@article {pmid41275232,
year = {2025},
author = {Sun, C and Li, J and Xu, H and Du, J and Muthusamy, P and Liu, K and Wei, S and Zhang, L},
title = {"Immunopause" no more: exercise to counter immunosenescence in aging.},
journal = {Immunity & ageing : I & A},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12979-025-00549-1},
pmid = {41275232},
issn = {1742-4933},
abstract = {The global demographic shift towards an aging population has amplified the public health challenge posed by immunosenescence, a progressive remodeling of the immune system that compromises host defenses. This age-related decline is characterized by a reduction in adaptive immunity, marked by a diminished pool of naïve T-cells and an increased susceptibility to infections and poor vaccine responses. Simultaneously, it is defined by a paradoxical state of chronic low-grade inflammation, or "inflammaging," which accelerates age-related pathologies. This review posits "immunopause" as a conceptual framework for a state of severe immune decline, a state often viewed as an inevitable consequence of aging. However, the evidence synthesized herein challenges this view by positioning physical exercise as a potent, non-pharmacological intervention capable of countering this process. The report systematically reviews the cellular, molecular, and systemic mechanisms through which exercise exerts its beneficial effects, including the rejuvenation of T-cell repertoires, the regulation of cytokine networks, and the modulation of multi-organ axes involving myokines and the gut microbiome. By improving the efficacy of existing immune cells and shifting the systemic inflammatory milieu, chronic physical activity promotes a more "youthful" and functional immune phenotype. This synthesis not only underscores exercise's potential to enhance vaccine efficacy and serve as an adjuvant therapy for age-related diseases but also argues for a paradigm shift: from viewing immune aging as an immutable process to recognizing it as a modifiable state. The report concludes that exercise provides a scientifically validated strategy to extend healthspan and prevent the pathological state of immunopause.},
}

@article {pmid41275194,
year = {2025},
author = {Yang, X and Liao, R and Cai, Y and Wang, J},
title = {Deep metaproteomic mapping of gingival crevicular fluid reveals distinct microbial community at prepubertal and circumpubertal stages.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07348-6},
pmid = {41275194},
issn = {1472-6831},
abstract = {BACKGROUND: Orthodontic diagnosis and treatment planning are closely associated with the pubertal growth spurt. Previously, we developed a simplified MS-based protocol for deep quantitative analysis of human gingival crevicular fluid (GCF) proteome for skeletal maturity indicators. The purpose of this study is to perform an in-depth and comparative analysis of the GCF metaproteome at prepubertal and circumpubertal stages to aid oral health and skeletal maturity evaluation.

METHODS: Based on our previously obtained and published LC-MS data, the GCF metaproteome of 45 children (24 subjects from prepubertal group and 21 subjects from circumpubertal group) were analyzed by searching against the Human Oral Microbiome Database using FragPipe software. Differentially expressed bacterial proteins between two groups were analyzed using Wilcoxon rank sum test. Differentially abundant taxa between two groups were evaluated using linear discriminant effect size (LEfSe) analysis.

RESULTS: A total of 192 genera were identified in GCF. Neisseria (Neisseriales), Comamonadaceae, Burkholderiales, Proteobacteria and Betaproteobacteria were the most abundant bacterial taxa at prepubertal stage. Firmicutes, Saccharibacteria_TM7_[G-1] (Saccharibacteria TM7), Bacterium_HMT349, Bacilli and Alphaproteobacteria were the most abundant bacterial taxa of GCF microbiota at circumpubertal stage. Compared to that in the prepubertal group, enrichment of Firmicutes (Bacillus) was observed in the circumpubertal group.

CONCLUSIONS: Based on our developed and already published single-pot, solid-phase enhanced sample-preparation (SP3)-based liquid chromatography (LC) - high-field asymmetric waveform ion mobility spectrometry (FAIMS)-MS protocol for deep quantitative analysis of human GCF metaproteome, we were able to generate the largest dataset of the human GCF metaproteome (14376 bacterial proteins) to date and revealed distinct microbial community at prepubertal and circumpubertal stages. The proposed protocol and findings will be useful to aid oral health and skeletal maturity evaluation for orthodontic diagnosis and treatment planning.},
}

@article {pmid41275070,
year = {2025},
author = {Gao, H and Wang, Y and Zhao, Y and Jiao, X and Guo, Z and Zheng, L and Li, Y and Su, Y and Wang, Z and Bai, J and Yao, J and Bushman, FD and Luo, S and Song, X and Liang, G},
title = {Human gut prophage landscape identifies a prophage-mediated fucosylation mechanism alleviating colitis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66733-5},
pmid = {41275070},
issn = {2041-1723},
support = {32200036//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82341116//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92474105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270945//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Functions of the human gut virome are little understood, particularly for the hyperabundant prophages integrated in prokaryotic genomes. Here we identified 254,273 prophage sequences in 47.7% of 289,232 human gut metagenomic genomes, significantly expanding the known taxonomic and functional diversity of prophages in the human gut microbiome. Analysis of 8503 gut metagenomic samples showed the ratios of lysogens (cells harboring prophages) to non-lysogens varied widely associated with age, health condition, and geography, with the latter linked to industrialization. Notably, the alterations of the prophage-encoded genes exhibited disease-specific patterns. For inflammatory bowel diseases, the prophage-encoded futC gene, encoding α-1,2-fucosyltransferase, was less prevalent in affected patients. This enzyme was experimentally validated to direct 2-fucosyllactose (2'-FL) biosynthesis in vitro. Here we show that 2'-FL could diminish colitis in mice induced by treatment with dextran sodium sulfate. Mechanistically, 2'-FL promoted maintenance of mucosal barrier integrity, leading to intestinal IgA secretion and intraepithelial CD4[+]CD8αα[+] T cell development mediated by the gut microbiome. Together, our findings thus link lysogeny to human age, geography, and disease, and demonstrate an immunomodulatory mechanism of prophage-encoded genes in alleviating colitis.},
}

@article {pmid41275034,
year = {2025},
author = {Qian, B and Fang, Z},
title = {The association between oral microbiome diversity and rheumatoid arthritis: a nationwide cross-sectional study.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {41275034},
issn = {1434-9949},
abstract = {OBJECTIVE: The association between oral microbiome diversity and rheumatoid arthritis (RA) remains unclear. This study aims to investigate the association between oral microbiome diversity and RA.

METHODS: In this nationwide cross-sectional study, 5284 participants from the 2009-2012 National Health and Nutrition Examination Survey (NHANES) cycles were included. To explore the potential association between α-diversity and self-reported RA, weighted logistic regression and weighted restricted cubic spline (RCS) analyses were carried out. Subgroup analysis was performed to examine the robustness of the results. Finally, β-diversity in non-RA and RA groups was examined using principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA).

RESULTS: Our findings suggested that α-diversity was negatively correlated with RA, and the subsequent RCS analysis supported that the lower the variety of bacteria, the higher the likelihood of having RA. In the subgroup analysis, no apparent interaction effect was detected. PCoA and PERMANOVA demonstrated significant differences in the composition of the oral microbiome between non-RA and RA groups in terms of β-diversity.

CONCLUSION: Oral microbiome diversity was significantly associated with RA. This finding may offer new clinical insights into the treatment and prevention of RA, while also enhancing our understanding of its relationship with periodontitis. Key Points • By utilizing NHANES data, this study reveals the association between oral microbiome diversity and RA. • Lower α-diversity was closely related to higher RA prevalence. • PCoA and PERMANOVA showed that β-diversity differed in non-RA and RA groups.},
}

@article {pmid41274892,
year = {2025},
author = {Pröschle-Donoso, T and Díaz, R and Vásquez-Dean, J and Serebrinsky-Duek, K and Pezoa-Soto, I and Martin, AJM and Garrido, D},
title = {Emergent roles of infant gut microbes during the utilization of human milk oligosaccharides.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00865-w},
pmid = {41274892},
issn = {2055-5008},
support = {Fondequip EQM190070//Agencia Nacional de Investigación e Innovación/ ; Fondecyt 1230764//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {Bifidobacterium spp. are representative species of the infant gut microbiome. Human milk oligosaccharides (HMOs) are complex carbohydrates in breast milk, guiding gut microbiome assembly by establishing complex microbial interactions. Here, a synthetic community of seven infant gut microbes was subjected to single species dropouts in bioreactors using three HMOs. Substrate use, acid production, biomass, and metatranscriptomics revealed that B. bifidum was critical for degradation product formation and supporting cross-feeding. Removing B. longum subsp. infantis, known for intracellular HMO use, accelerated global growth and HMO consumption, suggesting competitive interactions. Some dropouts led to the accumulation of sialic acid, fucose, or lactose. Metatranscriptomics showed niche expansion, upregulated central metabolism and cross-feeding dependencies when certain species were removed. Modeling highlighted that HMO degradation rates strongly influence community dynamics. Overall, this study identifies key ecological roles in infant gut microbes and deepens our understanding of how HMOs shape microbiota assembly and function.},
}

@article {pmid41274878,
year = {2025},
author = {Ferretti, P and Allert, M and Johnson, KE and Rossi, M and Heisel, T and Gonia, S and Knights, D and Fields, DA and Albert, FW and Demerath, EW and Gale, CA and Blekhman, R},
title = {Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66497-y},
pmid = {41274878},
issn = {2041-1723},
support = {R01HD109830//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R21HD099473//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; F32HD105364//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD080444//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
abstract = {The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as sole nutrition for the infant, little is known about how variation in the milk microbiome shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiomes using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. Microbial taxonomic overlap between milk and the infant gut was driven by Bifidobacterium longum, and infant microbiomes dominated by B. longum showed greater temporal stability than those dominated by other species. We identified numerous instances of strain sharing between milk and the infant gut, involving both commensal (e.g. B. longum) and pathobiont species (e.g. K. pneumoniae). Shared strains also included typically oral species such as S. salivarius and V. parvula, suggesting possible transmission from the infant's oral cavity to the mother's milk. At one month, the infant gut microbiome was enriched in biosynthetic pathways, suggesting that early colonisers might be more metabolically independent than those present at six months. Lastly, we observed significant overlap in antimicrobial resistance gene carriage within mother-infant pairs. Together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.},
}

@article {pmid41274873,
year = {2025},
author = {Peng, H and Andreu-Sanchez, S and Ruiz-Moreno, AJ and Fernández-Pato, A and Wu, J and Gacesa, R and Zhernakova, A and Wang, D and Fu, J},
title = {Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66612-z},
pmid = {41274873},
issn = {2041-1723},
abstract = {Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 338 individuals in the Lifelines-DEEP study collected ~4 years apart, using a newly developed workflow to detect recent HGT events from metagenome-assembled genomes. We identified 5,644 high-confidence HGT events occurring within the past ~10,000 years across 116 gut bacterial species. We find that species pairs with an HGT relationship were significantly more likely to maintain stable co-abundance relationships over the 4-year period, suggesting that gene exchange contributes to community stability. Notably, HGT and strain replacement act together to disseminate mobile genes in the population. Furthermore, our observation that an individual's mobile gene pool remains highly personalized and stable over time indicates that host lifestyles drive specific gene transfer. For example, proton pump inhibitor usage is linked to increased transfer of multidrug transporter genes. Our findings demonstrate, at the individual gut microbiome level, that HGT is both an integral and stabilizing force in the human gut ecosystem and an important mechanism for disseminating adaptive functions, underscoring HGT potential for tracking host lifestyle.},
}

@article {pmid41274681,
year = {2025},
author = {Imai, M and Kawachi, M and Wakui, A and Miyazawa, M and Sekiguchi, M and Kato, Y and Sato, H and Naruse, Y and Asano, N and Morohashi, M and Sano, H and Abiko, Y and Washio, J and Tanaka, K and Takahashi, N and Sato, T},
title = {Microbial profiling of bold green tea bottled beverages: A screening experiment.},
journal = {Journal of oral biosciences},
volume = {67},
number = {4},
pages = {100697},
doi = {10.1016/j.job.2025.100697},
pmid = {41274681},
issn = {1880-3865},
mesh = {Humans ; *Tea/microbiology ; Adult ; *Saliva/microbiology ; Young Adult ; *Beverages/microbiology ; Male ; *Bacteria/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Female ; DNA, Bacterial ; },
abstract = {OBJECTIVES: To explore the storage potential and drinking safety of leftover bottled tea beverages from various manufacturers after directly drinking from the bottle, we conducted a screening experiment on the growth of salivary bacteria in plastic bottles of bold green tea.

METHODS: Resting whole saliva (n = 14) was collected from each participant (aged 19-25 years). The saliva samples (1.0 mL of each diluted saliva sample [5.0 × 10[5] CFU/mL]), were inoculated into plastic bottles containing 280 mL of green tea, which included six types of bold green tea beverages. The bottles were stored at 37 °C for 24 h; subsequently, 1.0 mL of each sample was inoculated onto a blood agar plate and incubated anaerobically at 37 °C. Genomic DNA was extracted from the resulting individual colonies and the bacterial species were identified by 16S rDNA sequencing.

RESULTS: More than 60 % of the samples of six types of bold green tea beverages, Bold Oi Ocha®, Suntory Bold Green Tea Iyemon®, Bold Oi Ocha Premium Strong®, Healthya®, Bold Ayataka®, and Catechin Green Tea® showed low bacterial levels (<10[3] CFU/mL) after 1 day of storage. However, in some cases, former members of the genus Lactobacillus, such as Limosilactobacillus and Lactiplantibacillus spp., were specifically detected as the predominant bacteria (37.6-100 %), although these bacteria usually account for the minority among the oral microbiome.

CONCLUSIONS: Although the antibacterial effects of catechins may have affected the total bacterial counts and compositions, no clear correlation was observed between total tea catechin concentrations and total bacterial growth inhibitory effects.},
}

Humans
*Tea/microbiology
Adult
*Saliva/microbiology
Young Adult
*Beverages/microbiology
Male
*Bacteria/isolation & purification
RNA, Ribosomal, 16S/genetics
Female
DNA, Bacterial

@article {pmid41274528,
year = {2025},
author = {Canzian, J and Jacobs, F and Floreani, A and Miggiano, C and Tiberio, P and Pozzi, C and Santoro, A and Zambelli, A and Rescigno, M and De Sanctis, R},
title = {Intratumoral Microbiome in Breast Cancer: A Hidden Player in Tumor Development, Progression and Treatment response.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105035},
doi = {10.1016/j.critrevonc.2025.105035},
pmid = {41274528},
issn = {1879-0461},
abstract = {The intratumoral microbiome has recently emerged as a critical component of the tumor microenvironment in breast cancer (BC). BC exhibits a uniquely rich and diverse microbial community, characterized by phyla such as Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. In addition, distinct microbial signatures were observed in different molecular subtypes, with hormone receptor-positive BC showing the highest microbial diversity and the most robust microbiome. These microbial constituents interact with neoplastic and immune cells, influencing estrogen metabolism, DNA damage, epithelial-to-mesenchymal transition (EMT), inflammation, and response to anticancer therapy. For instance, Fusobacterium nucleatum is among the main microbial components implicated in BC, contributing to carcinogenesis, tumor growth, and metastasis through mechanisms involving DNA damage (e.g., activating the E-cadherin/β-catenin signaling pathway), EMT (e.g., inducing the expression of EMT markers, including cadherins and vimentin), and immunoregulatory effects (e.g., regulating IL-1β expression and activating the TLR4/NF-κB signaling pathway). It has also been shown to induce chemoresistance by enhancing cancer cell stemness and viability, whereas its elimination improves sensitivity to anticancer therapies and immunotherapy. Besides investigating the specific activity of microbial components, recent studies have focused on the intratumoral microbiome prognostic role. Methodological variability remains a significant barrier to standardization and cross-study comparisons. Nevertheless, subtype-specific microbial signatures have demonstrated prognostic and predictive value, correlating with stage, treatment response, and immune cell infiltration. Understanding the interplay between the intratumoral microbiome, host genetics, and treatment response may ultimately inform the development of microbiome-based biomarkers and therapeutic strategies, positioning the tumor microbiota as a potential modifiable target in personalized BC care.},
}

@article {pmid41274315,
year = {2025},
author = {Najjar, I and Gandolpho, LS and Santos, JPD and Siqueira, CP and Ikechukwu, MB and Ribeiro, ÁCDS and Roch, M and Sierra, R and Andrey, D and Arrais-Rodrigues, C and Gales, AC},
title = {Phage therapy for KPC-producing Klebsiella pneumoniae decolonization in high-risk patients : The KIDNAP Study Protocol - A prospective feasibility and proof of concept study in the Brazilian context.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107673},
doi = {10.1016/j.ijantimicag.2025.107673},
pmid = {41274315},
issn = {1872-7913},
abstract = {BACKGROUND: There has been renewed interest in phages amidst growing antimicrobial resistance. Their potential for intestinal decolonization is interesting due to their specificity, minimal side effects and microbiota preservation. In addition, phage-resistant bacterial mutants that arise during treatment may become more susceptible to antibiotics and less virulent, possibly leading to better clinical outcomes.

