@article {pmid41352345,
year = {2025},
author = {Rojas-Vargas, J and Wilcox, H and Monari, B and Gajer, P and Zuanazzi, D and Shouldice, A and Parmar, R and Haywood, P and Tai, V and Krakowsky, Y and Potter, E and Ravel, J and Prodger, JL},
title = {The neovaginal microbiota, symptoms, and local immune correlates in transfeminine individuals with penile inversion vaginoplasty.},
journal = {Cell reports},
volume = {},
number = {},
pages = {116546},
doi = {10.1016/j.celrep.2025.116546},
pmid = {41352345},
issn = {2211-1247},
abstract = {Transfeminine people (assigned male at birth) often undergo penile inversion vaginoplasty to create vulva, a clitoris and a vaginal canal (referred to as a neovagina). After vaginoplasty, transfeminine people frequently experience gynecological concerns, but their etiology is unknown due to a lack of knowledge of the neovaginal microenvironment. We characterized neovaginal microbiota and cytokines in 47 transfeminine participants. Participants self-reported sexual behaviors and symptoms, enabling correlation with bacterial (16S rRNA) and immune profiles. Four distinct clusters of co-occurring bacteria with unique immune profiles were identified. One cluster, which included Fastidiosipila, Ezakiella, and Murdochiella, was abundant, stable, and correlated with lower cytokines. Conversely, another cluster containing Howardella, Parvimonas, Fusobacterium, and Lawsonella was linked to higher cytokines. Although Lactobacillus was detected, Lactobacillus dominance was rare. These findings underscore the need for evidence-based clinical guidelines tailored to transfeminine gynecologic care, emphasizing the vital role of the neovaginal microbiome in symptom management and sexual health.},
}

@article {pmid41352344,
year = {2025},
author = {Monari, B and Wilcox, H and Haywood, P and Gajer, P and Rojas-Vargas, J and Zuanazzi, D and Rutt, L and Shouldice, A and Parmar, R and Waetjen, LE and Krakowsky, Y and Potter, E and Prodger, JL and Ravel, J},
title = {The vaginal microbiota, symptoms, and local immune correlates in transmasculine individuals using sustained testosterone therapy.},
journal = {Cell reports},
volume = {},
number = {},
pages = {116632},
doi = {10.1016/j.celrep.2025.116632},
pmid = {41352344},
issn = {2211-1247},
abstract = {Transmasculine individuals (assigned female at birth, masculine gender identity, TM) may use gender-affirming testosterone therapy, and some report adverse genital symptoms during treatment. In cis women, the vaginal microbiota is central to reproductive and sexual health. Lactobacillus-dominant communities are considered optimal, while diverse, Lactobacillus-depleted microbiota are non-optimal. Prior studies suggest Lactobacillus deficiency in TM vaginal microbiota, but associations with symptoms and immune markers remain unclear. We launched the TransBiota study to characterize the TM vaginal microbiota, soluble mediators of local inflammation, and self-reported symptoms over three weeks. Fewer than 10% of TM possess Lactobacillus-dominant microbiota, and most exhibit diverse, Lactobacillus-depleted microbiota. We identify 11 vaginal microbiota community state types (tmCSTs), with Lactobacillus-dominant tmCSTs unexpectedly linked to abnormal odor and elevated interleukin-1α. However, Lactobacillus dominance is not associated with other key symptoms, such as dyspareunia and vaginal dryness, underscoring that microbiome-symptom relationships in TM are more complex and warrant further research.},
}

@article {pmid41352125,
year = {2025},
author = {Taki, AG and Shareef, A and Arora, V and Oweis, R and Jyothi, SR and Singh, U and Sahoo, S and Chauhan, AS and Alimova, F and Sameer, HN and Yaseen, A and Athab, ZH and Adil, M},
title = {Unraveling the microbiome's role in breast cancer progression and treatment response.},
journal = {Current problems in cancer},
volume = {60},
number = {},
pages = {101264},
doi = {10.1016/j.currproblcancer.2025.101264},
pmid = {41352125},
issn = {1535-6345},
abstract = {The human microbiome, encompassing microbial communities in the gut and breast tissue, has emerged as a critical modulator of breast cancer (BC) initiation, progression, and treatment response. This review synthesizes current evidence on the microbiome's role in BC, highlighting its influence on tumorigenesis, tumor microenvironment (TME), and therapeutic outcomes. Breast cancer, the most prevalent malignancy among women globally, exhibits significant heterogeneity across its molecular subtype's hormone receptor-positive, HER2-enriched, and triple-negative-each with distinct clinical challenges. Recent studies reveal that microbial dysbiosis in the gut and breast tissue can drive oncogenesis through mechanisms such as immune modulation, estrogen metabolism, and inflammation. Gut microbes, via the "estrobolome," regulate circulating estrogen levels, impacting hormone-driven BC, while breast tissue microbiota contributes to local inflammation and DNA damage, promoting tumor progression. Specific microbial taxa, including Bacillus, Staphylococcus, and Escherichia coli, are enriched in BC patients, whereas beneficial species like Lactobacillus and Bifidobacterium are diminished. The microbiome also influences treatment efficacy, with gut microbial diversity linked to enhanced chemotherapy and immunotherapy responses, while antibiotic-induced dysbiosis may impair outcomes. Emerging research suggests microbiome signatures as potential biomarkers for predicting therapeutic success, with Akkermansia muciniphila and short-chain fatty acids showing promise in enhancing anti-tumor immunity. Probiotics, prebiotics, and fecal microbiota transplantation offerel therapeutic avenues, though challenges such as standardization, interindividual variability, and safety concerns remain. Integrating multi-omics and machine learning could elucidate microbiome-host interactions, paving the way for precision oncology. This review underscores the transformative potential of microbiome-based diagnostics and interventions in improving BC management, emphasizing the need for large-scale, longitudinal studies to validate these findings and address existing research gaps.},
}

@article {pmid41352001,
year = {2025},
author = {Hofsvang, A and Hanssen, EN and Muinck, EJ and Trosvik, P and Fonneløp, AE},
title = {Forensic geolocation of Norwegian soil samples using random forest analysis of microbiomes.},
journal = {Forensic science international. Genetics},
volume = {82},
number = {},
pages = {103408},
doi = {10.1016/j.fsigen.2025.103408},
pmid = {41352001},
issn = {1878-0326},
abstract = {Soil is a substrate easily picked up during everyday activities due to its ubiquity and adhesiveness. A method to determine the origin of soil precisely would therefore be useful in forensic casework as it can provide insight into a person`s or object`s previous whereabouts. To evaluate the potential of microbiomes for soil provenance determination, we collected soil samples from 15 locations in and around Oslo, Norway. Samples were collected multiple times from the same locations to assess changes in the microbiome over time. Additionally, a mock soil stain on clothing sample was collected at each site to validate this sample type. The microbial composition of samples was determined via amplicon sequencing of the V4 region of the 16S rRNA bacterial gene. Our results showed that the microbiomes were significantly impacted by location, with both soil and soil stain samples from the same site mainly exhibiting greater similarity than those from different sites. Notably, seasonal variations affected microbiome composition, leading to significant changes in some locations. Machine learning was employed to associate samples with their geographic origins, achieving classification accuracies above 85 % for both soil stain samples and soil samples collected within one week of each other. However, accuracies were lower for samples collected across different seasons, between 55 % and 64 %, indicating that temporal variation can limit the reliability of soil microbiome analysis when there is a delay between sample collection times.},
}

@article {pmid41351948,
year = {2025},
author = {Carnell, BH and Jayaraman, J and Dar Juan, JBP and Templeton, MD and Hay, ID},
title = {Understanding the dynamics of Pseudomonas syringae tailocin targeting allows for predictive protective microbial inoculation of Actinidia chinensis.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128401},
doi = {10.1016/j.micres.2025.128401},
pmid = {41351948},
issn = {1618-0623},
abstract = {The Pseudomonas syringae complex is an important group within the Gammaproteobacteria and comprises several pathovars of agricultural significance. Genome mining of the P. syringae species complex has uncovered high-molecular-weight phage tail complexes termed tailocins. Tailocins exert specific bactericidal action against both closely and more distantly related bacteria and significantly shape the ecology of the microbiome. Tailocin targeting specificity is currently understood to be dependent on tail-fibers (TFs) binding to specific molecular epitopes, including lipopolysaccharide (LPS) as a bacterial cell surface receptor for tailocin TF-targeting domains. Recent work in P. syringae has strongly correlated variation at the common polysaccharide antigen of LPS with tailocin sensitivity. Here we provide biochemical evidence for LPS as the major receptor for P. syringae tailocins; examine the mechanisms and genetic basis of tailocin TF targeting; and predict strains that can provide protective colonization of plants. We then use the understanding of these mechanisms that determine the tailocin targeting spectrum and genetic knockouts and complementation to modify the bacterial canker pathogen of kiwifruit plants to predict LPS-mediated tailocin targeting by naturally occurring host microbiota, and then demonstrate the efficacy of these applied microbiome-derived tailocin-carrying commensal strains as biocontrol agents.},
}

@article {pmid41351871,
year = {2025},
author = {Yu, L and Hu, Y and Du, W and Hu, X and Shen, Y},
title = {Mapping the Burn Injury Landscape with Omics Techniques.},
journal = {Journal of burn care & research : official publication of the American Burn Association},
volume = {},
number = {},
pages = {},
doi = {10.1093/jbcr/iraf223},
pmid = {41351871},
issn = {1559-0488},
abstract = {In this review, we studied the significance of multi-omics techniques in understanding the complex processes after burns. Severe burns result in both temporary local pathophysiological changes and long-term, profound, and extensive pathophysiological abnormalities. The utilization of multi-omics approaches to identify novel treatment targets or clarify the molecular mechanisms underlying pathophysiological alterations related to burn injury has significant promise. This review encapsulates recent advancements in the utilization of omics approaches to elucidate pathophysiological alterations and biomarkers associated with inflammation, wound healing, and metabolic pathways after burn injuries, encompassing the genome, transcriptome, proteome, metabolome, and microbiome. An enhanced comprehension of the pathophysiological alterations and biomarkers associated with burn injuries can promote the creation of more efficacious and focused therapeutic approaches.},
}

@article {pmid41351823,
year = {2025},
author = {Howard-Stone, R and Măndoiu, II},
title = {MHASS: Microbiome HiFi Amplicon Sequencing Simulator.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf656},
pmid = {41351823},
issn = {1367-4811},
abstract = {SUMMARY: Microbiome HiFi Amplicon Sequence Simulator (MHASS) creates realistic synthetic PacBio HiFi amplicon sequencing datasets for microbiome studies, by integrating genome-aware abundance modeling, realistic dual-barcoding strategies, and empirically derived pass-number distributions from actual sequencing runs. MHASS generates datasets tailored for rigorous benchmarking and validation of long-read microbiome analysis workflows, including ASV clustering and taxonomic assignment.

Implemented in Python with automated dependency management, the source code for MHASS is freely available at https://github.com/rhowardstone/MHASS along with installation instructions. Our code is also published on Zenodo at https://doi.org/10.5281/zenodo.17486364.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid41351803,
year = {2025},
author = {Kuang, R and Levinthal, DJ and Cummings, C and Ramos Rivers, C and Ghaffari, AA and Binion, DG},
title = {Pain and IBD: The Contributing Role of Diet and Nutrition.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41351803},
issn = {1573-2568},
abstract = {Pain is one of the most debilitating symptoms in patients with inflammatory bowel disease (IBD). We explore the impact of diet, nutrition, and malnutrition in the emergence and worsening of pain in patients with IBD, and potential strategies to prevent this complication. We propose that diet may impact pain in IBD through nociceptive, neuropathic, and nociplastic mechanisms. IBD-related nociceptive pain arises from intestinal inflammation, nerve sensitization, obstruction, and pressure due to chronic remodeling and strictures. Neuropathic pain in IBD may result from vitamin and micronutrient malabsorption. Surgery can leave patients with IBD particularly prone to vitamin B12 deficiency due to anatomical changes that hinder absorption. Nociplastic pain occurs through central pain sensitization and the experience of pain in the absence of inflammation and other known organic causes. The epidemiologic identification of a Western diet high in ultra-processed foods being associated with both IBD as well as neuropsychiatric illness may contribute to increased pain perception in patients through the gut-brain-axis. We highlight actionable clinical factors linking diet and nutrition to pain in IBD, along with emerging hypotheses on the complex interplay between diet, its prebiotic effects on the microbiome and metabolome, and disorders of gut-brain interaction that may exacerbate pain.},
}

@article {pmid41351790,
year = {2025},
author = {Coker, MO and Kreutzberg, R and Sam-Agudu, NA and Macodiyo, E and Jumare, J and Madan, J and Singhal, V and Li, Z and Robbins, R and Shiau, S},
title = {The State of the Science on Chronic Comorbidities and Aging in Children and Adolescents with perinatally-acquired HIV.},
journal = {Current HIV/AIDS reports},
volume = {22},
number = {1},
pages = {56},
pmid = {41351790},
issn = {1548-3576},
support = {R21DE032869//National Institutes for Health/NIDCR/ ; R21DE032869//National Institutes for Health/NIDCR/ ; },
mesh = {Humans ; *HIV Infections/complications/epidemiology/transmission/drug therapy ; Child ; Comorbidity ; *Aging ; Adolescent ; *Infectious Disease Transmission, Vertical ; Chronic Disease ; },
abstract = {The availability and global scale-up of suppressive antiretroviral therapy (ART) has transformed HIV from a fatal infection to a chronic disease. While long-term survival is a positive development for people living with HIV (PLWH), the increased life expectancy comes with age-related comorbidities. These comorbidities affect PLWH at relatively earlier ages than the general population, and examples include cardiometabolic conditions, renal toxicity, lung and respiratory dysfunction, neurocognitive deficits, malignancy, and oral/dental pathology. Anticipatory management of early markers of non-communicable diseases (NCDs) can be especially advantageous for children and adolescents with perinatally-acquired HIV (CAPHIV), the vast majority of whom live in low-and middle-income countries. However, evidence for the mechanisms underlying age-related comorbidities in PLWH and implications for CAPHIV represent a still-emerging area of investigation. In this article, we review the current literature on comorbidities and age-related conditions experienced by CAPHIV, discuss the role of inflammation and chronic immune activation, and highlight accelerated biological aging and/or disruptions to the microbiome as underlying mechanisms. We recommend that HIV clinical care and health policy should reflect evidence on aging and comorbidities to optimize growth, development, and long-term health for CAPHIV globally.},
}

Humans
*HIV Infections/complications/epidemiology/transmission/drug therapy
Child
Comorbidity
*Aging
Adolescent
*Infectious Disease Transmission, Vertical
Chronic Disease

@article {pmid41351781,
year = {2025},
author = {Gim, G and Lee, DG and Park, CH and Kim, OS and Han, K and Heo, YM and Lee, H},
title = {Antarctic soil microbiomes as a reservoir for cosmetic bioactives: continental-scale diversity and predicted functions.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41351781},
issn = {2092-9293},
support = {PI24020//Korea Polar Research Institute/ ; PI24120//Korea Polar Research Institute/ ; RS-2024-00343166//National Research Foundation of Korea (NRF)/ ; },
abstract = {BACKGROUND: Demand for clean beauty ingredients is driving discovery of safe, effective, and sustainable actives. Microbes inhabiting polar deserts produce biomolecules adapted to stress, relevant to skin protection and regeneration.

OBJECTIVE: To characterize taxonomic diversity and functional potential of Antarctic soil microbiomes from distinct biogeographic regions and identify microbial genes linked to cosmetic efficacy.

METHODS: Public 16S rRNA amplicon datasets from NCBI SRA were compiled and classified into four Antarctic Conservation Biogeographic Regions: North Antarctic Peninsula, East Antarctica, South Victoria Land, and Transantarctic Mountains. Functional profiles were predicted using PICRUSt2 and analyzed for antioxidant, anti-aging, moisturization, skin-barrier, and regeneration pathways via KEGG Orthology terms.

RESULTS: Analysis of 406 sequencing runs identified 54,523 amplicon sequence variants from 48 bacterial and 2 archaeal phyla. Actinobacteria dominated (36.1%), followed by Bacteroidetes (13.0%) and Proteobacteria (10.5%). East Antarctica exhibited highest diversity (Shannon index mean 8.97) and evenness (0.87), with region-distinct communities. Functional prediction revealed enriched antioxidant defense, skin-barrier maintenance, moisturization, and photoprotective genes. Taxonomic and functional ordinations partially decoupled, indicating functional convergence amid taxonomic divergence.

CONCLUSION: Antarctic soils are a rich source of microbial functions for cosmetic innovation, especially in East Antarctica. Multi-omics validation, strain isolation, and sustainable production may accelerate development of next-generation clean beauty actives compliant with access and benefit-sharing regulations.},
}

@article {pmid41351776,
year = {2025},
author = {Hussain, B and Javed, K and Ali, M and Ullah, S and Sun, S and Idris, AM and Singh, S},
title = {Impact of nanoparticles on biogeochemical processes in soil-plant system under heavy metals stress; exploring remediation mechanism and plant health status.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {1},
pages = {31},
pmid = {41351776},
issn = {1573-2983},
mesh = {*Metals, Heavy/toxicity/metabolism ; *Soil Pollutants/toxicity/metabolism/chemistry ; Soil/chemistry ; *Plants/drug effects/metabolism ; *Environmental Restoration and Remediation ; Biodegradation, Environmental ; Stress, Physiological ; *Metal Nanoparticles/chemistry/toxicity ; },
abstract = {Although, NPs have potential to improved plant resistance against abiotic stress, increased nutrient usage efficiency, and sustenance of agricultural production. However, reactions of NPs in soil matrices, particularly their movement, perseverance, and biogeochemical reactions in soil-plant system under heavy metals (HMs) were not well understood. Therefore, this review presents the latest research in order to clarify the molecular interactions, beneficial transformations, and detoxification processes of NPs in plants and evaluates their roles in these processes. It further aims to quantify the benefits and risks, and give future directions for NPs design and applications in environmental remediation and agriculture. NPs significantly enhanced agricultural outcomes through mechanisms such as regulating HMs uptake, boosting antioxidant enzyme activity (up to a 60% increase), altering soil properties, and optimizing physiological metabolism. NPs amendments raised crop output by 20-55% while reducing disease and nutrient leaching to 50% and 30%, respectively, and improving the soil's carbon sink by 15%. Meanwhile, green-synthesized nanomaterials offer eco-friendly alternatives in remediation through processes like adsorption, oxidation, coprecipitation, ion-exchange, photocatalysis, and nanophytoremediation, achieving 100% pollutant removal efficiency for elements like hexavalent chromium using iron NPs. However, challenges such as NPs accumulation in food chains, potential toxicity to non-target species, and physiological disruptions necessitate solutions like microbiome co-delivery and stimuli-responsive systems to balance safety and effectiveness. In order to increase the available resources and address the worldwide food safety issue, the use of NPs in agroecosystems might be a crucial step towards sustainable farming. Therefore, the influence of NPs on soil, and plant antioxidant defense systems and oxidative stress activation under HMs should be studied using molecular, physiological, and biochemical techniques. For this purpose, real-time polymerase chain reaction (RT-PCR) analysis, illumina MiSeq sequencing, pyrosequencing analysis, metagenomics, metabolomics, proteomics, and functional assays etc. could be most useful for NPs risk/benefit evaluation.},
}

*Metals, Heavy/toxicity/metabolism
*Soil Pollutants/toxicity/metabolism/chemistry
Soil/chemistry
*Plants/drug effects/metabolism
*Environmental Restoration and Remediation
Biodegradation, Environmental
Stress, Physiological
*Metal Nanoparticles/chemistry/toxicity

@article {pmid41351765,
year = {2025},
author = {Peters, M and Hegelmaier, T and Wegner, F and Höllerhage, M and Ye, L and Niesmann, C and Schneidereit, IV and Haghikia, A and Klietz, M},
title = {The role of the gut microbiome in the progression of Parkinson's disease: a systematic review of patient cohorts.},
journal = {Journal of neurology},
volume = {273},
number = {1},
pages = {8},
pmid = {41351765},
issn = {1432-1459},
mesh = {Humans ; *Parkinson Disease/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; *Disease Progression ; Dysbiosis ; },
abstract = {INTRODUCTION: Parkinson's disease (PD) is the second most common neurodegenerative disease. The etiology of PD is not yet fully understood. In recent years, the role of the gut microbiome in the progression of the disease came to attention. A deeper understanding of the relationship between the gut microbiome and the development and progression of PD may innovate therapeutic approaches.

AIM: The aim of the present literature analysis is to systematically evaluate alterations in gut microbiome in PD and its correlation with clinical symptoms.

MATERIALS AND METHODS: A search for publications via PubMed using the search terms "Parkinson's disease" AND "gut microbiome" AND "human" was performed. The main inclusion criteria were a subject number ≥ 30 per group, patients with clinically confirmed PD, an analysis of the gut microbiome in a case-control, cross-sectional or longitudinal study design.

RESULTS: The evaluation of the results showed that gut microbiome of PD patients is altered both in early stages of the disease and throughout its progression compared to healthy controls. These alterations correlate with clinical symptoms. In general, the diversity of micro-organisms in the gut is reduced in PD patients, and the composition of the gut microbiome differs significantly from healthy persons. Particularly a reduction in short-chain fatty acid (SCFA) producing genera such as Faecalibacterium and Roseburia and the increase in pro-inflammatory taxa such as Collinsella and Akkermansia is described.

