@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.},
}

@article {pmid41342934,
year = {2025},
author = {Bell, W and Jennings, A and Bondonno, NP and Franke, A and Bang, C and Both, M and Kassubek, J and Müller, HP and Borggrefe, J and Lieb, W and Kühn, T and Cassidy, A},
title = {The gut microbiome mediates the association between a flavonoid-rich diet and MASLD in a population-level analysis.},
journal = {European journal of nutrition},
volume = {65},
number = {1},
pages = {1},
pmid = {41342934},
issn = {1436-6215},
support = {22/CC/11147//Co-Centre for Sustainable Food Systems/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Flavonoids/administration & dosage ; Male ; Cross-Sectional Studies ; Female ; *Diet/methods ; Middle Aged ; *Fatty Liver/microbiology/prevention & control/epidemiology ; Adult ; Aged ; },
abstract = {PURPOSE: A growing body of evidence suggests diets rich in flavonoids may protect against metabolic-dysfunction associated steatotic liver disease (MASLD) development and progression. As the gut microbiome is important in the biotransformation of flavonoids to their constituent bioactive metabolites, studies on the potential mediating role of the gut microbiome in the association between dietary flavonoid intakes and MASLD are warranted but lacking. Thus, this study aims to examine the associations between a diet rich in flavonoids and MASLD, and assess the potential mediating role of the gut microbiome.

METHODS: In a cross-sectional analysis (n = 531), using the FlavoDiet score (FDS), we assessed the association between a flavonoid-rich diet and MASLD (ascertained by magnetic resonance imaging) using multivariable logistic and linear regression. Additionally, we used mediation analysis to identify and assess potential 16S-derived gut microbiome mediators.

RESULTS: Each doubling of the FDS was associated with a 27% lower odds of MASLD (OR: 0.73 [95% CI 0.54-0.98], p = 0.04) after multivariable adjustment. 9.2% of this association was mediated by a greater abundance of the genus Eisenbergiella (indirect effect ß = - 0.006 [95% CI - 0.019, to - 0.000], p = 0.04).

CONCLUSION: These findings suggest that a flavonoid-rich diet is associated with better liver health, and that the abundance of the Eisenbergiella taxa may in part explain the association between a flavonoid-rich diet and MASLD.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Flavonoids/administration & dosage
Male
Cross-Sectional Studies
Female
*Diet/methods
Middle Aged
*Fatty Liver/microbiology/prevention & control/epidemiology
Adult
Aged

@article {pmid41342739,
year = {2025},
author = {Shah, UA and Cogrossi, LL and Garces, JJ and Policastro, A and Castro, F and Derkach, A and Fei, T and DeWolf, S and Grioni, M and Sisti, S and Blaslov, J and Adintori, PA and Hosszu, KK and McAvoy, D and Baichoo, M and Cross, JR and Paredes, J and Anuraj, A and Raj, SS and Pohl, C and Zordan, P and Zinsmeyer, V and Jesus Faustino Ramos, RJ and Lorenzoni, M and Gipson, B and Maclachlan, KH and Gradissimo, A and Boiocchi, L and Aleynick, N and Marchigiani, C and Pagani, S and Salehi, E and Koche, RP and Chaligne, R and Block, T and Korde, N and Tan, CR and Hultcrantz, M and Hassoun, H and Shah, GL and Scordo, M and Lahoud, OB and Chung, DJ and Landau, HJ and Peled, JU and Clementi, N and Chesi, M and Bergsagel, PL and Mailankody, S and Pollak, MN and D'Souza, A and Landgren, O and Chimonas, S and Giralt, SA and Usmani, SZ and Iyengar, NM and Lesokhin, AM and van den Brink, MRM and Bellone, M},
title = {A High-Fiber Plant-Based Diet in Myeloma Precursor Disorders - Results from the NUTRIVENTION Clinical Trial and Preclinical Vk*MYC Model.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-25-1101},
pmid = {41342739},
issn = {2159-8290},
abstract = {Consumption of a western diet and high body mass index (BMI) are risk factors for progression from pre-malignant phenotypes to multiple myeloma, a hematologic cancer. In the NUTRIVENTION trial (NCT04920084), we administered a high-fiber, plant-based diet (meals for 12 weeks, coaching for 24 weeks) to 23 participants with myeloma precursor states and elevated BMI. The intervention was feasible, improved quality of life and modifiable risk factors: metabolic (BMI, insulin resistance), microbiome (diversity, composition), and immune (inflammation, monocyte subsets). Disease-progression trajectory improved (n=2) or was stable. Findings were translated to Vk*MYC mice modeling the myeloma-precursor state, in which a high-fiber diet delayed disease progression through improved metabolism and microbiome composition leading to increased short-chain fatty acid production that reinvigorated anti-tumor immunity and inhibited tumor growth. These effects from fiber consumption were independent of calorie restriction and weight loss. A high-fiber diet is a low-risk intervention that may delay progression to myeloma.},
}

@article {pmid41342539,
year = {2025},
author = {Song, W and Zhang, S and Perez, M and Li, J and Ma, H and Thomas, T and Qiu, J-W and Qian, P-Y},
title = {Distinct patterns of microbial association across deep-sea corals from the Western Pacific Magellan Seamounts.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0209325},
doi = {10.1128/spectrum.02093-25},
pmid = {41342539},
issn = {2165-0497},
abstract = {Ahermatypic corals are common inhabitants in the Magellan Seamounts of the Western Pacific Ocean, yet their microbiomes are largely unexplored. In the present study, we used 16S rRNA gene amplicon sequencing targeting the V4 variable region to characterize the microbiomes of 30 deep-sea coral samples from 9 coral families collected from this area, including members of the families Schizopathidae, Victorgorgiidae, and Chrysogorgiidae, whose microbiomes had not been previously described. Our analyses revealed distinct patterns of microbial association between the coral families, with most coral samples being dominated by single amplicon sequence variants belonging to 11 prokaryotic genera. Ammonia-oxidizing archaea of the genus Nitrosopumilus were abundant exclusively in schizopathid corals, with relative 16S rRNA gene read abundances ranging from 29.4% to 99.8%. In contrast, Nitrosopumilus was either absent or constituted no more than 5.3% of the reads in the remaining coral families. This may be attributed to the catabolism of the protein-rich zooplankton preferred by schizopathid corals, which could, in turn, facilitate ammonia-driven carbon fixation within the holobiont. Three cladopathid corals hosted abundant sequences of two distantly related bacteria capable of utilizing nitric oxide, which could be used by the symbionts either to generate oxygen for aerobic metabolisms or be reduced as a defense against the host's antibacterial activity. The distinct patterns of microbial association between coral taxa indicate that the microbiomes have differential roles in the adaptation of the hosts to specific ecological niches in the deep-sea environments.IMPORTANCEMicrobiomes play crucial roles in host development, physiology, and health, especially in the deep-sea environments. In this study, we collected 30 deep-sea corals from the Western Pacific Magellan Seamounts at depths ranging from 805 to 5,572 m. These samples spanned nine coral families, including three whose microbiomes have not been previously described. Our analyses revealed distinct patterns of microbial association between coral taxa. A majority of the deep-sea corals were dominated by single microbial species, indicating strong selection for certain microbial symbionts and thus functions, such as chemolithoautotrophy, the production of oxygen or secondary metabolites. Furthermore, we observed an overwhelming dominance of sequences from the ammonia-oxidizing archaeal genus Nitrosopumilus exclusively in black corals from the family Schizopathidae, a phenomenon not previously reported. This may be attributed to the catabolism of the protein-rich zooplankton preferred by the schizopathid corals, which could, in turn, facilitate ammonia-driven carbon fixation within the coral holobiont.},
}