OBJECTIVES: This study's primary objective is to measure the efficacy of phage-based intestinal decolonization of KPC-producing Klebsiella Pneumoniae (KPC-Kp) at 14 days post-treatment, as well as its feasibility, which is defined as >80% achieving at least 7 days of treatment. Secondary objectives will include phage safety at 14 days post-treatment, intestinal KPC-Kp load change over time, characterization of phage-resistant KPC-Kp mutants, microbiome changes, and infection-related outcomes and general clinical outcomes 3 months after the end of treatment.

METHODS: This feasibility and proof-of-concept study aims to include 15 high-risk patients recruited from a tertiary Hospital in São Paulo who will receive individualized phage combinations for a mean duration of 14 days. Safety data will be reviewed by an independent Safety Monitoring Board. Description of microbiological techniques is provided.

CONCLUSION: To the best of our knowledge this is the first published protocol that aims to establish a standardized, individualized phage-treatment framework for intestinal decolonization in a high-endemicity setting. It will also explore phage-bacterial interactions and their broader impact on bacterial virulence and susceptibility profiles. It represents a stepping stone towards implementing phage therapy in South America, and bringing knowledge and capacities to the countries most impacted by escalating AMR.},
}

@article {pmid41274275,
year = {2025},
author = {Zhang, T and Chen, SY and Zhang, C and Chen, R and Zhou, PF and Li, ZC and He, Q and Fu, XH and Wen, W and Zhang, CP and Yao, MY and Geng, JJ},
title = {HLA-B27 modulates the composition of the gut microbiota and drives a proinflammatory intestinal microecology.},
journal = {Human immunology},
volume = {87},
number = {1},
pages = {111616},
doi = {10.1016/j.humimm.2025.111616},
pmid = {41274275},
issn = {1879-1166},
abstract = {The pathogenesis of autoimmune diseases such as spondyloarthritis (SpA), rheumatoid arthritis (RA), and inflammatory bowel disease (IBD) involves genetic factors and gut microbiota dysbiosis, which have been widely reported in patients and animal models. Although genetic factors are known to reshape the gut microbiota, the mechanistic role of the host gene-reshaped gut microbiota in mediating inflammatory diseases remains poorly characterized. This study focused on HLA-B27 to investigate its impact on the gut microbial composition and its association with HLA-B27 related autoimmune inflammatory diseases. The expression of HLA-B27/β2M significantly altered the diversity of the gut microbiota in mice, leading to changes in bacterial species and their functions. Concurrently, HLA-B27/β2M profoundly modified the gut metabolic profile, resulting in increased levels of multiple prostaglandins and decreased levels of anti-inflammatory metabolites. Multi-omics integrated analysis demonstrated that HLA-B27/β2M promoted the synthesis of Gram-negative bacteria while suppressing Gram-positive bacteria, findings validated in both omics datasets. Further validation confirmed that these HLA-B27/β2M-driven alterations in the gut microbial composition caused a shift toward a proinflammatory microbial community. These findings first revealed that genetic factors significantly reshaped the gut microbiota composition and further drove the microbial ecosystem toward a proinflammatory state. This study provides a foundation for identifying gut microbial signature targets in HLA-B27 associated diseases.},
}

@article {pmid41274019,
year = {2025},
author = {Chen, R and Qian, J and Wang, Q and Li, Y and Xu, Z and Zhang, M and Wang, M and Nie, H and Yang, W and Tong, X and Yan, F},
title = {Periodontitis exacerbates metabolic dysfunction-associated steatotic liver disease via the gut microbiota-derived tryptophan metabolism-AHR axis in obesity.},
journal = {EBioMedicine},
volume = {122},
number = {},
pages = {106037},
doi = {10.1016/j.ebiom.2025.106037},
pmid = {41274019},
issn = {2352-3964},
abstract = {BACKGROUND: Periodontitis is linked to metabolic dysfunction-associated steatotic liver disease (MASLD); however, the underlying mechanisms remain unclear.

METHODS: Periodontitis was investigated in male mice with high-fat diet (HFD)-induced MASLD. Gut microbiome and metabolomic profiling were conducted using16S rRNA gene sequencing, along with both untargeted and targeted metabolomic profiling via liquid chromatography-tandem mass spectrometry. Intestinal barrier integrity was evaluated by histopathological analysis. Faecal microbiota transplantation was conducted and the vital role of the aryl hydrocarbon receptor (AHR) was confirmed using Ahr gene knockout (Ahr[-/-]) mice. The protective roles of tryptophan derivative indole-3-propionic acid (IPA) and the tryptophan-metabolising probiotic Limosilactobacillus reuteri were assessed following their administration via oral gavage. The impact of endotoxin-mediated hyperinflammation on hepatic mitochondrial dynamics was examined in vitro.

FINDINGS: Periodontitis promoted MASLD, gut microbiota dysbiosis, and tryptophan metabolism depletion, leading to intestinal barrier dysfunction, systemic inflammation, and endotoxin overexpression in HFD-fed mice. Periodontitis-accelerated MASLD was attenuated in HFD-fed Ahr[-/-] mice. In an AHR-dependent manner, IPA or L. reuteri alleviated the detrimental effects of periodontitis on MASLD progression, intestinal barrier impairment, systemic inflammation, and endotoxin translocation to the liver. Conditioned medium from endotoxin-stimulated THP-1 cells promoted mitochondrial fission in HepG2 cells by upregulating Drp1 expression.

INTERPRETATION: Periodontitis exacerbates MASLD by disrupting the gut microbiota-tryptophan metabolism-AHR axis, leading to intestinal barrier dysfunction, systemic inflammation, and endotoxin translocation. Endotoxin plays a pivotal role in promoting hepatic mitochondrial fission during the exacerbation of MASLD by periodontitis. AHR agonists offer a novel intervention strategy for patients with comorbid MASLD and periodontitis.

FUNDING: This work was supported by the Jiangsu Province Key Research and Development Program [No. BE2022670]; National Natural Science Foundation of China [No. 82270979]; Jiangsu Provincial Medical Key Discipline Cultivation Unit [No. JSDW202246]; and High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University [No. 0224C001].},
}

@article {pmid41273865,
year = {2025},
author = {Sahu, M and Kaushik, A and Mishra, AU and Rout, PK and Sundaresan, V and Shanker, K and Mani, DN and Shukla, AK},
title = {Aegle marmelos effectively attenuates DSS-induced colitis by restoring intestinal mucosal barrier and alleviating inflammation through modulation of gut microbiota in mice.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {149},
number = {},
pages = {157538},
doi = {10.1016/j.phymed.2025.157538},
pmid = {41273865},
issn = {1618-095X},
abstract = {BACKGROUND: In Ayurveda, Aegle marmelos fruit is described for its utility in alleviating gastrointestinal disorders due to its astringent, digestive, and stomachic properties.

PURPOSE: Here the aim was to explore the mechanism involved in the protective effect of A. marmelos against ulcerative colitis (UC) in murine model. The study also compared the anti-colitis efficacy of two distinct fruit morphotypes of A. marmelos available in India (oblate-spheroid, Lucknow; pyriform, Bengaluru). Further, it explored the role of the more effective one in modulating the gut microbiota in mice.

STUDY DESIGN: Aqueous, ethanolic and hydroalcoholic extracts of A. marmelos fruit were analyzed for efficacy against dextran sulfate sodium (DSS)-induced UC in mice at 200 mg/kg BW oral dose.

METHODS: The most efficacious extract was subjected to dose-dependent (100-500 mg/kg BW) analysis. Its best dose was analyzed in terms of restoration of cytokine levels, tight junction proteins, intestinal permeability, myeloperoxidase activity, transcript abundance of key genes and modulation of gut microbiota through NGS-based 16S rRNA analysis.

RESULTS: The aqueous extract of Lucknow fruit at 300 mg/kg BW (AM) ameliorated colitis symptoms in DSS-induced mice. It elevated relative abundance of Lactobacillus and Blautia but decreased that of Escherichia-Shigella, Clostridium sensu stricto 1 and Romboutsia in the gut microbiota. AM downregulated Tlr4 transcripts, upregulated Muc2 and Slc6a4 transcripts, ZO-1 protein and goblet cells in colon showing barrier protective properties against colon damage and inflammatory response. Moreover, it was found to be safe up to 3000 mg/kg BW.

CONCLUSION: This study has elucidated the potential of A. marmelos treatment in UC by modulation of gut microbiome and provided strong scientific evidence to validate its use in traditional medicine.},
}

@article {pmid41273632,
year = {2025},
author = {Bi, J and Li, J and Rahman, SU and Long, Y and Hui, N and Romantschuk, M and Zheng, J and Zhang, X and Hou, D and Tan, J and Bi, Q and Xia, H and Yu, X and Luo, L and Liu, X},
title = {Balancing water efficiency and crop productivity: rhizosphere microbiome shifts in drought-resistant rice.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {469},
pmid = {41273632},
issn = {1573-0972},
}

@article {pmid41273488,
year = {2025},
author = {Tiwari, S and Paramanik, V},
title = {Lactobacillus fermentum ATCC 9338 ameliorates immune dysregulation via indoleamine 2, 3-dioxygenase through modulating gut microbial diversity of chronic unpredictable mild stressed mouse.},
journal = {Metabolic brain disease},
volume = {40},
number = {8},
pages = {322},
pmid = {41273488},
issn = {1573-7365},
support = {2021//University Grants Commission/ ; 2021-11643//Indian Council of Medical Research/ ; },
mesh = {Animals ; *Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; *Gastrointestinal Microbiome/physiology/drug effects ; *Limosilactobacillus fermentum ; Mice ; *Stress, Psychological/metabolism/microbiology/immunology ; Tryptophan/analogs & derivatives/pharmacology ; Male ; *Probiotics/pharmacology ; Depression/metabolism ; Brain/metabolism ; Cytokines/metabolism ; Mice, Inbred C57BL ; },
abstract = {Gut microbiota (GM) plays a significant role in the pathophysiology of neuropsychiatric diseases like depression. A complex two-way system between gut and brain termed as gut-brain axis (GBA) dependent on intestinal GM and central nervous system (CNS). Alterations in the GM can affect behavior and brain neurochemistry including tryptophan metabolism through immune mediated pathways. Researchers focused to understand immune challenges involving kynurenine action via indoleamine-2,3-dioxygenase (IDO) induces depressive like "sickness behavior". This study examined the role of Lactobacillus fermentum (LF) and 1-methyl-D-tryptophan (1-MT) on IDO regulation, proinflammatory cytokine responses, and gut microbial diversity in chronic unpredictable mild stress (CUMS) depression model. LF (oral administration, 1 × 10[8] CFU/day/mouse for 28 days) and 1-MT (intraperitoneal, 15 mg/KgBW/day for 21 days) supplementation decreases the expression of cytokines and IDO in cortex, hippocampus, and medulla. Likewise, the mRNA and protein level of cytokines and IDO were modulated after LF and 1-MT administration. Additionally, 16 S rRNA gene sequencing showed that Lactobacillus fermentum restored gut microbial β-diversity and increased overall community richness, indicating a shift toward a balanced microbiome. These results suggest that LF alleviates stress-induced neuroinflammatory and immune changes by modulating IDO activity in the tryptophan pathway. The findings highlight the therapeutic potential of LF as a microbiota-based intervention for regulating neuroinflammation and mood disorders such as depression.},
}

Animals
*Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism
*Gastrointestinal Microbiome/physiology/drug effects
*Limosilactobacillus fermentum
Mice
*Stress, Psychological/metabolism/microbiology/immunology
Tryptophan/analogs & derivatives/pharmacology
Male
*Probiotics/pharmacology
Depression/metabolism
Brain/metabolism
Cytokines/metabolism
Mice, Inbred C57BL

@article {pmid41273394,
year = {2026},
author = {Irles, P and Sulbaran-Bracho, Y and Sarrazin, AF},
title = {The Ring-Legged Earwig, Euborellia annulipes (Dermaptera, Insecta): A Promising Model to Study Development and Reproductive Strategies of Hemimetabolous Insects.},
journal = {Results and problems in cell differentiation},
volume = {76},
number = {},
pages = {183-206},
pmid = {41273394},
issn = {0080-1844},
mesh = {Animals ; *Insecta/physiology/growth & development ; Reproduction/physiology ; Female ; Oogenesis/physiology ; Phylogeny ; },
abstract = {This chapter comprehensively reviews the phylogenetic position, morphology, reproductive strategies, and developmental biology of the ring-legged earwig Euborellia annulipes. Special reference is given to the embryonic and postembryonic development, as well as oogenesis, with particular emphasis on the role of the juvenile hormone in this process. Additionally, the influence of maternal care on offspring survival and microbiome transmission is explored. In the light of the presented and discussed analyses, E. annulipes emerges as a new model species suitable for studying the evolution of insect segmentation, anagenesis of insect ovaries, and parental investment in nonholometabolous insects.},
}

Animals
*Insecta/physiology/growth & development
Reproduction/physiology
Female
Oogenesis/physiology
Phylogeny

@article {pmid41273353,
year = {2025},
author = {de Sousa, LP and Silva, LDPE and Brandão, MM and Filho, OG},
title = {First report of the coffee leaf miner (Leucoptera coffeella) bacteriome in larval/adult stages and possible contribution of the plant host.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf133},
pmid = {41273353},
issn = {1574-6968},
abstract = {Coffee leaf mine, a small moth of the family Lyonetiidae, is considered one of the most important coffee pests. Despite its economic importance, almost nothing is known about its microbiome. Seeking to help fill this knowledge gap, in our study we investigated the bacteriome of the insect (larvae and adult) and coffee leaves by sequencing the 16S rRNA gene. We found that at the phylum level Pseudomonadota and Bacteroidota dominate. At the genus level, leaves were mainly dominated by Sphingomonas and Methylobacterium; the caterpillar were mainly dominated by Xanthomonas and Paracoccus; the adult moth were mainly dominated by Acinetobacter and Klebsiella. We estimate that the contribution to the bacteriome of adult moths comes from larvae, 50%, from leaves, 40%, and 10% from other sources. Several bacteria with the potential to degrade insecticides and secondary plant compounds were found, which leads to the expectation that they may help their hosts in resisting these toxic compounds. We hope that this work will contribute to encouraging further investigation of this important coffee pest.},
}

@article {pmid41273231,
year = {2025},
author = {Kuehn, JF and Zhang, Q and Heston, MB and Kang, JW and Harding, SJ and Davenport-Sis, NJ and Peter, DC and Kerby, RL and Vemuganti, V and Schiffmann, EC and Tallon, MM and Harpt, J and Hajra, A and Wheeler, JL and Shankar, S and Mickol, A and Zemberi, J and Chow, H and Zhang, E and Clements, E and Noughani, H and Forst, A and Everitt, G and Kollmorgen, G and Quijano-Rubio, C and Christian, BT and Carlsson, CM and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Ulland, TK and Rey, FE and Bendlin, BB},
title = {Fecal short-chain fatty acids vary by sex and amyloid status.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {11},
pages = {e70877},
doi = {10.1002/alz.70877},
pmid = {41273231},
issn = {1552-5279},
support = {//the Wisconsin Registry for Alzheimer's Prevention/ ; //the Wisconsin Alzheimer's Disease Research Center/ ; //NIH/NINDS/ ; //Wisconsin Partnership Program grant/ ; R01AG070973/AG/NIA NIH HHS/United States ; R01AG083883/AG/NIA NIH HHS/United States ; R21AG089348/AG/NIA NIH HHS/United States ; //the Swedish Research Council/ ; //Swedish Alzheimer's Foundation/ ; //Hjärnfonden, Sweden/ ; //the Swedish state under the agreement between the Swedish government and the County Councils/ ; //the ALF-agreement/ ; //the Alzheimer's Association 2021 Zenith Award/ ; //the Alzheimer's Association 2022-2025 Grant/ ; //La Fondation Recherche Alzheimer (FRA), Paris, France/ ; //the Kirsten and Freddy Johansen Foundation, Copenhagen, Denmark/ ; //Familjen Rönströms Stiftelse, Stockholm, Sweden/ ; //an anonymous philanthropist and donor/ ; //the European Union's Horizon Europe Research and Innovation Programme/ ; //Swedish State Support for Clinical Research/ ; //the European Union Joint Program for Neurodegenerative Disorders/ ; 2137424//National Science Foundation Graduate Research Fellowship Program/ ; //the Graduate School and the Office of the Vice Chancellor for Research, University of Wisconsin-Madison/ ; //the Wisconsin Alumni Research Foundation/ ; },
mesh = {Humans ; Female ; Male ; *Fatty Acids, Volatile/metabolism/analysis ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Alzheimer Disease/metabolism ; Aged ; Sex Factors ; Biomarkers/cerebrospinal fluid ; Cognitive Dysfunction ; },
abstract = {INTRODUCTION: Short-chain fatty acids (SCFAs), produced by gut microbes, influence Alzheimer's disease (AD) pathology in animals. Less is known about SCFAs and AD in humans. We profiled feces of adults along the AD continuum to investigate gut microbiome and SCFA associations with AD pathology and cognition.