CONCLUSIONS AND DISCUSSION: According to current evidence, the relationship between alterations in the gut microbiome and the pathogenesis of PD is not yet fully understood. Recent findings suggests that intestinal dysbiosis may contribute to the progression of PD.},
}

Humans
*Parkinson Disease/microbiology/physiopathology
*Gastrointestinal Microbiome/physiology
*Disease Progression
Dysbiosis

@article {pmid41351422,
year = {2025},
author = {Jiang, Y and Xu, H and Zhang, W and Jin, S and Piao, H and Yu, J and Yao, H and Shi, J and Liu, Q and Li, N and Shen, Y and Fu, J and Li, M},
title = {Advances in the Study of Intestinal Microbiota and Neuropathic Pain.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {11},
pages = {43051},
doi = {10.31083/FBL43051},
pmid = {41351422},
issn = {2768-6698},
support = {82104838//China National Natural Science Foundation/ ; XH-D001//China Promotion Foundation Spark Program/ ; 2024JH2/102500062//Liaoning Provincial Key Research and Development Programme/ ; 2025-MSLH-490//Liaoning Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *Neuralgia/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; },
abstract = {The intestinal microbiota, present in vast numbers within the human body, plays a pivotal role, with its composition and abundance varying significantly across individuals. This gut microbiota not only contributes to normal physiological development but also impacts the initiation, progression, resolution, and prognosis of various diseases. Recent studies have increasingly illuminated the connection between intestinal microbiota and pain, with a particular focus on the relationship between gut microbiota and neuropathic pain (NP). NP, an acute and chronic pain disorder arising from sensory nervous system injury, encompasses both peripheral and central neuropathic pain. Evidence suggests that intestinal microbiota influences NP occurrence and may modulate its severity. This review synthesizes current research findings on the microbiota-NP relationship, aiming to establish a theoretical foundation for future clinical investigations.},
}

Humans
*Neuralgia/microbiology
*Gastrointestinal Microbiome/physiology
Animals

@article {pmid41351421,
year = {2025},
author = {Li, Y and Chen, H and Zhou, S},
title = {Macrophages and Tissue Homeostasis: From Physiological Functions to Disease Onset.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {11},
pages = {42706},
doi = {10.31083/FBL42706},
pmid = {41351421},
issn = {2768-6698},
support = {32200755//National Natural Science Foundation of China/ ; 23JRRA696//Natural Science Foundation of Gansu Province/ ; 23YF1430600//Shanghai Rising-Star Program/ ; },
mesh = {Humans ; *Homeostasis ; Tumor Microenvironment/immunology ; *Macrophages/physiology/immunology/metabolism ; Animals ; *Neoplasms/immunology/pathology/metabolism ; Tumor-Associated Macrophages/immunology ; },
abstract = {The role of macrophages has transcended the traditional binary framework of M1/M2 polarization, emerging as "tissue microenvironment engineers" that dynamically govern organismal homeostasis and disease progression. Under physiological conditions, they maintain balance through phagocytic clearance, metabolic regulation (e.g., lipid and iron metabolism), and tissue-specific functions (such as hepatic detoxification by Kupffer cells and intestinal microbiota sensing), all meticulously orchestrated by epigenetic mechanisms and neuro-immune crosstalk. In pathological states, their functional aberrations precipitate chronic inflammation, fibrosis, metabolic disorders, and neurodegenerative diseases. Notably, this plasticity is most pronounced within the tumor microenvironment (TME): tumor-associated macrophages (TAMs) polarize toward a protumoral phenotype under conditions of low pH and high reactive oxygen species (ROS). They promote angiogenesis via vascular endothelial growth factor (VEGF), suppress immunity through interleukin-10 (IL-10)/programmed death-ligand 1 (PD-L1), and facilitate tumor invasion by degrading the extracellular matrix, ultimately fostering an immune-evasive niche. Novel intervention strategies targeting TAMs in the TME have shown remarkable efficacy: CRISPR-Cas9 spatiotemporal editing corrects aberrant gene expression; pH/ROS-responsive nanoparticles reprogram TAMs to an antitumoral phenotype; chimeric antigen receptor-macrophage (CAR-M) 2.0 enhances antitumor immunity through programmed death-1 (PD-1) blockade and IL-12 secretion; and microbial metabolites like butyrate induce polarization toward an antitumor phenotype. Despite persisting challenges-including the functional compensation mechanisms between tissue-resident and monocyte-derived macrophages, and obstacles to clinical translation-the macrophage-centered strategy of "microenvironmental regulation via cellular engineering" still holds revolutionary promise for the treatment of tumors and other diseases.},
}

Humans
*Homeostasis
Tumor Microenvironment/immunology
*Macrophages/physiology/immunology/metabolism
Animals
*Neoplasms/immunology/pathology/metabolism
Tumor-Associated Macrophages/immunology

@article {pmid41351413,
year = {2025},
author = {Xu, Y and Tao, Y and Pan, H and Wang, Z and Wang, H and Luo, Q},
title = {Microbiome Modulation in Lung Cancer Immunotherapy: Unveiling the Role of Respiratory and Gut Microbiota in the PD-1/PD-L1 Response.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {11},
pages = {41531},
doi = {10.31083/FBL41531},
pmid = {41351413},
issn = {2768-6698},
support = {24ZR1464400//Shanghai Municipal Natural Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Lung Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Tumor Microenvironment/immunology ; *B7-H1 Antigen/antagonists & inhibitors/immunology ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Dysbiosis/immunology ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Lung cancer, the leading cause of cancer-related mortality worldwide, poses considerable therapeutic challenges due to the varied responses to programmed death-1/programmed death-ligand 1 (PD-1/PD-L1) inhibitors. Emerging highlight the pivotal role of host-microbiome interactions in modulating antitumor immunity and influencing clinical outcomes. This review examines how the respiratory and gut microbiota contribute to the immunosuppressive tumor microenvironment through dysbiosis-induced T-cell exhaustion and regulatory cell activation, while certain commensals facilitate dendritic cell-mediated recruitment of cytotoxic T lymphocytes. Additionally, this review explores the molecular mechanisms by which microbial metabolites, such as short-chain fatty acids, influence myeloid-derived suppressor cells. Therapeutically, microbiota-modulation strategies-such as tailored probiotic formulations and precision fecal microbiota transplantation-offer potential to enhance immunotherapy efficacy. This review provides a foundation for microbiome-guided immunotherapy, advocating for biomarker-driven patient stratification and the use of engineered microbial consortia to counteract therapeutic resistance. These findings pave the way for the integration of microbiome science into next-generation precision oncology.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Lung Neoplasms/therapy/immunology/microbiology
*Immunotherapy/methods
Tumor Microenvironment/immunology
*B7-H1 Antigen/antagonists & inhibitors/immunology
Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology
Immune Checkpoint Inhibitors/therapeutic use
Dysbiosis/immunology
Animals
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid41351400,
year = {2025},
author = {Zhang, Y and Liu, Y and Liu, Q and Zhang, Q and Zhu, W and Ma, C and Zhu, Z and Fang, Z and Xu, X},
title = {Impact of Dapagliflozin on Gut Microbiota and Plasma Metabolomic Profiles in Patients With Heart Failure.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {11},
pages = {46142},
doi = {10.31083/FBL46142},
pmid = {41351400},
issn = {2768-6698},
support = {2022e07020058//2023 Chizhou City major science and technology special project and Anhui Provincial Key Research and Development Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Glucosides/therapeutic use/pharmacology ; *Benzhydryl Compounds/therapeutic use/pharmacology ; *Heart Failure/drug therapy/blood/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; Metabolomics/methods ; *Metabolome/drug effects ; *Sodium-Glucose Transporter 2 Inhibitors/therapeutic use/pharmacology ; Bacteria/genetics/classification/drug effects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Heart failure (HF) remains a leading cause of morbidity and mortality worldwide. Although dapagliflozin, a selective sodium-glucose cotransporter 2 (SGLT2) inhibitor, has demonstrated significant cardiovascular benefits in large clinical trials, the underlying mechanisms beyond glucose lowering remain incompletely understood. Increasing evidence suggests that gut microbiota and its metabolites may contribute to HF progression through gut-heart axis interactions.

METHODS: In this study, a total of 135 individuals with HF were recruited, comprising 84 patients treated with dapagliflozin (Y group) and 51 receiving conventional therapy (N group). Gut microbial communities were characterized through 16S rRNA gene sequencing to evaluate compositional structure, diversity metrics, and taxa differences between groups. Untargeted metabolomic profiling of plasma samples was conducted to identify significantly altered metabolites and enriched metabolic pathways. Furthermore, the interrelationships between gut bacterial taxa and circulating metabolites were systematically explored to delineate potential microbiome-metabolome interactions.

RESULTS: Dapagliflozin treatment significantly altered gut microbial composition (p < 0.05, permutational multivariate analysis of variance [PERMANOVA]), characterized by increased Prevotella, Akkermansia, Collinsella, and Fusobacterium, and reduced Bacteroides, Parabacteroides, Subdoligranulum, and Bifidobacterium in the dapagliflozin group, whereas control-enriched taxa included Lachnoclostridium and the Ruminococcus gauvreauii group. Fourteen plasma metabolites were differentially abundant between groups, including higher levels of O-phospho-L-threonine and epiandrosterone in the dapagliflozin group, while salicyluric acid and L- (+)-rhamnose were enriched in the control group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated alterations in amino acid and one-carbon metabolism, as well as carbohydrate and steroid-related pathways. Correlation analysis revealed that Collinsella was positively associated with fludarabine phosphate (p < 0.05), whereas Akkermansia and Paraprevotella showed negative correlations with maslinic acid and phospho-L-valine, respectively (p < 0.01 to p < 0.001).

CONCLUSION: Dapagliflozin modulates gut microbiota composition and circulating metabolic signatures in HF patients, supporting a potential gut-heart axis mechanism contributing to its cardioprotective effects.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Glucosides/therapeutic use/pharmacology
*Benzhydryl Compounds/therapeutic use/pharmacology
*Heart Failure/drug therapy/blood/microbiology/metabolism
Male
Female
Aged
Middle Aged
Metabolomics/methods
*Metabolome/drug effects
*Sodium-Glucose Transporter 2 Inhibitors/therapeutic use/pharmacology
Bacteria/genetics/classification/drug effects
RNA, Ribosomal, 16S/genetics

@article {pmid41351294,
year = {2025},
author = {Cai, Y and Zhou, T and Shi, W and Ding, X and Cai, X and Yu, L},
title = {Genetic Evidence Implicating Gut Microbiota and Circulating Cytokines in Sjögren's Syndrome.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e70136},
doi = {10.1002/jcla.70136},
pmid = {41351294},
issn = {1098-2825},
support = {82172234//National Natural Science Foundation of China/ ; 82401309//National Natural Science Foundation of China/ ; 2024409//Shanghai Post-doctoral Excellence Program/ ; 2025M771943//China Postdoctoral Science Foundation/ ; },
abstract = {BACKGROUND: This study investigates the potential interplay between gut microbiota and circulating cytokines in Sjögren's syndrome (SS) through a bidirectional and mediation Mendelian randomization (MR) approach.

METHODS: Summary-level statistics of 473 gut microbiota (n = 5959), 41 circulating cytokines (n = 8293), and SS (ncase = 2735, ncontrol = 399,355) were obtained from genome-wide association studies (GWAS) in European populations. A two-sample MR analysis was employed to investigate the bidirectional causal effects of gut microbiota and circulating cytokines on SS, and mediation analyses were applied to discover potential mediating gut microbiota and circulating cytokines. A series of sensitivity analyses were conducted to address heterogeneity and pleiotropy concerns.

RESULTS: Fifteen taxa were found to be causally associated with SS, and SS had a causal effect on 26 taxa. A bidirectional causal relationship was identified between CAG-269 sp001916065 and SS, and between UBA7703 and SS. Genetically predicted levels of five circulating cytokines-MIG, IL-5, IL-1RA, IL-2RA, and SCGF-β-were found to potentially affect SS, and genetically predicted SS was associated with increased levels of two circulating cytokines, IL-1β and IL-5. A bidirectional causal relationship was identified between circulating IL-5 and SS. Mediation analyses further revealed that circulating cytokines do not mediate the gut microbiome's influence on SS, and conversely, the gut microbiome does not influence circulating cytokines to affect SS.

CONCLUSION: This study provides compelling evidence for causal effects of gut microbiome composition and circulating cytokines on SS risk. Further mediation analysis suggests that these biological factors may operate independently to influence SS development.},
}

@article {pmid41351228,
year = {2025},
author = {Sun, JM and Liu, YX and Zheng, DN and Gao, Y and Zhang, YF and Yu, L},
title = {Ralstonia pickettii - The Potential and Substantial Impact in Capsular Contracture: Insights from 2bRAD-M Analysis and Murine Model.},
journal = {Plastic and reconstructive surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/PRS.0000000000012570},
pmid = {41351228},
issn = {1529-4242},
abstract = {BACKGROUND: Capsular contracture (CC) is one of the most common complications in augmentation mammaplasty with breast implant, but its etiology remains uncertain. We aimed to apply the 2bRAD-M technique to characterize the microbiome differences between normal and contracture capsules.

METHODS: 10 normal capsules and 10 contractured capsules were used for 2bRAD-M sequencing and corresponding histological evaluation. By constructing a mouse silicone implant infection model, histological staining was used to verify the influence of different microorganisms identified in sequencing results.

RESULTS: Histologic evaluation of patient samples revealed a marked increase in the thickness and stiffness of contracture capsules, along with increased infiltration of macrophages and T cells. Through 2bRAD-M sequencing, we found that the microbial composition of contracture capsules was significantly different from that of normal capsules, with the most significant difference of relative abundance value in Ralstonia pickettii. In vivo, Ralstonia pickettii could significantly increase the thickness, collagen content, and hardness of the capsules, which was more effective than the combined infection with Staphylococcus epidermidis and Cutibacterium acnes. Immunofluorescence results showed both bacterial infections caused increased infiltration of macrophages and T cells, and Ralstonia pickettii infection caused more infiltration of T cells.

CONCLUSION: This is the first study to use 2bRAD-M technique to characterize microbiome differences of relative abundance value between normal and contracture capsules. Ralstonia pickettii can recruit more macrophages and T cells to infiltrate. This study provides new etiological causes of capsular contracture and new clinical insights for the prevention and treatment of capsular contracture.},
}

@article {pmid41351139,
year = {2025},
author = {Park, C and Kim, J and Lee, J},
title = {Inference of causal interaction networks of gut microbiota using transfer entropy.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12384-1},
pmid = {41351139},
issn = {1471-2164},
support = {RS-2023-00220207//Ministry of Education/ ; NRF-2020R1A2C1005956//Ministry of Education/ ; },
}

@article {pmid41351056,
year = {2025},
author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ},
title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02236-1},
pmid = {41351056},
issn = {2049-2618},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; DE-AC05-76RL01830//U.S. Department of Energy/ ; },
abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.

RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.

CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.},
}

@article {pmid41350930,
year = {2025},
author = {Hashmi, AS and Gupta, ND and Khan, S and Agrawal, N and Ali, SA and Atif, M},
title = {Evaluation of mouthwash-induced antimicrobial resistance in the oral microbiome: a systematic review.},
journal = {British dental journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41415-025-9012-9},
pmid = {41350930},
issn = {1476-5373},
abstract = {Aim Antimicrobial resistance is an emerging global health challenge, driven largely by the overuse of antimicrobial drugs. However, the extent of mouthwash-induced antimicrobial resistance remains poorly understood. This systematic review aimed to assess the influence of commonly used mouthwashes on antimicrobial resistance, focusing on resistance genes, microbial alterations, and cross-resistance to antibiotics.Methods PubMed, Scopus, Web of Science, and grey literature, including Google Scholar, were searched for studies evaluating mouthwash-induced antimicrobial resistance. The search strategy included terms related to 'oral microbiome', 'mouthwash' and 'antimicrobial resistance', with Boolean operators tailored to each database. Risk of bias was assessed using In Vitro Critical Appraisal Tool for in vitro studies and the Modified Joanna Briggs Institute for ex vivo and in vivo studies, respectively.Results Twelve studies were analysed, comprising seven in vitro, four ex vivo and one in vivo study. A total of 91 patients and 213 bacterial isolates were assessed across various mouthwashes, including chlorhexidine digluconate, cetylpyridinium chloride, hydrogen peroxide and others. Due to heterogeneous outcomes, a meta-analysis was not conducted. The findings consistently revealed increased minimum inhibitory concentrations of oral bacteria and the presence of resistance genes, highlighting a potential rise in antimicrobial resistance.Conclusion This systematic review indicates a possible association between mouthwash use and resistance-related changes in the oral microbiome; however, the limited and heterogeneous evidence base warrants cautious interpretation. Further, longitudinal research is needed to elucidate the underlying mechanisms and inform evidence-based guidelines for mouthwash use.},
}

@article {pmid41350800,
year = {2025},
author = {Zheng, W and Yang, C and Bu, W and Wang, H and Ma, T and Bu, F},
title = {Age-dependent variations in leaf-endophytic microbiota and biocontrol potential in Camellia oleifera.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31248-y},
pmid = {41350800},
issn = {2045-2322},
support = {232102110050//the Henan Province Key Research and Development and Promotion Special Project (science and technology research)/ ; 23B22001//the Key Scientific Research Project of Henan Province Colleges and Universities/ ; XNKJTD-004//the Dabie Mountain Forestry Resources Innovation Theory and Technology innovation team of Xinyang Agriculture and Forestry University/ ; 2023XYZD05//Key Project of Xinyang Ecological Research Institute/ ; },
abstract = {Endophytic microorganisms play important roles in plant health, but their diversity and functions can vary with host developmental stage. Camellia oleifera, a major oil-producing crop in China, offers a valuable system for exploring these dynamics. We compared endophytic microbial communities in young (5-year) and old (15-year) C. oleifera leaves using high-throughput 16 S rRNA and ITS sequencing, supported by culture-dependent isolation and inhibition assays. Diversity indices, taxonomic composition, and predicted bacterial functions were analyzed with QIIME2 and PICRUSt2. Ten fungal and nine bacterial strains were isolated and tested for antagonism against key leaf pathogens in confrontation assays (n = 3 replicates). A total of 607 bacterial and 778 fungal ASVs were identified. Young leaves contained greater bacterial richness and diversity (Observed ASVs, Shannon, Simpson indices, P < 0.05), while old leaves hosted higher fungal richness. Beta diversity (Bray-Curtis PCoA) showed clear separation of bacterial communities by leaf age, with weaker separation for fungi. Bacterial functional prediction revealed enrichment of carbohydrate metabolism and amino acid biosynthesis in young leaves, while secondary metabolism and stress response pathways were more prominent in old leaves. Among isolated strains, Coniochaeta velutina inhibited Colletotrichum gloeosporioides, Alternaria alternata, and Botryosphaeria dothidea by 67.4%, 54.8%, and 65.2%, respectively. The bacterium Burkholderia ambifaria achieved the highest inhibition rate of 87.2% against B. dothidea. These findings suggest that leaf age shapes endophytic microbial diversity and bacterial functional potential in C. oleifera. Moreover, C. velutina and B. ambifaria represent promising candidates for biocontrol applications. While limited by small sample size (n = 3 replicates), this exploratory study provides foundational insights into age-associated shifts in endophyte communities and their biocontrol potential.},
}

@article {pmid41350794,
year = {2025},
author = {Huo, F and Liu, Q and Zhang, S and Liu, X and Lv, S and Zhao, M and Liu, Y and Zhu, X and Huang, C and Feng, S and Wang, H and Xu, S and Shen, J and Gao, J and Su, T and Wu, Y and Jiang, R and Zhu, JK and Liu, H},
title = {Circadian Rhythm Disorder-Related Dysfunctions are Exacerbated by Aging and Ameliorated by Time-Restricted Feeding.},
journal = {Neuroscience bulletin},
volume = {},
number = {},
pages = {},
pmid = {41350794},
issn = {1995-8218},
abstract = {Circadian rhythms are present in various species, and circadian rhythm disorder (CRD) affects people of all ages, especially those with age-related neurodegenerative diseases. Gut microbiota, which changes with age, also exhibits circadian rhythms. Disruption of gut microbial balance can trigger neurodegenerative diseases. This study explored the link between aging, CRD, and gut microbes by modeling CRD through light/dark cycle control. We found that aging worsened cognitive and mood disorders, along with gut microbial imbalance, intestinal barrier damage, and systemic inflammation in aged mice with CRD. Abnormal circadian gene expression increased oxidative stress. However, time-restricted feeding (TRF) improved CRD effects in aged mice by boosting Akkermansia muciniphila and inhibiting the NOD-like signaling pathway. This study shows that older mice exhibit increased behavioral and functional issues under CRD-related stress due to complex causes like systemic inflammation from a proinflammatory gut microbiome and oxidative stress from disrupted circadian genes. Maintaining a regular eating schedule significantly alleviates these CRD-induced issues in aged mice.},
}

@article {pmid41350753,
year = {2025},
author = {Kim, K and Park, S and Jinno, C and Ji, P and Liu, Y},
title = {Impact of dietary supplementation of Bacillus subtilis on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic Escherichia coli.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {167},
pmid = {41350753},
issn = {1674-9782},
abstract = {BACKGROUND: Our previous study demonstrated that dietary supplementation of Bacillus subtilis enhanced growth performance and intestinal integrity in weaned pigs challenged with enterotoxigenic Escherichia coli (ETEC). Therefore, this study aimed to explore the impact of Bacillus subtilis on gut health and its role in modulating host-microbe interactions in post-weaning pigs.

RESULTS: ETEC infection disrupted key metabolic pathways in distal colon, including glutathione, beta-alanine, and pyrimidine metabolism, indicating increased oxidative stress, impaired nucleotide balance, and amino acid catabolic stress. Bacillus subtilis supplementation induced distinct metabolomic and microbiome profiles in colon digesta of weaned pigs challenged with ETEC. Bacillus subtilis-treated pigs under ETEC challenge exhibited significant enrichment in amino acid- and energy-related pathways such as arginine biosynthesis, phenylalanine metabolism, pantothenate and CoA biosynthesis. ETEC infection induced microbial dysbiosis in the distal colon, resulting in decrease (P < 0.05) in abundance of Streptococcaceae and Enterobacteriaceae compared to healthy controls. Bacillus subtilis supplementation mitigated the ETEC-induced disruptions by increasing the relative abundance of beneficial bacterial families, including Lachnospiraceae and Bacteroidaceae.