@article {pmid41342438,
year = {2025},
author = {Yaqoob, A and Sharif, MK and Haider, U and Feng, Q},
title = {Quercetin Modulates Gut Microbiome and Immune Response to Mitigate Arsenic-Induced Toxicity: Insights From a Microbiome-Immune Study.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70330},
doi = {10.1002/mnfr.70330},
pmid = {41342438},
issn = {1613-4133},
abstract = {Arsenic exposure from contaminated food and water is a global nutritional issue. Nutritional interventions indicate that dietary polyphenols, such as quercetin, may reduce these toxic effects via antioxidant and immunomodulatory properties. This study examined the protective effect of quercetin against arsenic-induced toxicity in a Wistar rat model. Twenty-four adult Wistar rats were divided into four groups as follows: control (G0), arsenic-exposed (G1; 5 mg/kg/day NaAsO2), quercetin-treated (G2; approximately 50 mg/kg/day), and co-treated (G3; arsenic + quercetin). Over 28 days, catalase (CAT), glutathione peroxidase (GPx), glutathione S-transferase (GST), superoxide dismutase (SOD), cytokine gene expression (IL-1β, IL-6, TNF-α, IL-4, IL-10, TGF-β), claudin, occludin (CLDN1, OCLN), and fecal microbial profiles (q-PCR, diversity index) were assessed. Our results demonstrate that arsenic exposure significantly reduces antioxidant enzyme levels, elevates pro-inflammatory cytokines, disrupts tight junction protein expression, and causes dysbiosis and proliferation of Proteobacteria and E. coli, ultimately damaging intestinal structure. Quercetin treatment, especially in G3, restored antioxidant levels, balanced cytokine profiles, normalized tight junction gene expression, and maintained gut microbial diversity. Histopathological and correlation analyses also confirmed structural and functional recovery of gut tissues. These findings support quercetin's potential as a dietary intervention to counteract heavy metal-induced gut disorders, reinforcing its nutritional relevance in environmental toxins.},
}

@article {pmid41342432,
year = {2026},
author = {Gonciarz, M and Wiatrak, B and Lombard, I and Konecki, Ł and Sarbinowska, J},
title = {Therapeutic Potential of Melatonin in Gastrointestinal Cancers: Molecular Mechanisms, Preclinical Evidence and Clinical Implications.},
journal = {Journal of pineal research},
volume = {78},
number = {1},
pages = {e70101},
doi = {10.1111/jpi.70101},
pmid = {41342432},
issn = {1600-079X},
support = {//The authors received no specific funding for this work./ ; },
mesh = {*Melatonin/therapeutic use/pharmacology ; Humans ; Animals ; *Gastrointestinal Neoplasms/drug therapy/metabolism ; },
abstract = {Gastrointestinal (GI) cancers remain a leading cause of global morbidity and mortality, necessitating novel therapeutic strategies. Melatonin (MEL), an indoleamine with pleiotropic biological activities, has emerged as a promising adjuvant in oncology due to its antiproliferative, proapoptotic, and antioxidant properties. This review synthesizes current evidence on MEL's molecular mechanisms in GI carcinogenesis, including modulation of NF-κB, PI3K/AKT, and Wnt/β-catenin pathways, suppression of reactive oxygen species (ROS), and regulation of circadian rhythm-related genes (e.g., CLOCK, BMAL1). Preclinical studies demonstrate that MEL enhances chemoradiotherapy efficacy-reducing tumor volume by 70% in murine colorectal models and decreasing 5-fluorouracil (5-FU) resistance via miR-532-3p/β-catenin axis modulation. Clinical trials report a 23%-41% risk reduction in colorectal cancer among shift workers with MEL supplementation and a 53% decrease in radiotherapy-induced oral mucositis. Despite promising data, limitations persist: fewer than 15% of clinical trials focus on GI cancers, dosing remains unstandardized (10-40 mg/day), and molecular heterogeneity (e.g., KRAS mutations in pancreatic cancer) may limit therapeutic responses. Future research must prioritize phase III trials, chronotherapy optimization, and biomarker-driven approaches, including MT1/MT2 receptor expression and microbiome profiling. Given its low toxicity and putative synergy with immunotherapies, MEL should be regarded as an adjunct under investigation rather than an established option; to date, no GI-specific phase III randomized trials exist, and clinical signals come primarily from small, heterogeneous cohorts. Dosing is unstandardized and limited by low oral bioavailability (first-pass) and possible pharmacogenomic variability.},
}

*Melatonin/therapeutic use/pharmacology
Humans
Animals
*Gastrointestinal Neoplasms/drug therapy/metabolism

@article {pmid41342428,
year = {2026},
author = {Astan, R},
title = {Gut microbiome-metabolome interplay in nondipper hypertension: pathophysiological insights and clinical perspectives.},
journal = {Journal of hypertension},
volume = {44},
number = {1},
pages = {231-232},
doi = {10.1097/HJH.0000000000004170},
pmid = {41342428},
issn = {1473-5598},
}

@article {pmid41342427,
year = {2026},
author = {Ozbek, DA and Altun, B},
title = {Reply to correspondence 'Gut microbiome-metabolome interplay in nondipper hypertension: pathophysiological insights and clinical perspectives'.},
journal = {Journal of hypertension},
volume = {44},
number = {1},
pages = {231},
pmid = {41342427},
issn = {1473-5598},
}

@article {pmid41342324,
year = {2025},
author = {Silber, JL and Norman, JM and Kanno, T and Crossette, EM and Szabady, R and Menon, R and Marko, M and Hao, LY and Tomsho, L and Bhagat, S and Yuan, A and Olle, B and Lamousé-Smith, E},
title = {A randomized, double-blind, placebo-controlled, single- and multiple-dose phase 1 study of VE202, a defined bacterial consortium for treatment of inflammatory bowel disease: safety and colonization dynamics of a novel live biotherapeutic product in healthy adults.},
journal = {European journal of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MEG.0000000000003098},
pmid = {41342324},
issn = {1473-5687},
abstract = {OBJECTIVES: VE202 is an oral, defined 16-strain bacterial consortium with properties that may diminish dysbiosis and alleviate symptoms of inflammatory bowel disease. This phase 1 study evaluated VE202 safety and tolerability and assessed strain colonization.

METHODS: Thirty-one healthy adults received oral vancomycin 125 mg four times daily for 5 days to decrease gut microbial burden, followed by a single dose of VE202 at 1 × 109 or 1 × 1010 colony-forming units (CFUs), or 14-days of the lower dose (1.4 × 1010 total CFU). Adverse events were monitored through week 12, with follow-up at week 24. Stool was collected for VE202 strain detection and abundance during screening and pretreatment, day 2, day 4, day 7, day 14, week 4, week 8, week 12, and optionally at week 24.