METHODS: We measured SCFAs and bacterial abundances in fecal samples from 287 participants in the Wisconsin Alzheimer's Disease Research Center and Wisconsin Registry for Alzheimer's Prevention. We performed regressions examining associations between SCFAs or gut microbes and AD pathology and cognition.

RESULTS: Fecal propionate, isovalerate, and propionate-producing bacteria are inversely associated with amyloid status. Mediation analysis found that propionate mediates sex-specific associations between SCFAs and cerebrospinal fluid biomarkers. SCFA levels are associated with slower cognitive decline.

DISCUSSION: These results link SCFAs and propionate-producing bacteria with AD. This may inform efforts to leverage diet and specific bacteria to boost SCFA production and potentially ameliorate AD progression.

HIGHLIGHTS: Fecal SCFAs link to lower amyloid burden and microglial activation, notably in females. SCFA-producing gut microbes have reduced abundance in amyloid-positive participants. Fecal propionate mediates relationships between gut microbes and amyloid status. SCFAs are associated with slower plasma pTau217 accumulation in females. SCFAs are associated with slower cognitive decline.},
}

Humans
Female
Male
*Fatty Acids, Volatile/metabolism/analysis
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome/physiology
*Alzheimer Disease/metabolism
Aged
Sex Factors
Biomarkers/cerebrospinal fluid
Cognitive Dysfunction

@article {pmid41273085,
year = {2025},
author = {Kruger, R and Oler, E and Saha, S and Poelzer, J and Han, S and Punsalan, MP and Green, B and Bushra, F and Kyes, M and Disu, F and Wakoli, J and Woudstra, R and Tejol, E and Fakutan, O and Wang, F and Lee, BL and Sajed, T and Tian, S and Torres-Calzada, C and Berjanskii, M and MacKay, S and Karu, N and Kadurrah-Daouk, R and Wishart, DS},
title = {MiMeDB 2.0: the Human Microbial Metabolome Database for 2026.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1272},
pmid = {41273085},
issn = {1362-4962},
support = {//NIH/ ; AG063744/AG/NIA NIH HHS/United States/AG/NIA NIH HHS/United States ; CFI MSIF 42495//Canada Foundation for Innovation/ ; CRC TIER1 100628//Canada Research Chairs/ ; //Genome Alberta, a division of Genome Canada/ ; ALLRP 597259-24//Natural Sciences and Engineering Research Council of Canada/ ; UBC F23-05862 WFF//Weston Family Foundation/ ; 2007-2024-1003//Social Sciences and Humanities Research Council of Canada/ ; //Genome Alberta/ ; },
abstract = {The Microbial Metabolome Database (MiMeDB) (https://mimedb.org) is a comprehensive, freely accessible resource linking human-associated microbes to the metabolites they produce, along with their connections to human health, disease, and diet. Since the release of MiMeDB 1.0 in 2023, the database has been substantially expanded and redesigned. Major updates include the systematic addition of millions of newly annotated genes and pathways, thousands of new metabolites, significantly expanded pathway and reaction coverage, along with broader representation of eukaryotic gut microbes. MiMeDB 2.0 now contains >12.9 million annotated microbial genes, over 23.1 million microbial pathways, 29 295 metabolites, 21 829 metabolic reactions, 3725 microbial species and strains, and 514 076 new experimental and predicted nuclear magnetic resonance and mass spectrometry spectra of microbial metabolites. New features, such as detailed microbial descriptions, metabolite origin tags, refined search filters, and species-specific reaction queries, have been added to enhance usability. Likewise, redesigned network and genome viewers have been implemented to support more comprehensive, intuitive, and integrated visualization of complex, multi-omic relationships. The significant addition of more metabolite spectral data and improved spectral search capabilities further strengthen metabolite identification and discovery. Together, these improvements make MiMeDB 2.0 one of the most comprehensive and user-friendly platforms for investigating the human microbiome at a molecular level and exploring the roles of microbes and microbial metabolites in human health, diet, and disease.},
}

@article {pmid41272772,
year = {2025},
author = {Yang, Y and Yang, L and Yang, R and Deng, F and Tian, Q and Yu, Z and Zhang, L},
title = {Gut microbiome restoring biogenic ferritin mineral as an effective oral iron supplement for iron deficiency anemia.},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {726},
pmid = {41272772},
issn = {1477-3155},
support = {2024M754229//China Postdoctoral Science Foundation/ ; 31971315//National Natural Science Foundation of China/ ; },
mesh = {*Anemia, Iron-Deficiency/drug therapy ; Humans ; Caco-2 Cells ; *Gastrointestinal Microbiome/drug effects ; *Ferritins/metabolism/chemistry ; *Ferric Compounds/chemistry/pharmacology ; Dietary Supplements ; Animals ; *Iron/metabolism ; Administration, Oral ; Mice ; Dysbiosis/drug therapy ; Male ; Nanoparticles/chemistry ; },
abstract = {Traditional iron supplements for iron deficiency anemia (IDA) have several limitations, including suboptimal absorption, gastrointestinal discomfort, and concerns regarding long-term safety. In this study, we synthesized monodisperse 6-line ferrihydrite as an innovative iron supplement, featuring a structure analogous to the natural "iron core" present in ferritin. Notably, 6-line ferrihydrite (6-Fh) was internalized by Caco-2 cells via a process independent of divalent metal transporter 1 (DMT1). Additionally, its stability as nanoparticles within the gastrointestinal tract prevents the irritation typically associated with metal ions, thereby significantly enhancing iron utilization efficiency. Consequently, compared to FeSO4 (a traditional oral iron supplement), 6-Fh effectively stabilized cellular free iron with low ROS toxicity and high biosafety, thereby effectively maintaining intestinal barrier integrity and avoiding liver injury. Furthermore, it restored intestinal dysbiosis caused by IDA and increased the proportion of beneficial bacterial strains, which was superior to FeSO4. Characterized by low toxicity, efficient cellular absorption, intestinal stability, and superior iron supplementation efficacy compared with conventional iron supplements, 6-Fh demonstrates compelling therapeutic advantages and holds great promise for medical applications.},
}

*Anemia, Iron-Deficiency/drug therapy
Humans
Caco-2 Cells
*Gastrointestinal Microbiome/drug effects
*Ferritins/metabolism/chemistry
*Ferric Compounds/chemistry/pharmacology
Dietary Supplements
Animals
*Iron/metabolism
Administration, Oral
Mice
Dysbiosis/drug therapy
Male
Nanoparticles/chemistry

@article {pmid41272710,
year = {2025},
author = {Mukhtar, H and Easterly, AC and Bachle, KB and Ozorio, D and Creech, CF and Schachtman, DP},
title = {Peptide nucleic acid (PNA) clamps enhance root microbiome profiling in wheat and maize.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {148},
pmid = {41272710},
issn = {2524-6372},
support = {2019-08314//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Peptide Nucleic Acid (PNA) clamps represent a crucial molecular tool for reducing host DNA contamination during plant tissue microbiome profiling. This is particularly important when there is sequence similarity between the host organellar DNA (e.g., mitochondrial) and the targeted PCR sequences. However, the effectiveness and optimal concentration of universal PNA clamps can vary between plant species, necessitating a case-by-case evaluation. Here, we assessed the effectiveness of five concentrations (0.0, 0.25, 1.0, 2.0 and 4.0 µM) of mitochondrial and chloroplast PNA blockers (mPNA and pPNA) in reducing the amplification of organellar DNA and enhancing the profiling of prokaryotic communities across root tissues from 34 maize and 27 wheat samples cultivated under various soil and climatic conditions.

RESULTS: We observed that host plant contamination in root samples was consistently high, with an average rate exceeding 95% across all samples. The application of PNA clamps significantly reduced plant host contamination by 2.4-27.2 times in a concentration-dependent manner. This reduction was more pronounced in maize samples than in wheat samples, particularly at lower doses (PNA ≤ 1.0 µM). PNA clamps also increased the read abundance of more than half of the observed microbiome phyla in the root tissues. The most substantial increase in prokaryotic read abundance was observed at a PNA concentration of 1.0 µM, without introducing significant bias to the prokaryotic community.

CONCLUSIONS: In conclusion, the introduction of universal PNA clamps during PCR assays significantly reduced amplification of host contamination and enhanced the detection of low-abundance microbiome and the depth of microbial profiling in both maize and wheat root tissues, with effects being concentration- and crop-specific.},
}

@article {pmid41272493,
year = {2025},
author = {Nourazarain, A and Vaziri, Y},
title = {Nutrigenomics meets multi-omics: integrating genetic, metabolic, and microbiome data for personalized nutrition strategies.},
journal = {Genes & nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12263-025-00790-9},
pmid = {41272493},
issn = {1555-8932},
abstract = {The integration of multi-omics technologies with computational biology has had a profound impact on nutritional science, enabling the development of precision nutrition strategies tailored to individual biochemical profiles. This review synthesizes recent advances in integrating genomic, epigenetic, transcriptomic, proteomic, metabolomic, and microbiome data for personalized dietary interventions. The present study analyzed machine learning approaches, with a particular focus on transformer and graph neural networks, for the processing of multi-omics data and prediction of metabolic outcomes. Advanced computational models have demonstrated an accuracy rate of over 90% in predicting individual metabolic responses to dietary interventions. Large-scale clinical trials (PREDICT, FOOD4ME, and PRECISION-HEALTH) have demonstrated significant improvements in weight management, glycemic control, and dietary adherence compared with conventional approaches. Digital health technologies, including continuous glucose monitoring and artificial intelligence (AI)-powered applications, facilitate real-time physiological monitoring and enable dynamic nutritional adjustments in patients with diabetes. The paradigm shift from population-based dietary recommendations to individualized interventions is represented by multi-omics-driven precision nutrition. The integration of sophisticated computational methodologies with comprehensive biological profiling provides a unique opportunity to prevent and manage chronic diseases via targeted dietary interventions. However, the successful implementation of such a system necessitates interdisciplinary collaboration among biologists, computational scientists, clinicians, and policymakers to ensure equitable access and ethical deployment of the technology. Future research should focus on developing scalable implementation frameworks, establishing evidence-based clinical practice guidelines to standardize multi-omics applications in precision nutrition, and identifying strategies to address potential disparities in access to these applications.},
}

@article {pmid41272435,
year = {2025},
author = {Dandachi, I and Alawdah, L and Aljabr, W},
title = {Comparative meta-transcriptomic analysis of nasal and anal microbiota in respiratory syncytial virus mono and co-infected children.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {768},
pmid = {41272435},
issn = {1471-2180},
mesh = {Humans ; Male ; Female ; *Respiratory Syncytial Virus Infections/microbiology/virology ; Infant ; *Coinfection/microbiology/virology ; Child, Preschool ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Nose/microbiology ; Child ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Respiratory Syncytial Virus, Human ; },
abstract = {BACKGROUND: Respiratory syncytial virus is among the most common viruses causing respiratory infections in children. It has been suggested that imbalance of the respiratory microbiota could be involved in the prognosis of RSV illness. The aim of this work is to explore dysbiosis of nasal/anal microbiota in children upon RSV infection, compared to controls.

RESULTS: Fifty-nine subjects were enrolled in this study and included: 23 controls, 17 infected only with RSV, and 19 RSV infected together with other respiratory viruses. Multi-infected subjects had non-statistically significant, higher rates of ICU admission (8 versus 3), oxygen supplementation (13 versus 9), and longer hospital stay (20 versus 15 mean days), compared to those single infected with RSV (P > 0.05). Meta-transcriptomic analysis revealed that the nasal microbiota of multi-infected RSV patients had significantly lower alpha richness compared to RSV mono-infected and control group. Principal component analysis revealed the distinct clustering of the nasal microbiome based on the infectious category (P < 0.05). Following the control of confounders i.e. age, gender, comorbidities and antimicrobial intake, Pseudomonas were significantly increased in RSV patients compared to controls. Lactobacillus, Bacteroides, and Staphylococcus were significantly decreased in multi-infected compared to the control subjects. For the anal microbiota, multi-RSV-infected patients had significantly lower alpha richness according to the observed indices, when compared only to the control group. RSV patients had both significantly lower abundance of Spirochaetes and Actinobacteria compared to the control group (P < 0.05). However, following the control of confounders, no significant difference was observed (P > 0.05).

CONCLUSION: Our study revealed that multi-infected RSV subjects revealed the highest difference in microbial composition of the nasal microbiota compared to single infected and control subjects. Whether the observed microbiome difference is related to increased disease severity is yet to be explored in future studies. Moreover, the potential use of Lactobacillus and Bacteroides as probiotics for the treatment and prevention of RSV infection should be explored in future research.},
}

Humans
Male
Female
*Respiratory Syncytial Virus Infections/microbiology/virology
Infant
*Coinfection/microbiology/virology
Child, Preschool
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Nose/microbiology
Child
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Respiratory Syncytial Virus, Human

@article {pmid41272314,
year = {2025},
author = {Yang, X and Yang, T and Zhang, Z and Zhang, Y and Mei, X and Gao, Y and Wang, N and Jiang, G and Xu, Y and Shen, Q and Medema, MH and Jousset, A and Wei, Z},
title = {Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {41272314},
issn = {2397-334X},
abstract = {Understanding how plant-associated microbiomes resist phytopathogen invasion remains a key challenge in natural ecosystems. Here we combined genome-scale metabolic models with synthetic community experiments, both in vitro and in planta, to unravel the mechanisms driving pathogen suppression. We developed curated genome-scale models for each strain, incorporating 48 common resource utilization profiles to fully capture their metabolic capacities. Trophic interactions inferred from models effectively predicted pathogen invasion outcomes across diverse microbial communities and nutrient environments. Importantly, considering both substrate and metabolite features provided a more holistic understanding of pathogen suppression. In particular, cross-feeding metabolites within the native community emerged as crucial yet often overlooked predictors of community resistance, disproportionally favouring native species over invaders. This study lays the foundation for designing disease-resistant microbiomes, with broad implications for mitigating pathogen exposure in diverse environments.},
}

@article {pmid41272144,
year = {2025},
author = {Al-Rajhi, AMH and Alsalamah, SA and Alruhaili, MH and Gattan, HS and Alharbi, MT and Kafy, SM and Selim, S and Qanash, H and Bazaid, AS and Abdelghany, TM},
title = {Innovative vaginal wash formulation with Chitosan nanoparticles targets microbial pathogens, ovarian cancer and inflammation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41445},
pmid = {41272144},
issn = {2045-2322},
mesh = {*Chitosan/chemistry/pharmacology ; Female ; *Nanoparticles/chemistry ; Humans ; *Ovarian Neoplasms/drug therapy ; *Vagina/microbiology ; *Inflammation/drug therapy ; Microbial Sensitivity Tests ; Anti-Infective Agents/pharmacology/chemistry ; Cell Line, Tumor ; },
abstract = {Pathogenic microorganisms, ovarian cancer, and inflammation represent significant health challenges, as infections can disrupt the vaginal microbiome, chronic inflammation contributes to cancer progression. This study explored the enhancement of the therapeutic efficacy of vaginal wash (VW) incorporate chitosan nanoparticles (Chit) (VW + Chit) to create a multifunctional formulation targeting microbial infections, inflammation, and ovarian cancer. Gas Chromatography-Mass Spectrometry analysis identified 42 chemical constituents in the vaginal wash, including bioactive alcohols, esters, ethers, and fatty acids, with major components including 1,2-benzenedicarboxylic acid, diethyl ester (24.83%) and Diethylene glycol monododecyl ether (7.10%). Transmission electron microscopy imaging revealed that VW + Chit nanoparticles exhibited improved morphology, reduced agglomeration, and increased particle size (~ 41 nm), indicating successful interaction and encapsulation. Fourier transform infrared spectroscopy confirmed strong intermolecular bonding between chitosan and vaginal wash components, suggesting enhanced structural stability. Antimicrobial testing showed that VW + Chit achieved significantly greater inhibition zones and lower MIC/MBC/MFC values across multiple pathogens, particularly Staphylococcus aureus, Enterococcus faecalis, and Candida albicans, outperforming both its individual components and standard antibiotics. The formulation VW + Chit also demonstrated potent anti-inflammatory activity, with COX-1 and COX-2 inhibition reaching 92.9% and 94.3%, with lowest IC50 values 20.92 ± 0.1 and 9.23 ± 0.1 µg/mL, respectively compared to IC50 values of utilize VW (47.52 ± 0.4 and 43.73 ± 0.1 µg/mL) and Chit alone (27.39 ± 0.1 and 21.67 ± 0.1 µg/mL), respectively. Cytotoxicity assays on SKOV3 ovarian cancer cells revealed that VW + Chit exerted the strongest dose-dependent cytotoxic effect, with the lowest IC50 (147.3 µg/mL) and significant G1 phase cell cycle arrest, indicating antiproliferative potential. In conclusion, the VW + Chit composite shows enhanced antimicrobial, anti-inflammatory, and anticancer activities, highlighting its potential as a novel therapeutic formulation. These findings warrant further investigation through formulation refinement and in vivo studies to validate its clinical applicability for gynecological use.},
}