CONCLUSION: Supplementation of Bacillus subtilis improves intestinal health and resilience against ETEC challenge by mitigating infection-induced metabolic disruptions and gut dysbiosis in weaned pigs.},
}

@article {pmid41350681,
year = {2025},
author = {Lin, L and Zhou, X and Peng, B and Ma, J and Zheng, Z and Jiang, C and He, Z and Li, S and Fang, W and Wu, C and Jiang, Z and Chen, Y and Zhong, L and Kwan, HY and Shen, C and Gong, S and Zhao, X},
title = {Extracellular vesicles derived from Kaempferia Galanga L. show promise for targeted oral therapy in the treatment of ulcerative colitis.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-025-03897-8},
pmid = {41350681},
issn = {1477-3155},
support = {20221260//Guangdong Traditional Chinese Medicine Special Fund/ ; 82405279//National Natural Science Foundation of China/ ; 82405279//National Natural Science Foundation of China/ ; 20231800913372//Science and Technology Program of Dongguan/ ; 2023A1515110757//Natural Science Foundation of Guangdong Province/ ; 2023A1515010720//Natural Science Foundation of Guangdong Province/ ; 81830117//the Key Project of the National Natural Science Foundation of China/ ; },
abstract = {Ulcerative colitis (UC) is characterised by chronic intestinal inflammation and its global prevalence is increasing. Although a variety of drugs have been approved for the clinical treatment of UC, their application is often limited by unsatisfactory long-term effects, side effects, and high treatment costs. Therefore, there is an urgent need for the development of effective drugs with fewer side effects. In this study, we found that the extracellular vesicles extracted and purified from rhizomes of Kaempferia galanga L. (KGEVs) exhibit promising therapeutic effects in treating UC disease. With an average diameter of 133.8 nm, KGEVs are rich in functional components, including lipids, proteins, and pharmacologically and immunologically active molecules. In vivo experiments revealed that KGEVs accumulated in the colorectal region 6 h after oral administration, demonstrating targeted enrichment at the site of enteritis. Moreover, we found that KGEVs effectively alleviate DSS-induced colitis in mice, as indicated by reductions in body weight loss, DAI score, spleen index and colon length shortening. Mechanistically, KGEVs may alleviate colitis by repairing the intestinal barrier, inhibiting oxidative stress and colonic inflammation regulating gut microbiota and inhibiting the polarisation of macrophages into pro-inflammatory M1 macrophages during the inflammatory response, indicating significant anti-inflammatory effects. These results suggest the potential of KGEVs as a promising, cost-effective, and efficient oral therapeutic agents for UC treatment.},
}

@article {pmid41350670,
year = {2025},
author = {Huang, Y and Huang, Y and Xu, B and Lin, C and Chen, X and Li, Y and Wang, Y and Liu, X},
title = {The association between a newly proposed gut microbiota dietary index and obesity among U.S. adults: a cross-sectional analysis based on NHANES 1999-2020.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {181},
pmid = {41350670},
issn = {1475-2891},
support = {2022QH1268//Fujian Medical University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Obesity/epidemiology/microbiology ; Cross-Sectional Studies ; Male ; Female ; Adult ; Nutrition Surveys ; Middle Aged ; *Diet ; United States/epidemiology ; Young Adult ; Body Mass Index ; Aged ; },
abstract = {OBJECTIVE: Obesity is linked to gut microbiota dysbiosis, and diet is a key determinant influencing the gut microbiome. This study examined the association between a newly proposed Dietary Index for Gut Microbiota (DI-GM) and obesity in the National Health and Nutrition Examination Survey (NHANES) from 1999 to 2020.

METHODS: A total of 41,159 adults aged ≥ 20 years were included, with 15,327 individuals classified as obese (BMI ≥ 30 kg/m²) and 25,832 as living without obesity. DI-GM comprises 13 components deemed either beneficial or unfavorable to the gut microbiome, yielding a total score ranging from 0 to 13. Weighted logistic regression assessed the relationship between DI-GM (continuous and categorical) and obesity, adjusting for demographic and lifestyle factors plus comorbidities. Restricted cubic spline, stratified analyses, multiple imputation, and propensity score matching were also performed.

RESULTS: Participants with obesity had a significantly lower mean DI-GM score than those without obesity (4.32 vs. 4.65, P < 0.001). Each 1-point increase in DI-GM was associated with 13% lower obesity odds (OR = 0.87, 95% CI: 0.85-0.88) in the crude model, remaining robust (OR = 0.88, 95% CI: 0.87-0.90, P < 0.001) after full adjustment. Higher DI-GM scores were linearly linked to lower odds of obesity, supported by multiple imputation and propensity score matching (P < 0.001).

CONCLUSION: In this nationally representative U.S. population, a more microbiota-oriented diet, as proxied by higher DI-GM scores, was independently associated with lower odds of obesity. Prospective and randomized trials are warranted to verify causality and investigate underlying mechanisms.},
}

Humans
*Gastrointestinal Microbiome
*Obesity/epidemiology/microbiology
Cross-Sectional Studies
Male
Female
Adult
Nutrition Surveys
Middle Aged
*Diet
United States/epidemiology
Young Adult
Body Mass Index
Aged

@article {pmid41350615,
year = {2025},
author = {Alkan, EN and Hekim, N and Gunes, S and Asci, R and Henkel, R},
title = {Evaluation of the semen microbiome for fertility in men with obesity using next-generation sequencing.},
journal = {Basic and clinical andrology},
volume = {35},
number = {1},
pages = {47},
pmid = {41350615},
issn = {2051-4190},
support = {PYO.TIP.1904.22.022//Ondokuz Mayis Üniversitesi/ ; PYO.TIP.1904.22.022//Ondokuz Mayis Üniversitesi/ ; },
abstract = {BACKGROUND: The study aimed to evaluate the microbial content and diversity in semen samples of men with obesity, determine the differences between infertile and fertile groups, and investigate the effect of seminal microbiota on semen parameters, sperm DNA fragmentation, sperm chromatin condensation, and total antioxidant capacity.

RESULTS: The study included thirteen infertile men with obesity as subjects and five fertile men with obesity as the control group (aged 18-55 years, body mass index > 30 kg/m²). The most abundant bacteria in both groups were seen to be belonging to the phylum of Bacillota, Pseudomonadota, Actinomycetota and Bacteroidota. The most common bacteria at the genus level were Pseudescherichia, Staphylococcus, Paenibacillus, Streptococcus, Klebsiella, and Moraxella, which had similar distributions in both groups. A negative correlation was observed between the percentage of aniline-positive sperm and motility (p < 0.0001), sperm concentration (p = 0.0001) and total sperm count (p = 0.001). It was found that Brevibacterium, Paenibacillus, Alistipes, Lactiplantibacillus, Rhizobacter, Sphingomonas and Venlonella genera were correlated with sperm DNA fragmentation; Pantoea, Devosia, Bacteroides, Acidovorax were correlated with total antioxidant capacity, Fusobacterium was correlated with the histone-rich sperm, and Corynebacterium, Hydrogenophaga, and Paenalcagenes were associated with body mass index.

CONCLUSION: Bacterial species in semen may play a role in male infertility by affecting semen quality, sperm DNA fragmentation or total antioxidant capacity.},
}

@article {pmid41350593,
year = {2025},
author = {Hegelmaier, T and Duscha, A and Desel, C and Fuchs, S and Shapira, M and Amidror, S and Shan, Q and Stangl, GI and Hirche, F and Kempa, S and Maifeld, A and Würtele, LM and Peplinski, J and Jauk, D and Naim, G and Shidlovsky, N and Cohen, A and Bennet, Y and Paschold, L and Dumitru, CA and Obermüller-Jevic, U and Hustvedt, SO and Timmesfeld, N and Gold, R and Zapf, A and Binder, M and Sandalcioglu, IE and Mostaghim, S and Przuntek, H and Segal, E and Yissachar, N and Haghikia, A},
title = {Supplementation with short-chain fatty acids and a prebiotic improves clinical outcome in Parkinson's disease: a randomized double-blind prospective study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29692-x},
pmid = {41350593},
issn = {2045-2322},
abstract = {BACKGROUND: Parkinson's disease is associated with a dysbiotic, proinflammatory gut microbiome, disruptions to intestinal barrier functions, and immunological imbalance. Microbiota-produced short-chain fatty acids, such as propionic and butyric acid promote gut barrier integrity and immune regulation, but their impact on Parkinson's disease pathology remains mostly unknown.

METHODS: In a randomized double-blind prospective study, 72 people with Parkinson's disease received propionic and butyric acid and/or the prebiotic fiber 2'-fucosyllactose supplementation over 6 months in combination with existing Parkinson's disease-specific therapy. Patients underwent complete neurological assessment and provided blood and stool samples before as well as 3 and 6 months after supplementation.

RESULTS: We observed a robust improvement in motor symptoms, with all intervention groups achieving clinically meaningful reductions. These motor benefits were paralleled by clinically relevant reductions in levodopa medication. In contrast, effects on nonmotor symptoms were more heterogeneous. Notably, the interventions also modulated peripheral immune responses and enhanced mitochondrial respiration in immunocytes. Postintervention microbiota remodeled inflammatory and barrier-related gene sets in gut organ cultures and improved in vitro barrier functions. Treatment response was associated with microbiome composition, distinct patterns of colonic transcription and permeability ex vivo. Multiobjective analysis revealed immune parameters associated with an optimal response to supplementation.

CONCLUSION: Short-chain fatty acids ameliorate clinical symptoms in Parkinson's disease patients and modulate intestinal and peripheral immunity.

REGISTRATION: This clinical trial was retrospectively registered with the German Clinical Trials Register (DRKS), registration number DRKS00027061 on 11/19/2021.},
}

@article {pmid41350579,
year = {2025},
author = {Tarracchini, C and Longhi, G and Gennaioli, E and Muscò, A and Rizzo, SM and Viappiani, A and Vitale, SG and Mancabelli, L and Lugli, GA and Angioni, S and Turroni, F and van Sinderen, D and Milani, C and Ventura, M},
title = {Compiling an early life human gut microbiome atlas and identification of key microbial drivers.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00868-7},
pmid = {41350579},
issn = {2055-5008},
abstract = {During the first year after birth, the infant gut microbiome undergoes a rapid and profound compositional and functional transformation, impelled by an intricate network of intrinsic and extrinsic factors. This process results in increased taxonomic and functional diversification, alongside greater interindividual variability. To better understand this early-life ecosystem, this study assessed the interindividual variability of the infant gut microbiome using a comprehensive infant gut microbiome database of 5288 fecal metagenomic data from healthy, full-term infants across various geographical locations. Our study identified six reference microbial communities, termed Early-Life Community State Types (ELi-CSTs), which not only capture specific compositional profiles and heterogeneity of the infant gut microbiome, but also record the extensive transformation experienced by this developing microbial community during the first year of human life. Indicative Species analysis and Random Forest modeling assisted the precise identification of unique, key taxonomic signatures that are critical to the structure of each ELi-CST, highlighting microbial taxa with pivotal roles in shaping the infant gut microbiota. To complement these findings, we established a bacterial biobank through dedicated cultivation efforts of the infant microbiota, comprising 182 genome-sequenced isolates corresponding to key taxa involved in early life gut microbiota assembly. This biobank provided the basis for co-cultivation experiments combined with transcriptome analyses, thereby enabling in vitro investigations into microbial cross-talk among key modulators, and yielding novel insights into the molecular interactions and cooperative dynamics behind early microbiome development.},
}

@article {pmid41350554,
year = {2025},
author = {Protic, D and Bascarevic, D and Dimitrijevic, S and Pesovic, J and Nikolic, V and Nikolic, S and Novicevic, V and Markovic, J and Arandjelovic, I and Savic-Pavicevic, D and Diricks, M and Belheouane, M and Merker, M},
title = {Microbiome modulation and behavioural improvements in children with fragile X syndrome following probiotic intake: A pilot study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29896-1},
pmid = {41350554},
issn = {2045-2322},
}

@article {pmid41350543,
year = {2025},
author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL},
title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43215},
pmid = {41350543},
issn = {2045-2322},
support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.},
}

*Soil Microbiology
Manure/microbiology
Fertilizers
*Soil/chemistry
Animals
Agriculture/methods
Poultry
Microbiota
Metagenomics
*Drug Resistance, Bacterial/genetics
Humans
Gene Transfer, Horizontal

@article {pmid41350482,
year = {2025},
author = {Farley, MJ and Scanlon, B and Crichton, M and Bigaran, A and Barnes, A and Hart, NH and Yates, PM and Eastgate, M and Alexander, K},
title = {Non-pharmacological Supportive Care Interventions during Immunotherapy for People with Cancer: A Systematic Scoping Review and Future Directions.},
journal = {Current oncology reports},
volume = {},
number = {},
pages = {},
pmid = {41350482},
issn = {1534-6269},
abstract = {PURPOSE: Immunotherapy has transformed cancer treatment and outcomes. Patients receiving immunotherapy often encounter immune-related and treatment-related adverse events, leading to substantial supportive care needs. Currently, no recommendations exist to guide the use of non-pharmacological supportive care interventions for people with cancer undergoing immunotherapy treatments. This review aims to summarise the available evidence regarding non-pharmacological supportive care strategies to inform future clinical management and research directions.

METHODS: Six electronic databases (PubMed, CINAHL, EMBASE, PsycInfo, Web of Science and Scopus) were systematically searched for studies on non-pharmacological supportive care interventions for adults undergoing immunotherapy, published from October 2014 to October 2024.

RESULTS: A total of 5383 studies were screened, with 14 meeting the inclusion criteria. Five were interventional studies and ten were observational. The interventional studies included three physical activity and exercise interventions, two dietary interventions, and one multimodal intervention. Most interventions were found to be feasible, acceptable, and demonstrate preliminary efficacy at improving quality of life, symptom burden, and clinical outcomes. Observational evidence demonstrated associations between physical activity and dietary factors and improved quality of life, reduced symptom burden, and improved clinical outcomes.

CONCLUSION: Growing observational and preliminary interventional evidence suggests a multimodal supportive care intervention that includes regular symptom monitoring, dietary support and exercise to address the physical and psychosocial needs of cancer patients undergoing immunotherapy may be beneficial. However, further high-quality trials are needed to confirm their efficacy and inform clinical implementation.},
}

@article {pmid41350437,
year = {2025},
author = {Wang, H and Li, C and Hu, Z and Feng, H and Chen, L and Ding, K and Nan, J and Wu, Y and Sheng, J and Xiong, X},
title = {Genetics-mediated regulation of intestinal gene expression on microbiome contributes to human disease heritability.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {41350437},
issn = {1744-4292},
support = {32422017//MOST | National Natural Science Foundation of China (NSFC)/ ; 32370609//MOST | National Natural Science Foundation of China (NSFC)/ ; 92353301//MOST | National Natural Science Foundation of China (NSFC)/ ; 2024YFF1207600//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; 2023YFA1800700//MOST | Dream Project of Ministry of Science and Technology of the People's Republic of China (Dream Project of MOST of China)/ ; LR25C060002//MOST | NSFC | NSFC-Zhejiang Joint Fund | | Natural Science Foundation of Zhejiang Province (ZJNSF)/ ; 226-2025-00176//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; 2024R01024//Zhejiang Provincial Leading Innovation and Entrepreneurship Team Introduction and Cultivation Program/ ; NA//Benyuan Foundation/ ; NA//K.C.Wong Education Foundation/ ; 012024002//The State Key Laboratory of Transvascular Implantation Devices/ ; },
abstract = {The gut microbiome plays fundamental roles in physiological and pathological processes, yet its interaction with host gene expression and contribution to disease remain underexplored. Here, we integrate the genetic regulatory maps of 116 microbial genera with gene expression quantitative trait loci (eQTLs) and DNA methylation QTLs (mQTLs) in three intestinal tissues to dissect host-microbiome interaction. We identify 6088, 5810, and 2398 gene-to-microbiome regulatory loci in the transverse colon, sigmoid colon, and ileum, respectively. Among these, 13.2% of genes show broad regulatory effects on multiple genera, with functional enrichments in developmental, metabolic, and immune-related pathways. Integrative analysis with genome-wide association studies (GWASs) reveals 283 microbiome-dependent disease loci. We observe pleiotropic effects mediated by the gene-to-microbiome regulation at both microbiome and disease layers. Notably, we predict and experimentally validate the suppressive effect of Allisonella on depression through regulating bile acid abundance, and the regulation of Parasutterella on short-chain fatty acid and its contribution to allergic rhinitis. The gene-microbiome-disease regulatory maps are available at our interactive database (https://xiongxslab.github.io/microbiomeMR/).},
}

@article {pmid41350154,
year = {2025},
author = {Vonaesch, P and Garneau, JR and Dominguez-Bello, MG},
title = {From global to local: rethinking the design of probiotic intervention strategies.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.11.009},
pmid = {41350154},
issn = {1878-4380},
abstract = {The human microbiome plays a crucial role in maintaining homeostasis and influencing disease development, yet its composition varies across geography, age, and lifestyle. These differences challenge the efficacy of universal probiotic treatments and call for more personalized or regionally adapted approaches. In this review we examine the limitations of universal probiotics, emphasizing the importance of considering host-microbe co-adaptation, local dietary practices, and ecological context. We argue that probiotic design must account for microbial diversity, strain-level adaptation, and functional redundancy, and we explore how these factors affect colonization success and therapeutic potential. Finally, we discuss ways to re-center microbiome knowledge within diverse ecological, cultural, and epistemic traditions for a global, inclusive approach allowing for microbiome-targeted therapies that are both effective and accessible.},
}

@article {pmid41350118,
year = {2025},
author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.},
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.70099},
pmid = {41350118},
issn = {1600-0714},
abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.

METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.

RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.

CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.},
}

@article {pmid41350098,
year = {2025},
author = {Puca, P and Coppola, G and Parello, S and Capobianco, I and Colantuono, S and Scaldaferri, F and Papa, A},
title = {Atherosclerotic cardiovascular disease and inflammatory bowel disease: epidemiology, pathogenesis and risk assessment.},
journal = {Best practice & research. Clinical gastroenterology},
volume = {78},
number = {},
pages = {102056},
doi = {10.1016/j.bpg.2025.102056},
pmid = {41350098},
issn = {1532-1916},
mesh = {Humans ; Risk Assessment ; *Inflammatory Bowel Diseases/epidemiology/complications/drug therapy ; *Atherosclerosis/epidemiology/etiology ; Risk Factors ; },
abstract = {Inflammatory bowel diseases (IBD) are systemic inflammatory conditions increasingly recognized to confer excess risk of atherosclerotic cardiovascular disease (ASCVD), particularly in younger patients and during periods of active disease. We here synthesize evidence across epidemiology, mechanisms, risk stratification, and management at the IBD-ASCVD interface. Across population cohorts and meta-analyses, IBD associates with modest but consistent increases in ischemic heart disease, cerebrovascular events, and peripheral arterial disease, with higher relative risks for mesenteric ischaemia and for premature events; risk escalates with inflammatory burden and flares, while traditional factors alone partially explain the association. Prolonged corticosteroid exposure correlates with adverse vascular outcomes, whereas effective control of intestinal inflammation, particularly with anti-TNF biologics, appears protective; the absolute cardiovascular risk with Janus kinase inhibitors seems largely determined by baseline risk profile and is low in appropriately selected patients. Proposed drivers include dysbiosis and microbially derived metabolites (e.g., trimethylamine-N-oxide, imidazole propionate), intestinal barrier failure with low-grade endotoxemia and Toll-like receptor-4 activation, neutrophil- and platelet-mediated thromboinflammation, and inflammasome pathways that accelerate atherothrombosis. For risk stratification, non-invasive vascular measures (arterial stiffness, carotid intima-media thickness, coronary artery calcium) and general calculators (SCORE2/ASCVD) are informative, though underestimation in younger patients is possible; expert guidance emphasizes mitigation of inflammatory activity, smoking cessation, prudent steroid use, and lipid monitoring with small-molecule therapy. In conclusion, IBD confers clinically relevant ASCVD risk through immune-microbiome-barrier interactions superimposed on traditional factors. Routine cardiovascular assessment, aggressive control of intestinal inflammation, lifestyle optimization, and judicious therapy selection should be embedded in IBD care, while prospective studies refine prediction tools and test targeted preventive strategies across phenotypes and ages.},
}

Humans
Risk Assessment
*Inflammatory Bowel Diseases/epidemiology/complications/drug therapy
*Atherosclerosis/epidemiology/etiology
Risk Factors

@article {pmid41350095,
year = {2025},
author = {Deleu, S and Sabino, J},
title = {Cutting edge developments and novel targets in IBD: Microbiome in IBD.},
journal = {Best practice & research. Clinical gastroenterology},
volume = {78},
number = {},
pages = {102060},
doi = {10.1016/j.bpg.2025.102060},
pmid = {41350095},
issn = {1532-1916},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; *Inflammatory Bowel Diseases/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Crohn Disease/microbiology/therapy ; *Colitis, Ulcerative/microbiology/therapy ; Synbiotics/administration & dosage ; },
abstract = {Inflammatory bowel disease (IBD), a non-communicable disease encompassing Crohn's disease and ulcerative colitis, is a chronic disorder with increasing prevalence and complex etiology. Emerging evidence highlights the gut microbiome's pivotal role in IBD pathogenesis, driving interest in microbiome-targeted therapeutic strategies. This narrative review explores the latest advancements in microbiome modulation for IBD management, encompassing antibiotics, prebiotics, probiotics, synbiotics, postbiotics, and fecal microbiota transplantation. Additionally, dietary interventions, physical activity, as well as non-bacterial microbiota components such as fungi, archaea, and bacteriophages are examined for their potential roles in restoring microbial equilibrium and mitigating intestinal inflammation. As research progresses, a multimodal approach integrating microbiota-targeted therapies with lifestyle modifications and conventional pharmacologic treatments may offer a personalized and effective strategy for IBD management.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Prebiotics/administration & dosage
*Inflammatory Bowel Diseases/therapy/microbiology
Anti-Bacterial Agents/therapeutic use
*Crohn Disease/microbiology/therapy
*Colitis, Ulcerative/microbiology/therapy
Synbiotics/administration & dosage