RESULTS: VE202 and vancomycin pretreatment were well tolerated. Among VE202 recipients, the most frequent adverse events (>20% of subjects) were abdominal discomfort, diarrhea, headache, and fatigue. Most treatment-related adverse events were gastrointestinal. Two serious adverse events were reported; these were not treatment-related and occurred weeks after dosing completion. VE202 strain detection and relative abundance in the vancomycin-perturbed gut occurred as soon as day 2, sustained through 2 weeks postdosing, then declined slowly but remained substantially above baseline through week 24. Colonization was dose- and duration-dependent, with 14-day dosing providing more durable VE202 colonization.

CONCLUSION: VE202 was well tolerated. Following antibiotic pretreatment, rapid and durable gut colonization of VE202 strains was observed, most significantly in participants administered multiple doses (NCT03931447).},
}

@article {pmid41341909,
year = {2025},
author = {Yang, L and Wang, Y and Yuan, L and Tang, W},
title = {Advances in research on congenital and hereditary intestinal diseases: From molecular mechanisms to precision medicine.},
journal = {Intractable & rare diseases research},
volume = {14},
number = {4},
pages = {258-265},
pmid = {41341909},
issn = {2186-3644},
abstract = {Congenital and hereditary intestinal diseases are a group of major disorders caused by gene mutations or embryonic developmental anomalies and are characterized by diverse clinical manifestations and complex management. This review systematically explores the molecular genetic basis and pathogenic mechanisms of common intestinal diseases, including familial adenomatous polyposis (FAP), Peutz-Jeghers syndrome (PJS), Lynch syndrome (LS), Hirschsprung disease (HSCR), congenital short bowel syndrome (SBS), and cystic fibrosis (CF). It focuses on cross-disease commonalities in translational research frontiers such as gene-environment interactions, organoid-based precision medicine, the immune microenvironment, and metabolic and microbiome remodeling. The review also forecasts future directions, including gene therapy, targeted drugs, and other cutting-edge research advances.},
}

@article {pmid41341501,
year = {2025},
author = {Deng, X and Wu, X and Wang, R and Qiao, X and Cao, T and Xu, Y and Jin, Q and Jia, L and Liang, W},
title = {Gut microbiota-based biomarkers for precision subtype classification and mechanistic understanding of biliary and hyperlipidemic acute pancreatitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1695811},
pmid = {41341501},
issn = {1664-302X},
abstract = {BACKGROUND: Acute pancreatitis (AP) is an inflammatory disorder with distinct etiological subtypes, yet the role of gut microbiota in disease pathogenesis remains poorly understood. We hypothesized that biliary acute pancreatitis (BAP) and hyperlipidemic acute pancreatitis (HLAP) exhibit etiology-specific gut microbiota signatures that correlate with disease severity and metabolic dysfunction.

METHODS: We conducted a cross-sectional study in which stool samples were collected from 20 BAP patients, 20 HLAP patients, and 20 healthy controls (HC) for 16S rRNA gene sequencing to compare gut microbiota profiles among the three groups. Microbial diversity, taxonomy, and functional genes were analyzed using bioinformatics pipelines. Clinical-microbial correlations were assessed, and the construction of RF and logistic regression models evaluated diagnostic biomarker potential.

RESULTS: Both AP groups showed significantly reduced microbial diversity compared to controls, with HLAP patients exhibiting more severe dysbiosis. HLAP patients showed enrichment of pro-inflammatory taxa, including Escherichia-Shigella and Collinsella, alongside depletion of beneficial genera Faecalibacterium and Bifidobacterium. As a key SCFA-producing genus, Faecalibacterium exhibited comprehensive correlations with inflammatory markers, pancreatic enzymes, and lipid profiles in Spearman correlation analysis. Functional analysis revealed compromised short-chain fatty acid biosynthesis capacity, as evidenced by significant downregulation of acetate (ackA, pta) and butyrate (buk, but) synthesis genes in AP patients, which may have partially mediated the observed differences in microbiota composition. Furthermore, our findings reveal that multi-species biomarker panels provide superior diagnostic performance compared to single-species predictors for BAP and HLAP subtype classification.

CONCLUSION: BAP and HLAP patients exhibit distinct gut microbiota signatures with progressive dysbiosis, functional impairment, and strong host associations. These findings establish a novel framework linking gut microbial composition to AP pathophysiology, providing insights for microbiome-targeted precision medicine strategies.},
}

@article {pmid41341495,
year = {2025},
author = {Rana, TS and Bansode, RR and Rana, JP and Williams, LL},
title = {A systematic review: polyphenol's effect on food allergy via microbiome modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1673472},
pmid = {41341495},
issn = {1664-302X},
abstract = {INTRODUCTION: Food allergy is an increasing health concern worldwide. Microbes, food allergies, and polyphenols are found to be interrelated. However, studies relating polyphenols' effect on food allergy via microbiome modulation are scarce, and there is a lack of common signature microbiome modulation patterns. Thus, this review aims to summarize the effect of polyphenols on food allergy via microbiome modulation.

METHODS: Research articles were searched from Scopus, PubMed, ScienceDirect, and Web of Science database. The in vivo and in vitro studies were assessed via SYRCLE risk of bias and modified CONSORT checklist, respectively. The population characteristics and experimental details were extracted, and the data were synthesized narratively.

RESULTS: The included studies were free of selective reporting of results. The allergy of egg (ovalbumin), milk (𝛽-lactoglobulin), soybean (𝛽-conglycinin), and shrimp allergy contributed to 54%, 23%, 15%, and 8% of the total included studies, respectively. The used compounds were a different source or types of polyphenols such as cocoa, cyanidin-3-O-glucoside (C3G), avenanthramide's (AVA), rosmarinic acid (RA), neohesperidin, and fermented apple juice for egg allergy, luteolin, and green tea polyphenol (GTP) for soybean allergy, and flavonoids (Luteolin, myricetin and hyperoside), ferulic acid, and luteolin for milk allergy. Allergies of milk, egg, wheat, and shrimp occurred with the reduction of Lactobacillus, Alistipes, Odaribactor, Akkermansia, Bacteroides, and Lachnospiraceae_NK4A136_group and an increase of Prevotella, Alloprevotella, Faecalibaculum, Helicobactor, Blautia, Clostridium, and Staphylococcus. The polyphenols modulated these microbes in order to attenuate the food allergies.