*Chitosan/chemistry/pharmacology
Female
*Nanoparticles/chemistry
Humans
*Ovarian Neoplasms/drug therapy
*Vagina/microbiology
*Inflammation/drug therapy
Microbial Sensitivity Tests
Anti-Infective Agents/pharmacology/chemistry
Cell Line, Tumor

@article {pmid41272004,
year = {2025},
author = {Komorniak, N and Cembrowska-Lech, D and Wiechowska-Kozłowska, A and Gaweł, K and Pawlus, J and Skonieczna-Żydecka, K and Sulikowski, T and van Kley, AM and Stachowska, E},
title = {Changes in microbiota associated with the use of intragastric balloons.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-27652-z},
pmid = {41272004},
issn = {2045-2322},
support = {WNoZ/330-01/2025//Pomeranian Medical University in Szczecin, Poland/ ; WNoZ/330-01/2025//Pomeranian Medical University in Szczecin, Poland/ ; },
abstract = {Obesity is a chronic disease characterized by excessive accumulation of adipose tissue. Intragastric balloon (IGB) implantation is one of the methods used to treat obesity. The aim of the study was to investigate whether the composition of the balloon-associated microbiota changes based on the duration of implantation and whether there is an association between changes in microbiota and weight loss results. In patients who lost weight, the microbial community was more diverse. The individuals who had an IGB for 12 months and lost weight exhibited a distinct microbiome shift, with increased levels of beneficial or metabolically flexible taxa. Bacteroides uniformis (11%) and Blautia massiliensis (9%) were abundant, while Anaerostipes hadrus was present at 6.2%. Ruminococcaceae species and Faecalibacterium prausnitzii were also detected at moderate levels. Over time, the intragastric balloon might influence the distribution and availability of nutrients, favoring the growth of specific bacteria like Oscillibacter, Eubacterium, and Blautia. Certain bacteria may become more competitive and increase in abundance after prolonged adaptation. These findings indicate that in this small cohort extended IGB therapy may shift the microbial community toward higher levels of certain Bacillota, while also reducing specific Eubacterium populations that may be more prevalent at earlier time points.},
}

@article {pmid41271838,
year = {2025},
author = {Zhou, Y and Gong, T and Yi, C and Yang, W and Ye, G and Xiao, D and Cao, Y and Xiong, Y and Ibáñez, E and Cifuentes, A and Ren, L and Lu, W},
title = {Gut microbiota-driven diseases and intervention strategies - lessons from China.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {249},
pmid = {41271838},
issn = {2396-8370},
support = {32402105//National Natural Science Foundation of China/ ; 62306083//National Natural Science Foundation of China/ ; 82104173//National Natural Science Foundation of China/ ; },
abstract = {Complicated relationships exist among lifestyles, gut microbiome (GM), and human health. Lifestyles can modulate the composition and function of GM, hence influencing the development of non-communicable diseases (NCDs). Recently, the socio-economic growth in China has led to the emergence of urbanized lifestyles, including unbalanced eating patterns and a sedentary lifestyle, causing an increased incidence of lifestyle-related NCDs among the Chinese population. In this review, we discussed the impact of lifestyle specific to the Chinese population on the GM and highlighted the mechanistic evidence that the commensals and their metabolites prevent or promote the pathogenesis of common lifestyle-related NCDs in China. Additionally, we described several microbiome-targeted therapies derived from traditional Chinese health practices, including traditional Chinese medicine treatments, the intake of fermented foods and tea, and Tai Chi intervention. In conclusion, we emphasized the significance of lifestyle-induced dysbiosis in the etiology of prevalent NCDs in China and provided relevant solutions, which should offer new insight into the treatment of these diseases to improve the overall health status of Chinese citizens.},
}

@article {pmid41271801,
year = {2025},
author = {Aminian-Dehkordi, J and Montazeri, F and Tamadon, A and Mofrad, MRK},
title = {Systems biology and microbiome innovations for personalized diabetic retinopathy management.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {133},
pmid = {41271801},
issn = {2056-7189},
mesh = {Humans ; *Diabetic Retinopathy/therapy/microbiology ; *Systems Biology/methods ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; *Microbiota ; Probiotics/therapeutic use ; },
abstract = {Diabetic retinopathy (DR), a complex condition driven by inflammation, oxidative stress, and metabolic imbalances, calls for innovative treatment strategies. Engineered probiotics delivering angiotensin-converting enzyme 2 (ACE2) offer a promising strategy by leveraging gut microbiome-retina association. Advances in synthetic biology and computational techniques enable personalized, data-driven therapies. This review discusses computational approaches at multiple scales and presents an integrated framework for promoting personalized, systems-level DR management.},
}

Humans
*Diabetic Retinopathy/therapy/microbiology
*Systems Biology/methods
*Precision Medicine/methods
*Gastrointestinal Microbiome
*Microbiota
Probiotics/therapeutic use

@article {pmid41271774,
year = {2025},
author = {Qin, W and Mei, Q and Wang, G and Wang, R and Huang, Z and Fu, Y and Xu, B and Huang, C and Ai, L and Zeng, Y},
title = {Faecalibacterium prausnitzii alleviates experimental recurrent acute pancreatitis by producing oleic acid to regulate MAPK/NF-κB signaling and Th17/Treg balance.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00845-0},
pmid = {41271774},
issn = {2055-5008},
support = {No.82200714//National Natural Science Foundation--Youth Foundation/ ; No. 82300731//National Natural Science Foundation--Youth Foundation/ ; No.10-21-308-420//USST Medical-engineering Cross-project/ ; No. 32025029//National Science Foundation for Distinguished Young Scholars of China/ ; No. 82270671//Natural Science Foundation of China/ ; CCTR-2022B02//Shanghai General Hospital Characteristic Research Program/ ; },
abstract = {Acute pancreatitis (AP) is a complex gastrointestinal disorder associated with disruptions in the gut microbiome. However, the gut microbial and metabolomic profiles in recurrent acute pancreatitis (RAP), which is a clinically distinct subtype of AP, remain unclear. This study integrated microbiome-metabolome analysis to identify the key gut microbial species and metabolic pathways associated with RAP. The findings reveal that the abundance of Faecalibacterium prausnitzii (Fp) is significantly diminished in RAP patients, exhibiting a strong negative correlation with disease severity. Consistent with this observation, fecal microbiota transplantation enriched with Fp significantly ameliorated pancreatic injury in RAP mice. We further isolated Fp Ai 3-16 strain from the stool of healthy volunteers. Functional validation using experimental AP models demonstrates that Fp Ai 3-16 and its metabolite oleic acid (OA) can effectively attenuate pancreatitis by modulating MAPK/NF-κB signaling pathways and restoring the intestinal Th17/Treg balance. Importantly, these results extend beyond the context of RAP, as they highlight the broader significance of the gut-pancreas axis in the pathogenesis of AP. Thus, the elucidation of the underlying molecular mechanisms offers novel therapeutic avenues for RAP management and provides a foundation for further investigations into the intricate interplay between the gut microbiome and the pancreas.},
}

@article {pmid41271607,
year = {2025},
author = {Nazari, M and Fathinejad, A and Mohammadi, MH and Bickel, S and Berg, G and Carminati, A},
title = {The origin and evolution of root mucilage.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70770},
pmid = {41271607},
issn = {1469-8137},
abstract = {Mucilage, a polysaccharide-rich substance secreted by root cap and border cells, is a key mediator of plant-soil interactions. This review traces the evolutionary origins of root mucilage from ancestral secretion mechanisms in streptophyte algae to its diverse roles in modern vascular plants. We highlight how mucilage biosynthesis relies on conserved gene families involved in polysaccharide assembly, whose phylogenomic distribution suggests that components of this machinery were already present in algal ancestors. Combining genetic, functional, and ecological evidence, we infer a stepwise evolutionary trajectory in which mucilage initially facilitated hydration and anchorage, later supporting soil structuring, plant-microbe interactions, nutrient availability, root water uptake, and drought tolerance. Fossil and comparative evidence indicates that both the secretion of mucilage and its regulatory mechanisms are deeply conserved traits. By connecting ancestral molecular and physiological functions to modern ecological roles, we demonstrate that mucilage has been a critical adaptation enabling plants to colonize and thrive in terrestrial environments over geological timescales.},
}

@article {pmid41271605,
year = {2025},
author = {},
title = {Jun Yuan ().},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70755},
pmid = {41271605},
issn = {1469-8137},
}

@article {pmid41271552,
year = {2025},
author = {Knapp, DG and Sunde, J and BakhshiGanje, M and Witzell, J},
title = {Bacterial Communities Associated With Acute Oak Decline of Sessile Oak (Quercus petraea) in Southern Sweden.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70244},
doi = {10.1111/1758-2229.70244},
pmid = {41271552},
issn = {1758-2229},
support = {20221014//Crafoordska Stiftelsen/ ; //The Bridge partnership between Södra, IKEA, and Linnaeus University/ ; },
mesh = {*Quercus/microbiology ; Sweden ; *Bacteria/classification/genetics/isolation & purification ; *Plant Diseases/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Plant Bark/microbiology ; Phylogeny ; },
abstract = {Acute oak decline (AOD) is a rapidly progressing disease affecting various oak species (Quercus spp.). Recent studies have shown that AOD is associated with a consortium of Gram-negative, facultatively anaerobic bacteria (e.g., in Enterobacterales) in the United Kingdom and continental Europe. However, there is limited information on the bacterial contributions and key genera associated with oak diseases and broadleaf forest ecosystems in Nordic countries. The primary objective of this brief study was to collect the first data on the bark microbiomes of symptomatic, declining sessile oaks (Q. petraea) in Sweden. Pairs of healthy and diseased bark samples were collected from symptomatic trees near Ankarsrum (Kalmar County), Sweden. After total DNA extraction, the bacterial 16S rDNA region was amplified, and Oxford Nanopore Technologies was used for long-read high-throughput DNA metabarcoding of the bacterial microbiome. We found a dominance of enterobacterial phytopathogens, including two of the typical genera associated with AOD, Brenneria and Rahnella, exclusively in the diseased bark samples. Our findings extend the known distribution of AOD-associated bacteria to Sweden and Scandinavia and show that diseased oaks in this region host a microbiome similar to those found in other parts of Europe.},
}

*Quercus/microbiology
Sweden
*Bacteria/classification/genetics/isolation & purification
*Plant Diseases/microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
Plant Bark/microbiology
Phylogeny

@article {pmid41271235,
year = {2025},
author = {Barry, D and Thachuk, C and Trink, J},
title = {Integrating gut microbiome and host transcriptomics for the personalized management of IBD.},
journal = {Epigenomics},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/17501911.2025.2591594},
pmid = {41271235},
issn = {1750-192X},
abstract = {Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affects an estimated 6.8 million individuals worldwide. Although biological or small molecule drug therapies can improve patient outcomes, loss of response to treatment over time remains high, highlighting the need for new precision medicine strategies. Dysbiosis of the gut microbiome is characterized by the loss of beneficial microbes and an overgrowth of pro-inflammatory pathobionts. In IBD, gut dysbiosis contributes to chronic intestinal inflammation via altered metabolite profiles and epithelial barrier disruption. Recent advancements in multi-omics integration offer approaches to better understand the pathogenesis of IBD. Epigenomic studies have revealed disease-specific DNA methylation and enhancer activation patterns that reshape immune pathways and compromise epithelial barrier integrity, key mechanisms in IBD pathophysiology. These molecular signatures allow for the stratification of IBD patients into distinct subgroups, allowing for more targeted therapeutic strategies. Here we explore the potential benefits of integrating gut microbiome and both host transcriptomics and epigenomics to improve disease management in IBD patients. While challenges remain - such as data standardization, computational complexity, and cost - the progression of multi-omics methodologies is expected to improve patient outcomes by reducing high treatment failure rates in IBD patients.},
}

@article {pmid41271113,
year = {2025},
author = {Ferrando, ML and Busonero, F and Crobu, F and Sanna, S},
title = {Aging in Women - the Microbiome Perspective.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102950},
doi = {10.1016/j.arr.2025.102950},
pmid = {41271113},
issn = {1872-9649},
abstract = {Menopause is a hallmark of women's aging and is frequently portrayed as a medical issue. It also encompasses social and biological aspects often neglected and not well-understood, leaving women with insufficient support and attention. With the decline in estrogen levels, starting years before menopause is fully established, women experience various physical symptoms, and the risk of many age-related diseases increases sharply soon after these hormonal changes occur. Notably, these hormonal shifts also significantly impact the vaginal and gut microbiomes, contributing to dysbiosis and influencing the onset and progression of several diseases. Here, we examined the complex and dynamic relationship among aging, menopause, and microbiome changes with a particular focus on the vaginal and gut ecosystems. Emerging research highlights diet as a potential modulator for maintaining microbiome health during menopause. A deeper understanding of microbiome changes across life stages suggests the potential for microbiome-targeted strategies to support well-aging in women.},
}

@article {pmid41270950,
year = {2025},
author = {Yuan, S and Bremmer, A and Yang, X and Hu, Q},
title = {Microbiota metabolism and immune regulation: From mechanisms to immunotherapeutic applications in cancer.},
journal = {Seminars in cancer biology},
volume = {117},
number = {},
pages = {168-183},
doi = {10.1016/j.semcancer.2025.11.023},
pmid = {41270950},
issn = {1096-3650},
abstract = {The human microbiome plays a pivotal role in shaping immune responses by producing bioactive metabolites such as bile acids (BAs) and short-chain fatty acids (SCFAs). These microbial metabolites influence a broad range of cell types, including innate and adaptive immune cells and non-immune cells. Emerging evidence suggests that microbiome metabolism is a crucial factor affecting the success of cancer immunotherapy. Promising therapeutic approaches, such as the use of probiotics, engineered bacteria, metabolite supplementation, and bile acid sequestrants, are being explored to enhance immunotherapeutic outcomes. This review critically evaluates current insights into how microbiome-derived metabolites modulate cellular functions, with a particular focus on immune cells within the tumor microenvironment, and highlights their potential to improve the efficacy of cancer immunotherapy.},
}

@article {pmid41267089,
year = {2025},
author = {Somphot, T and Sirithaweesuk, T and Dubas, L and Tungkijanansin, N and Tunvirachaisakul, C and Maes, M and Sirinara, P and Kulsing, C},
title = {Metabolomic profiling of sweat VOCs for occupational stress surveillance in firefighters: a GC-MS pilot study.},
journal = {Journal of occupational medicine and toxicology (London, England)},
volume = {20},
number = {1},
pages = {42},
pmid = {41267089},
issn = {1745-6673},
support = {012/1621//The Medical Council of Thailand/ ; },
abstract = {BACKGROUND: With limited access to mental health specialists for diagnosis, current stress tracking methods rely on questionnaire results. These self-report questionnaires often obtain untruthful answers, especially in beneficial situations such as career hiring or promotion. This study aimed to evaluate an alternative method for stress screening based on analysis of sweat volatile organic compounds.

METHODS: Sweat samples of 44 firefighters were collected using headspace-solid phase microextraction (HS-SPME). Sweat VOCs were analyzed using gas chromatography-mass spectrometry (GC-MS). The compounds were identified by comparing the experimental retention indices (I) and MS spectra with the database from the National Institute of Standards and Technology (NIST) library.