@article {pmid41350090,
year = {2025},
author = {Petito, V and Deleu, S and Lopetuso, LR and Pizarro, TT and Scaldaferri, F},
title = {The way forward: Towards pragmatic preclinical microbiome research in inflammatory bowel disease.},
journal = {Best practice & research. Clinical gastroenterology},
volume = {78},
number = {},
pages = {102054},
doi = {10.1016/j.bpg.2025.102054},
pmid = {41350090},
issn = {1532-1916},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/therapy ; *Gastrointestinal Microbiome ; Animals ; Disease Models, Animal ; Translational Research, Biomedical ; },
abstract = {Clinical trials for inflammatory bowel disease are primarily randomized clinical trials, which have been the gold standard since the 1940s. However, these trials often focus on a specific group of patients, are expensive, and focus on one treatment option over a short period. Challenges in IBD research include environmental triggers, preclinical mechanisms, novel technologies, precision medicine, and pragmatic clinical research. Pragmatic research aims to generate evidence for real-world clinical practice by including diverse patient populations and assessing outcomes that matter to patients and healthcare providers. Advancements in biomedical research require high-quality translational research and successfully preclinical models able to convert promising laboratory results into clinical applications. Such approaches increase external validity of results, informs decision-making, optimizes care strategies, and improves outcomes for IBD patients. Specifically, increasing both internal and external validity remains a challenge in both in vitro/ex vivo and in vivo preclinical research. Therefore, we here aim to give an overview of recent advances in preclinical research models for IBD both in vitro/ex vivo and in vivo and pragmatic strategies to implement with a specific focus on microbiome research. While each model has its limitations, combining and implementing various techniques can provide a comprehensive preclinical evaluation. Advances in the field, such as personalized gut-on-a-chip models and humanized spontaneous animal models, will facilitate more pragmatic and effective strategies for identifying, evaluating, and predicting responses to potential new therapeutics in future research.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/therapy
*Gastrointestinal Microbiome
Animals
Disease Models, Animal
Translational Research, Biomedical

@article {pmid41350062,
year = {2026},
author = {Wang, Y and Chen, L and Wu, X and Gong, B and Lv, G and Zhang, J and Shen, W and Gao, X and Xu, A and Gao, H},
title = {Bacillus velezensis SF-10 modulates the rhizosphere core microbiome by stimulating the probiotic community to control tomato wilt disease.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 2},
pages = {106805},
doi = {10.1016/j.pestbp.2025.106805},
pmid = {41350062},
issn = {1095-9939},
mesh = {*Solanum lycopersicum/microbiology ; *Bacillus/physiology ; *Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; *Probiotics ; Soil Microbiology ; *Microbiota ; Fusarium/physiology ; },
abstract = {Tomato wilt disease, caused by Fusarium spp., is one of the most harmful soil-borne diseases globally. Biological control is an environmentally friendly and effective strategy, but its success largely depends on the type of bacterial strain used and its ability to regulate rhizosphere soil microorganisms. In this study, a new bacterium Bacillus velezensis SF-10 was from rhizosphere of healthy tomato plants grown in wilt-infested fields, which showed a high control effect of 74.14 % against wilt disease in tomato seedlings. The SF-10 can produce amylase, cellulase, siderophores, and IAA, and has demonstrated stable colonization via a constructed rifampicin resistance marker system. However, it is currently unknown how SF-10 inoculation regulates soil microbial communities and plant metabolites to achieve disease resistance, especially during the seedling stage. Here, we used amplicon sequencing and metabolite profiling revealed that B. velezensis SF-10 significantly altered the structure of the rhizosphere microbiota in plants challenged with the wilt pathogen. During this process, B. velezensis SF-10 recruits various beneficial soil bacteria, particularly Sphingomonas and Flavobacterium, to suppress F. oxysporum. These beneficial bacteria exhibited significant positive correlations with secondary metabolites such as total phenols, flavonoids, and lignin. In summary, B. velezensis SF-10 enhancing plant resistance by regulating the rhizosphere microbial community and increasing secondary metabolite content, providing valuable insights for the biological control of soil-borne diseases in vegetables.},
}

*Solanum lycopersicum/microbiology
*Bacillus/physiology
*Rhizosphere
*Plant Diseases/microbiology/prevention & control
*Probiotics
Soil Microbiology
*Microbiota
Fusarium/physiology

@article {pmid41349926,
year = {2025},
author = {Zhao, W and Zhou, X and Cai, H and Tang, T and Shen, Y and Sun, Z and Zhu, J and Yu, Y},
title = {The relation between gut microbiota, brain structure and cognitive function in metabolic syndrome.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106209},
doi = {10.1016/j.bbi.2025.106209},
pmid = {41349926},
issn = {1090-2139},
abstract = {Metabolic syndrome (MetS) can lead to accelerated brain aging and cognitive decline. Evidence has suggested the involvement of the microbiota-gut-brain axis in the relationship between MetS and cognitive dysfunction, but the underlying mechanisms are unclear. Using magnetic resonance imaging and 16S rRNA gene amplicon sequencing, we collected data of brain structure (gray matter volume and white matter integrity) and gut microbiome from 97 patients with MetS and 103 sex-, age- and education-matched healthy controls. The Trail-making Test A and auditory verbal learning test were used to assess executive function and memory. Group differences in gut microbiome, brain structure, and cognitive function as well as their plausible interactive links in patients with MetS were examined. We found that patients with MetS exhibited impaired executive function and memory ability, both depleted short-chain fatty acids (SCFA)-producing bacteria and enriched inflammation-triggering bacteria, gray matter atrophy of several brain regions and microstructural integrity damage of multiple white matter tracts. Of more importance, correlation and mediation analyses demonstrated that the abnormal brain structure mediated the associations between the depleted anti-inflammatory bacteria (i.e., Clostridium XlVa, Kineothrix and Acetivibrio) and the impaired cognitive function in patients with MetS. Our findings not only point to new hypotheses about potential neurobiological pathways by which gut microbial dysbiosis may lead to cognitive dysfunction in the context of MetS, but also highlight the potential therapeutic value of targeting gut microbiota for cognitive impairments in patients with MetS.},
}

@article {pmid41349815,
year = {2025},
author = {Ma, X and Wang, D and Kuang, Y and Nan, S and Niu, Y and Wu, Y and Zhang, W},
title = {Resveratrol ameliorates early-weaning stressed calves via alterations in gut microbiome and metabolome.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27101},
pmid = {41349815},
issn = {1525-3198},
abstract = {Early weaning disrupts gut microbiota homeostasis and increases oxidative stress and inflammation in calves, thus negatively affecting their growth performance and health. Resveratrol is a polyphenol with antioxidant and anti-inflammatory properties that modulates gut microbiota and metabolites. In the present study, we investigated the effects of resveratrol on growth performance, immune function, antioxidant capacity, gut microbiota, and metabolic pathways in early-weaning calves. Thirty-six newborn Simmental × Holstein F1 generation female calves were randomly assigned to one of 3 treatment groups: conventional weaning at 63 d of age (CON), early weaning at 49 d of age (EW), or early weaning at 49 d of age with 2 g/d resveratrol supplementation from d 7 to d 49 (EWR). The results revealed that the final BW, ADG, and feed efficiency were greater in the EWR group than in the CON group, and diarrhea incidence was significantly reduced. The EWR treatment decreased the concentrations of the proinflammatory cytokine IL-1β and the oxidative damage product malondialdehyde. Meanwhile, resveratrol supplementation increased the anti-inflammatory cytokine IL-4, catalase, and the total antioxidant capacity in early-weaning calves, which were not significantly different from CON group. In addition, EWR increased the abundance of Parabacteroides, Eubacterium_coprostanoligenes_group, Christensenella, and Ruminococcaceae, as well as increased concentration of butyric acid, valeric acid, isobutyric acid, isovaleric acid, and total branched short-chain fatty acids. Metabolomic analysis revealed that resveratrol significantly enhanced the tryptophan metabolic pathway. Correlation analysis suggested that Parabacteroides was closely related to the modulatory effects of resveratrol in early-weaning calves through its involvement in tryptophan metabolism. In conclusion, dietary resveratrol supplementation improves growth performance and reduces diarrhea in early-weaning calves by alleviating inflammation and oxidative stress, modulating gut microbiota, and enhancing microbial tryptophan metabolism.},
}

@article {pmid41349670,
year = {2025},
author = {Liu, T and Li, J and Wang, F and Meng, J},
title = {Enhanced caproic acid production through electro-fermentation: A novel approach for resource utilization of lignocellulosic waste.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123505},
doi = {10.1016/j.envres.2025.123505},
pmid = {41349670},
issn = {1096-0953},
abstract = {Caproic acid production from lignocellulosic biomass as sole substrate via anaerobic fermentation is a promising technology, but limited by low yields and selectivity. This study proposed using electro-fermentation to enhance caproic acid production from rice straw, and analyzed the underlying mechanisms of the enhancement. Cathodic electro-fermentation (CEF) significantly increased both the concentration and selectivity of caproic acid, approximately doubling the levels observed in open-culture fermentation. Transfer cultures of microbiome within the CEF system further enhanced the caproic acid production performance. After straw loading and cathode potential optimization, the maximum caproic acid concentration and selectivity reached 6.96 ± 0.42 g/L and 33.5 ± 2.27%, respectively. Microbial community analysis and functional prediction indicated that CEF enriched caproic acid synthesis genus, including Caproiciproducens, Rummeliibacillus, and Oscillibacter. The reverse β-oxidation pathway (RBO) pathway and the synthesis pathway for acetyl-CoA were also strengthened. Straw loading and cathode potential were key factors influencing caproic acid production. This study introduces a method for enhancing caproic acid production from lignocellulosic waste and contributes to understanding the mechanisms behind CEF-enhanced fermentation of raw waste biomass.},
}

@article {pmid41349548,
year = {2025},
author = {Zarour, HM and Trinchieri, G},
title = {Harnessing the Microbiome in Cancer Immunotherapy: Regulation, Prediction, and Therapeutic Targeting.},
journal = {Annual review of immunology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-immunol-082323-114522},
pmid = {41349548},
issn = {1545-3278},
abstract = {Humans are metaorganisms, composed of both host (human) cells and a roughly equal number of commensal microorganisms-collectively known as the microbiome-residing primarily at epithelial barrier surfaces. This review considers human cancer as a disease of the metaorganism, to which the microbiome contributes by influencing genome stability, tissue organization, inflammation, immunity, tumor initiation and promotion, metastasis formation, and therapeutic response. We summarize evidence demonstrating that machine learning models trained on patients' microbiome features moderately predict clinical response to immunotherapy and the development of immune-related adverse events. We review results from single-arm and randomized clinical trials wherein fecal microbiome transplantation from therapy-responsive patients or healthy donors, when combined with therapy targeting programmed cell death 1 (PD-1), improved outcomes in PD-1-refractory patients or served as an effective first-line intervention. We conclude by highlighting the emerging opportunities and ongoing challenges in leveraging the microbiome to enhance the efficacy and safety of cancer immunotherapy.},
}

@article {pmid41349479,
year = {2025},
author = {Chau, D and Turni, C and Roura, E and Omaleki, L},
title = {Use of non-bound proteinogenic amino acids to modulate the growth of pathogenic bacteria from broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106121},
doi = {10.1016/j.psj.2025.106121},
pmid = {41349479},
issn = {1525-3171},
abstract = {Pathogenic bacteria can inhabit the chicken intestinal tract and potentially cause disease and mortality in chickens. Proteinogenic amino acids are major nutrients available in the intestine that have diverse growth-modulating effects on bacteria. However, limited knowledge exists about the direct association between amino acids and the growth of bacteria in the microbiome of the chicken's intestinal tract. The present study evaluated the growth-modulating effects of the 20 proteinogenic amino acids on chicken pathogens. Seven bacterial species were tested, including avian pathogenic Escherichia coli (APEC), Salmonella enterica., Staphylococcus aureus, Clostridium perfringens, Enterococcus cecorum, Enterococcus faecalis, and Enterococcus faecium. All bacteria were tested in minimal nutrient medium (MNM) in an in vitro model, with or without the addition of each amino acid. Bacterial growth was measured by absorbance (OD600) and visualised as growth curves. l-cysteine significantly (p ≤ 0.05) inhibited the growth of APEC, extended the lag phase and increased the maximum density of C. perfringens, Salmonella enterica. and S. aureus. In contrast, l-glutamine and l-glutamic acid significantly shortened the lag phase and increased both the growth rate and maximum density of C. perfringens, Glycine and l-serine significantly (p ≤ 0.05) increased the maximum density of S. aureus. The effect of amino acids was insignificant (p ≥ 0.05) on the total growth of Enterococcus spp. These findings suggested that l-cysteine has inhibiting effects on APEC, C. perfringens, S. enterica and S. aureus. l-glutamine and l-glutamic acid promoted the growth of C. perfringens, while glycine and l-serine promoted the growth of S. aureus.},
}

@article {pmid41349354,
year = {2025},
author = {Tokallou, MA and Mahmoudi, M and Kheder, RK and Azghadi, SF and Rastgoo, E and Sabouri, A and Esmaeili, SA},
title = {Probiotics and the immune landscape: An ally in breast cancer combination therapy.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {143},
number = {},
pages = {113011},
doi = {10.1016/j.nut.2025.113011},
pmid = {41349354},
issn = {1873-1244},
abstract = {Breast cancer is the second cause of death among women in the world. Breast cancer deaths are anticipated to increase to 3.2 million by 2050. Although treatment methods such as surgery, chemotherapy, radiation, targeted therapies, and immunotherapy have advanced, survivors still face long-term problems. Probiotics are increasingly recognized as a promising therapeutic modality in cancer management, primarily through their capacity to modulate the gut microbiota and enhance host immune responses, in addition to their direct antitumor effects. Some probiotic strains also block cancer cell growth by promoting cancer cell apoptosis and reducing cell proliferation. Moreover, probiotics can also boost the effect of medications such as immune checkpoint inhibitors by boosting patients' immune systems against cancer cells. The objective of this review is to investigate the influence of probiotics on the immune system, their direct effects on cancer cells, and their potential in the treatment of breast cancer therapies.},
}

@article {pmid41349338,
year = {2025},
author = {Bastías, DA and Johnson, LJ and Jáuregui, R and Applegate, ER and Liu, X and Mace, WJ and Card, SD},
title = {Paenibacillus taichungensis strain E222: Mother and progeny plant growth promotion and association with an Epichloë fungal endophyte.},
journal = {Plant physiology and biochemistry : PPB},
volume = {230},
number = {},
pages = {110851},
doi = {10.1016/j.plaphy.2025.110851},
pmid = {41349338},
issn = {1873-2690},
abstract = {There are limited publications evaluating the effects of bacteria on plant-fungal symbioses. We evaluated the effects of a bacterium (designated strain E222) on perennial ryegrass (Lolium perenne) symbiotically associated with an Epichloë endophyte. Within this tripartite symbiosis, E222 was characterised as an ectosymbiont of Epichloë sp. AR135, the latter a mutualistic endophytic fungus of L. perenne. We hypothesised that (i) E222 would promote host plant growth and not interfere with the in planta production of AR135-derived antiherbivore alkaloids and AR135 growth and (ii) the Epichloë hyphal colonisation of plant seeds would facilitate the E222 entry into the progeny seeds. Via whole genome analysis, E222 was identified as Paenibacillus taichungensis and predicted to possess plant growth-promoting traits. E222 was inoculated on seeds of perennial ryegrass associated with AR135 and the bacterium was systemically present in the subsequent seedlings. E222 promoted the growth of AR135-associated plants, as expected, but reduced AR135-derived alkaloid concentrations and decreased the AR135 biomass at an early plant stage. AR135, but not E222, was detected in the progeny seeds and in line with the absence of E222, growth of progeny seedlings was not affected by the bacterial inoculation of mother plants. The bacterial effects on plants and Epichloë may be explained by the predicted abilities of E222 to promote plant growth (e.g., auxin production) and compete with AR135 for alkaloid precursors (e.g., tryptophan).},
}

@article {pmid41349311,
year = {2025},
author = {Manfreda, C and Ghidini, S and Fuschi, A and Remondini, D and Guarneri, F and Alborali, GL and Fernández-Trapote, E and Cobo-Dìaz, JF and Alvarez-Ordóñez, A and Ianieri, A},
title = {In-depth characterization of microbiome and resistome of carcasses and processing environments in a swine slaughterhouse.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110820},
doi = {10.1016/j.vetmic.2025.110820},
pmid = {41349311},
issn = {1873-2542},
abstract = {Antimicrobial resistance represents a critical global health challenge. Within the swine production chain, all stages have been identified as potential reservoirs for antimicrobial resistance genes. In the present study whole metagenomic sequencing technology was applied in a swine slaughterhouse and pig carcasses to investigate microbial communities and their associated antimicrobial resistance genes. Actinomycetota and Pseudomonadota were the dominant phyla across all samples, while Bacillota, Bacteroidota, and Campylobacteriota were more prevalent in the dirty zone and carcass samples than in the clean zone. Key antimicrobial-resistant bacteria included genera such as Acinetobacter, Aeromonas, and Streptococcus, with Acinetobacter spp., Streptococcus suis, and Aliarcobacter cryaerophilus identified as high-priority species for food safety due to their persistence and antimicrobial resistance genes associations. Several genera showed strong correlations with resistance to macrolides, lincosamides, and beta-lactams. Moreover, the plasmid-borne and lateral gene transfer events were associated with dirty zone and carcass samples in comparison to clean zone samples, suggesting the potential dissemination of antimicrobial resistance genes, especially for macrolides and sulphonamides resistance genes. Tetracycline, beta-lactam, and aminoglycoside resistance genes were the most abundant antimicrobial resistance genes across all samples, consistent with a pig slaughterhouse environment. This study highlights distinct microbiome profiles across environmental zones of a pig slaughterhouse, reflecting the adaptation of bacterial taxa to specific processing conditions. The findings have significant implications for food business operators who have to apply appropriate hygienic measures to reduce the dissemination of bacterial food-borne pathogens and to mitigate the risk of antimicrobial resistance transfer along the food chain.},
}

@article {pmid41349248,
year = {2025},
author = {Darzi, A and Shokouhfar, M and Farajee, N and Ghafari, A and Deldar, F and Eini, P and Vanan, AG and Bahrami, N},
title = {Immune checkpoint inhibition in renal cell carcinoma: Mechanisms of resistance and emerging therapeutic strategies.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {193},
number = {},
pages = {118875},
doi = {10.1016/j.biopha.2025.118875},
pmid = {41349248},
issn = {1950-6007},
abstract = {Renal cell carcinoma (RCC) represents a major therapeutic challenge due to its highly immunosuppressive tumor microenvironment. Over the past decade, immune checkpoint inhibitors (ICIs) have revolutionized the management of advanced RCC, shifting treatment paradigms from cytokine- and VEGF-based therapies toward immunotherapy-driven strategies. This review highlights the mechanisms of immune evasion in RCC, focusing on the roles of tumor-associated macrophages, regulatory T cells, and cancer-associated fibroblasts, as well as the key checkpoints PD-1/PD-L1 and CTLA-4. We summarize pivotal clinical trials that established ICIs as the standard of care, including monotherapy and combination regimens with tyrosine kinase inhibitors (TKIs) and mTOR inhibitors, which have demonstrated superior objective response rates, progression-free survival, and overall survival compared to conventional therapies. Despite these advances, primary and acquired resistance remain significant barriers, driven by adaptive signaling pathways and immune exhaustion. Emerging strategies such as dual checkpoint blockade, metabolic and angiogenic co-targeting, and biomarker-guided personalization are under investigation to overcome resistance. Furthermore, the integration of multi-omics profiling, artificial intelligence, and microbiome modulation may refine patient selection and optimize therapeutic outcomes. Collectively, ICIs have transformed RCC treatment, yet future progress will depend on deeper biological insight, rational combination design, and individualized immunotherapy approaches.},
}

@article {pmid41349172,
year = {2025},
author = {Gupta, K and Rahaman, J and Mukherjee, D},
title = {Gut and oral microbiota in oral bone tissue engineering: Impact of mechanistic and molecular pathways.},
journal = {Differentiation; research in biological diversity},
volume = {147},
number = {},
pages = {100919},
doi = {10.1016/j.diff.2025.100919},
pmid = {41349172},
issn = {1432-0436},
abstract = {The influence of the oral-gut microbiota on craniofacial bone healing is increasingly recognised, as its interactions with host osteoimmune pathways are now understood to shape the course of regeneration. These microbiota play an important role in maintaining bone mass via immune modulation, metabolite production, and nutrient resorption. Under conditions of dysbiosis, inflammatory signalling through NF-κB, NLRP3, and the RANKL/OPG axis is amplified, while Wnt/β-catenin and BMP/Smad pathways are suppressed, resulting in heightened oxidative stress, increased osteoclast activity, and progressive alveolar bone loss. In contrast, a balanced microbial community is associated with the production of short-chain fatty acids, through which epithelial barrier stability is supported, Th17/Treg equilibrium is restored, and osteoblast differentiation and mineralisation are promoted. In this review, mechanistic, preclinical, and emerging clinical evidence are integrated to illustrate how these microbial interactions regulate bone remodelling and influence the performance of engineered scaffolds. Therapeutic opportunities involving probiotics, prebiotics, synbiotics, engineered microbial strains, and microbiome-responsive biomaterials are emphasized. Cellular and molecular pathways controlling bone homeostasis, including the composition of the oral and gut microbiota, impacting oral bone health, have been summarized. Overall, the microbiome is positioned as a central biological determinant of oral bone regeneration, and its targeted modulation in addition to microbiome-based therapeutic strategies for bone tissue regeneration is proposed as a personalized approach for improving outcomes in craniofacial tissue engineering.},
}

@article {pmid41349014,
year = {2025},
author = {Huang, Z and Ou-Yang, J and Zhou, Z and Sun, H and Wang, L and Chen, Y and He, G and Zhang, Y},
title = {Plant compartments and regional variations shape the community structures and functional composition of endophytic fungi of Citrus aurantium.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0237},
pmid = {41349014},
issn = {1480-3275},
abstract = {Although Citrus aurantium has enormous medicinal and ecological value in southern China, little research has been conducted into the composition and functions of endophytic fungi in it. To better explore the characteristics of the endophytic fungal community in C. aurantium, ITS rRNA gene analyses were used to characterise the endophytic fungal microbiome across 3 plant compartments and 3 regions. The results shown that a total of 12109 OTUs were obtained and further divided into 15 phyla and 768 genera. Ascomycota was the dominant phylum. Fusarium, Alternaria, Mortierella, Plectosphaerella, Cladosporium, Colletotrichum, Trichomerium, Botryotrichum, and Aspergillus were the dominant genera. The endemic and dominant genera of endophytic fungi in C. aurantium exhibited plant compartment specificity. The assembly of endophytic fungal communities was dominated by homogeneous selection of deterministic processes. The endophytic fungal genera of C. aurantium predominantly exhibited positive interactions (with a proportion > 99%). The dominant functions of endophytic fungi in C. aurantium were pathotroph and saprotroph. The composition (niche: R2=0.09, P=0.001; site: R2=0.06, P=0.021) and functional components (niche: R2=0.117, P=0.002; site: R2=0.122, P=0.006) exhibited significant plant compartment and region specificity. The results of this study reveal the characteristics of the endophytic fungal community of C. aurantium, and provide a theoretical reference for the further development and utilization of endophytic fungal resources.},
}