DISCUSSION: The types of polyphenols, food allergies, animal model used, and taxonomic resolution of the microbiome studies lead to variation in the results. Thus, by increasing the studies on effect of polyphenols on individual food allergies, and combining with higher taxonomic resolution techniques such as shotgun metagenomics along with metabolomics would increase reliability of the results of the future studies.},
}

@article {pmid41341407,
year = {2025},
author = {Arshad, MT and Maqsood, S and Hossain, MS and Awlqadr, FH and Rauf, A and Ullah, I and Ikram, A and Bibi, A and Mukhtar, S and Abdullahi, MA},
title = {Integrating Microbiomes for Regenerative Food Systems: Recent Insights, Implementations, and Emerging Trends.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71312},
pmid = {41341407},
issn = {2048-7177},
abstract = {Microbiomes play a central role in food science by influencing food quality, safety, sustainability, and human health. This review brings together contemporary advancements in the understanding and use of microbiomes in the food system, with a focus on sustainable agriculture, fermentation, food safety, and nutrition. We discuss both traditional approaches (e.g., natural fermentation and soil management) and new high-tech strategies, including precision microbiome engineering, synthetic biology, and machine learning. The major applications under consideration are microbiome-based food preservation, biofertilisers and biopesticides, waste valorisation, and alternative protein production. The socioeconomic context is also being considered, recognizing that while recent advances are more pragmatic in high-income countries, traditional and low-input approaches are still critical in low- and middle-income country (LMIC) settings. The emphasis in this review is laid on food science and food systems, and nutrition and health effects are considered as downstream consequences. The readership includes food scientists, microbiologists, agricultural researchers, and policy decision-makers who care about the integration of microbiome science into resilient and sustainable food systems. By presenting a fair representation of standard and advanced microbiome techniques, this review delineates the prospects and challenges in the application of microbial communities in shaping the future of food.},
}

@article {pmid41341259,
year = {2025},
author = {Wang, Y},
title = {Linear Dimensionality Reduction Methods for Analyzing Structured Biomedical Data: Existing Research and Future Opportunities.},
journal = {Wiley interdisciplinary reviews. Computational statistics},
volume = {17},
number = {3},
pages = {e70045},
pmid = {41341259},
issn = {1939-5108},
abstract = {High-dimensional biomedical data often exhibit complex structural features that challenge traditional analytical methods. These features include distributional structures, such as count and sparse data in single-cell RNA-seq studies; correlation structures among biomarkers, such as phylogenetic relationships in microbiome studies; and correlation structures among samples, such as spatial correlations in spatial transcriptomics. Dimensionality reduction methods that account for these structures are essential for extracting biologically meaningful insights. This article provides a selected review of existing linear dimensionality reduction methods for both supervised and unsupervised analysis of structured data. Leveraging a unified framework based on low-rank-plus-noise models, we conduct theoretical and numerical comparisons of these methods. Our review aims to equip researchers with a deeper understanding of the strengths and limitations of various structured dimensionality reduction techniques, aiding in the selection of the most suitable approach for their data. Finally, this review highlights several promising directions for future research, offering opportunities for advancements in dimensionality reduction methods tailored to the unique complexities of structured biomedical data. This article is categorized under: Statistical Learning and Exploratory Methods of the Data Sciences > Modeling MethodsStatistical and Graphical Methods of Data Analysis > Multivariate AnalysisStatistical and Graphical Methods of Data Analysis > Dimension Reduction.},
}

@article {pmid41341205,
year = {2025},
author = {Yue, Z and Li, C and Yan, F and Guan, S and Fan, Y and Chen, X},
title = {The oral microbiome in aging: a window into health and longevity.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2589648},
pmid = {41341205},
issn = {2000-2297},
abstract = {BACKGROUND: Aging is characterized by progressive physiological decline and increased susceptibility to age-related diseases. The oral microbiome, a complex community of microorganisms, has been increasingly recognized as a potential key player in the aging process.

OBJECTIVE: This review aims to explore and summarize the relationship between the oral microbiome and aging, with a specific focus on contrasting microbial changes in healthy and unhealthy aging populations.

DESIGN: We conducted a comprehensive review of the current literature to synthesize evidence on oral microbiome shifts during aging, the influencing factors, associations with age-related conditions, and potential interventions.

RESULTS: Evidence indicates that the composition of the oral microbiome changes with age, although findings on diversity are inconsistent, with reports of both increases and decreases in older adults. These shifts are influenced by factors such as diet, oral hygiene, and immune function. Unhealthy aging, including conditions like frailty, neurodegenerative diseases, and sarcopenia, is associated with distinct oral dysbiosis. Potential mechanisms linking the oral microbiome to aging include chronic inflammation and immunosenescence. Interventions targeting the oral microbiome, such as probiotics and dietary modifications, show promise in promoting healthspan.

CONCLUSIONS: The oral microbiome is significantly altered during aging and is implicated in age-related health status. It represents a promising target for strategies aimed at promoting healthy aging. Future research should prioritize elucidating the functional mechanisms of oral microbiota and developing targeted microbiome-based interventions.},
}

@article {pmid41340927,
year = {2025},
author = {Samuel David, AV and María Del Rocío, PR},
title = {Termites and their gut microbiome in animal nutrition: Advances and biotechnological applications.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {527-534},
pmid = {41340927},
issn = {2405-6383},
abstract = {Since the late 20th century, termites have attracted attention due to the vast potential of their gut microbiome and digestive enzymes, which enable them to efficiently degrade lignocellulosic biomass, making them a promising resource for animal nutrition, particularly for recovering fibrous waste. Termite gastrointestinal symbionts and enzymes are highly effective at decomposing plant fiber, thus positioning them as natural bioreactors with significant biotechnological potential. This review examines the evolving applications of termites in animal feed, including their incorporation as protein sources in diets for monogastric animals and fish, as well as the utilization of bacteria, fungi, and enzymes derived from their guts as additives to enhance the digestibility of agricultural byproducts in both ruminants and non-ruminants. Furthermore, recent developments have demonstrated the identification and heterologous expression of lignocellulolytic enzymes and metabolites with prebiotic and detoxifying properties. The diversity of termite species offers an exceptional source of microbial communities. These communities highly adaptable to various fibrous substrates due to their diet, which enhances their potential despite existing limitations in cultivation and process standardization. However, their gut microbiota remains an untapped resource with immense potential to improve feed efficiency, promote sustainability, and reduce reliance on conventional inputs. It is concluded that at larger scale in vivo studies are needed to fully realize the potential of these symbiotic systems in animal nutrition.},
}

@article {pmid41340567,
year = {2025},
author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M},
title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593050},
doi = {10.1080/19490976.2025.2593050},
pmid = {41340567},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Vegan ; Male ; Female ; Adult ; Czech Republic ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; Italy ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Vegans ; Metagenome ; Multiomics ; },
abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.},
}

Humans
*Gastrointestinal Microbiome
*Diet, Vegan
Male
Female
Adult
Czech Republic
Cross-Sectional Studies
*Metabolome
Middle Aged
Italy
*Bacteria/classification/metabolism/genetics/isolation & purification
Vegans
Metagenome
Multiomics

@article {pmid41340403,
year = {2025},
author = {Park, J and Cheon, JH},
title = {The epidemiology of inflammatory bowel disease: exploring the impacts of environmental factors.},
journal = {The Korean journal of internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.3904/kjim.2025.083},
pmid = {41340403},
issn = {2005-6648},
abstract = {Inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn's disease, are distinct chronic immune-mediated intestinal inflammatory disorders. The pathogenesis of IBD is complex and involves a combination of genetic and environmental factors, the gut microbiome, and the host immune system. Despite significant progress in identifying the genetic factors of IBD, the increasing IBD incidence in recent decades, along with findings from immigrant and twin studies, suggest the involvement of environmental factors on IBD susceptibility. In this review, we summarize various up-to-date environmental factors, including early-life influences; diet, food, and nutritional exposures; urbanization and air pollution; smoking; appendectomy; medications; psychological stress; sleep; and latitude and geography.},
}