RESULTS: The obtained data were correlated with the standardized questionnaire-based Thai version of the perceived stress scores (T-PSS-10) of the volunteers. The significant peaks were then selected based on the individual accuracy and t-test. Six possible volatile features for high stress (PSS score ≥ 32) samples were revealed. Their potential sources could involve human and microbiome metabolism/catabolism. By using partial least square discriminant analysis (PLS-DA), these markers could be combined into a single feature. The feature value thresholds were then varied for construction of receiver operating characteristic (ROC) curves. With the optimum threshold, the combined marker offered the accuracy, sensitivity, selectivity and area under curve (AUC) of 84%, 87%, 81% and 91%, respectively.

CONCLUSIONS: This pilot study demonstrates the feasibility of using sweat VOC profiling via HS-SPME GC-MS as a rapid and non-invasive method for occupational stress screening. The technique provides objective biochemical markers that could enhance the reliability of conventional questionnaire-based assessments in high-risk occupational groups.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12995-025-00486-1.},
}

@article {pmid41267045,
year = {2025},
author = {Deng, G and Wu, L and Xiong, S and Zhou, J and Li, Z},
title = {Host stress proteins shape hemorrhagic shock via gut microbiota: evidence from Mendelian randomization and animal models.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1324},
pmid = {41267045},
issn = {1479-5876},
support = {NO.YC2024-S175//Graduate Innovative Special Fund Projects of Jiangxi Province/ ; },
abstract = {BACKGROUND: Hemorrhagic shock (HS) is a severe condition involving stress proteins, inflammation, and gut microbiota dysbiosis. Understanding whether regulatory proteins influence HS through microbial pathways is crucial for improving therapeutic strategies.

METHODS: We used Mendelian randomization (MR) combined with animal experiments to investigate the role of regulatory proteins in HS. Two-sample MR was performed to assess the impact of various stress-related proteins. Additionally, 16 S rRNA sequencing was conducted in a rat HS model to analyze gut microbiota diversity and composition at baseline, 24 h, and 72 h after hemorrhage.

RESULTS: Two-sample MR identified HSPB1 and HIF1A as protective proteins, while APAF1, F7, and F10 increased susceptibility to HS. In the rat model, microbiota alpha diversity decreased at 24 h but partially recovered by 72 h, with significant shifts in beta diversity. Genus-level analysis revealed transient expansion of Lactobacillus, followed by dominance of Blautia and Romboutsia. Stage-specific predictions from PICRUSt2 suggested enrichment of amino acid metabolism and protein synthesis, particularly at 72 h, implicating microbial regulation in cellular recovery and stress adaptation.

CONCLUSIONS: Our findings support a “protein-microbiota-HS” regulatory framework, highlighting the gut microbiota as key mediators of host stress responses. This integrative approach provides mechanistic insights into HS pathogenesis and suggests potential microbiome-targeted therapeutic strategies. We propose that targeting specific microbial communities, such as Blautia and Lactobacillus, could enhance recovery from HS.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07364-8.},
}

@article {pmid41270896,
year = {2025},
author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M},
title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.},
journal = {Gene},
volume = {},
number = {},
pages = {149913},
doi = {10.1016/j.gene.2025.149913},
pmid = {41270896},
issn = {1879-0038},
abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.

METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) to elucidate their microbial diversity and relative abundance.

RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2] = 0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY:aerobactin biosynthesis.

CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.},
}

@article {pmid41270740,
year = {2025},
author = {Yi, X and Cai, H and Liu, H and Xu, S and Meng, R and Rao, J and Wu, M and Yang, L and Shi, Y and Zhang, J and Zhu, T and Yang, Y and Wen, P and Qin, Y and Song, W and Li, JT and Shu, W and Dai, J and Sun, J and Lin, L and Guan, WJ and Brightling, CE and Zheng, XY and Wang, Z},
title = {Environmental exposure augments the abundance and transferability of antibiotic resistance genes in the respiratory tract.},
journal = {Cell reports},
volume = {},
number = {},
pages = {116517},
doi = {10.1016/j.celrep.2025.116517},
pmid = {41270740},
issn = {2211-1247},
abstract = {Exposure to environmental pollutants has been linked to increased antibiotic resistance, a critical global health challenge. The respiratory microbiome constitutes a key reservoir of antibiotic resistance genes (ARGs). Here, we constructed a respiratory ARG catalog from sputum metagenomes of 1,128 individuals. We demonstrate that exposures, particularly to cigarette smoke and biofuels, are associated with increased abundance and enhanced mobility of respiratory ARGs. These resistome alterations correlate inversely with lung function, with elevated mobile ARG abundance detectable even in individuals with mild airflow limitation within normal spirometry. Specific ARGs, including opmD and tet(K), interact with smoking in relation to lung function impairment. Murine experiments recapitulate these findings, showing exposure-induced increases in homologous ARGs that confer heightened phenotypic resistance in cultured respiratory bacteria. Our results elucidate a pathway through which environmental pollutants augment the respiratory resistome, suggesting the need for actions to mitigate the antimicrobial resistance burden by addressing environmental pollution.},
}

@article {pmid41270737,
year = {2025},
author = {Long, X and Wang, H and Lu, Y and Gao, X and Xiao, Y and Zhang, M and Guo, J and Yang, J and Zhang, R and Li, Q and Zhou, G and Yang, R and Chen, F and Wu, Q and Sun, L and Chu, C and Zhu, X and Wu, Z and Ren, Q and You, C and Liu, Z and Li, Q and Liu, D and Cheng, D and Kang, P and Chen, A and Wu, Q and Fang, Q and Wei, L and Zhang, L and Li, J and Panagiotou, G and Jia, W and Zeng, R and Ni, Y and Chen, L and Li, H},
title = {Interindividual variability in gut microbiome mediates the efficacy of resistant starch on MASLD.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.10.017},
pmid = {41270737},
issn = {1932-7420},
abstract = {Our randomized, placebo-controlled trial showed resistant starch (RS), a type of prebiotic, has therapeutic effects in metabolic dysfunction-associated steatotic liver disease (MASLD). Here, we observed its heterogeneous efficacy, where 30% of participants exhibited limited benefits, which was replicated in a multi-center trial (ChiCTR2300074588). Multi-omics analysis and fecal microbiota transplantation identified baseline microbiota as a dominant contributor of response. Further population stratification and network analysis combined with in vitro and in vivo experiments revealed Prevotella as the key cause of low response by inhibiting RS-degrading bacteria, thereby impairing RS utilization. Conversely, Bifidobacterium pseudocatenulatum RRP01, a strain isolated from our cohort, restored RS degradation and improved Prevotella-attenuated RS response. Furthermore, we developed a predictive model integrating baseline microbial and clinical features (area under the curve [AUC] = 0.74-0.87), enabling stratification for personalized interventions. Our study indicates that gut microbiota determines the heterogeneity in RS efficacy and offers possibilities for novel microbiota-oriented precision therapeutics for MASLD.},
}

@article {pmid41270734,
year = {2025},
author = {Tibocha-Bonilla, JD and Santibáñez-Palominos, R and Weng, Y and Kumar, M and Zengler, K},
title = {Metabolism and gene expression models for the microbiome reveal how diet and metabolic dysbiosis impact disease.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101451},
doi = {10.1016/j.cels.2025.101451},
pmid = {41270734},
issn = {2405-4720},
abstract = {The gut microbiome plays a critical role in human health, spurring extensive research using multi-omic technologies. Although these tools offer valuable insights, they often fall short in capturing the complexity of microbial interactions that associate with disease onset, progression, and treatment. Thus, integration of multi-omics datasets with metabolic models is needed to predict associations between microbial activity and disease. Here, we automated the reconstruction of 495 metabolic and gene expression models (ME-models), overcoming the main limitation preventing the wide use of this approach. We integrated them with multi-omics data from patients with inflammatory bowel disease (IBD), identifying taxa associated with variations in amino acids, short-chain fatty acids, and pH in the gut of IBD patients. In general, this approach provides testable hypotheses of the metabolic activity of the gut microbiota, and the automated pipeline opens the opportunity to study microbial interactions in other biologically relevant settings using ME-models.},
}

@article {pmid41270627,
year = {2025},
author = {Li, L and Huang, S and Bai, Z and Xu, H and Ji, Q and Song, W},
title = {Combined transcriptome and microbiome characterization highlights digestive system development involved in the metabolism and immunity of the large yellow croaker (Larimichthys crocea).},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128394},
doi = {10.1016/j.micres.2025.128394},
pmid = {41270627},
issn = {1618-0623},
abstract = {The development of the digestive system and its interaction with microbiota are critical for fish growth and health. Transcriptomic and 16S rRNA sequencing analyses were conducted to investigate the gene expression profiles of the digestive system and microbial community dynamics in Larimichthys crocea from the embryonic stage to day 28 to elucidate their potential roles in larval and juvenile development and their associations with immune and metabolic functions. The results revealed stage-specific changes in gene expression and microbial composition during development, and two critical transitional phases were identified: day 1 vs embryonic stage (C1 vs CE) and day 15 vs day 9 (C15 vs C9). Microbial succession demonstrated clear temporal characteristics: Pseudoalteromonas were dominant during the embryonic stage (CE), which was succeeded by Stenotrophomonas after hatching (C1, C3, C4, and C9), by Cohaesibacter on day 15 (C15), and by Psychrobacter as the core genus after formulated feed introduction on day 19. Functional enrichment analyses revealed predominant enrichment of differentially expressed genes in immune- and metabolic-related pathways, such as calcium signaling, steroid biosynthesis, and amino acid metabolism. Weighted gene co-expression network and correlation analyses revealed significant associations between specific genera (e.g., Rhodococcus and Psychrobacter) and immune- and metabolism-related genes. This study analyzed the developmental patterns of the digestive system of L. crocea and revealed significant correlations between shifts in the microbiota and host metabolism and immunity, highlighting the close association between the microbiota and metabolic and immune responses.},
}

@article {pmid41270591,
year = {2025},
author = {Zahn, G and Hjelmen, CE and Wainwright, BJ},
title = {Distinct temporal trajectories of bacterial and fungal networks during agricultural rewilding.},
journal = {The Science of the total environment},
volume = {1008},
number = {},
pages = {180999},
doi = {10.1016/j.scitotenv.2025.180999},
pmid = {41270591},
issn = {1879-1026},
abstract = {Tropical land-use change from native forests to oil palm plantations has created widespread biodiversity loss, soil degradation, and disruption of microbial communities. As rewilding initiatives emerge to restore ecosystem function in post-agricultural landscapes, understanding microbial community assembly, diversity dynamics, and interaction networks is essential for informing effective restoration strategies. However, the pace and predictability of microbial reorganization following intensive monoculture remain poorly understood, particularly in tropical systems. We examined microbial reassembly across a five-year tropical rewilding chronosequence in a former oil palm plantation, using full-length 16S and ITS amplicon sequencing, ecological network modeling, and soil chemistry analyses. Bacterial and fungal alpha diversity increased over time, though with domain-specific trajectories. Generalized dissimilarity models revealed that soil phosphorus and carbon were dominant environmental filters shaping community turnover. Co-occurrence networks showed increasing complexity over time, with bacterial networks becoming progressively more interconnected, while fungal networks exhibited earlier but less sustained restructuring. These patterns suggest that microbial community coalescence during rewilding is asynchronous, structured, and shaped by deterministic environmental filtering and legacy effects of past land use. Our results provide evidence that tropical rewilding can rapidly reorganize soil microbial communities, enhancing diversity, connectivity, and compositional structure within just a few years. Full recovery is likely to require longer time frames, these early trajectories highlight the potential for rewilding to promote functional microbial reassembly in degraded tropical systems. By identifying taxonomic and network-based indicators of microbial reorganization, this study advances our understanding of community assembly theory and offers guidance for restoration practices in post-agricultural landscapes.},
}

@article {pmid41270390,
year = {2025},
author = {Chen, L and He, W and Gao, L and Lu, Y and Zhu, L},
title = {Shouhui Tongbian Capsules ameliorate heart failure and atrial fibrillation via gut microbiota regulation.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {149},
number = {},
pages = {157549},
doi = {10.1016/j.phymed.2025.157549},
pmid = {41270390},
issn = {1618-095X},
abstract = {BACKGROUND: Heart failure (HF) with atrial fibrillation (AF) poses a significant therapeutic challenge due to its complex pathophysiology. Shouhui Tongbian Capsules (SHTB) contain multiple active components that have been proven to affect HF or AF through the intestinal flora. However, the specific therapeutic effects of this drug on HF combined with AF, as well as whether these effects are achieved by regulating the intestinal flora, still require systematic research.

PURPOSE: This study aimed to elucidate the cardioprotective effects of SHTB in a doxorubicin (DOX)-induced HF/AF rat model, focusing on gut microbiota modulation and myocardial transcriptome regulation.

METHODS: Rats were randomized into control, model (DOX-induced HF/AF), SHTB treatment (low/medium/high doses), and metoprolol groups. Pharmacodynamically, cardiac function was assessed via echocardiography and electrocardiography. And myocardial fibrosis was quantitatively evaluated using pathomorphology analysis. Mechanistically, microvascular integrity was examined via immunofluorescence, while the neural activity ligand-receptor interaction pathway-related protein expression was analyzed by immunohistochemistry. Additionally, gut microbiota composition was determined via 16S rRNA sequencing, and myocardial transcriptome profiling was performed using RNA sequencing. Furthermore, fecal microbiota transplantation (FMT) experiments were performed to validate the role of gut microbiota in the observed effects.

RESULTS: The SHTB intervention significantly improved the cardiac function and electrophysiological stability of HF/AF rats, along with enhancing microvascular maturation and reducing myocardial fibrosis. The analysis of the intestinal microbiota showed that SHTB effectively restored the microbial ecological balance, especially regulating the abundance of key genera (such as Turicibacter) closely related to disease progression and treatment efficacy. Transcriptional analysis identified the neural activity ligand-receptor pathway as the key mechanism, and FMT experiments demonstrated that SHTB modulates the Edn1-Agtr1a-Bdkrb2 axis through gut microbiota, ultimately leading to improved cardiac function. The synergistic effect of the composition of the intestinal microbiota and myocardial molecular targets jointly contributed to the improvement of cardiac remodeling in HF/AF.