@article {pmid41348832,
year = {2025},
author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A},
title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337760},
doi = {10.1371/journal.pone.0337760},
pmid = {41348832},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; },
abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.},
}

Animals
*Gastrointestinal Microbiome
Humans
Mice
*Fecal Microbiota Transplantation/methods
*Virome
Male
Diet, High-Fat/adverse effects
Obesity/therapy/microbiology
*Feces/virology
Mice, Inbred C57BL
*Glucose/metabolism
Metabolic Syndrome/therapy/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics

@article {pmid41348596,
year = {2025},
author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA},
title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf638},
pmid = {41348596},
issn = {1477-4054},
support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; },
mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; },
abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.},
}

*Virome
*Workflow
*Metagenomics/methods
*Software
High-Throughput Nucleotide Sequencing
*Computational Biology/methods
*Viruses/genetics/classification
Metagenome
Microbiota
Genome, Viral
Reproducibility of Results

@article {pmid41348595,
year = {2025},
author = {Jiang, L and Li, Y and Xie, B and Wang, L and Chen, S},
title = {In silico approaches for discovering microbial antiviral defense systems.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf619},
pmid = {41348595},
issn = {1477-4054},
support = {2022YFA0912200//National Key Research and Development Program of China/ ; 32125001//National Natural Science Foundation of China/ ; 32220103001//National Natural Science Foundation of China/ ; 32430006//National Natural Science Foundation of China/ ; ZDSYS20230626090759006//Shenzhen Science and Technology Program/ ; },
mesh = {*Computational Biology/methods ; *Computer Simulation ; Bacteriophages/genetics ; *Bacteria/virology/genetics ; },
abstract = {Prokaryotes possess a remarkably diverse and dynamic repertoire of antiviral defense systems, enabling them to withstand phage predation. However, their frequent horizontal gene transfer, extensive sequence diversity, modular genomic organization, and rapid evolution make purely experimental discovery challenging. Coupled with the massive influx of microbial genomes from high-throughput sequencing, computational strategies have become indispensable complementary tools that can enhance the efficiency and scope of defense systems discovery. In this review, we categorize computational approaches into four major strategies: (i) Sequence homology-based methods, which reliably annotate known defense systems through protein sequence similarity but are limited in detecting highly divergent or novel systems; (ii) Structure-guided approaches, which leverage conserved protein folds to uncover remote homologs and single-gene defense proteins, providing sensitivity beyond sequence-based identification, albeit at high computational cost; (iii) Genomic context-based strategies, which exploit gene co-localization and defense islands to uncover multi-gene defense clusters and previously uncharacterized defense modules; and (iv) Artificial intelligence-powered methods, which integrate sequence-derived embeddings with genomic context information to predict low-homology proteins and reconstruct candidate defense systems at scale, enabling discovery of novel systems beyond the reach of conventional approaches. We further discuss emerging tools and frameworks, such as the conserved gene cluster discovery tool and genomic foundation models, which hold strong potential to extend conventional approaches for identifying novel defense systems and supporting the generative design of synthetic modules. By comparing methodological principles, strengths, and limitations, this review provides a practical framework for the systematic exploration of microbial immune systems, guiding applications such as rational phage therapy, microbiome engineering, and synthetic biology.},
}

*Computational Biology/methods
*Computer Simulation
Bacteriophages/genetics
*Bacteria/virology/genetics

@article {pmid41348443,
year = {2025},
author = {Luu, LDW and Bryant, C and Brown, J and Turner, M and Pham, TH and Mazraani, R and Burke, C and Jury, B and Shrestha, M and Fleming, K and Bateson, D and Russell, D and Bassett, F and Ong, E and Hocking, JS and Sweeney, S and Huston, WM},
title = {Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001574},
pmid = {41348443},
issn = {2057-5858},
mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Case-Control Studies ; *Vagina/microbiology ; Adult ; *Cervix Uteri/microbiology ; Vaginosis, Bacterial/microbiology ; Gardnerella vaginalis/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Young Adult ; },
abstract = {Pelvic inflammatory disease (PID), which involves infection and inflammation of the female reproductive tract, can lead to sequelae including chronic pelvic pain, ectopic pregnancy and tubal factor infertility. A causative pathogen is not identified in many PID cases (idiopathic PID) and does not develop in all women with a sexually transmitted infection or bacterial vaginosis. Therefore, there is a need to better understand the pathogenesis of PID. A case-control study was conducted to explore microbiome, antibiotic resistance and immune gene expression in PID. Microbial profiling using both 16S rRNA gene amplicon and metagenomic approaches revealed that bacterial vaginosis-associated bacteria such as Gardnerella vaginalis, Fannyhessea vaginae, Ureaplasma parvum and members of the Prevotella spp. were significantly enriched in PID cases, while healthy controls were associated with Lactobacillus (L.) crispatus. Quantitative analysis with species-specific quantitative real-time PCR (qPCR) indicated that a high copy number of L. crispatus (measured using calibrated copy estimates by qPCR) was strongly associated with cervical samples from women in the control group, whereas PID cases with this organism had low copies when measured using qPCR. Antibiotic resistance to tetracyclines was more frequently predicted in metagenome-assembled genomes from PID cases, and corresponding isolates cultured from cases were less susceptible to doxycycline (L. iners). Overall, this study supports that PID is associated with cervicovaginal dysbiosis and an absence or low quantity of L. crispatus.},
}

Humans
Female
*Pelvic Inflammatory Disease/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Case-Control Studies
*Vagina/microbiology
Adult
*Cervix Uteri/microbiology
Vaginosis, Bacterial/microbiology
Gardnerella vaginalis/genetics
Metagenomics
*Bacteria/genetics/classification/isolation & purification
Young Adult

@article {pmid41348173,
year = {2025},
author = {Dos Anjos Almeida, JV and de Medeiros Oliveira, M and Kuniyoshi, TM and Mamani Sanca, FM and Nóbrega Mendonça, CM and Cabrera Matajira, CE and Louvisi, AL and de Souza Oliveira, RP and de Mello Varani, A},
title = {Genome-Resolved in Silico Analysis of Poultry and Swine Lactobacillales Provides a Data-Driven Framework for Elucidating Metabolic Complementary interactions in Multi-Strain Probiotics.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41348173},
issn = {1867-1314},
support = {2024/05163-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/04372-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/05677-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2020/13271-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/14986-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2024/07246-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/25511-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/25511-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 312923/2020-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 304367/2022-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Probiotics are live microorganisms that provide health benefits to the host by improving digestion, enhancing nutrient absorption, and modulating the immune system. Among them, lactic acid bacteria are known for producing vitamins and short-chain fatty acids, both essential for intestinal health. In this in silico study, we performed high-fidelity (PacBio HiFi) whole-genome sequencing and comprehensive comparative genomic analysis of five Lactobacillales strains (Enterococcus lactis, Enterococcus mundtii, Ligilactobacillus agilis, Limosilactobacillus reuteri, Limosilactobacillus vaginalis) isolated from the intestinal microbiota of chickens and pigs. The assembled genomes ranged from 1.8 to 2.8 Mb, with more than 98% completeness and less than 1.31% contamination. Taxonomic classification, presence of antimicrobial resistance genes, bacteriocin biosynthetic potential, carbohydrate-active enzyme repertoires and vitamin biosynthesis pathways, and capacity to degrade plant polysaccharides were investigated. Functional characterization identified 65 families of carbohydrate-active enzymes, with E. mundtii presenting the greatest diversity (43 families) and absolute number (100 terms) of enzymes. Metabolic reconstruction suggested functional specialization among strains, with xylooligosaccharide degradation exclusive to E. mundtii and pectin utilization limited to E. lactis. Genes related to the biosynthesis of B-complex vitamins, including riboflavin, folate, and menaquinone, showed heterogeneous and complementary distribution among strains. These findings suggest the potential for metabolic complementarity and cross-feeding, where metabolites produced by one strain serve as precursors for biosynthetic pathways in others. Collectively, these genome-resolved insights offer a data-driven framework for designing multi-strain probiotics aimed at improving intestinal health and feed efficiency in poultry and swine.},
}

@article {pmid41347891,
year = {2025},
author = {Delannoy, J and Ferraris, L and Labellie, C and Dupire, L and Ilavska, D and Butel, MJ and Barbut, F and Aires, J},
title = {Commensal Clostridia in the preterm gut as reservoirs of antimicrobial resistance: susceptibility profiles, and resistance genes.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf122},
pmid = {41347891},
issn = {1574-6941},
abstract = {The gut microbiome of preterm infants is highly vulnerable to perturbations. Members of the class Clostridia are among the first anaerobes colonizing the preterm gut, yet their ecological roles and antimicrobial resistance (AMR) properties remain poorly understood. We characterized 98 Clostridia isolates from fecal samples of preterm infants, spanning 17 species and 11 genera. Isolates were identified by MALDI-TOF and 16S rRNA sequencing, colonization levels were quantified, and antimicrobial susceptibility was assessed by disk diffusion and E-test. Resistance determinants were screened by PCR and sequenced. We focused on Clostridia that were present at low colonization levels (mean 5.3 log10 CFU g-1 of feces). While most isolates were susceptible to amoxicillin-clavulanic acid, imipenem, and metronidazole, resistance to tetracycline (12%), clindamycin (35%), and cefotaxime (35%) was observed. Distinct species-specific resistance included linezolid (Clostridium argentinense), chloramphenicol (Clostridium innocuum), and tigecycline (Paeniclostridium sordellii), and a one Robinsonella peoriensis isolate displayed vancomycin resistance. The detection of tet and erm genes corresponded with phenotypic resistance, while β-lactamase activity was uncommon. Although colonizing at low levels, these findings highlight the ecological significance of rarely studied commensal Clostridia and their contribution to the neonatal resistome, acting as underappreciated reservoirs of AMR genes during a critical window of microbiome assembly.},
}

@article {pmid41347608,
year = {2025},
author = {Ran, Q and Dong, C and Long, X and Peng, S and Luo, J and Liang, H and Han, Y},
title = {Microbiota on football surfaces: providing fresh insights into football sports management.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/10934529.2025.2597719},
pmid = {41347608},
issn = {1532-4117},
abstract = {Football is one of the most popular, widely participated in, and age-spanning sports in the world. The role of scientific management in football is crucial for safeguarding the health of the athletes.However, There is limited understanding of the potential relationship between microbiota and athletes. This study employed 16S rRNA amplicon sequencing to characterize the microbiota on football surfaces used by different user groups (schools of different grade levels.). The results indicate that there were no significant differences in the α-diversity of football surface microbiota among different groups, however, there were significant differences in β-diversity and microbial co-occurrence network patterns. Enterobacteriaceae spp and Stenotrophomonas were the designated microbial markers within the primary school (PS). The designated microbial markers in middle school (MS) were Lactobacillus, Escherichia, Bacteroides, and Staphylococcus. In university (UN), Serratia serve as the indicative microorganisms. Nursery school (NS) was characterized by Pantoea and Exiguobacterium as its microbial markers, while Acinetobacter was the designated microbial marker in residential quarters (RQ). These microbial markers are even opportunistic pathogens. Storage temperature, storage relative humidity, and the frequency of utilization will accelerate the reproduction of opportunistic human pathogens. This study suggests disinfection management for footballs.},
}

@article {pmid41347333,
year = {2025},
author = {Harding, C and Da Silva, A and Khasriya, R and Khullar, V and Lombardo, R and Malde, S and Nambiar, A and Rademakers, K and Werneburg, G},
title = {Is There Adequate Evidence for Intracellular Bacteria Being a Significant Cause of rUTIs and Thereby Justifying Targeted Treatments Such as Bladder Fulguration or Intravesical Therapies? ICI-RS 2025.},
journal = {Neurourology and urodynamics},
volume = {},
number = {},
pages = {},
doi = {10.1002/nau.70200},
pmid = {41347333},
issn = {1520-6777},
support = {//The authors received no specific funding for this work./ ; },
abstract = {AIMS: Recurrent urinary tract infections are a common medical problem and current guidelines recommend both antibiotic and non-antibiotic preventative treatments. However, for a significant proportion of patients with this condition these second-line treatments are not effective. As a result, there has been recent focus on more targeted treatment such as intravesical instillations and bladder fulguration procedures. We aim to report discussions regarding these targeted treatments for recurrent urinary tract infections that took place at the International Consultation on Incontinence - Research Society meeting in Bristol 2025.

METHODS: We undertook a think-tank session during this multi-disciplinary meeting specifically designated for discussion regarding targeted treatments for UTI prevention. We discussed the incidence and prevalence of recurrent UTIs in the general population and recognise that up to 25% of patients are not adequately treated with currently recommended preventive strategies. We also explored the increasing knowledge base surrounding the urinary microbiome and discussed the concept of chronic urinary tract infection. Finally we outlined the current evidence to support the use of the targeted treatments of intravesical instillation of both antibiotics and glycosaminoglycan (GAG) replacement compounds and the surgical procedure of bladder fulguration. This led to the generation of research ideas which hope to shape future UTI research within this topic area.

RESULTS: We describe the discussions that took place and document the important research questions that were generated during the International Consultation on Incontinence-Research Society meeting in Bristol 2025.

CONCLUSIONS: Although the use of targeted treatments is becoming more widespread the evidence base is currently insufficient for strong guideline recommendation. This must be balanced against the significant need for second-line treatments when current guideline recommended treatments are unsuccessful, particularly in the design of clinical pathways for patients with refractory recurrent UTIs.},
}

@article {pmid41347246,
year = {2025},
author = {Mishra, S and Shukla, AC and Craven, KD},
title = {Editorial: Microbial symbionts of lower plants.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1727008},
doi = {10.3389/fmicb.2025.1727008},
pmid = {41347246},
issn = {1664-302X},
}

@article {pmid41347241,
year = {2025},
author = {Lowe, MS and Peek, RM},
title = {Microbial oncogenesis within the gastric niche: how the gastric microbiota influences H. pylori-induced disease progression.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1691080},
pmid = {41347241},
issn = {1664-302X},
abstract = {Chronic pathogens incur a significant public health burden, contributing to the development of 1 in 5 cancer cases worldwide. Helicobacter pylori, a Gram-negative bacterium that colonizes the gastric mucosa, is the strongest known risk factor for gastric adenocarcinoma, the fifth leading cause of cancer-related mortality. H. pylori colonizes almost half of the world's population; however, despite its high prevalence, only approximately 1-3% of infected individuals progress to this malignancy. These data suggest that H. pylori colonization alone may be insufficient to fully drive oncogenic progression. Previously considered a sterile environment, the stomach is now recognized to harbor a diverse microbial ecosystem, which plays a crucial role in human health and disease. Emerging research highlights the complex interplay between H. pylori and the gastric microbiota, with several commensal bacterial species now identified as modulators of disease progression. Clinical data have defined key variations in gastric microbiota composition between H. pylori-infected individuals who progress toward gastric cancer and those who simply develop gastritis alone, further suggesting that the gastric microbiota affects cancer risk in synergy with H. pylori. In this review, we will discuss microbial species identified within the stomach of H. pylori-infected persons that orchestrate detrimental or protective interactions, which influence the host response and alter cancer risk.},
}

@article {pmid41347161,
year = {2025},
author = {Wu, M and Shu, H and Wang, M and Xu, Y and Zhang, Y and Jiang, X and Zhang, L and Chen, X and He, L},
title = {Protective effects of Angelica sinensis polysaccharide on chemotherapy-injured rats with premature ovarian insufficiency and its impact on gut microbiota.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1685281},
pmid = {41347161},
issn = {1663-9812},
abstract = {OBJECTIVE: This study aimed to investigate the therapeutic effects and action mechanisms of Angelica sinensis polysaccharides (ASP) on a chemotherapy-induced premature ovarian insufficiency (POI) rat model along with screening for the optimal therapeutic dose.

METHODS: Sprague-Dawley female rats were used to establish a POI rat model via intraperitoneal injection of cyclophosphamide and busulfan. The rats were treated with ASP at doses of 80, 160, and 320 mg/kg/d for 21 d. The ovarian histomorphology and follicular development were examined by hematoxylin and eosin staining, and the serum levels of follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), anti-Müllerian hormone (AMH), and inflammatory cytokines (IL-6, IL-1β, and TNF-α) were measured. The ovarian oxidative stress was assessed via malondialdehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and reactive oxygen species (ROS) levels. The composition of the gut microbiota was analyzed by 16S rDNA sequencing, and the associations between differential microbiota and ovarian indicators were assessed using Spearman correlation analysis.

RESULTS: ASP treatment improved sex hormone secretion in the chemotherapy-induced POI rats, in addition to increased E2 and AMH levels, decreased FSH and LH levels, improved ovarian tissue structure, and increased follicle growth at all stages. ASP treatment also improved the serum inflammatory levels in POI rats by reducing the IL-6, IL-1β, and TNF-α levels; it decreased oxidative stress levels in the ovarian tissue, inhibited ROS and MDA activities, and increased SOD and GSH-Px activities. The gut microbiota differential analysis showed that chemotherapy-induced POI rats exhibited dysbiosis of the gut microbiota. After ASP treatment, the α and β diversities of the gut microbiota changed, thereby increasing the relative abundance of beneficial bacteria and decreasing the relative abundance of harmful bacteria. Spearman's correlation analysis was performed between the main differential microbiota as well as serum sex hormone, proinflammatory cytokine, and ovarian tissue oxidative stress levels; accordingly, the results showed that some beneficial bacteria were positively correlated with E2, AMH, SOD, and GSH-Px levels while being negatively correlated with FSH, LH, MDA, IL-6, IL-1β, and TNF-α levels.

CONCLUSION: ASP ameliorates chemotherapy-induced POI in rats by improving the serum hormone levels, promoting follicular development, as well as suppressing inflammation and oxidative stress, with medium and high treatment doses showing significant efficacies. Furthermore, ASP reshapes the gut microbiome; the altered gut microbiota are strongly correlated with ovarian function indicators, suggesting that they may serve as a new therapeutic approach for POI.},
}

@article {pmid41346779,
year = {2025},
author = {Orsud, H and Zoughbor, S and AlDhaheri, F and Hajissa, K and Refaey, M and Ajab, S and Alswaider, K and Mohamed, N and Alkaabi, O and Al Rasbi, Z},
title = {Multi-marker comparative analysis of 18S, ITS1, and ITS2 primers for human gut mycobiome profiling.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1690766},
pmid = {41346779},
issn = {2673-7647},
abstract = {BACKGROUND: Gut fungi play crucial roles in human health. The profiling of the human gut mycobiome continues to progress. However, adjustments in the selection of ribosomal DNA marker regions can substantially affect the taxonomic resolution of a population. In particular, the impact of using primers' combinations is insufficiently defined. In this study, we investigated the performance of three targeted sequencing regions, ITS1, ITS2 and 18S rRNA, separately and in combination.

METHODS: Eight fecal samples from healthy individuals (n = 4) and cancer patients (n = 4) were selected as proof of principle for amplicon-based sequencing conducted with the DNBSEQ™ sequencing system. Quality-filtered reads were grouped into operational taxonomic units (OTUs) via USEARCH and categorized using the SILVA (18S) and UNITE (ITS) databases. Downstream bioinformatics encompassed diversity analyses, principal component analysis (PCA), and biomarker detection via linear discriminant analysis effect size (LEfSe). To improve taxonomic coverage and compositional understanding, data were examined using ALDEx2 with centered log-ratio (CLR) transformation, facilitating reliable differential abundance and effect size assessment in small sample metagenomic contexts.

RESULTS AND DISCUSSION: Among primers, ITS2 and ITS1 enhanced the coverage of identified taxa, with operational taxonomic unit quantities of 183 and 158, respectively, compared to 58 OTUs of 18S. Accordingly, among primer combinations tested, the triple integration of ITS1-ITS2-18S produced the highest fungal richness, while the dual ITS1-ITS2 combined datasets enhanced group discrimination analysis, showing enrichment of Candida albicans and scarcity of Penicillium sp. in cancer patients. Our findings based on ITS sequencing and the combination of ITS1 and ITS2 provide instructive information on the composition and dynamics of gut fungi in our initial test subjects, enhancing our understanding of their roles in gut homeostasis and the microbial shifts associated with cancer. Despite our approach being conducted with a limited cohort to establish methodological feasibility, it brings attention to multi-marker strategies, demonstrating that integrated primer datasets surpass traditional single-marker methods in both taxonomic coverage and biomarker detection sensitivity in low-biomass fecal samples. Our research provides a reliable starting point for future studies on gut mycobiome in both healthy and diseased individuals, which could lead to better diagnostics and treatments based on microbiome profiles.},
}

@article {pmid41346725,
year = {2025},
author = {Yao, Y and O'Sullivan, B and Mondal, TK and Uddin, MN and Manley, K and Graf, J and Lawrence, DA},
title = {Mitochondrion-Mediated Metabolism and Microbiome Biodiversity Influence Autism-alike Behaviors.},
journal = {Journal of neurology & translational neuroscience},
volume = {10},
number = {1},
pages = {},
pmid = {41346725},
abstract = {BACKGROUND: The BTBR T [+] Itpr3[tf] /J (BTBR) strain has autism spectrum disorder (ASD)-like behaviors, which has been associated with mitochondrial dysfunction. Therefore, a new mouse strain was developed. The BTBR-mt[B6] strain has the nuclear genome of BTBR but mitochondria from C57BL/6J (B6) mice, which have normal behaviors and immunity. The BTBR-mt[B6] strain had more normal behavios and immunity. Therefore, the mechanisnisms associated with the improvements were investigated.

AIM: Since replacement of mitochondria in BTBR mice improved behavior and some immune differences, the associated mechanisms were researched.