@article {pmid41340205,
year = {2025},
author = {Chakraborty, S and Guo, Z},
title = {Invisible contaminants, irreversible consequences? LDPE residues twist the Arabidopsis holobiome.},
journal = {Journal of experimental botany},
volume = {76},
number = {22},
pages = {6569-6572},
doi = {10.1093/jxb/eraf388},
pmid = {41340205},
issn = {1460-2431},
support = {NE/B000187/1//UKRI NERC Independent Research Fellowship/ ; EP/X525662/1//Engineering and Physical Sciences Research Council/ ; 202106300062//China Scholarship Council/ ; },
}

@article {pmid41340173,
year = {2025},
author = {Zhang, X and Dong, TS and Gee, GC and Kilpatrick, LA and Beltran-Sanchez, H and Wang, MC and Vaughan, A and Church, A},
title = {Social bonds and health: exploring the impact of social relations on oxytocin and brain-gut communication in shaping obesity.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2566978},
doi = {10.1080/19490976.2025.2566978},
pmid = {41340173},
issn = {1949-0984},
mesh = {Humans ; *Oxytocin/blood ; *Obesity/psychology/microbiology/metabolism ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/physiology ; *Brain/physiology/metabolism ; Body Mass Index ; Feeding Behavior/psychology ; Middle Aged ; Young Adult ; *Brain-Gut Axis ; *Interpersonal Relations ; },
abstract = {Social relationships play a crucial role in shaping health. To better understand the underlying mechanisms, we explored the independent and interactive effects of perceived emotional support (PES) and marital status on body mass index (BMI), eating behaviors, brain reactivity to food images, plasma oxytocin, and alterations in the brain-gut microbiome (BGM) system. Brain responses to food stimuli, fecal metabolites, and plasma oxytocin levels were measured in 94 participants. Structural equation modeling was used to determine the integrated pathways linking social factors to obesity-related outcomes. Marital status and PES interact and independently influence lower BMI, healthier eating behaviors, increased oxytocin levels, food-cue reactivity in frontal brain regions involved in craving inhibition and executive control, and tryptophan-pathway metabolites related to inflammation, immune regulation, and energy homeostasis. These findings suggest that supportive human relationships, particularly high-quality marital bonds, may regulate obesity risk through oxytocin-mediated alterations in brain and gut pathways.},
}

Humans
*Oxytocin/blood
*Obesity/psychology/microbiology/metabolism
Male
Female
Adult
*Gastrointestinal Microbiome/physiology
*Brain/physiology/metabolism
Body Mass Index
Feeding Behavior/psychology
Middle Aged
Young Adult
*Brain-Gut Axis
*Interpersonal Relations

@article {pmid41340151,
year = {2025},
author = {Kropp, DR and Glover, ME and Samanta, R and Unroe, KA and Clinton, SM and Hodes, GE},
title = {Perinatal citalopram exposure alters the gut composition and microbial metabolic profiles of Sprague-Dawley rat dams and female offspring but not male offspring.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-025-00794-5},
pmid = {41340151},
issn = {2042-6410},
support = {R01MH105447-01/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Selective serotonin reuptake inhibitors are widely prescribed during pregnancy. Their main route of administration is through the gut. However, their impact on the maternal and offspring gut microbiome and microbial metabolic pathways remains poorly understood. This study used metagenomic shotgun sequencing to examine the effects of perinatal citalopram exposure in rat dams and their offspring on gut composition and downstream metabolic pathways.

METHODS: We treated pregnant and nursing rat dams with either citalopram or vehicle (water). Their feces were collected, DNA from these samples was extracted and then sequenced using shotgun metagenomic sequencing. The BioBakery suite of microbiome analysis tools was utilized in tandem with RStudio to analyze the gut composition and microbial metabolic pathways of the rat dams and their offspring.

RESULTS: Pregnant and nursing dams treated with citalopram exhibited marked shifts in microbial community structure, including phylum-level alterations in Proteobacteria and Defferibacteria. Citalopram treated dams displayed significantly altered beta diversity. Species level alterations due to treatment were composed of five significantly altered microbes, two of which belong to the Proteobacteria phylum. These changes were highly diverse and were not congruent with microbe-level alterations observed in offspring. Alpha diversity of microbial metabolic pathways was compared using the Gini-Simpson index, which was significantly increased in dams suggesting greater metabolic functional diversity with age. Female offspring perinatally exposed to citalopram showed significant changes in gut beta diversity, with seven significant alterations at the microbe level. These microbial shifts were accompanied by twenty-one significantly altered microbial metabolic pathways. In contrast, male offspring showed no significant differences in microbial composition or beta diversity and only minor metabolic changes.

CONCLUSIONS: These findings demonstrate that maternal citalopram exposure during pregnancy and lactation has lasting, sex-specific impacts on the offspring's gut microbiome and microbial metabolic pathways. The pronounced alterations in female, but not male offspring, suggest that host sex may be a critical determinant in the developmental response to citalopram exposure. This work underscores the value of metagenomic approaches in uncovering complex host-microbiome interactions and highlights the need to consider offspring sex in evaluating the safety and long-term effects of antidepressant use during pregnancy.},
}

@article {pmid41340133,
year = {2025},
author = {Abavisani, M and Sajjadi, SM and Ebadpour, N and Karav, S and Sahebkar, A},
title = {Gut microbiota-cholesterol crosstalk in cardiovascular diseases: mechanisms, metabolites, and therapeutic modulation.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-025-01051-7},
pmid = {41340133},
issn = {1743-7075},
abstract = {Cardiovascular diseases (CVD) are one of the leading causes of death worldwide. Genetic factors, and various environmental factors, including nutrition and the composition of the gut microbiota, have been identified as important factors in the initiation of CVD. Among them, the pivotal role of the gut microbiota in modulating cholesterol metabolism and influencing cardiovascular outcomes has recently been highlighted. Extensive research has confirmed that the gut microbiota has direct and indirect regulatory effects on host cholesterol homeostasis. Recent studies have shown that the microbiota can influence blood cholesterol levels and thus the risk of CVD through various pathways, such as the production of certain metabolites such as bile acids (BAs), SCFAs, and TMAO, the activation of nuclear and membrane-bound receptors such as farnesoid X receptor (FXR), the regulation of gene expression involved in lipid metabolism and inflammatory responses, as well as microbial enzymatic pathways. These complex regulatory mechanisms make the gut microbiota a potential therapeutic target in cholesterol-related diseases and CVD. Microbiota-modulating strategies, including the use of probiotics, prebiotics, fecal microbiota transplantation (FMT), and selective antibiotics, have shown beneficial effects in previous studies. In this regard, in this study, we conducted an in-depth investigation of the regulatory effect of intestinal microbiota on cholesterol metabolism and their impact on the development and progression of atherosclerosis and CVD, and described potential therapeutic pathways based on the regulation of intestinal microbiota in CVD.},
}

@article {pmid41340088,
year = {2025},
author = {Hu, J and Guo, P and Yu, J and Zhang, T and Yang, X},
title = {Oral and fecal microbiota in Chinese adults with obesity reveal potential niche-specific microbiota associated with obesity.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04561-9},
pmid = {41340088},
issn = {1471-2180},
abstract = {BACKGROUND: Obesity has emerged as a global health crisis. Increasing evidence suggests that imbalances in gut and oral microbiota are linked to obesity, with specific microbial profiles influencing metabolic dysfunction and weight gain. Given the distinct ecological niches and the importance of gut and oral microbiota in obesity, this study analyzed both oral and fecal microbiota in adults with obesity, aiming to identify potential niche-specific microbial signatures associated with the condition.