CONCLUSION: SHTB ameliorates HF with AF by synergistically modulating the gut-heart axis, involving gut microbiota restoration, myocardial fibrosis suppression, and vascular tension regulation via the Edn1-Agtr1a-Bdkrb2 axis. This multi-target mechanism substantiates SHTB's potential as a promising adjunct therapy for HF/AF.},
}

@article {pmid41270103,
year = {2025},
author = {Shannon, KC and Colwell, FS and Crump, BC and Brennan, E and St John, G and Gould, R and Hartzell, C and Wasley, M and Nichols, C and Kraft, CE and Suffridge, CP},
title = {Bacimethrin, an allelopathic vitamin B1 antagonist, is linked with microbial gene expression patterns in a hypereutrophic watershed.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335861},
doi = {10.1371/journal.pone.0335861},
pmid = {41270103},
issn = {1932-6203},
mesh = {*Thiamine/antagonists & inhibitors/metabolism ; *Cyanobacteria/genetics/drug effects/metabolism ; Harmful Algal Bloom/drug effects ; *Gene Expression Regulation, Bacterial/drug effects ; Microbiota/drug effects/genetics ; },
abstract = {Freshwater cyanobacterial harmful algal blooms (cyanoHABs), often dominated by Aphanizomenon, Dolichospermum, and Microcystis, are intensifying in eutrophic watersheds globally. A potential control on bacterioplankton dynamics in these systems is the availability of the essential metabolic cofactor thiamin (vitamin B1) and presence of the allelopathic thiamin antagonist bacimethrin, which causes competitive inhibition of thiamin-requiring enzymes. We examined dissolved concentrations of thiamin chemical congeners and bacimethrin, 16S amplicon-based microbiome compositions, prokaryotic mRNA-based metatranscriptomes, and reference genomes in hypereutrophic Upper Klamath Basin before and during seasonal cyanoHABs. Our objective was to connect bacterioplankton community compositions and gene expression patterns with thiamin congener and bacimethrin availability under different cyanoHAB conditions. Bacimethrin was present in all samples at similar concentrations to the thiamin precursor, HMP, suggesting that similar mechanisms influence the availability of both compounds. Additionally, bacimethrin concentrations were positively correlated with cyanoHAB species abundance (cells mL-1) and the expression of microbial thiamin biosynthesis genes. Samples with high cyanoHAB abundance also displayed elevated transcription of genes in key biochemical pathways such as the pentose phosphate pathway, photosynthesis, and glycogen biosynthesis. Bacterioplankton such as Limnohabitans spp. that are unable to synthesize thiamin, and are thus vulnerable to bacimethrin allelopathy, showed reduced gene expression when cyanoHAB abundance was high. Reference genomes of cyanoHAB and many picocyanobacteria strains contained complete thiamin biosynthesis gene pathways, implicating these taxa as major thiamin sources. These results suggest that bacimethrin provides a competitive advantage to bacterioplankton that do not require exogenous thiamin by eliminating the risk of bacimethrin uptake with thiamin transporters, potentially facilitating cyanoHAB dominance in Upper Klamath Basin and broader eutrophic watersheds.},
}

*Thiamine/antagonists & inhibitors/metabolism
*Cyanobacteria/genetics/drug effects/metabolism
Harmful Algal Bloom/drug effects
*Gene Expression Regulation, Bacterial/drug effects
Microbiota/drug effects/genetics

@article {pmid41269658,
year = {2025},
author = {Daniel, RC and Okeugo, B and Armbrister, SA and Saleh, ZM and Wang, J and Luo, M and Taylor, CM and Lundberg, LE and Giorgberidze, S and Yin, Z and Roos, S and Rhoads, JM and Liu, Y},
title = {Limosilactobacillus reuteri Strains Differentially Stimulate Immunity in Response to Human Milk Oligosaccharides in Newborn Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41269658},
issn = {1867-1314},
abstract = {Probiotic Limosilactobacillus reuteri DSM 17938 reduces autoimmunity in mouse models. Recently, a novel strain, L. reuteri DSM 32846 (BG-R46®), derived from DSM 17938 was found to have unique properties including bile acid tolerance and enhanced adenosine production. Human milk oligosaccharides (HMOs) help establish the intestinal microbiome and assist immune and neurodevelopment. The objective of the study was to explore the differential effects of each strain (with or without HMOs) with respect to innate and adaptive immunity in the intestine of mice during early development at postnatal d8 (early stage), d14 (rapid growth stage), and d21 (at weaning). C57BL/6J mice received intragastric DSM 17938 or DSM 32846 individually or in combination with HMOs, a mixture of 2`-FL and 6`-SL, daily from d7 to d20. We subsequently assessed circulating and intestinal immune cell markers at d8, d14 and d21. Both strains promoted development of intestinal macrophages, natural killer cells, and activated T and B cells. The cellular responses in the intestine of d8 mice were boosted within one day of treatment with DSM 17938, as opposed to 1-2 weeks after treatment with DSM 32846. This delay could be reversed by supplementing HMOs along with DSM 32846. Both DSM 32846 and DSM 17938 facilitated dendritic cell maturation and enhanced regulatory T cell numbers in the intestines of these newborns. However, HMOs enhanced the effects of DSM 32846, but not DSM 17938. Therefore, an early-life boost of intestinal immune cells by probiotics was observed which could be essential to protection against neonatal inflammatory conditions. This novel difference between two strains of the same species in immune modulation could provide a rationale for co-administration in an HMO-rich environment.},
}

@article {pmid41269457,
year = {2025},
author = {Younis, NK and Alfarttoosi, KH and Sanghvi, G and Roopashree, R and Kashyap, A and Krithiga, T and Taher, WM and Alwan, M and Jawad, MJ and Ali Al-Nuaimi, AM},
title = {Attenuating Neurotoxicity Through Fecal Microbiota Transplant: Mechanisms and Therapeutic Potential.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {128},
pmid = {41269457},
issn = {1559-1182},
mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; Animals ; *Gastrointestinal Microbiome/physiology ; *Neurotoxicity Syndromes/therapy/microbiology ; },
abstract = {Neurotoxicity, triggered by drugs, environmental pollutants, metabolic disorders, or infections, can cause lasting neurological dysfunction and cognitive impairment. Recent research highlights the gut microbiota's crucial role in regulating brain health and vulnerability to neurotoxic damage, sparking interest in fecal microbiota transplantation (FMT) as a potential treatment. This review examines how FMT may counteract neurotoxicity and assesses its therapeutic potential for neurodegenerative diseases, neuroinflammation, and cognitive decline. The gut-brain axis-a bidirectional communication system between the gut and the central nervous system (CNS)-acts as the primary route through which gut microbes influence brain function. Growing evidence suggests that microbiota imbalances can exacerbate neuroinflammation, oxidative stress, blood-brain barrier disruption, and altered neurotransmitter production, all of which contribute to neurotoxicity. FMT, the transfer of donor fecal microbes to a recipient's gut, has demonstrated promise in restoring microbial equilibrium and reducing neurotoxic effects in both animal studies and human trials. The review also explores microbial profiles tied to neuroprotection versus those linked to neurotoxic conditions, along with the prospects of tailored microbiome therapies. Despite its potential, FMT faces challenges, including protocol standardization, donor selection criteria, and long-term efficacy. More research is needed to unravel the intricacies of gut-brain interactions and optimize FMT for clinical use. If these hurdles are addressed, FMT could become a transformative therapy for neurotoxicity-related disorders.},
}

*Fecal Microbiota Transplantation/methods
Humans
Animals
*Gastrointestinal Microbiome/physiology
*Neurotoxicity Syndromes/therapy/microbiology

@article {pmid41269281,
year = {2025},
author = {Yazhini, A and Morice, É and Jochheim, A and Lieser, B and Söding, J},
title = {Evaluation of metagenome binning: advances and challenges.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf617},
pmid = {41269281},
issn = {1477-4054},
support = {101111457//Marie Skłodowska-Curie Actions/ ; //Horizon Europe programme of the European Union and from the Max Planck Society/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Deep Learning ; Computational Biology/methods ; Humans ; Algorithms ; },
abstract = {Several recent deep learning methods for metagenome binning claim improvements in the recovery of high-quality metagenome-assembled genomes. These methods differ in their approaches to learn the contig embeddings and to cluster them. Rapid advances in binning require rigorous benchmarking to evaluate the effectiveness of new methods. We have benchmarked newly developed state-of-the-art deep learning binners on CAMI2 and real metagenomic datasets. The results show that SemiBin2 and COMEBin give the best binning performance, although not always the best embedding accuracy. Interestingly, post-binning reassembly consistently improves the quality of low-coverage bins. We find that binning coassembled contigs with multi-sample coverage is effective for low-coverage dataset, while binning sample-wise assembled contigs with multi-sample coverage (multi-sample) is effective for high-coverage samples. In multi-sample binning, splitting the embedding space by sample before clustering showed enhanced performance compared with the standard approach of splitting final clusters by sample. Deep-learning binners using contrastive models emerged as the top-performing tools overall, with MetaBAT2 and GenomeFace demonstrating superior speed. To facilitate future development, we provide workflows for standardized benchmarking of metagenome binners.},
}

*Metagenome
*Metagenomics/methods
*Deep Learning
Computational Biology/methods
Humans
Algorithms

@article {pmid41268538,
year = {2025},
author = {Jiao, JM and Liu, CG and Zang, D and Chen, J},
title = {Gut microbiota and metabolites: emerging prospects in the treatment of non-small cell lung cancer.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1638942},
pmid = {41268538},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Carcinoma, Non-Small-Cell Lung/therapy/metabolism/microbiology ; *Lung Neoplasms/therapy/metabolism/microbiology ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Animals ; },
abstract = {Non-small cell lung cancer (NSCLC) is the most prevalent form of lung cancer, accounting for approximately 85% of all cases, and is associated with a poor prognosis. Despite significant advancements in treatment modalities, therapeutic efficacy remains suboptimal, underscoring the urgent need for novel strategies. In recent years, increasing attention has been directed toward the pivotal role of gut microbiota-host interactions in the treatment of NSCLC. This review systematically examines the influence of current NSCLC therapies on gut microbiota and metabolism, explores the relationship between the microbiome and therapeutic response, and highlights the critical functions of probiotics, microbial metabolites, fecal microbiota transplantation (FMT), and dietary interventions in NSCLC management. By elucidating the mechanisms through which gut microbiota and their metabolites modulate treatment efficacy, we investigate the potential of exogenous interventions targeting the gut ecosystem to enhance therapeutic outcomes and mitigate adverse effects. Modulating the intestinal microbiota represents a promising clinical avenue and offers a new frontier for the development of future NSCLC treatment strategies.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Carcinoma, Non-Small-Cell Lung/therapy/metabolism/microbiology
*Lung Neoplasms/therapy/metabolism/microbiology
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Animals

@article {pmid41268503,
year = {2025},
author = {Wang, L and Garland, GM and Ge, T and Guo, S and Kebede, EA and He, C and Hijri, M and Plaza-Bonilla, D and Stringer, LC and Davis, KF and Lee, SJ and Feng, S and Wang, L and Wei, Z and Cao, H and Wang, Z and Xu, J and Siddique, KHM and Gan, GY and Zhao, M},
title = {Integrated strategies for enhancing agrifood productivity, lowering greenhouse gas emissions, and improving soil health.},
journal = {Innovation (Cambridge (Mass.))},
volume = {6},
number = {11},
pages = {101006},
pmid = {41268503},
issn = {2666-6758},
abstract = {Global agrifood systems face three interconnected challenges: ensuring food security, promoting environmental sustainability, and restoring soil health in the face of climate change. Conventional practices have prioritized productivity over ecological resilience, leading to soil degradation, increased greenhouse gas (GHG) emissions, and inefficient resource utilization. Here, we introduce a "triple-goal" agrifood framework that enhances food production, soil health, and GHG mitigation simultaneously through integrated innovations. Using a second-order meta-analysis of 104 meta-analyses that cover 39,162 studies and 300,139 global field comparisons, we identified key interventions, including optimized fertigation, diversified cropping systems, organic amendments, and precision N management, that increased productivity by 14%-28% while reducing environmental impacts. Diversified systems boosted yields by 19.6% and reduced land use by 19%. Integrating legumes and cover crops lowered N2O emissions by 18%-65%, while organic amendments increased soil organic carbon stocks by 7%-13%. Structural equation modeling identified nitrogen use efficiency and microbial activity as central to the food-soil-emissions nexus. However, tradeoffs remain; yield-focused strategies can elevate emissions if not tailored to local conditions. By integrating agronomic, biological, and technological interventions such as conservation tillage, biofertilization, and digital agriculture, this triple-goal framework supports a 15%-30% reduction in anthropogenic CO2-equivalent emissions. These findings underscore the need for policy reform and multi-stakeholder collaboration to scale up the adaptation of integrated strategies in alignment with the UN's Sustainable Development Goals and the "One Health" initiative. The triple-goal framework provides a transformative pathway to climate-smart, equitable, and resilient agrifood systems that strike a balance between productivity and planetary health.},
}

@article {pmid41268305,
year = {2025},
author = {Choi, S and Pham, TTD and Jeong, TK and Kang, JG and Lee, SW and Heo, BY and Park, JH and Koh, JS and Lee, MW and Lim, DS and Song, IC and Kwon, J},
title = {Korean red ginseng extract suppresses food allergy by remodeling the gut microbiota and restoring immune homeostasis in IL4ra[F709] mice.},
journal = {Journal of ginseng research},
volume = {49},
number = {6},
pages = {746-757},
pmid = {41268305},
issn = {1226-8453},
abstract = {BACKGROUND: Food allergy (FA) is a growing health concern with limited therapeutic options. While Korean Red Ginseng Extract (KRGE) exhibits immunomodulatory and microbiota-modulating properties, its specific effects and mechanisms in FA are not fully understood.

METHODS: We evaluated the anti-allergic efficacy of KRGE in IL4ra[F709] mice, a model genetically predisposed to IgE-mediated anaphylaxis. Mice were sensitized with ovalbumin(OVA) and staphylococcal enterotoxin B (SEB) and challenged with OVA. KRGE was administered orally prior to and during sensitization. Clinical symptoms, serum IgE levels, IL-33 levels, and intestinal histology were assessed. Mesenteric lymph nodes and Peyer's patches immune cell populations were analyzed by flow cytometry. Fecal microbiota composition was profiled using 16S rRNA sequencing and quantitative PCR; correlations between phenotype and microbiota were investigated.

RESULTS: Results showed KRGE significantly suppressed anaphylactic symptoms, including hypothermia and mortality, and reduced OVA-specific IgE and IL-33 levels. KRGE restored intestinal epithelial integrity and normalized Peyer's patch hypertrophy. Immunologically, it decreased IL-13-producing T follicular helper cells and rebalanced dendritic cell subsets, increasing tolerogenic CD103[+] cDC1 and reducing pro-allergic CD11b[+] cDC2. Microbiome analysis revealed that OVA/SEB increased pro-inflammatory Lachnospiraceae and Ruminococcaceae while depleting beneficial Lactobacillaceae and Bifidobacteriaceae. KRGE reversed these changes, notably enriching Akkermansia muciniphila and Lactobacillus gasseri. Correlation analysis revealed that Akkermansia, Lactobacillus, and Christensenellaceae were negatively correlated with allergic markers and positively correlated with epithelial integrity. In contrast, Oscillospiraceae (Eubacterium_g8, Acetobacter, and Pseudoflavonifractor) was associated with allergy exacerbation.

CONCLUSION: KRGE mitigates FA in IL4ra[F709] mice by restoring gut microbiota balance and immune homeostasis, suggesting its potential as a microbiota-targeted intervention for FA.},
}

@article {pmid41268133,
year = {2025},
author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C},
title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.},
journal = {Topics in spinal cord injury rehabilitation},
volume = {31},
number = {4},
pages = {111-129},
pmid = {41268133},
issn = {1945-5763},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; },
abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.

OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).

METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).

RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.

CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism
Male
Female
*Metabolome
Adult
Middle Aged
*Diet, High-Protein Low-Carbohydrate
*Diet, High-Protein

@article {pmid41268108,
year = {2025},
author = {Peregrina, S and Aubalat, AP and Manohar, A and Benavente, A and Torres-Carvajal, M and Gabaldón, T},
title = {Effects of removable clear dental aligners on the composition of the oral microbiome.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2579836},
pmid = {41268108},
issn = {2000-2297},
abstract = {Proper tooth alignment is important for oral and periodontal health, allowing better hygiene and reducing plaque build-up. While traditional braces are effective, clear aligners offer an aesthetic advantage and are also thought to promote better oral hygiene. However, their specific impact on the oral microbiome is not yet fully understood. This longitudinal study used 16S amplicon sequencing to study the oral microbiome (from saliva, subgingival, and supragingival samples) of 11 patients undergoing clear aligner treatment. Samples were collected at three time points: before treatment and at 3 and 6 months during therapy. Our results revealed large differences between the microbiomes of different oral sites but no significant overall changes in the oral microbiome composition due to orthodontic treatment. While some species-specific changes were observed, their effect sizes were very small. Although these results should be confirmed in a larger and more diverse cohort, they suggest that the treatment had a small or negligible impact. Given the observed stability of the oral microbiome in all three studied niches throughout the treatment and the known benefits to oral hygiene, clear aligners may present a favorable therapeutic alternative compared to fixed appliances.},
}

@article {pmid41267933,
year = {2025},
author = {Tincati, C and Bono, V and Nozza, S and Bandera, A and Tosi, D and Sala, V and Ancona, G and Calcagno, A and Muscatello, A and Rusconi, S and Augello, M and Rovito, R and Gianelli, U and Pescia, C and Santoro, A and Falleni, M and Gori, A and Marchetti, G},
title = {Three-Month cART Initiated During Primary HIV Does Not Correct the Structural, Immune, and Microbial Abnormalities within the Gastrointestinal Tract.},
journal = {Pathogens & immunity},
volume = {10},
number = {2},
pages = {263-285},
pmid = {41267933},
issn = {2469-2964},
abstract = {BACKGROUND: HIV infection leads to profound alterations of gut structure, immunity, and microbiome, resulting in immune activation and inflammation, which drive the development of non-infectious comorbidities. The introduction of combination antiretroviral therapy (cART) in the chronic stages of disease does not correct such abnormalities; however, the effect of viro-suppressive treatment in the gastrointestinal tract during primary HIV infection (PHI) is largely unknown. We studied the effects of 12-week cART on gastrointestinal (GI) structure, immunity, and mucosal microbiome in people living with HIV (PLWH) with PHI.

METHODS: Eleven participants with PHI enrolled in the INACTION trial underwent colonoscopy with ileum and colon biopsies, as well as peripheral blood mononuclear cell (PBMC) and plasma collection, prior to and at 12 weeks of cART. Gut biopsies were stained with CD14, CD68, CD163, and E-cadherin antibodies and Masson trichrome. Flow cytometry was performed on lamina propria and PBMCs to characterize CD4, γδ T, Treg, and Th17 cells. Gut tissue-associated microbiome analysis was conducted on colon and ileum biopsies. Ten untreated individuals with chronic HIV infection (CHI) were also studied for comparative analysis.