METHODS: Since mitochondria functions affect gut microbiota and metabolomics, the bacteria in fecal samples and metabolites in the blood and organs including the brain were investigated. Microbiome sequences were retrieved from Illumina BaseSpace. Genetic and molecular changes incuding metabolomics were assayed.

RESULTS: The fecal microbiomes of BTBR, B6 and BTBR-mt[B6] mice were different from each other. The serum and brain cholesterol levels were intermediate between males of the BTBR and B6 strain. The liver PPARγ level also was intermediate between the BTBR and B6 strain which may relate to the BTBR-mt[B6] intermediate amount of lipid in the liver. The BTBR-mt[B6] mice also had an intermediate number of T cells in the white adipose tissue compared to the BTBR and B6 mice. Complex IV of the ETC in the liver was slightly lower in the BTBR-mt[B6] mice than B6 mice. The BTBR-mt[B6] strain lost production of IgG to brain antigen that is observed in BTBR mice.

CONCLUSION: The mitochondrial shift is shown to affect fecal microbiota, mitochondrion-dependent metabolism affecting lipid accumulation, the levels of cholesterol in the brain and serum, and brain expression of myelin basic protein (MBP) and 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase), which improves myelination in BTBR-mt[B6] brains. The metabolite and microbiome differences likely relate to mitochondrial/nuclear differences affecting metabolism, immunity, and behavior.},
}

@article {pmid41346685,
year = {2025},
author = {He, N and Zhong, J and Deng, S and Liang, J and Li, Q and Chen, K},
title = {The impact of trans fatty acids on ADHD in relation to the gut microbiome.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1641574},
pmid = {41346685},
issn = {2296-861X},
abstract = {Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder (NPDs) caused by the interaction of genetic and environmental factors. Trans-fatty acids (TFAs), mainly from chemically hydrogenated vegetable oils, are an environmental factor with increased exposure risk in modern diets. Recent studies suggest that TFAs may contribute to ADHD development through two pathways: inducing neurodevelopmental damage and indirectly affecting neural function by altering gut microbiota, though specific mechanisms remain unclear. This review focuses on two critical neurodevelopmental phases (perinatal period and adolescence) to explore the relationship between TFA exposure and ADHD, and to investigate the pathways through which TFAs affect ADHD by disrupting gut microbiota homeostasis. Although the association between TFA exposure during adolescence and ADHD is controversial, the harm of perinatal TFA exposure is undisputed. Shared neurodevelopmental damage mechanisms across both stages support reducing TFA intake during critical neurodevelopment. TFAs also impair neurodevelopment and brain function through the microbiota-gut-brain axis (MGBA) by disrupting gut microbiota homeostasis and activating neural, immune, and endocrine pathways. Thus, based on the harmful effects of TFAs during critical periods and the functional network by which TFAs contribute to ADHD pathogenesis through gut microbiota, this review supports dietary TFAs restriction as an ADHD prevention strategy.},
}

@article {pmid41346600,
year = {2025},
author = {Zhai, C and Wang, Z and Bai, L and Han, H and Ma, B},
title = {Characteristics and differences in immune response capacity and gut microbiome between wild and captive Amur grayling (Thymallus grubii): New insights into endangered fish conservation.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1654437},
pmid = {41346600},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Endangered Species ; Liver/immunology/metabolism ; *Fishes/immunology/microbiology ; RNA, Ribosomal, 16S/genetics ; Animals, Wild/immunology/microbiology ; Conservation of Natural Resources ; Cytokines/genetics/metabolism ; },
abstract = {INTRODUCTION: Endangered species recovery hinges on evaluating captivity-induced shifts in the adaptive traits of candidates slated for reintroduction. Gut microbiota is one such trait and is particularly important for Amur grayling (Thymallus grubii).

METHODS: The present study aimed to systematically investigate the differences in intestinal and liver health in Amur grayling from two water environments (wild and captive) by feeding habits, biochemical parameters and 16S ribosomal RNA gene sequencing.

RESULTS: Compared with captive fish, the wild Amur grayling in the liver and gut had higher lysozyme activity (P < 0.05), and alkaline phosphatase, catalase activity and glutathione content in gut was significantly higher (P < 0.05). In addition, the cultured fish showed lower relative expression levels of hepatic IgM, il-6, il-10, il-lβ, myd88, NF-kB, and Tnf-α mRNA expressions than those of wild fish (P < 0.05). In the intestine tissue, the mRNA level of C3, il-6, il-10, il-lβ, tlr1, tlr3, Tnf-α, and LYZ increased in the wild fish while the expression of IgM was significantly elevated (P < 0.05). For gut microbiota, the cultured group displayed higher percentages of Pseudomonadota phylum and lower percentages of Bacillota phylum than the wild group (P < 0.05) .

DISCUSSION: Overall, wild Amur grayling had higher immune capacity and intestinal barrier functions than cultured Amur grayling. This study displayed that responses and adaptations to diverse aquatic environments were shown by liver-gut-microbiota axis in Amur grayling. Our findings could provide a promising direction for the improve its adaptability of wild population in reintroduction project and propose the conservation strategy for biodiversity recovery.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Endangered Species
Liver/immunology/metabolism
*Fishes/immunology/microbiology
RNA, Ribosomal, 16S/genetics
Animals, Wild/immunology/microbiology
Conservation of Natural Resources
Cytokines/genetics/metabolism

@article {pmid41346595,
year = {2025},
author = {Liang, Y and Zheng, Y and Zeng, Y and Hu, C and Si, Y and Fan, X and Chen, Q},
title = {Immune checkpoint inhibitors in melanoma: mechanisms, immune cell interactions, and the tumour microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1691608},
pmid = {41346595},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Melanoma/immunology/drug therapy/pathology/metabolism ; *Cell Communication/immunology/drug effects ; Animals ; Immunotherapy/methods ; *Skin Neoplasms/immunology/drug therapy ; },
abstract = {Melanoma is a highly aggressive and metastatic malignant tumor originating from melanocytes, with globally rising incidence rates that pose significant challenges to patient prognosis. Traditional therapies for advanced melanoma have limited efficacy. In recent years, the emergence of immune checkpoint inhibitors (ICIs) has significantly altered this landscape by reactivating the body's antitumor immune response through blocking interactions between immune checkpoint proteins and their ligands, demonstrating remarkable therapeutic outcomes. However, some patients do not respond to ICIs or develop resistance, indicating that treatment responses involve complex interactions between tumors, immune cells, and the tumor microenvironment. This review comprehensively summarizes the mechanisms of ICIs, delves into the roles of various immune cells (including T cells, NK cells, macrophages, T helper cells, dendritic cells, and B cells) and the tumor microenvironment (TME), and explores their impact on ICI efficacy. It further distinguishes the application of ICBs across different disease stages (primary, adjuvant, neoadjuvant, and metastatic) and highlights the role of skin-specific immune cells (e.g., TRM, Langerhans cells) and microenvironmental components (e.g., skin microbiome). This review focuses on the mechanisms of ICIs in melanoma therapy, exploring the interactions between immune cells and the skin microenvironment in melanoma development and their impact on ICI efficacy. It aims to provide new insights and theoretical foundations for optimizing immunotherapy strategies in melanoma treatment.},
}

Humans
*Tumor Microenvironment/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Melanoma/immunology/drug therapy/pathology/metabolism
*Cell Communication/immunology/drug effects
Animals
Immunotherapy/methods
*Skin Neoplasms/immunology/drug therapy

@article {pmid41346456,
year = {2025},
author = {Yong, SB and Chang, YF and Chen, HY and Chen, YJ and Yang, CY and Liao, PL and Chen, PC and Wu, LS and Wei, JC and Wang, JY},
title = {The impact of COVID-19 on the incidence of allergic diseases in the pediatric population: A retrospective cohort study from TriNetX United States collaborative network.},
journal = {Asia Pacific allergy},
volume = {15},
number = {4},
pages = {255-262},
pmid = {41346456},
issn = {2233-8276},
abstract = {BACKGROUND: Allergic diseases, including asthma, allergic rhinitis (AR), and atopic dermatitis (AD), affect nearly 20% of the global population and are influenced by complex immune mechanisms. The COVID-19 pandemic, driven by SARS-CoV-2 and its evolving variants, has reshaped clinical and immunological landscapes. Previous evidence regarding the interaction between COVID-19 and allergic diseases remains inconsistent, necessitating large-scale real-world investigations.

OBJECTIVE: This study aimed to investigate the association between COVID-19 infection and the subsequent development of allergic diseases (AD, AR, and asthma) in pediatric populations, while exploring subgroup variations and testing robustness through sensitivity analyses.

METHODS: We performed a retrospective cohort study using TriNetX electronic health records from 56 U.S. healthcare facilities. Children <18 years with ≥2 visits and Polymerase chain reaction (PCR) testing (2020-2022) were included, excluding those with prior allergic disease. COVID-19 was defined by ICD-10 U07.1 and RNA positivity. Propensity score matching (1:1) balanced baseline characteristics. The primary outcome was the incident allergic disease within 1 year, assessed using Cox models; subgroup and sensitivity analyses tested robustness.

RESULTS: After matching, 412,017 patients were included in each cohort (COVID-19 vs non-COVID-19). Children with COVID-19 exhibited a significantly higher risk of developing allergic diseases (Hazard ratio (HR) = 1.211, 95% confidence interval [CI]: 1.189-1.235; P < 0.001). Elevated risks were observed across all categories: AD (HR = 1.179, 95% CI: 1.140-1.219), asthma (HR = 1.252, 95% CI: 1.216-1.290), and AR (HR = 1.223, 95% CI: 1.188-1.259). Kaplan-Meier curves demonstrated consistently higher cumulative incidence in the COVID-19 cohort. Subgroup analyses stratified by sex, age, and race yielded concordant results, while sensitivity analyses-including competing risks, extended follow-up to 2-3 years, stricter visit definitions, and exclusion of vaccinated individuals-confirmed robustness.

CONCLUSION: COVID-19 infection was linked to a higher risk of allergic diseases in children, suggesting postviral immune dysregulation and microbiome changes as possible mechanisms. Further studies are needed to clarify causality and guide prevention and management.},
}

@article {pmid41346440,
year = {2025},
author = {Müller, L and Di Benedetto, S and Müller, V},
title = {Neuroimmune dynamics and brain aging: mechanisms and consequences.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1715045},
pmid = {41346440},
issn = {1663-4365},
abstract = {Brain aging is accompanied by profound changes in neuroimmune interactions that shape the balance between resilience and vulnerability. Under healthy conditions, glial cells, neurons, vascular elements, and peripheral immune inputs cooperate to sustain homeostasis. With advancing age, however, immune remodeling and systemic inflammaging drive shifts in microglial surveillance, astrocytic reactivity, and neuronal susceptibility, creating conditions that compromise synaptic function and cognitive performance. These processes unfold along a continuum, from subtle impairments in normal aging to maladaptive dynamics that accelerate neurodegenerative disease. Sex differences, epigenetic regulation, and systemic influences-including the gut microbiome, metabolic state, and lifestyle factors-further modulate these trajectories. Here, we synthesize current knowledge on the cellular, systemic, and molecular mechanisms that govern neuroimmune aging, emphasizing how their dysregulation contributes to cognitive decline and disease vulnerability. We also highlight emerging conceptual frameworks, such as multilayer network modeling and resilience biomarkers, that provide a foundation for integrative approaches to brain aging. Understanding these interconnected systems underscores the necessity of viewing brain aging not solely through a CNS-centric lens, but as a networked process influenced by distal organs, circulating immune cells, microbial communities, and lifestyle factors-setting the stage for integrative models of neuroimmune dynamics in aging. Clarifying how these dynamic interactions unfold and what their consequences are is essential for developing strategies to preserve cognitive health and mitigate the burden of neurodegeneration in an aging society.},
}

@article {pmid41346362,
year = {2025},
author = {Barb, JJ and Hughes, AN and Nanda, S and Tuason, RTS and Wallen, GR and Maki, KA},
title = {Longitudinal assessment of oral and gut microbiome overlap in patients with Alcohol Use Disorder undergoing inpatient treatment.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1681781},
pmid = {41346362},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Alcoholism/microbiology/therapy ; Longitudinal Studies ; Female ; Inpatients ; Adult ; Feces/microbiology ; Middle Aged ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Alcohol Use Disorder (AUD) is a condition associated with compulsive alcohol consumption and disruption across multiple physiological systems. This brief report builds on previously published research separately examining longitudinal changes in the oral and gut microbiomes of treatment-seeking individuals with AUD. Twenty-two participants diagnosed with severe AUD were enrolled in an inpatient treatment protocol (NCT02231840) and provided oral and stool samples over 28 days (goal 10 samples/participant). The aim of this brief report was to explore within-person overlap and compositional similarity of the oral and gut microbiomes at the genus level, using the Sorenson-Dice Index and Robust Aitchison Distance. Results indicated that the oral and gut microbiomes became less similar during the first week of treatment, with both the number of shared genera and Sorenson-Dice Index values decreasing significantly (p <.001). However, the Robust Aitchison Distance also decreased over time (p <.05), suggesting increased compositional similarity among the shared genera. These findings suggest early divergence of oral and gut microbiota during AUD treatment, where individuals were abstinent of alcohol, followed by stabilization of overlapping communities. This study highlights dynamic shifts in microbiome structure during a period of abstinence and underscores the importance of evaluating site-specific and cross-site microbial changes in AUD populations.},
}

Humans
*Gastrointestinal Microbiome
Male
*Alcoholism/microbiology/therapy
Longitudinal Studies
Female
Inpatients
Adult
Feces/microbiology
Middle Aged
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification

@article {pmid41346331,
year = {2025},
author = {Preenanka, R and Sivam, V and Sasikala, R and Koombankallil, R and Raveendran, K and Jacob, J and Devadas, AL and Ravikumar, NK and Anbalakan, M and Chigilipalli, H and Thangaraj, RS and Basha, AK and Joseph, TC and Badireddy, MR and Vaiyapuri, M},
title = {Muscle Microbiome Analysis of Indian Mackerel (Rastrelliger kanagurta) Delineated Classical and Novel Spoilage Bacteria.},
journal = {Journal of food science},
volume = {90},
number = {12},
pages = {e70751},
doi = {10.1111/1750-3841.70751},
pmid = {41346331},
issn = {1750-3841},
support = {BT/PR46349/AAQ/3/1063/2022// Department of Biotechnology/ ; // Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Perciformes/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Seafood/microbiology ; Food Packaging/methods ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; *Muscles/microbiology ; Vacuum ; Metagenomics ; Food Storage ; },
abstract = {Metagenomics allows a comprehensive insight into the spoilage-associated muscle microbiome shifts in the air-packed and vacuum-packed Indian mackerel. This study explored the microbial composition and diversity of spoilage flora in air-packed (T1M, T2M, and T3M) and vacuum-packed (T4M, T5M, and T6M) Indian mackerel (Rastrelliger kanagurta) stored at 0 ± 2°C (iced), 5 ± 2°C (chilled), and 30 ± 2°C (abused) temperatures through metagenomics, targeting the V1-V9 region of 16s rRNA. Total Volatile Base Nitrogen and Thiobarbituric Acid were analyzed to confirm the spoilage threshold limit, and accordingly, the fish muscle tissue on the spoilage day was selected for microbiome analysis. Metagenomic analysis revealed distinct variation in the relative abundance and spoilage microbiome between the air-packed and vacuum-packed Indian mackerel stored at iced, chilled, and abused temperatures. The predominant bacterial species responsible for spoilage were Cetobacterium ceti, Clostridium polyendosporum, and Gilliamella apicola in vacuum-packed mackerel, whereas Shewanella arctica, S. aquimarina, S. baltica, Staphylococcus xylosus, and Burkholderia cepacia played a major role in the spoilage of air-packed samples. The observed bacterial population dynamics across different temperatures and packaging significantly influenced the microbiome diversity in Indian mackerel. Summing up, this study emphasizes the unique and diverse microbes contributing to spoilage and provides a valuable guide for the flora that need to be controlled for extending the shelf life of Indian mackerel.},
}

Animals
*Perciformes/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Seafood/microbiology
Food Packaging/methods
Food Microbiology
RNA, Ribosomal, 16S/genetics
*Muscles/microbiology
Vacuum
Metagenomics
Food Storage

@article {pmid41346294,
year = {2025},
author = {Salinas-Velarde, ID and Donaciano-Domínguez, JM and Oros-Pantoja, R and Aguirre-Garrido, JF and González-Cervantes, RM and Munguía-Cervantes, JE and López, MG and Bustos-Martínez, J and Soto-Piña, AE},
title = {Narrative Review: Gut Microbiota and Its Impact on α-syn Function in Parkinson's Disease.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70173},
doi = {10.1002/mbo3.70173},
pmid = {41346294},
issn = {2045-8827},
support = {//This review was funded by the "Consorcios Proyectos de Colaboración Interinstitucional UAM-IPN -UAEMEX" (grant number 7152/2024ECON) and publication grant 34503067 (UAM-Xochimilco). Additionally, I.D.S.V. received a grant from the Consejo Mexiquense de Ciencia y Tecnología (COMECYT, grant number CAT2024-0080)./ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Parkinson Disease/microbiology/therapy/metabolism ; Humans ; *alpha-Synuclein/metabolism ; Fecal Microbiota Transplantation ; Animals ; Bacteria/metabolism/classification ; },
abstract = {Gut microbiota (GM) plays a pivotal role in human health and disease, and its alterations have been implicated in various neurological disorders, including Parkinson's disease (PD). Growing evidence reveals correlations between the abundance of specific bacterial taxa and the severity of motor symptoms and intestinal dysfunction in PD. Moreover, bacterial metabolites have been shown to influence α-synuclein (α-syn) aggregation and neurodegeneration. This narrative review aims to explore the current understanding of the gut-brain axis in PD, specifically the connection between GM and α-syn function in PD experimental models and patients. Several therapeutic strategies aimed at modulating gut microbiota, such as dietary interventions, fecal microbiota transplantation, and targeted bacterial therapies with the goal of alleviating or preventing PD symptoms, are examined. Understanding the mechanisms through which GM influence neurodegeneration, including inflammation, immune modulation, and microbial metabolite production, offers promising avenues for the development of novel therapeutic strategies targeting the microbiome.},
}

*Gastrointestinal Microbiome/physiology
*Parkinson Disease/microbiology/therapy/metabolism
Humans
*alpha-Synuclein/metabolism
Fecal Microbiota Transplantation
Animals
Bacteria/metabolism/classification

@article {pmid41345980,
year = {2025},
author = {Jiang, Y and Che, L and Li, SC},
title = {Deciphering the personalized functional redundancy hierarchy in the gut microbiome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02273-w},
pmid = {41345980},
issn = {2049-2618},
support = {JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Functional redundancy (FR) in the human gut microbiome is crucial for maintaining stability and resilience, exhibiting a hierarchical structure. However, the precise configuration and functional implications of this hierarchy remain elusive and limited by single-metric measurements. We aimed to develop a method that comprehensively characterizes the hierarchical organization of functional redundancy in personalized microbiomes.

RESULTS: We represented functional redundancy as a network and developed a structural entropy (SE)-based approach to elucidate FR hierarchy, revealing functional redundancy clusters (FRCs)-groups of species capable of independently executing specific metabolic pathways. Through controlled simulations and cross-cohort analyses spanning 4912 gut metagenomes across 28 disease cohorts, we established that our approach offers higher resolution, more comprehensive measurement, and greater robustness in detecting disease-associated functional patterns than traditional FR methods. In healthy individuals, we observed FR network polycentric structure, which shifted to monocentric structure in non-alcoholic steatohepatitis patients. Vitamin biosynthesis FRCs correlated with microbiota transplantation efficiency, while FRCs specialized in short-chain fatty acid production predicted immunotherapy response and patient survival. Permutation tests validated the causal relationship between SE differences and disease phenotypes, while perturbation experiments revealed that FR keystone species exert disproportionate influence on the system's resilience.

CONCLUSIONS: Our SE-based approach to functional redundancy analysis provides superior sensitivity compared to conventional metrics by integrating multiple hierarchical levels of functional organization. This methodology establishes a novel perspective for understanding microbiome stability through personalized FR networks, positioning FRCs as promising diagnostic markers and therapeutic targets for microbiome-associated diseases. Video Abstract.},
}

@article {pmid41345979,
year = {2025},
author = {Sakanaka, A and Furuno, M and Ishikawa, A and Katakami, N and Inoue, M and Mayumi, S and Kurita, D and Nishizawa, H and Omori, K and Taya, N and Isomura, ET and Kudoh, M and Takeuchi, H and Amano, A and Shimomura, I and Fukusaki, E and Kuboniwa, M},
title = {Diabetes alters the supragingival microbiome through plasma-to-saliva migration of glucose and fructose.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02256-x},
pmid = {41345979},
issn = {2049-2618},
support = {22H03300, 22H00487, 22K10311, 21K18281//Japan Society for the Promotion of Science/ ; JP16gm0710005//Japan Agency for Medical Research and Development/ ; },
abstract = {BACKGROUND: Dental caries, a dysbiotic biofilm disease driven by polymicrobial acidogenesis, often coexists with type 2 diabetes (T2D). Previous studies suggest covarying relationships between circulating and salivary metabolites in patients with T2D. However, the role of hyperglycemia-induced saccharide migration from plasma to saliva in caries pathogenesis remains unclear. Here, we developed a novel method for untargeted metabolomics profiling of trace saliva from sublingual and submandibular glands, comparing this profile with those of plasma and whole saliva in participants with T2D (n = 31) and those with normoglycemia (n = 30). This comparison aimed to determine how circulating saccharide migration into the oral cavity and its subsequent microbial consumption are linked to dental caries. Additionally, shotgun metagenomic sequencing was combined with this analysis to investigate the cariogenic impact of circulating saccharide migration on the composition and function of supragingival biofilm using MetaPhlAn4 and HUMAnN3 pipelines.