RESULTS: The comparison of fecal and oral microbiota communities between individuals with obesity and non-obese controls revealed significant differences in microbial composition and diversity. The predominant genera identified in both sample types were Prevotella, Faecalibacterium, Streptococcus, and Porphyromonas. A notable restructuring of microbial communities was observed between fecal and oral samples, regardless of obesity status. Furthermore, obesity-associated changes in microbial co-occurrence networks were found to be niche-specific, with reduced modularity in stool samples. In contrast, saliva microbial networks appeared to be more compartmentalized than those in stool. MaAsLin 3 and ANCOM-BC2 analyses identified five niche-specific taxa associated with obesity. These included positive associations in saliva with Granulicatella sp902479935, Lancefieldella sp938036925, Peptostreptococcus stomatis, Rothia sp916715725, as well as a negative association in saliva with Faecalibacterium sp934503275. Mediation analysis indicated that the second principal component partially mediated these effects, with Lancefieldella sp938036925 and others serving as positive contributors. The taxa Wolinella, Phocaeicola, and Bulleidia, which exhibited high abundance in saliva, were consistently selected by all machine learning models.

CONCLUSIONS: This study contributes to the growing body of literature investigating the relationship between obesity and microbial communities. Using 16 S rRNA gene amplicon sequencing, we characterized distinct microbial compositions in both saliva and fecal samples from individuals with obesity compared to normal-weight controls within a defined geographic population. The results suggest that the salivary microbiome may contain potential associative biomarkers indicative of obesity risk, warranting further in-depth investigation.},
}

@article {pmid41340070,
year = {2025},
author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM},
title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {249},
pmid = {41340070},
issn = {2049-2618},
mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.

RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.

CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.},
}

*Air Microbiology
*Metagenomics/methods
Humans
*Bacteria/genetics/classification/isolation & purification
*Aircraft
*Masks/microbiology
*Microbiota/genetics
*Air Filters/microbiology
Metagenome

@article {pmid41340067,
year = {2025},
author = {Parmar, A and Nigam, SK and Cai, K and Falah, K and Ermakov, VS and Wang, K and Ferguson, CJ},
title = {Developmentally dynamic chromatin state at loci regulating organ crosstalk by remote sensing and signaling.},
journal = {Epigenetics & chromatin},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13072-025-00648-9},
pmid = {41340067},
issn = {1756-8935},
support = {R01DK109392/DK/NIDDK NIH HHS/United States ; },
abstract = {BACKGROUND: Interorgan communication, metabolite regulation and drug handling require fine-tuned small molecule transport across membranes. The Remote Sensing and Signaling (RSS) theory, which has found applicability in chronic kidney disease and uric acid disorders, emphasizes the central role of solute carrier (SLC) and ATP-binding cassette (ABC) transporters, enzymes and transcription factors in organ crosstalk. Based on prior network biology studies, ~ 1000 protein-coding genes are predicted to mediate RSS. This gene set largely overlaps with genes that are important for absorption, digestion, metabolism and excretion (ADME) of small molecules. However, it is not known how epigenetic regulation of these loci changes during the development of the liver and kidney, which control the small molecule composition of the blood, or the brain, whose physiology relies upon this process. Epigenetic regulation of these genes is also critical for understanding pharmacokinetics.

RESULTS: We profiled chromatin state at 1034 RSS/ADME genes in the mouse kidney, liver and brain at the embryonic and adult stages. Using the high-resolution chromatin mapping method CUT&RUN, we examined the activating histone modifications H3K4me3, H3K27ac and H3K9ac, and the repressive modification H3K27me3. Activating modifications were most dynamic at the chromatin level in the liver and least dynamic in the brain. Acetylated histone modifications were more dynamic overall than methylation marks in all three tissues. Hierarchical clustering demonstrated that a subset of RSS/ADME genes undergoes a coordinated program of activation during kidney and liver development that correlates with changes in transcript abundance.

CONCLUSIONS: Defining the changes in chromatin that occur after birth within this gene set provides insight into tissue-specific regulation of RSS. Our findings carry implications for how the body acquires autonomous functionality through organ crosstalk mediated by transport of endogenous small molecules. Given their critical roles in ADME as well as handling of exogenous toxins, medications and metabolites derived from the gut microbiome, our analysis has ramifications for both precision pharmacology and diseases such as chronic kidney disease, metabolic syndrome and gout, in which dysregulation of RSS drives pathophysiology.},
}

@article {pmid41339959,
year = {2025},
author = {McAdams, ZL and Campbell, EJ and Dorfmeyer, RA and Turner, G and Shaffer, S and Ford, T and Lawson, J and Terry, J and Raju, M and Coghill, L and Cresci, L and Lascola, K and Pridgen, T and Blikslager, A and Barrell, E and Banse, H and Paul, L and Gillen, A and Nott, S and VandeCandelaere, M and van Galen, G and Townsend, KS and Martin, LM and Johnson, PJ and Ericsson, AC},
title = {A novel dataset of 2,362 equine fecal microbiomes from veterinary teaching hospitals across three countries reveals effects of geography and disease.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {124},
pmid = {41339959},
issn = {2524-4671},
abstract = {BACKGROUND: Horses and other equids are reliant on the gut microbiome for health, and studies have reported associations between certain clinical conditions and features of the fecal microbiome. However, research to date on the equine fecal microbiome has often relied on small sample sizes collected from single and relatively localized geographic regions. Previous work also largely employs single timepoint analyses, or horses selected based on limited health criteria.

RESULTS: To address these limitations and expand our understanding of the core microbiome in health, and the changes associated with adverse outcomes, the Equine Gut Group (EGG) has collected and performed 16S rRNA sequencing on 2,362 fecal samples from 1,190 healthy and affected horses. This resource of 16S rRNA sequencing data with accompanying demographic and clinical metadata represent a diverse equine population in health and disease. We identified features making up the core microbiome of healthy equids and metadata factors influencing the relative abundance of those features. We then identified microbial markers of acute gastrointestinal disease at the community and taxonomic levels.