RESULTS: Despite treatment of PHI, gut barrier damage (E-cadherin loss, collagen deposition) progressed, with a partially preserved distribution of intestinal macrophages. Treated PHI showed stable CD4+ and γδ T-cell frequencies and decreased activation of these subsets in the colon, with no effect on intestinal Th17 and Treg cells. No major changes in peripheral inflammation and intestinal barrier integrity markers were observed. Gut tissue-associated microbiome composition evolved during cART treatment in PHI.

CONCLUSION: Despite early initiation, 12-week cART is unable to correct the HIV-mediated gut damage. Since gut injury drives systemic inflammation, which in turn fosters the pathogenesis of non-communicable comorbidities, our findings provide pathogenetic evidence of limited efficacy of early cART in reverting the HIV-associated pro-inflammatory signature and clinical risk.},
}

@article {pmid41267780,
year = {2025},
author = {Sharma, I and Sudarsanan, D and Moonah, S},
title = {The gut microbiome as a major source of drug-resistant infections: emerging strategies to decolonize and target the gut reservoir.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1692582},
pmid = {41267780},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; *Bacterial Infections/microbiology/therapy/prevention & control ; *Drug Resistance, Bacterial ; Phage Therapy ; *Bacteria/drug effects ; Antimicrobial Peptides/therapeutic use ; },
abstract = {Infections caused by antimicrobial-resistant bacteria represent a significant global health crisis that continues to worsen, creating an urgent need for alternative treatment and prevention strategies. A major source of drug-resistant bacteria is the human gut. The gut microbiota consists of bacteria that are frequently exposed to antibiotics, leading to selective pressure that promotes the development of resistant strains such as carbapenem-resistant Enterobacterales (CRE) and vancomycin-resistant enterococci (VRE). These drug-resistant bacteria can spread from the gut to other body sites, leading to hard-to-treat and potentially life-threatening infections such as bacteremia, surgical site infections, and urinary tract infections. Targeting the gut reservoir is essential in the fight against antimicrobial resistance. In this review, we focus on emerging non-antibiotic strategies aimed at eliminating drug resistant bacteria from the gut before they cause invasive infections, with particular emphasis on clinical evidence. Approaches discussed include fecal microbiota transplantation, bacteriophage therapy, antimicrobial peptides, probiotics, and dietary interventions. Optimizing these strategies, while continuing to explore newer approaches, will be essential to combat the growing threat of drug-resistant infections.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Anti-Bacterial Agents/pharmacology/therapeutic use
Fecal Microbiota Transplantation
Probiotics/therapeutic use
*Bacterial Infections/microbiology/therapy/prevention & control
*Drug Resistance, Bacterial
Phage Therapy
*Bacteria/drug effects
Antimicrobial Peptides/therapeutic use

@article {pmid41267737,
year = {2025},
author = {Surendranath, A and Gupta, A and Singhal, S},
title = {Impact of Dementia on Patients Admitted With Complicated Diverticular Disease: A U.S. Nationwide Analysis.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94971},
pmid = {41267737},
issn = {2168-8184},
abstract = {Background Emerging research has suggested a link between diverticular disease and dementia, potentially mediated by alterations in the gut microbiome and chronic systemic inflammation. This study aimed to evaluate in-hospital outcomes in patients admitted with complicated diverticular disease (CDD) and pre-existing dementia. Methods We used the 2021 National Inpatient Sample (NIS), which reflects 97% of the U.S. population. Patients admitted with CDD, defined as diverticulitis, abscess, perforation, or bleeding, were identified and stratified by the presence or absence of a prior dementia diagnosis. In-hospital mortality was compared between groups. Subgroup analysis evaluated the impact of specific complications (perforation/abscess vs. diverticulitis/bleeding) on mortality among patients with dementia. Multivariable logistic regression was used to adjust for potential confounders. Results Of 221,460 patients admitted with CDD, 9,160 (4.1%) had a comorbid dementia diagnosis. Patients with dementia were older (mean age 82.5 years), predominantly female (64.9%), and more likely to have multiple comorbidities. Overall, in-hospital mortality was higher in the dementia group (unadjusted OR 3.41; 95% CI: 2.38-4.90; p < 0.01), though this was not statistically significant after adjustment (aOR 1.45; 95% CI: 0.97-2.16; p = 0.07). Subgroup analysis revealed that dementia was significantly associated with increased mortality among patients with perforation or abscess (aOR 2.07; 95% CI: 1.07-4.04; p = 0.03), but not in those with diverticulitis or bleeding alone. Conclusion Pre-existing dementia was associated with higher unadjusted mortality, but it was not statistically significant after adjustment, except in patients with CDD who presented with perforation or abscess.},
}

@article {pmid41267628,
year = {2025},
author = {Chamedjeu, RR and Jani, K and Jetter, K and Wilhelm, K and Schäfer, P and Wilfert, L and Sommer, S and Riedel, CU},
title = {Impact of Fertilisation on the Bacterial Core Microbiome of Grassland Soils: Abundance in the Field and Growth In Vitro.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70235},
doi = {10.1111/1758-2229.70235},
pmid = {41267628},
issn = {1758-2229},
support = {ID-18 IMPALA//Baden-Württemberg Stiftung/ ; },
mesh = {*Soil Microbiology ; *Grassland ; *Bacteria/genetics/growth & development/classification/isolation & purification ; *Microbiota ; *Fertilizers/analysis ; RNA, Ribosomal, 16S/genetics ; Animals ; DNA, Bacterial/genetics/chemistry ; Soil/chemistry ; Swine ; Phylogeny ; },
abstract = {Anthropogenic activities may have profound impacts on the soil microbiome with consequences for soil health, agriculture and food production. Here, we investigated the impact of different fertilisation regimes on the composition of the bacterial soil microbiome in grassland ecosystems by 16S rRNA gene amplicon sequencing and in vitro growth experiments with culturable representatives of the bacterial core microbiota. We observed a large proportion of taxa shared across fertilisation regimes without significant differences in their evenness, but shifts in the composition of the bacterial core microbiome by fertilisation. These effects were most pronounced for fertilisation with pig slurry (PS). Analysis of microbiome multivariable association with linear models identified bacterial biomarker taxa for different fertilisation regimes. This enabled the selection of several culturable representatives for in vitro growth experiments. Consistent with the relative abundances of Bradyrhizobium, Nocardioides, and Solirubrobacter in field samples, the growth of Bradyrhizobium japonicum was inhibited by PS, while Nocardioides albus and Solirubrobacter pauli exhibited enhanced growth in its presence. Our results suggest that culturable representatives of the bacterial core soil microbiota can be identified and used to investigate the effects of specific parameters linked to anthropogenic impacts under controlled laboratory conditions.},
}

*Soil Microbiology
*Grassland
*Bacteria/genetics/growth & development/classification/isolation & purification
*Microbiota
*Fertilizers/analysis
RNA, Ribosomal, 16S/genetics
Animals
DNA, Bacterial/genetics/chemistry
Soil/chemistry
Swine
Phylogeny

@article {pmid41267490,
year = {2025},
author = {Sharma, P and Dagariya, S and Sharma, S and Singh, M},
title = {Uncovering the nexus of human health hazards of nanoplastics, gut-dysbiosis and antibiotic-resistance.},
journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis},
volume = {},
number = {},
pages = {1-60},
doi = {10.1080/26896583.2025.2578871},
pmid = {41267490},
issn = {2689-6591},
abstract = {Nanoplastics (1-1000 nm) (NPs) represent a novel and insidious class of emerging contaminants with the potential to profoundly disrupt gut microbial ecology and accelerate the spread of antibiotic resistance two critical and converging threats to global health. While prior studies have examined the toxicokinetics of NPs and their general microbial interactions, this review provides the first comprehensive synthesis specifically focused on the nexus between NPs, gut dysbiosis, and the propagation of antibiotic resistance genes (ARGs). This review highlights how NPs alter gut microbiota composition, suppressing beneficial microbes while fostering opportunistic pathogens and how such imbalances may contribute to human health issues. Importantly, emerging evidence also suggests that NPs may serve as unrecognized vectors for horizontal gene transfer (HGT), enabling the rapid dissemination of ARGs via conjugation, transformation, transduction, and extracellular vesicles within the gastrointestinal tract. In addition, this review also identifies urgent methodological gaps in detecting NPs in biological matrices and the environment, as well as assessing their mechanistic impacts, calling for innovation in analytical approaches. By presenting an interdisciplinary perspective that bridges nanotoxicology, microbiome science, and antimicrobial resistance, this article sheds light on an underexplored yet urgent frontier in environmental health, offering novel insights to guide future research, risk assessment, and policy development.},
}

@article {pmid41267409,
year = {2025},
author = {van der Hulst, R and Borra, LCP and Verschoor, SP and Hundscheid, IHR and Nienaber, WC and Quaak, FCA and Verschraagen, M and Oostra, RJ and Touw, DJ},
title = {The influence of 13 weeks of burial on morphine and metabolite distribution in human remains.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.70233},
pmid = {41267409},
issn = {1556-4029},
abstract = {When human remains are in an advanced stage of decomposition, drug concentrations are altered. In five decedents morphine, morphine-3-glucuronide (M3G), and morphine-6-glucuronide (M6G) concentration changes and bacterial DNA were investigated after 13 weeks of burial. Femoral blood (FB), musculus quadriceps femoris (QM), adipose tissue (AT), synovial fluid (SF), and vitreous humor (VH) were collected on arrival at the morgue (t1), 15-24 h later (t2), and after burial of 13 weeks (t3). At t3 FB, QM, AT, and BM were sampled during autopsy, along with additional samples. Morphine, M3G, and M6G concentrations were determined. The median morphine concentration change, expressed as t2/t1 ratios in FB, VH, SF, QM, and AT was 0.96 (0.87->1.1), 1.1 (0.90-1.2), 0.92 (0.86-1.02), 1.1 (0.90-1.6), and 1.4 (1.2-1.8), respectively. At t3 the concentrations showed wide variability, with the least in QM. The median(range) morphine to FB (t1) ratios in matrices collected at t3 from the torso (central) and outside the torso (peripheral) were 4.8 (1.0-70) and 1.3 (0.02->3.1), respectively, and were significantly different. The central and peripheral median M3G to morphine t3/t1 ratios were 0.31 (0.01-1.2) and 1.4 (range 0.34-13), respectively, suggesting postmortem deconjugation of M3G. Bacterial DNA was detected in all matrices. At t3 most matrices examined had a higher bacterial DNA concentration compared to t1. The measured t2/t1 morphine ratios suggest stability of morphine concentrations between t1 and t2. At t3 morphine concentrations in peripheral matrices are lower than in central matrices, where QM and BT are possible alternatives to analyze at extended PMIs.},
}

@article {pmid41267291,
year = {2025},
author = {Wang, X and Ma, X and Su, D and Zhang, Y and Miao, J and Liu, X and Yu, Y and Leng, K},
title = {The effect of short-term storage on Antarctic krill (Euphausia superba) quality: Insights into microbial characteristics, volatile flavor compounds, trimethylamine oxide and its derivatives.},
journal = {Food research international (Ottawa, Ont.)},
volume = {222},
number = {Pt 1},
pages = {117709},
doi = {10.1016/j.foodres.2025.117709},
pmid = {41267291},
issn = {1873-7145},
mesh = {Animals ; *Euphausiacea/microbiology/chemistry ; *Methylamines/analysis/metabolism ; *Food Storage/methods ; *Volatile Organic Compounds/analysis ; Microbiota ; Antarctic Regions ; Odorants/analysis ; Bacteria/classification/metabolism ; *Seafood/microbiology/analysis ; *Food Quality ; Taste ; Food Microbiology ; },
abstract = {Under suboptimal storage conditions, the conversion of trimethylamine oxide (TMAO) into undesirable metabolites seriously impairs the edible quality, safety, and market value of aquatic foods. This study aims to assess the microbiome variations related to spoilage and its relationship with volatile flavor compounds and TMAO metabolites in Antarctic krill simulated deck environment storage by bio-chemical examination and correlation analysis. Compared to storage at 4 °C and 0 °C, Antarctic krill stored at -20 °C maintained better freshness, with significant reductions in L*, a*, lipid oxidation, carotenoid degradation, texture deterioration, and excessive proteolysis. A total of 60 volatile compounds flavor were identified, of which 12 were identified as important flavor contributors with relative odor active value (ROAV) greater than 1. Bacterial diversity indicated that Proteobacteria, Actinobacteriota and Firmicutes were dominant bacterial phyla. According to Pearson correlation analysis, dominant bacterial genera may mediate changes in volatile compounds through amino acid and fatty acid metabolism. Concurrently, they synergistically drove quality deterioration during storage via multiple pathways, including altered nitrogenous compound metabolism, accelerated lipid oxidation, and induced pigment degradation. These findings offer critical insights into the relationships between quality indicators, volatile flavor compounds, TMAO/its derivatives and bacterial diversity, providing theoretical support for optimizing storage conditions to enhance the flavor and quality of Antarctic krill.},
}

Animals
*Euphausiacea/microbiology/chemistry
*Methylamines/analysis/metabolism
*Food Storage/methods
*Volatile Organic Compounds/analysis
Microbiota
Antarctic Regions
Odorants/analysis
Bacteria/classification/metabolism
*Seafood/microbiology/analysis
*Food Quality
Taste
Food Microbiology

@article {pmid41267258,
year = {2025},
author = {Tiwari, S and Shah, IA and Devi, PB and Suryavanshi, MV and Rani, PU and Rawat, A and Harini Nivedhitha, M and Kondepudi, KK and Bhanuprakash Reddy, G and Kavitake, D and Shetty, PH},
title = {Evaluating the prebiotic potential of a glucan EPS from Enterococcus hirae OL616073: Digestive resistance, probiotic growth stimulation, and gut microbiome modulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {222},
number = {Pt 1},
pages = {117649},
doi = {10.1016/j.foodres.2025.117649},
pmid = {41267258},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Prebiotics ; *Probiotics ; *Glucans/metabolism/pharmacology ; Fermentation ; Feces/microbiology ; *Enterococcus hirae/metabolism/chemistry ; Lacticaseibacillus rhamnosus/growth & development ; *Digestion ; Oligosaccharides ; Bifidobacterium breve/growth & development ; Escherichia coli/growth & development ; Humans ; *Polysaccharides, Bacterial/pharmacology ; },
abstract = {Earlier we have reported extraction, purification and characterization of glucan exopolysaccharide (EPS) from Enterococcus hirae OL616073. In this study, we investigate the potential of glucan EPS as a prebiotic biomolecule through in vitro gastrointestinal (GI) digestion, probiotic growth promotion, and fecal fermentation studies. The glucan EPS showed higher resistance (11.5 % hydrolysis) compared to standard fructooligosaccharide (FOS;18.5 % (p ≤ 0.05)). The impact of various growth media on the viability of Bifidobacterium breve, Lacticaseibacillus rhamnosus, and Escherichiacoli was examined. Glucose stimulated the growth of commensal bacteria, such as E. coli (log 8.69 ± 0.06), whereas with glucan EPS and FOS, the growth of E. coli was lower compared to probiotics. The growth viability for E.coli in the presence of EPS and FOS was log 7.97 ± 0.05 and log 7.85 ± 0.02, respectively while the values were log 8.2 ± 0.05 (p ≤ 0.05) for both the probiotics (B. breve and L. rhamnosus). During in vitro fecal fermentation glucan EPS showed a significant drop in pH from 7.56 to 4.60 after 48 h. Further, fermentation of glucan has produced high concentrations of key short chain fatty acids (SCFAs) that have several health benefits. Microbiome analysis after fecal fermentation demonstrated that glucan EPS impacts gut microbiota modification differently than FOS and a non-sugar control. A substantial increase in Bacillota abundance (33.94 to 54.32 % over 24 h) was observed with glucan EPS, indicating improved nutrition utilization and energy metabolism. Together, these findings highlight glucan EPS as a promising prebiotic agent with the potential to modulate gut microbiota and support metabolic health.},
}

*Gastrointestinal Microbiome/drug effects
*Prebiotics
*Probiotics
*Glucans/metabolism/pharmacology
Fermentation
Feces/microbiology
*Enterococcus hirae/metabolism/chemistry
Lacticaseibacillus rhamnosus/growth & development
*Digestion
Oligosaccharides
Bifidobacterium breve/growth & development
Escherichia coli/growth & development
Humans
*Polysaccharides, Bacterial/pharmacology