RESULTS: The metabolomics profiles of glandular saliva showed intermediate dissimilarity between plasma and whole saliva, reflecting cardiometabolic traits more sensitively than whole saliva. Glucose and fructose showed a decreasing positive correlation with glycemic parameters in the order of plasma, glandular saliva, and whole saliva, suggesting systemic-to-oral migration and subsequent microbial consumption. Saccharide migration was more pronounced in participants with dental caries and plaque accumulation, coinciding with shifts in supragingival microbiota, including depletion of Streptococcus sanguinis, Corynebacterium durum, and Rothia aeria, and enrichment of Streptococcus mutans, Veillonella parvula, and Actinomyces sp. oral taxon 448. Glycolytic potential increased at the community level. Improved glycemic control reduced fructose migration and mitigated dysbiosis, decreasing fructose phosphotransferase abundance and shifting the S. mutans-S. sanguinis balance. Experimental validation demonstrated that fructose promotes S. mutans dominance over S. sanguinis in dual-species biofilms.

CONCLUSIONS: This study establishes saccharide migration as a metabolic driver of supragingival dysbiosis in T2D. The findings highlight the role of both glucose and fructose in caries pathogenesis and suggest that glycemic control could serve as an effective strategy as part of caries control. Video Abstract.},
}

@article {pmid41345974,
year = {2025},
author = {Anthony, MA and Röckel, N and Traistaru, A and Krishna, A and Meesenburg, H and Wagner, M and Jacob, F and Gessler, A and Waldner, P and Schaub, M and Ferretti, M and Schmitz, A and van den Bulk, P and Hensen, A and Hupperts, SF and Bialic-Murphy, L and Averill, C},
title = {Soil microbial community differences drive variation in Pinus sylvestris physiology, productivity, and responses to elevated CO2.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00828-w},
pmid = {41345974},
issn = {2524-6372},
abstract = {BACKGROUND: Soil microbial communities can affect plant nutrient uptake, productivity, and may even confer resistance to global change. Elevated atmospheric CO2 is widely expected to stimulate plant productivity; however, this will depend on the availability of growth limiting nutrients such as nitrogen. Soil microbial communities are the main mediators of soil nitrogen cycling and should therefore play a key role in influencing plant responses to elevated CO2.

RESULTS: To test this, we conducted a controlled, growth chamber experiment with Pinus sylvestris to evaluate how soil microbiome variation influences plant physiology, productivity, and responses to elevated CO₂ (eCO₂; 800 ppm versus 400 ppm in the ambient treatment). Field soils were collected from six forests with varying tree growth rates and were used as an inoculant source, either sterilized or living, into a common growth medium seeded with P. sylvestris. After seven months of growth, we measured plant carbon assimilation, photosynthetic nitrogen use efficiency, above- and belowground productivity, and we measured soil microbial biodiversity using DNA metabarcoding. Our findings demonstrate that seedling productivity was stimulated under eCO2 conditions and that this was supported by improved plant photosynthetic nitrogen use efficiency, but only in the presence of living versus sterilized soil inoculant. The magnitude of this response was also dependent on the forest soil microbial inoculant source and was linked to a 70% increase in bacterial species richness, increased relative abundances of bacteria known to have positive effects on plant growth (e.g., Lactobacillus, Bacillus, Flavobacterium), and with a concomitant shift in saprotrophic fungal community composition and root growth. Variation in inorganic nitrogen cycling which favored the accumulation of nitrate under eCO2 was also correlated with a twofold reduction in photosynthetic nitrogen use efficiency, suggesting a decoupling of nitrogen availability and assimilation efficiency with distinct implications for plant growth responses to elevated CO2.

CONCLUSIONS: Our results show that soil microbial community variation directly affects P. sylvestris physiology, productivity, and responses to eCO2, and may enhance plant growth through improved nitrogen use efficiency. Surprisingly, growth with different microbial communities even more strongly impacted plant productivity than a doubling of atmospheric CO2 concentrations. The soil microbiome therefore plays a key role in supporting plant nutrition and growth under ambient and eCO2 conditions, and in turn, may confer increased forest resistance to climate change.},
}

@article {pmid41345748,
year = {2025},
author = {Maher, RL and Ayala, AC and Crandall, GA and Vinton, AL and Harvell, CD},
title = {Eelgrass microbiome and disease dynamics under field and lab heat stress.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00826-y},
pmid = {41345748},
issn = {2524-6372},
support = {DBI-2149705//Division of Biological Infrastructure/ ; OCE-2109607//Division of Ocean Sciences/ ; },
abstract = {BACKGROUND: The interaction between host microbiomes, pathogen diversity, and environmental stress is a critical but understudied mechanism shaping disease outcomes in marine foundation species. Eelgrass (Zostera marina) suffering from wasting disease, caused by the protist Labyrinthula zosterae, offers a powerful system with which to probe this interaction. We conducted complementary laboratory experimentation and field surveys to examine three main questions: (1) whether thermal stress compromises the eelgrass microbiome and exacerbates disease outcomes; (2) whether different isolates of L. zosterae differ in virulence and their effects on the host microbiome; and (3) whether laboratory-derived microbiome signatures of heat stress correspond with those observed in the field. In the lab, we exposed eelgrass pieces to two temperature regimes (11 °C vs. 19 °C) and inoculated with two L. zosterae strains. We tracked lesion development, pathogen load via qPCR, and epiphytic microbiome dynamics via 16S rRNA gene sequencing. In parallel, we tagged and sampled intact intertidal eelgrass in situ at Fourth of July Beach, San Juan Island, Washington, before and after a three-day heat stress event, tracking tissue damage, growth, and microbiome dynamics.

RESULTS: In the lab, elevated temperature significantly heightened wasting disease severity across both pathogen isolates, with no significant difference in virulence between them. High temperatures in the lab also led to more pronounced diseased-induced microbiome dysbiosis: community composition shifted, and a greater number of microbial taxa changed in abundance relative to controls, including Colwelliaceae. Both lab and field heat stress decreased microbiome diversity with intertidal eelgrass experiencing extensive tissue damage and reduced growth.

CONCLUSIONS: Warming accelerates wasting disease progression in Z. marina by some combination of microbiome disruption, enhanced pathogen virulence, or compromised host defenses. Although pathogen strain identity had limited influence, temperature emerged as a dominant driver of both disease outcomes and microbiome shifts. While temperature stress in the lab and field was not comparable in duration and intensity, we show consistent trends towards microbiome dysbiosis characterized by changes in diversity and taxon abundance. Exploring the four-way interaction among host, microbiome, pathogen, and environment promises deeper insights for forecasting disease outbreaks and bolstering resilience in eelgrass ecosystems.},
}

@article {pmid41345737,
year = {2025},
author = {Li, F and Yan, M and Su, D and Peng, J and Wang, X and Hao, J and Ma, T and Lin, Y and Shi, H},
title = {Integrated meta-omics reveals AFB1 dose-dependent remodeling of the rumen microbiome-virome-metabolome axis driving metabolic impairment in goats.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02291-8},
pmid = {41345737},
issn = {2049-2618},
support = {grant no. 31902187//National Natural Science Foundation of China/ ; SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Meat Goat and Sheep/ ; },
abstract = {BACKGROUND: Aflatoxin B1 (AFB1), a highly carcinogenic and hepatotoxic mycotoxin frequently contaminating animal feed, presents serious health risks to both humans and livestock. Although AFB1's hepatotoxicity and other organ damage are extensively characterized, how this mycotoxin influences ruminal microbiota dynamics and functional activities in ruminants remains underexplored. Although some studies suggest that AFB1 reduces nutrient digestibility and performance in ruminants, the underlying mechanisms are unclear. To aid in developing effective mitigation strategies for aflatoxicosis in ruminants, this study randomly divided Saanen goats into three groups. The CON group received the standard ration without additives, whereas LD and HD groups were provided identical basal diets fortified with 50 or 500 μg/kg AFB1. Throughout the study, alterations in ruminal fermentation parameters, microbiome, and metabolome profiles were analyzed.

RESULTS: With increasing AFB1 levels, ruminal pH, the concentration of total volatile fatty acids (VFA), acetate, and propionate decreased quadratically, while butyrate decreased linearly. Metagenomic profiling indicated suppressed populations of Pelagibacter and Flavobacterium following AFB1 exposure, contrasting with promoted growth of Cryptobacteroides. Additionally, seven carbohydrate-active enzymes (CAZymes), specifically GT92, GT20, CE7, GT32, GT35, GT57, and GT50, were found to be more prevalent in the rumen of the CON group. Statistically higher viral loads characterized the HD group when benchmarked against CON group. Metabolomics analysis identified 1197 differential metabolites among the CON, LD, and HD groups, including cytochalasin Ppho and chrysophanol, both known for their teratogenic properties and their ability to induce cell death.

CONCLUSIONS: This study indicates that dietary AFB1 exposure can alter the ruminal microbial and metabolomic profiles, induce prophage activation, and impact carbohydrate degradation and microbial protein turnover. These alterations may contribute to reductions in ruminal pH and volatile fatty acid concentrations, thereby impairing feed digestibility and animal performance. The findings provide valuable insights into AFB1's effects on rumen health, and further investigations of these metabolic pathways may help develop precision interventions to mitigate AFB1-induced rumen dysfunction and productivity losses. Video Abstract.},
}

@article {pmid41345720,
year = {2025},
author = {Parpex, G and Nicco, C and Chassaing, B and Santulli, P and Chouzenoux, S and Bourdon, M and Maignien, C and Doridot, L and Batteux, F and Chapron, C and Marcellin, L},
title = {Microbiota insights in endometriosis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {251},
pmid = {41345720},
issn = {2049-2618},
mesh = {*Endometriosis/microbiology/immunology/physiopathology/therapy ; Humans ; Female ; Animals ; *Gastrointestinal Microbiome ; Vagina/microbiology ; Endometrium/microbiology ; *Microbiota ; Quality of Life ; },
abstract = {Endometriosis affects approximately 10% of women of reproductive age and is characterized by the presence of endometrial-like tissue outside the uterine cavity, leading to chronic pelvic pain, infertility, and a significant reduction in quality of life. Beyond its local manifestations, endometriosis is increasingly recognized as a systemic, immune-mediated condition with multifactorial origins. In this narrative review, we provide an updated and comprehensive overview of the disease, including its pathophysiology, clinical features, and evolving conceptual frameworks. Considering the frequent digestive symptoms observed in affected patients, we summarize key findings from both animal and human studies that investigate alterations in the gut microbiota. We also review the profound immune dysregulation associated with endometriosis and explore its potential bidirectional relationship with the microbiota. Furthermore, we examine recent insights into the endometrial microbiota-an emerging field of interest given its early involvement in the disease process and its strong interconnection with the vaginal microbiome. Lastly, we highlight studies exploring the gynecological microbiota and present an updated discussion of novel therapeutic strategies, including microbiota-targeted approaches that may shape future management of this complex disease. Video Abstract.},
}

*Endometriosis/microbiology/immunology/physiopathology/therapy
Humans
Female
Animals
*Gastrointestinal Microbiome
Vagina/microbiology
Endometrium/microbiology
*Microbiota
Quality of Life

@article {pmid41345617,
year = {2025},
author = {Franco-Duarte, R and Saati-Santamaría, Z and Choowong, P and Dharmarathne, G and Menéndez, E and Soares, P and Rito, T and Cheung, W and Spahr, A and Eberhard, J and Jayasinghe, TN},
title = {Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07285-4},
pmid = {41345617},
issn = {1472-6831},
}

@article {pmid41345534,
year = {2025},
author = {Abbà, S and Vallino, M and Cirrincione, S and Lamberti, C and Aiuto, B and Romaniello, F and Galetto, L and Marzachì, C and Bosco, D and Rossi, M},
title = {Rewiring the proteome of the Euscelidius variegatus holobiont in response to Flavescence dorée phytoplasma.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30920-7},
pmid = {41345534},
issn = {2045-2322},
support = {Metodi Innovativi per la DIfesa e gestione della Flavescenza Dorata della vite 2 (MIDI-FD3)//Regione Piemonte/ ; 2022BPB5A8//PRIN 2022 Italian Ministry of University and Research/ ; },
abstract = {The leafhopper Euscelidius variegatus is a laboratory vector of the phytoplasma associated to Flavescence dorée, a severe grapevine disease that threatens viticulture in Europe. Transcriptomic studies have already provided valuable insights into the mechanisms of insect-phytoplasma interactions, but proteomics can offer immediate insights into the cellular functions and metabolic adaptations of the insect and its microbiome to the presence of this plant bacterium. Here, the generation of new genomic data of the E. variegatus holobiont was instrumental in elaborating the first comprehensive proteomic profile of its response to Flavescence dorée phytoplasma (FDp). Both data-dependent acquisition and data-independent acquisition mass spectrometry were used to explore the complex molecular interactions between the insect host, its microbial community, and the phytoplasma. Results indicated a critical role of the insect mitochondria as a shared interface exploited by phytoplasmas for survival and propagation. Additionally, it appeared that the presence of FDp had a detrimental impact on the reciprocal metabolic support between the insect host and its two primary endosymbionts, predominantly resulting in a perturbation in amino acid synthesis and exchange. Proteins upregulated in response to FDp may represent promising targets for disrupting phytoplasma acquisition and transmission, either through rationally designed agrochemicals or gene silencing approaches.},
}

@article {pmid41345403,
year = {2025},
author = {Vivarelli, S and Formica, T and Puliatti, Y and Spatari, G and Fenga, C},
title = {Night shift work and breast cancer: from etiopathology to precision risk analysis.},
journal = {NPJ breast cancer},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41523-025-00863-3},
pmid = {41345403},
issn = {2374-4677},
support = {PNRR-MAD-2022-12376823//National Recovery and Resilience Plan (PNRR)/ ; PNRR-MAD-2022-12376823//National Recovery and Resilience Plan (PNRR)/ ; },
abstract = {The increasing prevalence of night shift work (NSW) in our current professional landscape has raised significant public health concerns, particularly regarding its potential role in breast cancer (BC) development among women. Recognized by the International Agency for Research on Cancer (IARC) as a probable human carcinogen, NSW is believed to contribute to carcinogenesis primarily through circadian disruption induced by exposure to light at night. This review explores three key areas: (1) the biological mechanisms potentially linking NSW to BC, including melatonin suppression, oxidative stress, immune dysregulation, chronic inflammation, clock gene alterations, epigenetic modifications, telomere shortening, estrogen signaling disruption, vitamin D deficiency, and gut microbiome imbalance; (2) the emergence of novel putative biomarkers with might be relevant to early detection and precision risk analysis; and (3) the latest epidemiological evidence from case-control and cohort studies evaluating BC risk in female night shift workers, while considering the heterogeneity caused by exposure misclassification and other confounding factors. Altogether, these insights underscore the importance of integrating mechanistic, molecular, and epidemiological data, not only to deepen our understanding of the strength and nature of the relationship between NSW and BC, but also to support a precision medicine framework. This integrated approach is essential for improving individual risk stratification, guiding occupational health policies, and developing targeted preventive strategies for high-risk workers.},
}

@article {pmid41345366,
year = {2025},
author = {Hanaoka, M and Hanaoka, K and Yamada, M},
title = {Effect of improvement in the endometrial microbiome on in vitro fertilization outcomes.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
pmid = {41345366},
issn = {1573-7330},
abstract = {PURPOSE: The uterine microbiome of in vitro fertilization (IVF) patients was analyzed using next-generation sequencing (NGS) targeting 16S rRNA. Lactobacillus spp. were examined, with a special focus on Lactobacillus iners. The effects of antibiotic therapy on pregnancy outcomes were investigated.

METHODS: A total of 257 IVF patients underwent endometrial microbiome testing. Patients were initially classified based on the percentage of Lactobacillus spp. into the Lactobacillus-dominant microbiome (LDM) group and the non-LDM group using a cutoff of 90%. Treatment was provided to non-LDM patients. Treated patients who improved on the second test were included in the Post-treatment group, and their pretreatment status was also examined.

RESULTS: Lactobacillus was dominant in many IVF patients, but some patients showed Gardnerella or other bacteria associated with bacterial vaginosis. The treatment improvement rate for the non-LDM group was 81.4%, with an equivalent or better pregnancy success rate compared with the LDM group. The effect on pregnancy outcomes of Lactobacillus may differ by species, with L. crispatus and L. gasseri tending to act positively, whereas L. iners at ≥ 74.2% acts negatively.

CONCLUSIONS: This study shows that the recovery of an LDM in non-LDM IVF patients improves the composition of the endometrial microbiome, and pregnancy outcomes approach those of patients initially having an LDM. Furthermore, in LDM cases, L. iners species were also associated with lower pregnancy rates. These findings suggest that both the presence and type of Lactobacillus species are important for IVF success and that targeted microbiome treatment may improve reproductive outcomes.},
}

@article {pmid41345336,
year = {2025},
author = {Antoł, W and Surmacz, B and Ostap-Chec, M and Stec, D and Miler, K},
title = {Do Shifts in Honeybee Crop Microbiota Enable Ethanol Accumulation? A Comparative Analysis of Caged and Foraging Bees.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {137},
pmid = {41345336},
issn = {1432-184X},
support = {Sonata 17 grant 2021/43/D/NZ8/01044//National Science Center in Poland/ ; },
mesh = {Animals ; Bees/microbiology/physiology/metabolism ; *Ethanol/metabolism/analysis ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Microbiota ; Plant Nectar/metabolism ; *Gastrointestinal Microbiome ; Fermentation ; },
abstract = {Honeybees encounter low environmental doses of ethanol, primarily through fermenting nectar, which can have both beneficial and detrimental effects on their functioning. Yet, ethanol traces can also be detected in the crop of caged bees with no access to environmental food sources. This raises the possibility that endogenous ethanol accumulation could occur under restricted conditions, with microbial contributions as a potential mechanism. The crop microbiota, although less diverse than that in other gut segments, plays important roles in food fermentation and pathogen defense. We hypothesized that captivity-induced shifts in crop microbiota may facilitate fermentation, resulting in measurable ethanol. To test this, we compared the crop contents of naturally foraging hive bees and caged bees reared without access to the natural environment. Ethanol levels were low in both groups and did not differ significantly, but non-zero measurements were more frequently observed in caged bees. Microbial community structure differed strongly in α- and β-diversity. Caged bees showed reduced abundance of nectar-associated genera (e.g., Apilactobacillus) and an increase in genera that include known ethanol-producing strains, such as Gilliamella and Bifidobacterium. While we did not directly assess metabolic activity, our results suggest that captivity alters microbial communities in ways that may influence ethanol levels. This raises broader questions about how microbe-host interactions modulate host phenotypes under different environmental conditions.},
}

Animals
Bees/microbiology/physiology/metabolism
*Ethanol/metabolism/analysis
*Bacteria/classification/metabolism/genetics/isolation & purification
*Microbiota
Plant Nectar/metabolism
*Gastrointestinal Microbiome
Fermentation

@article {pmid41345261,
year = {2025},
author = {Ma, J and Kim, N and Cha, JH and Kim, W and Kim, CY and Lee, YH and Kim, HS and Han, YD and Yong, D and Han, E and Yang, S and Beck, S and Lee, I},
title = {A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41345261},
issn = {2058-5276},
support = {2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; 2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; },
abstract = {Understanding the human gut microbiome requires comprehensive genomic catalogues, yet many lack geographic diversity and contain medium-quality metagenome-assembled genomes (MAGs) missing up to 50% of genomic regions, potentially distorting functional insights. Here we describe an enhanced Human Reference Gut Microbiome (HRGM2) resource, a catalogue of near-complete MAGs (≥90% completeness, ≤5% contamination) and isolate genomes. HRGM2 comprises 155,211 non-redundant near-complete genomes from 4,824 prokaryotic species across 41 countries, representing a 66% increase in genome count and a 50% boost in species diversity compared to the Unified Human Gastrointestinal Genome catalogue. It enabled improved DNA-based species profiling, resolution of strain heterogeneity and survey of the human gut resistome. The exclusive use of these genomes improved metabolic capacity assessment, enabling high-confidence, automated genome-scale metabolic models of the entire microbiota and revealing disease-associated microbial metabolic interactions. This resource will facilitate reliable functional insights into gut microbiomes.},
}

@article {pmid41345243,
year = {2025},
author = {Ste Marie, J and Mays, C and Guo, B and Radniecki, TS and Waite-Cusic, J and Navab-Daneshmand, T},
title = {Longitudinal replicated metagenomic analysis of biosolids-amended soils reveals enrichment of ARGs, virulence factors, and ESKAPE pathogens.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {96},
pmid = {41345243},
issn = {2731-8745},
support = {2018-67017-27631//USDA National Institute of Food and Agriculture, Agricultural and Food Research Initiative Competitive Program, Agriculture Economics and Rural Communities/ ; },
abstract = {Biosolids land application introduces antibiotic resistance genes (ARGs) and clinically relevant pathogens into agricultural soils, raising concerns about long-term environmental and public health impacts. Despite growing interest in biosolids reuse, there remains a critical need for replicated, longitudinal studies to assess how biosolids amendments shape soil microbiomes and resistomes during crop cultivation. In this replicated longitudinal greenhouse study, we used shotgun metagenomics to characterize the impact of biosolids amendment on the soil microbiome, resistome, virulence factors, and ESKAPE pathogens during carrot cultivation. Biosolids-amended soils exhibited increased richness of microbial genera (e.g., Rhodanobacter, Dyella, and Thermomonas), ARG subtypes (resistance to sulfonamide, tetracycline, fosmidomycin, and macrolides), and virulence factors compared to pristine controls. Notably, all six ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp., were detected at elevated relative abundances (1.4- and 3.4-fold) in biosolids-amended soils and remained detectable throughout the 11-week cultivation period. Network analysis revealed statistically supported co-occurrences between microbial taxa and ARGs (with resistance to tetracyclines, beta-lactams, chloramphenicol, and multidrugs), suggesting possible host associations. These findings underscore the ecological and clinical relevance of biosolids amendment and highlight the need for integrated surveillance frameworks to mitigate antimicrobial resistance dissemination in agricultural environments.},
}

@article {pmid41345102,
year = {2025},
author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M},
title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10051},
pmid = {41345102},
issn = {2041-1723},
support = {27/2023//Chronic Disease Research Foundation (CDRF)/ ; },
mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; },
abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.},
}

Humans
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome/physiology
*Diet
Male
Female
Metabolome
Middle Aged
Metabolomics/methods
Aged
Metagenomics
Adult
Machine Learning