CONCLUSIONS: Here we present the EGG database and demonstrate its utility in characterizing the equine microbiome in health and acute gastrointestinal disease. The EGG 16S rRNA database is a valuable resource to study the equine microbiome and its role in equine health.},
}

@article {pmid41339940,
year = {2025},
author = {Parwin, N and Dixit, S and Das, S and Sahoo, RK and Subudhi, E},
title = {Metagenomic analysis of microbiome spatial dynamics in urban river confluence affected by city wastewater.},
journal = {Genomics & informatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s44342-025-00054-3},
pmid = {41339940},
issn = {1598-866X},
abstract = {BACKGROUND: Environmental pollutants have a profound impact on microbial dynamics. This study highlights the influence of anthropogenic activity on the shift in bacterial diversity in the catchment area compared to upstream and downstream at Kathajodi, using a metagenomic approach for the first time in River Kathajodi.

METHODS: Water samples were collected from upstream, catchment, and downstream locations and transported at 4°C to the laboratory for DNA extraction, library preparation, sequencing, and physicochemical analysis employing inductively coupled plasma. The extracted DNA was sequenced via the Illumina HiSeq platform and analyzed through MG-RAST for taxonomic and functional classification using KEGG and COG annotations. Statistical diversity analysis, including rarefaction curves, alpha- and beta-diversity indices, and Venn diagrams, provided insights into microbial composition and community variations across sites.

RESULTS: A significant abundance of pollution indicator members of phylum Bacteroidetes (29.82%) in the catchment (CM), highly contaminated with metals, fecal, and other organic pollutants, could be attributed to their high metabolic capabilities to degrade them. The pristine upstream (US) exhibited an abundance of Shewanella (25.04%), Pseudomonas (17.35%), and Synechococcus (5.62%). The CM, influenced by high anthropogenic activity, showed higher abundances of Flavobacterium (5.20%), Arcobacter (4.05%), and Bacteroides (3.88%). In contrast, downstream (DS), with fewer anthropogenic activities, displayed higher abundances of Aeromonas (4.40%), Acidovorax (0.52%), and Acidimicrobium (0.32%). The highest bacterial diversity of CM could be due to the influence of the physicochemical properties of city waste effluent. From the Venn diagram, 73 common OTUs at the genera level were observed in all three sites, which indicates that the native microflora of the river water niche remains unaffected irrespective of the temporary changes in the vicinity. The functional profiling through KEGG and COG revealed that CM was enriched in carbohydrate metabolism (12.11%), while DS exhibited higher contributions to amino acid metabolism, along with the highest relative abundance of general function prediction (R) (12.89%), all indicative of stress adaptation and metabolic flexibility under polluted conditions. The clean upstream is home to oxygen-loving helpful bacteria, the catchment supports nutrient-hungry and sewage-linked microbes, while the downstream is dominated by metal-tolerant and possibly harmful bacteria, showing the clear impact of human activities along the river.

CONCLUSIONS: The marked shift in bacterial diversity between US, CM, and DS regions highlights the ecological consequences of anthropogenic impact. These findings emphasize the need for effective environmental management to safeguard water quality and prevent undesirable health issues.},
}

@article {pmid41339867,
year = {2025},
author = {Chen, YT and Sui, J and Yang, Y and Zhang, H and Wesselius, A and Shen, Y and Qin, QR and Sun, GJ and Wang, SK and Wang, XD and Wang, S and Li, WC and Cheng, KK and James, ND and Bryan, RT and Zeegers, MP and Chen, L and Xia, H and Yu, EY},
title = {Integration of gut microbiome and lipid metabolism reveals the anti-cancer effects of pentadecanoic acid on bladder cancer.},
journal = {BMC medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12916-025-04554-5},
pmid = {41339867},
issn = {1741-7015},
support = {82574191; 82204033//National Natural Science Foundation of China/ ; BK20220826//Natural Science Foundation of Jiangsu Province/ ; 2242022R10062/3225002202A1//Fundamental Research Funds for the Central Universities/ ; 2242023R40031//Zhishan Young Scholar Award at the Southeast University/ ; AHWJ2023A20172; AHWJ2023BAa20055//The Scientific Research Project for Health Commission of Anhui Province/ ; 2024AH050663//Natural Science Research Project of Anhui Educational Committee/ ; SSCBS20220169//Jiangsu Provincial Double-Innovation Doctor Program/ ; },
abstract = {BACKGROUND: Pentadecanoic acid (PEA), an odd-chain fatty acid derived from diet by the gut microbiome, has garnered increasing attention for its systemic health-promoting properties. Its potential role in bladder cancer (BC) occurrence and invasion, however, remains unclear.

METHODS: Large-scale cohorts' analyses were performed to assess the association between dietary PEA and BC occurrence and invasion. In vitro and in vivo experiments, including EJ and T24 BC cell assays and a BBN-induced mouse model, were conducted to experimentally assess the impact of PEA on BC. Serum proteomics, gut microbiome, and targeted fecal lipidomics analyses were employed to explore the underlying mechanisms.

RESULTS: Dietary PEA was negatively associated with BC occurrence and invasion in cohort analyses. PEA suppressed EJ and T24 BC cell migration, invasion, and proliferation, while inhibiting BC development in a BBN-induced mouse model. In vivo serum proteomics identified differentially expressed lipid-related proteins (e.g., Apoe and Apob) following PEA treatment, implicating its modulation of lipid metabolism pathways. Considering the essential role of the gut-bladder axis, the gut microbiome analysis exhibited that PEA markedly altered bacteria (e.g., g_Alistipes) and fungi (e.g., o_Erysiphales, g_Teberdinia, and g_Gibberella), with concomitant lipid metabolism changes. Furthermore, targeted fecal lipidomics demonstrated the shifts in key lipids, such as phosphatidylethanolamines (PE) involved in essential lipid clusters, suggesting regulation by gut microbiome linked to BC development.

CONCLUSIONS: Collectively, our findings demonstrate that PEA mitigates BC by reshaping the gut microbiome and modulating lipid metabolism, providing new insights into its molecular and therapeutic potential.},
}

@article {pmid41339801,
year = {2025},
author = {Yang, T and Wang, Y and Zhang, Y and Liu, C and Zeng, Y and Shi, P and Zhou, J and Li, Y and Wei, H},
title = {Haemophilus influenzae dominance in fungal ball microbiome revealed through multi-niche metagenomic sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04546-8},
pmid = {41339801},
issn = {1471-2180},
support = {7222026//Natural Science Foundation of Beijing Municipality/ ; },
abstract = {OBJECTIVE: This study employed metagenomic sequencing to characterize the sinonasal microbiome in patients with unilateral maxillary sinus fungal ball (MSFB), with specific emphasis on bacterial-fungal interactions and functional pathways implicated in fungal ball pathogenesis.

METHODS: The study enrolled 30 MSFB patients and 30 healthy controls. Nasal secretion samples were obtained from three anatomical sites in MSFB cases: fungal ball cavity (FC), affected middle nasal meatus (AM), and contralateral unaffected middle nasal meatus (UM). And in the control group, samples were obtained from the healthy middle nasal meatus (HM). Metagenomic sequencing of microbial DNA was performed using the Illumina Novaseq platform. Taxonomic and functional analyses were conducted using Kraken2, Bracken, and HUMAnN2.