@article {pmid41344956,
year = {2025},
author = {Jia, D and Wang, L},
title = {Opportunities and challenges in applying microbiota to clinical cancer immunotherapy.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.11.011},
pmid = {41344956},
issn = {1878-4380},
abstract = {Fundamental research has elucidated the indispensable role of gut microbiota in modulating cancer immunotherapy efficacy. Despite promising preclinical findings, few related approaches have reached clinical trials. In this opinion, we provide insights based on current clinical trials using fecal microbiota transplant or specific bacterial strains as adjuvants to enhance immune checkpoint blockade therapy. We also systematically analyze the challenges in trial design, with a focus on donor selection, patient enrollment, implantation procedures, antibiotic use, safety assessment, and endpoint evaluation. Moving forward, we offer a comprehensive '4D' framework (diversity, diffusion, depth, and delicacy) for accelerating the bench-to-bedside translation. It is hoped that this opinion will help researchers and clinicians aiming to harness microbiome-based strategies to improve cancer immunotherapy outcomes.},
}

@article {pmid41344748,
year = {2025},
author = {Suzuki, T and Ding, H and Yuan, F and Li, Y and Ren, J and Zhan, H and Israr, MZ and Sun, X and Qiu, Z and Sheng, H},
title = {Association of Gut Microbiome Biomarkers With Mortality in Chinese Patients With Acute/Worsening Heart Failure.},
journal = {JACC. Asia},
volume = {5},
number = {12},
pages = {1634-1637},
doi = {10.1016/j.jacasi.2025.09.023},
pmid = {41344748},
issn = {2772-3747},
}

@article {pmid41344619,
year = {2025},
author = {Li, Y and Li, T and Zhang, Y and Wang, Y and Wu, G and Tan, Y},
title = {Microbial metabolites in the gut-brain axis: their impact on depression pathophysiology and treatment.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2025.12.002},
pmid = {41344619},
issn = {1873-7544},
abstract = {Gut microbiota influences major depressive disorder (MDD) via the microbiota-gut-brain axis through various metabolites, but a systematic understanding of their neuroregulatory mechanisms is lacking. This review categorizes gut microbial metabolites according to their metabolic origin and physiological function, clarifies their roles in depression-related neurobiological processes, and explores their therapeutic potential. Following PRISMA-ScR guidelines, a scoping review screened 1,249 records from five databases (2020-2025), including 23 studies on tryptophan metabolism, short-chain fatty acids (SCFAs), gamma-aminobutyric acid (GABA), and other metabolites that regulate depression-related neurobiological pathways; tryptophan metabolism affects serotonin/kynurenine pathways, causing neuroinflammation and neurotransmitter imbalance; SCFAs(primarily butyrate, less so propionate) modulate gene expression, neuroinflammation, and microglial function as histone deacetylase (HDAC) inhibitors; GABA-producing bacteria influence synaptic plasticity and suppress hypothalamic-pituitary-adrenal (HPA) axis hyperactivity; and other metabolites (e.g., homovanillic acid and β-hydroxybutyrate) have neuroprotective effects and affect neurotransmitter dynamics. Notably, this review advances the field via an integrative cross-pathway perspective, a critical appraisal of evidence strength across animal/human studies, and translational implications. Microbiome-modifying interventions (like probiotics, prebiotics, and dietary changes, are promising in animal models for correcting metabolite dysregulation and alleviating depressive symptoms.},
}

@article {pmid41344580,
year = {2025},
author = {Tariq, F and Zhao, L and Hussain, S and Riaz, MW and Wu, C and Zhang, J and Li, P and Gowda, M and Nair, SK and Prasanna, BM and Zhang, X and Wang, X and Gangurde, SS},
title = {Plasticity and adaptive architecture of roots for enhanced salinity tolerance in crops.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108773},
doi = {10.1016/j.biotechadv.2025.108773},
pmid = {41344580},
issn = {1873-1899},
abstract = {Soil salinization poses a major challenge to global food security, affecting over one billion hectares of arable land and severely constraining crop productivity. As the primary interface between plants and soil, roots play a pivotal role in sensing and adapting to salinity stress through remarkable structural and functional plasticity. This review integrates recent advances in root system architecture (RSA) dynamics, suberin biosynthesis, hormonal regulation, and microbiome interactions to elucidate how plants achieve salinity resilience. We discuss key genes and regulatory modules controlling primary root elongation, lateral root patterning, and barrier formation, emphasizing transcriptional networks involving MYB, NAC, and WRKY families and their coordination with ABA, auxin, and ethylene signaling. Special attention is given to the biosynthesis and deposition of suberin as a dynamic ion-selective barrier governed by hormonal crosstalk and lipid metabolism. We further highlight how beneficial microbes such as Azospirillum, Bacillus, and arbuscular mycorrhizal fungi enhance salt tolerance by modulating phytohormones, antioxidant systems, and ionic homeostasis. Integrating multi-omics and CRISPR-based tools with microbiome engineering offers new avenues to design salt-resilient root ideotypes. We propose a conceptual framework linking molecular regulation, hormonal dynamics, and rhizosphere ecology to root system plasticity, providing a blueprint for engineering next-generation crops capable of maintaining growth and productivity in saline environments.},
}

@article {pmid41344505,
year = {2025},
author = {Rizwan, A and Karim, S and Andrabi, IL and Mushtaq, M and Farooqi, H},
title = {Fermentation Alters the Anticancer Properties of Dietary Polyphenols in Pulses.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.11.023},
pmid = {41344505},
issn = {1541-6100},
abstract = {Pulses are a rich dietary source of polyphenols, compounds increasingly known for their role in disease prevention and overall health. Recent advances show that fermentation can not only improve the bioavailability of pulse polyphenols but can also generate new metabolites. This review explores how these fermentation-driven molecular transformations enhance the anticancer effect of pulse polyphenol, highlighting newly identified microbial metabolite pathways. We also describe how fermented polyphenols interact with the gut microbiome, influencing pathways linked to cancer. Looking ahead, precision fermentation and multi-omics profiling promise to accelerate the development of next-generation functional foods and support cancer therapeutics, bridging the gap between laboratory innovation and clinical application.},
}

@article {pmid41344385,
year = {2025},
author = {Piccolo, L and Sligar, K and Kuster, A},
title = {Reevaluating Neonatal Erythromycin Prophylaxis Policy Amid Advances in Sexually Transmitted Infection Screening, Antenatal Treatment, and Antibiotic Stewardship.},
journal = {Journal of obstetric, gynecologic, and neonatal nursing : JOGNN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jogn.2025.11.003},
pmid = {41344385},
issn = {1552-6909},
abstract = {Long-standing mandates in the United States require universal ophthalmic prophylaxis with erythromycin for all neonates, although recent evidence has led to reconsideration of this practice. This intervention was originally adopted to prevent blindness caused by Neisseria gonorrhoeae (gonococcal ophthalmia neonatorum, GON) and Chlamydia trachomatis (chlamydial ophthalmia neonatorum, CON). Today, however, prenatal screening and treatment have rendered such infections rare at birth. Current population data indicate that GON is exceedingly uncommon in the United States and that erythromycin is ineffective at preventing CON. Moreover, concerns regarding antimicrobial resistance, medication shortages, and early microbiome disruption call into question the rationale for maintaining this policy. In this analysis, we integrate contemporary epidemiologic and policy evidence to support the conclusion that continuing universal prophylaxis provides minimal clinical benefit, exposes newborns to unnecessary antibiotics, and conflicts with modern principles of antibiotic stewardship. Risk-based prevention models already adopted in many high-income countries offer a safer and more evidence-aligned alternative. Nurses are uniquely positioned to lead this transition through patient education, antibiotic stewardship, and advocacy for evidence-based neonatal care.},
}

@article {pmid41344333,
year = {2025},
author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B},
title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.087},
pmid = {41344333},
issn = {1879-0445},
abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.},
}

@article {pmid41344294,
year = {2025},
author = {Sazykina, M and Lanovaya, O and Barabashin, T and Azhogina, T and Klimova, M and Karchava, S and Khmelevtsova, L and Khammami, M and Polinichenko, A and Sazykin, I},
title = {Ecotoxicity and antibiotic resistance genes in hydrobionts of the Azov Sea.},
journal = {Marine environmental research},
volume = {214},
number = {},
pages = {107759},
doi = {10.1016/j.marenvres.2025.107759},
pmid = {41344294},
issn = {1879-0291},
abstract = {Antimicrobial resistance is a major global health problem. Natural ecosystems, especially aquatic environments and aquatic animals, are important reservoirs of ARGs and antibiotic-resistant bacteria (ARB). The presence of ARGs in the microbiome of seafood may lead to their transfer to human bacteria. While most ARG research focus on water and sediments, the role of aquatic organisms (fish, shellfish, jellyfish) as reservoirs and vectors of ARGs is poorly understood. The aim of this work is to assess ARGs distribution in bacteria associated with aquatic organisms in different ecological niches of the Azov Sea (mollusks, jellyfish and fish) using PCR analysis and to study toxicity of aquatic organisms' tissues using a battery of whole-cell bacterial lux-biosensors, as well as to search for a correlation between samples toxicity and ARGs content in them. We also evaluate the potential relationship between toxicity levels in aquatic organisms, the frequency of ARGs and mobile genetic elements (MGEs) detected. In the course of the work, it was found that the most common are the genes that determine resistance to monobactams blaCTX-M and carbapenems blaVIM-1. Microbial communities of mollusks and fish are characterized by gill bacteria being more contaminated with ARGs than the gut microbiome, which is due to the constant and direct contact of the gill epithelium with polluted aquatic environment. Statistical analysis revealed a positive link between the toxicity of the organs in which the bacteria are localized and the presence of a number of ARGs was found; these findings highlight that tissue toxicity caused by endogenous toxins or external xenobiotic pollutants creates an unfavorable internal environment. A correlation was also discovered between the content of individual genes, which probably indicates their colocalization on the same mobile elements of the genome. This information may be useful for better understanding the spread of antimicrobial resistance genes in aquatic animals.},
}

@article {pmid41344253,
year = {2025},
author = {Zhao, Y and An, J and Wang, Y and Chang, J and Zeng, H and Liu, S and Ding, Y and Zhou, X and Jia, S},
title = {Mechanistic insights into ozone-slurry ice synergy for preserving the quality of Litopenaeus vannamei during chilled storage.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147318},
doi = {10.1016/j.foodchem.2025.147318},
pmid = {41344253},
issn = {1873-7072},
abstract = {Rapid post-harvest deterioration of Litopenaeus vannamei during chilled storage limits its economic value. Here, we assessed the combined treatment of ozone and slurry ice (referred to as SIO) as a preservation strategy at 4 °C, integrating physicochemical, structural and microbiome analyses. Compared with conventional icing, SIO markedly suppressed increases in total volatile basic nitrogen, K value, and total viable count. Meanwhile, SIO preserved inosine monophosphate by inhibiting acid phosphatase activity, while mitigating protein degradation to maintain myofibrillar integrity. High-throughput sequencing revealed that SIO decreased the relative abundance of Cupriavidus, and suppressed the proliferation of spoilage-associated genera Psychrobacter, Vibrio, and Shewanella. The K value in the CK group exceeded 60 % by day 5, whereas SIO postponed this threshold to day 7, effectively extending shelf life by 2 days. These findings demonstrate that SIO provides synergistic microbial suppression and biochemical stabilization, offering a scalable, residue-free approach for maintaining the quality of seafood.},
}

@article {pmid41344097,
year = {2025},
author = {Montoro-Dasi, L and Lorenzo-Rebenaque, L and Marco-Fuertes, A and Sisquella, L and Gomez, M and Soler, P and Marco-Jiménez, F and Marin, C},
title = {Dual Salmonella vaccination attenuates microbiota dysbiosis and enhances microbiota functionality in poultry challenged with S. Typhimurium.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106140},
doi = {10.1016/j.psj.2025.106140},
pmid = {41344097},
issn = {1525-3171},
abstract = {Salmonella is a leading cause of gastrointestinal illness and foodborne outbreaks worldwide, with poultry products such as eggs as the primary source of infection. In this context, live attenuated vaccines play a critical role in reducing the risk of infection in poultry flocks. However, their impact on the gut microbiota remains poorly understood. Thus, the aim of this study was to evaluate the effects of a live attenuated combined vaccine against Salmonella Enteritidis and Salmonella Typhimurium on the gut microbiota of chicks challenged with S. Typhimurium, including the study of microbial balance and functionality. The trial involved 40 specific pathogen-free chicks, divided into vaccinated and control groups, all challenged with S. Typhimurium at 14 days of age. Afterwards, caecal content of 10 animals per group was collected at 7 and 14 days post infection. Then, the composition, diversity and functionality of the microbiota were analyzed using 16S rRNA sequencing and bioinformatic analysis. The results of the taxonomic analysis revealed 1,261 bacterial taxa, with Firmicutes and Proteobacteria as the dominant phyla. In addition, vaccination resulted in significant changes in microbiota composition, with marked differences in microbial diversity between groups. PLS-DA and Bayesian analysis identified key species such as Clostridium innocuum in vaccinated chicks and Eubacterium coprostanoligenes in the control group. Results also showed that vaccination promoted the growth of beneficial genera such as Lactobacillus and Blautia, which was associated with reduced Salmonella colonization and shedding. Alpha diversity analysis revealed significantly higher microbial richness and evenness in the control group. Finally, functional annotation revealed shared microbial functions between the groups, with potentially pathogenic bacteria, including Salmonella, present in both. These results suggest that vaccination improves microbiota stability and supports the protective role of beneficial bacteria against Salmonella, highlighting the importance of vaccination in improving poultry health and pathogen control throughout the food chain.},
}

@article {pmid41343929,
year = {2025},
author = {Jemimah, S and Majdalawieh, AF and Hamad, M and Mahasneh, AA},
title = {Differential analysis of microbial profiles in colorectal cancer reveals modulations corresponding to immune subtypes.},
journal = {Computers in biology and medicine},
volume = {200},
number = {},
pages = {111346},
doi = {10.1016/j.compbiomed.2025.111346},
pmid = {41343929},
issn = {1879-0534},
abstract = {The proximity of the gut microbiome to the tumor microenvironment (TME) in colorectal cancer (CRC) presents a unique ecological niche. A systematic study of tumor-microbiome interactions will facilitate a deeper understanding of the heterogeneity in immune response and clinical outcomes in CRC. Previous studies have identified specific microbial species such as Fusobacterium nucleatum, pks[+] Escherichia coli, and enterotoxigenic Bacteroides fragilis as contributors to CRC initiation and progression. However, the extent to which interactions between the microbiome and immune landscape affect prognosis and tumor heterogeneity remains poorly understood. To address this, immune subtypes from The Cancer Genome Atlas (TCGA) were integrated with microbial profiles from The Cancer Microbiome Atlas (TCMA) to examine the relationship between immune subtypes and the tumor microbiome in CRC. A cohort of 631 TCGA CRC cases with clinical, microbial and immune subtype data was analyzed. Differential abundance analysis indicated significant associations between specific taxa and immune subtypes. We demonstrate that pathogenic genera such as Selenomonas, Butyricimonas and Centipeda are significantly enriched (padjusted < 0.05) in the C2 IFN-ɣ dominant subtype. Our findings show that the abundance of pathogenic genera may play a critical role in driving the paradoxically poorer survival observed in CRC patients with the C2 subtype.},
}

@article {pmid41343559,
year = {2025},
author = {George, NA and Bradford, L and Hinz, A and El Kadi, M and Xing, L and Doukhanine, E and MacFadden, DR and Nott, C and Fralick, M and Kassen, R and Wong, A and Hug, LA},
title = {SARS-CoV-2 detection is independent of microbiome composition on surfaces in a major Ontario hospital.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0326403},
doi = {10.1371/journal.pone.0326403},
pmid = {41343559},
issn = {1932-6203},
mesh = {Ontario/epidemiology ; *COVID-19/epidemiology/virology/diagnosis/microbiology ; *SARS-CoV-2/isolation & purification/genetics ; Humans ; *Microbiota ; Hospitals ; },
abstract = {The SARS-CoV-2 pandemic has resulted in considerable mortality in hospital settings. Built environment surveillance can provide a non-invasive indicator of SARS-CoV-2 status in hospitals, but we have a limited understanding of SARS-CoV-2's microbial co-associations in the built environment, including any potential co-occurrence dynamics with pathogenic and antimicrobial-resistant microorganisms. Here we examine the microbial communities on floors and elevator buttons across several locations in two major tertiary-care Ontario hospitals during a surge in SARS-CoV-2 cases in 2020. Total microbial community composition, prevalence and type of detected antimicrobial resistance genes, and virulence factor distributions were governed by sample source rather than SARS-CoV-2 detection status. Fifteen microorganisms were identified as indicator species associated with positive SARS-CoV-2 signal, including three opportunistic pathogens (i.e., two Corynebacterium sp. and a Sutterella sp). Key clinically relevant antimicrobial resistance genes showed varying prevalence across sites within the hospital, suggesting that our workflow could inform resistance burden in hospitals. Overall, these results indicate limited or only weak interactions between microbiome composition and SARS-CoV-2 detection status in the hospital built environment.},
}

Ontario/epidemiology
*COVID-19/epidemiology/virology/diagnosis/microbiology
*SARS-CoV-2/isolation & purification/genetics
Humans
*Microbiota
Hospitals

@article {pmid41343511,
year = {2025},
author = {Mahalak, KK and Narrowe, AB and Liu, L and Firrman, J and Lemons, JMS and Van den Abbeele, P and Baudot, A and Yao, Y and Li, Y and Yu, L},
title = {The ex vivo effects of ethanolic extractions of black cumin seed, turmeric root, and Ceylon cinnamon bark on the human gut microbiota.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0334824},
doi = {10.1371/journal.pone.0334824},
pmid = {41343511},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Plant Extracts/pharmacology/chemistry ; *Curcuma/chemistry ; *Cinnamomum zeylanicum/chemistry ; Plant Roots/chemistry ; Plant Bark/chemistry ; Male ; Adult ; Seeds/chemistry ; Fatty Acids, Volatile/metabolism ; Ethanol/chemistry ; Female ; *Nigella sativa/chemistry ; },
abstract = {Black cumin, turmeric root, and Ceylon cinnamon bark are spices that have been used for both culinary purposes and in traditional medicine practices. These spices are frequently connected with providing antidiabetic, antimicrobial, anti-inflammatory, and gastroprotective properties. However, most studies on potential health effects have not been performed in humans. Since many of the health effect claims relate to gastrointestinal health, we explored the impact of black cumin extract (BCE), turmeric root extract (TRE), and Ceylon cinnamon extract (CCE) on the human gut microbiota ex vivo using the SIFR® technology. The impact on the gut microbiota were determined using shotgun sequencing and flow cytometry, while the health-related short-chain fatty acids (SCFA) were analyzed to assess the metabolic output. While TRE and CCE had very little effect on the gut microbiota, BCE significantly increased acetate (+ 8.7mM), butyrate (+1.3mM), and propionate (+3mM) production. This related to specific increases of Alistipes onderdonkii, Alistipes shahii and particularly Candidatus Cibiobacter qucibialis, CCE and TRE increased the health related Faecalibacterium prausnitzii and Dysosmobacter welbionis, respectively, with CCE also increasing Enterococcus and Veillonella species. Overall, these findings indicate these spices may have an impact on the human gut microbiome that could explain their purported health effects.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Plant Extracts/pharmacology/chemistry
*Curcuma/chemistry
*Cinnamomum zeylanicum/chemistry
Plant Roots/chemistry
Plant Bark/chemistry
Male
Adult
Seeds/chemistry
Fatty Acids, Volatile/metabolism
Ethanol/chemistry
Female
*Nigella sativa/chemistry

@article {pmid41343437,
year = {2025},
author = {Ramírez-Larrota, JS and Juyoux, P and Guerra, P and Eckhard, U and Gomis-Rüth, FX},
title = {Correction: Biochemical and structural characterization of the human gut microbiome metallopeptidase IgAse provides insight into its unique specificity for the Fab' region of IgA1 and IgA2.},
journal = {PLoS pathogens},
volume = {21},
number = {12},
pages = {e1013742},
doi = {10.1371/journal.ppat.1013742},
pmid = {41343437},
issn = {1553-7374},
abstract = {[This corrects the article DOI: 10.1371/journal.ppat.1013292.].},
}

@article {pmid41343181,
year = {2025},
author = {Roth, TD and Russo-Savage, L and Bahojb Habibyan, Y and Keenan, CM and Wallace, LE and Nasser, Y and Mawe, GM and Lavoie, B and Sharkey, KA},
title = {Microbial dysbiosis alters serotonin signaling in a post-inflammatory murine model of visceral pain.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00240.2025},
pmid = {41343181},
issn = {1522-1547},
support = {FDN148380//Canadian Institutes of Health Research (CIHR)/ ; DK113800//HHS | National Institutes of Health (NIH)/ ; AT011203//HHS | National Institutes of Health (NIH)/ ; },
abstract = {Serotonin (5-HT) is a multifunctional signaling molecule in the gastrointestinal (GI) tract. 5-HT synthesis is regulated by the gut microbiota. Microbial dysbiosis has been implicated in visceral pain and persistent alterations in gut function that occur following inflammation. Here we tested the hypothesis that alterations in gut microbiota in a post-inflammatory model of visceral pain contribute to dysregulated 5-HT signaling. We used mice treated with dextran sodium sulfate (DSS) 42 days earlier (post-colitis) or untreated mice as donors for fecal microbiota transplants (FMTs) into germ-free mice to explore changes in enterochromaffin (EC) cell populations, expression of 5-HT synthesis, transport, and degradation genes, levels of 5-HT and its major metabolite, 5-hydroxyindoleacetic acid (5-HIAA), and 5-HT release. Significant differences were observed in EC cells, Tph1, Slc6a4, and Maoa gene expression, 5-HT and 5-HIAA levels and 5-HT release between germ-free mice and mice receiving an FMT from either control or post-colitis donor mice. We observed no differences in the total number of EC cells, Tph1, or Slc6a4 gene expression of mice after FMT from post-colitis or control mice. However, there was a significant increase in Maoa gene expression in the terminal ileum, an increased 5-HIAA/5-HT ratio in the proximal colon and reduced 5-HT release to mechanical and chemical stimulation in the proximal and distal colon after FMT from post-colitis mice. Collectively, these findings provide additional evidence that the gut microbiota regulates 5-HT signaling. Moreover, they reveal functional changes in EC cell sensitivity in the presence of an altered microbiota after recovery from inflammation.},
}