RESULTS: Bacteria dominated the microbiome in the FC group (98.53%), with Haemophilus influenzae identified as a key biomarker (LDA score > 5). A negative correlation between H. influenzae and Aspergillus flavus was observed in the FC group (r = -0.46, P = 0.013). Functional pathways enriched in the FC group included amino acid biosynthesis (map00290), lipopolysaccharide biosynthesis (map00540), and fatty acid biosynthesis (map00061), supporting H. influenzae survival and immune modulation. FC microbiota showed reduced diversity and distinct composition compared to other groups (PERMANOVA, P < 0.001). No significant differences were found in the composition of the microbiota between the bilateral middle nasal meatus groups of MSFB.

CONCLUSION: This study highlights H. influenzae as a critical bacterial biomarker in MSFB. The inverse relationship between H. influenzae and A. flavus may suggest competitive or immune-mediated interactions. These findings advance understanding of non-invasive fungal sinusitis. Future validation in larger fungal ball cohorts or invasive fungal sinusitis is warranted.},
}

@article {pmid41339745,
year = {2025},
author = {Zhang, L and Marfil-Sánchez, A and Kuo, TH and Seelbinder, B and van Dam, L and Depetris-Chauvin, A and Jahn, LJ and Sommer, MOA and Zimmermann, M and Ni, Y and Panagiotou, G},
title = {Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41339745},
issn = {2058-5276},
support = {Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; Excellent Young Scientists Fund (project ID 24HAA01325)//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Food, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example, Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case-control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomics and metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state.},
}

@article {pmid41339732,
year = {2025},
author = {Vogel, SC and Querdasi, FR and Callaghan, BL and Brito, NH},
title = {Examining associations among caregiver stress, social support, and the infant gut microbiota.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30553-w},
pmid = {41339732},
issn = {2045-2322},
abstract = {Maternal stress is a growing societal concern, with implications for both maternal wellbeing and infant development. One of the mechanisms by which maternal stress is thought to impact infant development is by shaping the development of the infant gut microbiome. Here, we examined how measures of maternal stress and social support were associated with alpha diversity, beta diversity, and relative abundance of individual bacterial taxa in the gut microbiota at 12 months of age in a community-based sample of infants and their biological mothers (n = 34) from New York. Maternal social support was negatively associated with alpha diversity of the infant gut microbiota and was associated with abundance of bacteria from several genera. We did not find associations between caregiver perceived stress and markers of infant gut microbiota diversity or composition. Results suggest that greater social support for new parents may be associated with infant health via changes in the diversity and composition of the infant gut microbiota.},
}

@article {pmid41339713,
year = {2025},
author = {Valdin, H and Gray, B and Cook, G and Creamer, M and Yu, L and LeBlanc, Z},
title = {Primary Prevention of Clostridioides difficile Infection With Oral Vancomycin in Pediatric Hematopoietic Stem Cell Transplant Patients.},
journal = {Pediatric transplantation},
volume = {29},
number = {8},
pages = {e70246},
doi = {10.1111/petr.70246},
pmid = {41339713},
issn = {1399-3046},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation ; *Vancomycin/administration & dosage/therapeutic use ; Retrospective Studies ; Female ; *Clostridium Infections/prevention & control/epidemiology ; Male ; Child ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Child, Preschool ; Adolescent ; Administration, Oral ; Incidence ; Infant ; *Antibiotic Prophylaxis/methods ; *Primary Prevention/methods ; Clostridioides difficile ; *Postoperative Complications/prevention & control ; },
abstract = {BACKGROUND: Clostridioides difficile infection (CDI) poses a significant risk to pediatric hematopoietic stem cell transplant (HSCT) due to microbiome disruption, mucosal injury, and graft versus host disease (GVHD). While oral vancomycin prophylaxis (OVP) is effective for preventing recurrent CDI, evidence for its role in preventing initial infection is limited. Our institution employs empiric OVP during the first HSCT admission to prevent initial CDI.

OBJECTIVES: We sought to describe the incidence of CDI among pediatric HSCT recipients receiving OVP and to evaluate secondary outcomes related to OVP exposure.

METHODS: We conducted a single center, retrospective observational study of 84 pediatric HSCT recipients at our institution receiving OVP during their initial transplant admission. Chart review captured demographics, transplant information, and clinical outcomes. The primary outcome was CDI incidence during hospitalization. Secondary outcomes included VRE infections, refractory CDI following cessation of OVP, and acute GI GVHD.

RESULTS: Only one patient developed CDI (1.19%) while on OVP, despite universal exposure to high-risk antibiotics among the entire cohort. No VRE infections were observed. Rates of GI aGVHD were consistent with national averages. Nine patients (10.7%) developed CDI after discontinuing OVP, all managed with standard treatment.

CONCLUSION: Empiric OVP during pediatric HSCT hospitalization was associated with a markedly low CDI incidence. Despite theoretical risks of microbiome disruption, no adverse effects were identified in this cohort, including long-term follow-up beyond 5 years. These findings support the safety and potential efficacy of OVP as primary CDI prophylaxis in pediatric HSCT patients.},
}

Humans
*Hematopoietic Stem Cell Transplantation
*Vancomycin/administration & dosage/therapeutic use
Retrospective Studies
Female
*Clostridium Infections/prevention & control/epidemiology
Male
Child
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Child, Preschool
Adolescent
Administration, Oral
Incidence
Infant
*Antibiotic Prophylaxis/methods
*Primary Prevention/methods
Clostridioides difficile
*Postoperative Complications/prevention & control

@article {pmid41339624,
year = {2025},
author = {Lamichhane, S and Dickens, AM and Buchacher, T and Lou, T and Charron-Lamoureux, V and Kattelus, R and Karmacharya, P and da Silva, LP and Kråkström, M and Rasool, O and Sen, P and Walker, C and Patan, A and Gentry, EC and Zuffa, S and Arzoomand, A and Lakshmikanth, T and Mikeš, J and Mebrahtu, A and Vatanen, T and Raffatellu, M and Zengler, K and Hyötyläinen, T and Xavier, RJ and Brodin, P and Lahesmaa, R and Dorrestein, PC and Knip, M and Orešič, M},
title = {Microbiome-derived bile acid signatures in early life and their association with islet autoimmunity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66619-6},
pmid = {41339624},
issn = {2041-1723},
support = {363417//Academy of Finland (Suomen Akatemia)/ ; },
abstract = {Emerging studies reveal that gut microbes can conjugate diverse amino acids to bile acids, known as microbially conjugated bile acids. However, their regulation and health effects remain unclear. Here, we analyzed early-life microbially conjugated bile acid patterns and their link to islet autoimmunity. We quantified 110 microbial bile acids in 303 stool samples collected longitudinally (3-36 months) from children who developed one or more islet autoantibodies and controls who remained autoantibody-negative. We identified distinct age-dependent trajectories of these bile acid amidates and correlated them with gut microbiome composition. We found that altered levels of ursodeoxycholic and deoxycholic acid conjugates were linked to islet autoimmunity as well as modulated monocyte activation in response to immunostimulatory lipopolysaccharide and Th17/Treg cell balance. These findings suggest that microbially conjugated bile acids influence immune development and type 1 diabetes risk.},
}