@article {pmid41267246,
year = {2025},
author = {Huang, X and Li, R and Zhang, L and Chen, X and Gong, X and Kang, J},
title = {Exploring the rare and abundant bacterial community structures and their metabolic differences in various types of qula cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {222},
number = {Pt 1},
pages = {117633},
doi = {10.1016/j.foodres.2025.117633},
pmid = {41267246},
issn = {1873-7145},
mesh = {*Cheese/microbiology ; *Bacteria/classification/metabolism/genetics ; *Microbiota ; *Food Microbiology ; Animals ; Tibet ; Fermentation ; Metabolomics ; Cattle ; Milk/microbiology ; },
abstract = {Qula is a fermented cheese-like product made from yak milk. Although the bacterial communities in qula have been well documented, the diversity and functions of both abundant and rare bacterial subcommunities are still unclear. Here, our study examines the community structures of abundant and rare taxa, as well as their metabolite profiles, in the distinct qula samples from Tibet, China, employing high-throughput sequencing and untargeted metabolomics. Our results indicate that rare bacterial taxa account for 98.15 % of total operational taxonomic units and 48 % of total sequences. Dominant bacteria from abundant taxa consist of Lactococcus, Lactobacillus, and Acetobacter, while rare taxa contain Prevotella, Ruminococcus, and Butyrivibrio. Furthermore, we show that stochastic processes predominantly influence bacterial assembly in qula microbial communities. Specifically, stochastic processes have a more significant impact on community assembly for rare taxa, while deterministic processes are more important for abundant taxa. Moreover, we evaluate the contributions of rare taxa to network complexity and community stability, identifying potential keystone species. By analyzing metabolic profiles, we further compared the differences in metabolic functions between rare and abundant taxa in the qula microbiome. Our study shows that, along with abundant taxa, rare taxa in the qula microbiome play a significant role in community assembly and interactions, offering valuable insights into the microbial ecosystems of traditional fermented foods.},
}

*Cheese/microbiology
*Bacteria/classification/metabolism/genetics
*Microbiota
*Food Microbiology
Animals
Tibet
Fermentation
Metabolomics
Cattle
Milk/microbiology

@article {pmid41267138,
year = {2025},
author = {Zafari, R and Goudarzi, N and Kamroo, A and Tafti, MF and Ghorbani, A and Talebian, N and Najafi, S and Shahbazian, S and Rahmanian, M and Parvardeh, S and Dargahi, L and Nassiri-Asl, M},
title = {The effects of polyphenols on gut microbial metabolites and composition in neurodegenerative diseases: a systematic review.},
journal = {Nutrition & metabolism},
volume = {22},
number = {1},
pages = {142},
pmid = {41267138},
issn = {1743-7075},
}

@article {pmid41267120,
year = {2025},
author = {Ahannach, S and Gehrmann, T and Spacova, I and Wittouck, S and Hiers, J and Bron, PA and Vander Donck, L and Cromphout, M and Swayambhu, M and Arora, N and Schuh, L and Tournoy, I and Smeers, I and Wuestenbergs, J and Bekaert, B and Decorte, R and Jehaes, E and Lebeer, S},
title = {Microbial and seminal traces of sexual intercourse and forensic implications.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {237},
pmid = {41267120},
issn = {2049-2618},
support = {Lacto-Be 26850/ERC_/European Research Council/International ; DOCPRO 37054//Universiteit Antwerpen/ ; 1277222N//Fonds Wetenschappelijk Onderzoek/ ; 11A0620N//Fonds Wetenschappelijk Onderzoek/ ; 1SD0622N//Fonds Wetenschappelijk Onderzoek/ ; FN701000004//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Coitus ; *Semen/microbiology ; *Microbiota ; Male ; Adult ; Sex Offenses ; Retrospective Studies ; Rape ; Longitudinal Studies ; Young Adult ; Machine Learning ; },
abstract = {BACKGROUND: The increasing numbers of sexual violence and unresolved rape cases require alternative approaches with higher evidential value to complement existing forensic tools. Predicting recent intercourse is crucial in forensic casework on sexual assaults. In this work, we assessed whether sexual intercourse can be predicted based on the vaginal microbiome and compared it to the gold standard method of semen detection.

RESULTS: Using a prediction model based on microbiome of 3043 women, intercourse was predicted with 71% accuracy in a balanced cross-validation machine learning setting. This prediction model was validated in a longitudinal intervention study and tested on forensic sexual assault cases. The developed predictor could accurately establish intercourse in 82% of the studied cases. Yet, underwear was found to hold an even greater evidential value and replace the more invasive vaginal sampling for semen detection in some cases with an accuracy of 95%. This was substantiated through a retrospective analysis of 207 forensic sexual assault cases.

CONCLUSIONS: Taken together, this study revealed that the vaginal microbiome is better at predicting recent sexual intercourse, while the victim's underwear has a clear value as additional biological trace evidence for semen detection. These findings are particularly useful in cases with delayed reporting and are obtained with less invasive sampling. Video Abstract.},
}

Humans
Female
*Vagina/microbiology
*Coitus
*Semen/microbiology
*Microbiota
Male
Adult
Sex Offenses
Retrospective Studies
Rape
Longitudinal Studies
Young Adult
Machine Learning

@article {pmid41266962,
year = {2025},
author = {Patridge, E and Gorakshakar, A and Molusky, MM and Ogundijo, O and Julian, C and Hu, L and Antoine, G and Vuyisich, M and Wohlman, R and Banavar, G},
title = {Altered gut microbial functional pathways in people with irritable bowel syndrome enable precision health insights.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {823},
pmid = {41266962},
issn = {1471-230X},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Adult ; Female ; Male ; Middle Aged ; Feces/microbiology ; Transcriptome ; Precision Medicine ; },
abstract = {BACKGROUND: Functional gastrointestinal disorders present diagnostic and therapeutic challenges, and there is a strong need for molecular markers that enable early health insights and intervention. Herein, we present an approach to assess the gut microbiome with stool-based gut metatranscriptome data from a large adult human population (n = 80,570), using irritable bowel syndrome as an example that features both an abnormal gut microbiome and a spectrum of distinct conditions.

METHODS: We develop a suite of eight gut microbial functional pathway scores, each of which represents the activity of a set of interacting microbial functional features (based on KEGG orthology) relevant to known gut biochemical activities. We use a normative approach within a subpopulation (n = 9,350) to define "Good" and "Not Optimal" activities for these transcriptome-based gut pathway scores.

RESULTS: We hypothesize that Not Optimal scores are associated with irritable bowel syndrome (IBS) and its subtypes (i.e., IBS-Constipation, IBS-Diarrhea, IBS-Mixed Type). We show that Not Optimal functional pathway scores are associated with higher odds of IBS or its subtypes within an independent cohort (n = 71,220) using both the Rome IV Diagnostic Questionnaire as well as self-reported phenotypes.

CONCLUSIONS: Rather than waiting to diagnose IBS after symptoms appear, these functional pathway scores can help to provide early health insights into molecular pathways that may contribute to IBS. These molecular endpoints could also assist with measuring the efficacy of practical interventions, developing related algorithms, providing personalized nutritional recommendations, diagnostic support, and treatments for gastrointestinal disorders like IBS.},
}

Humans
*Irritable Bowel Syndrome/microbiology
*Gastrointestinal Microbiome/genetics/physiology
Adult
Female
Male
Middle Aged
Feces/microbiology
Transcriptome
Precision Medicine

@article {pmid41266961,
year = {2025},
author = {Wang, L and Qi, G and Shi, Y and Ma, Y and Gao, J},
title = {A systematic longitudinal study of microbiome: integrating temporal-spatial dimensions with causal and deep learning models.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {1068},
pmid = {41266961},
issn = {1471-2164},
support = {Grant No. 12271216, 11831015, 92370131//National Natural Science Foundations of China/ ; },
mesh = {*Deep Learning ; Humans ; Biomarkers ; Longitudinal Studies ; *Microbiota ; Gastrointestinal Microbiome ; },
abstract = {Longitudinal microbiome data provide a unique opportunity to explore dynamic interactions between microbial communities and disease progression. However, these data are often characterized by missing values, sparse signals, and limited interpretability, which impede effective biomarker discovery and accurate disease modeling. Therefore, we propose SysLM, a comprehensive deep learning framework for systematic analysis of longitudinal microbiome data. It comprises two synergistic modules: SysLM-I and SysLM-C. SysLM-I focuses on the task of missing-value inference, combines metadata and three feature enhancement strategies, and comprehensively captures temporal causality and long-term dependence through Temporal Convolutional Network and Bi-directional Long Short-Term Memory modules. SysLM-C integrates deep learning with causal inference modeling to construct three causal spaces to accomplish the tasks of classification and screening of multiple types of biomarkers, including differential biomarkers of microbiomes, network biomarkers, core biomarkers, dynamic biomarkers, disease-specific biomarkers, and shared biomarkers. SysLM demonstrates superior performance in imputation, classification, and biomarker discovery across multiple datasets. Importantly, it uncovers novel microbial mechanisms underlying ulcerative colitis, highlighting its value for precision medicine. By integrating deep learning with causal modeling, SysLM offers a promising approach to advance microbiome-based disease research and facilitate the development of targeted therapeutic strategies.},
}

*Deep Learning
Humans
Biomarkers
Longitudinal Studies
*Microbiota
Gastrointestinal Microbiome

@article {pmid41266917,
year = {2025},
author = {Huang, JS and Zhang, ZY and Zhong, QH and Guo, FL and Wu, JY and Chen, S and Lin, WW and Lin, JB},
title = {Tumor-Intrinsic Microbiome-Based Subtyping of Esophageal Cancer as Predictive Biomarkers for Postoperative Survival.},
journal = {Annals of surgical oncology},
volume = {},
number = {},
pages = {},
pmid = {41266917},
issn = {1534-4681},
abstract = {OBJECTIVE: This study aims to investigate the impact of different treatment regimens on the intratumoral microbiota (ITM) composition in esophageal cancer patients and its association with prognosis.

METHODS: Tumor tissue samples from 107 esophagectomy patients were analyzed by using 5R 16S rRNA sequencing. Patients were classified into esophagotype A and B via hierarchical clustering, and the relationship between microbiota and prognosis was assessed through Kaplan-Meier survival analysis and Cox regression.

RESULTS: Significant differences in ITM diversity and composition were observed between the neoadjuvant chemoimmunotherapy (nCIT) and surgery alone groups. Esophagotype A was enriched with Firmicutes and Lactobacillus, while esophagotype B with Proteobacteria and Fusobacterium. Survival analysis revealed that patients with esophagotype B had significantly worse outcomes compared with esophagotype A. The 3- and 5-year overall survival rates for esophagotype A were 73 and 69.2%, respectively, significantly higher than those for esophagotype B (57 and 37.5%; p < 0.05 and p < 0.01, respectively). Similarly, the 3- and 5-year recurrence-free survival rates for esophagotype A were both 80.7% compared with 64 and 50.1% for esophagotype B. Multivariable Cox regression confirmed microbial clustering within esophageal cancer subtypes as an independent prognostic factor.

CONCLUSIONS: This study classifies esophageal cancer based on ITM signatures, highlighting the microbiota's prognostic significance and supporting the potential of microbiome-based strategies for personalized treatment.},
}

@article {pmid41266864,
year = {2025},
author = {Tan, H and Li, S and Yan, H and Li, F and Yao, Y and Li, Y and Feng, Q},
title = {Mendelian Randomization Unlocks Stroke Therapeutics: Dioscin Inhibits CD27-Driven Neuroinflammation via Gut Microbiota Modulation.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {110},
pmid = {41266864},
issn = {1559-1182},
support = {2022ZL20//the hospital-level research project of the affiliated Hospital of Xuzhou Medical University/ ; XWKYHT20230067//the medical science and technology innovation project of Xuzhou Municipal Health Commission/ ; LCZX202412//the Construction Project of High Level Hospital of Jiangsu Province/ ; XZSYSKF2022020//the Project Funded by Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)/ ; KC22243//the Xuzhou Science and Technology Program/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Stroke/drug therapy/genetics/microbiology ; *Mendelian Randomization Analysis/methods ; *Tumor Necrosis Factor Receptor Superfamily, Member 7/metabolism/antagonists & inhibitors ; *Neuroinflammatory Diseases/drug therapy/genetics ; },
abstract = {Research on the gut-brain-immune axis shows it plays a critical role in ischemic stroke, but the exact causal links between gut bacteria imbalance, immune system problems, and brain blood vessel damage remain unclear. To investigate this, we combined multiple types of biological data using a statistical method called Bayesian weighted Mendelian randomization (BWMR). We analyzed large genetic datasets covering 731 immune cell traits, 91 inflammatory proteins, 412 gut microbes and their pathways, and ischemic stroke cases. Shared genetic variants were confirmed using colocalization, and we used computer simulations to explore potential treatments. The analysis found that genetically predicted higher levels of the protein CD27 on specific memory B cells (CD24[+] CD27[+] and IgD[-] CD38[dim]) directly increased the risk of stroke caused by large-artery atherosclerosis. Computer modeling indicated that a compound called Dioscin could potentially block CD27 effectively. Conversely, bacteria from the order Burkholderiales (specifically at the family, genus, and species level Burkholderiales_bacterium_1_1_47) showed strong protective effects against small-vessel stroke. Further analysis revealed that about 12.6% of the protective effect of the gut bacterium g_Odoribacter worked through the signaling protein FGF19. This study identifies CD27-positive B cells as key drivers of brain inflammation in stroke and suggests Dioscin as a promising treatment candidate. It also demonstrates a protective mechanism where specific gut microbes communicate with blood vessels in the brain via FGF19, providing a foundation for new stroke therapies targeting the microbiome and immune system.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Stroke/drug therapy/genetics/microbiology
*Mendelian Randomization Analysis/methods
*Tumor Necrosis Factor Receptor Superfamily, Member 7/metabolism/antagonists & inhibitors
*Neuroinflammatory Diseases/drug therapy/genetics

@article {pmid41266809,
year = {2025},
author = {Docter-Loeb, H},
title = {Waste not: how researchers harness pee and poo for science.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41266809},
issn = {1476-4687},
}

@article {pmid41266796,
year = {2025},
author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R},
title = {Calculating fast differential genome coverages among metagenomic sources using micov.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1624},
pmid = {41266796},
issn = {2399-3642},
mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; },
abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.},
}

*Metagenomics/methods
*Genome, Bacterial
*Metagenome
*Microbiota/genetics
Humans

@article {pmid41266667,
year = {2025},
author = {Horseman, TS and Parajuli, B and Murthy, V and Holmes-Hampton, GP and Sukumar, G and Dalgard, CL and Anderson, JA and Burmeister, DM},
title = {A multi-omics approach exploring the gut-liver axis following combined radiation exposure and burn injury in a Sinclair minipig model.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41111},
pmid = {41266667},
issn = {2045-2322},
support = {RHE-24-01//United States Army Medical Research and Development Command's Combat Casualty Care Program/ ; RHE-24-01//United States Army Medical Research and Development Command's Combat Casualty Care Program/ ; RHE-24-01//United States Army Medical Research and Development Command's Combat Casualty Care Program/ ; RHE-24-01//United States Army Medical Research and Development Command's Combat Casualty Care Program/ ; },
mesh = {Animals ; *Burns/metabolism/pathology/genetics/microbiology/complications ; Swine ; *Liver/metabolism/radiation effects/pathology ; Swine, Miniature ; *Gastrointestinal Microbiome/radiation effects ; Disease Models, Animal ; Transcriptome ; *Radiation Exposure/adverse effects ; *Radiation Injuries, Experimental ; Multiomics ; },
abstract = {While radiation and burn injury have distinct local and systemic effects, they both negatively impact intestinal permeability/function. In a nuclear attack, combined thermal burns and radiation exposure (e.g., combined injury (CI)) would be a dominant injury pattern. Despite this, how burns affect gastrointestinal acute radiation syndrome, and vice versa, has been largely unstudied. Next-generation sequencing has revealed a strong bidirectional link between the liver and gut. Here, we used a porcine model to evaluate the impact of burn, radiation, and CI on the gut microbiota and liver transcriptomics to determine if this link exists in these injury patterns. Sinclair minipigs were randomly divided into three groups: burn (n = 8), hemibody radiation (n = 7), and CI (n = 8). Animals were monitored for 14 days with longitudinal rectal swab and blood collection. CI increased weight loss, diarrhea, inappetence and lethargy compared to either injury pattern alone. Jejunum histology revealed increased mucosal apoptosis in burn and CI groups compared to radiation. CI led to elevated levels of NLRP3 and IL1β in the jejunum. Intestinal barrier disruption was indicated by decreasing circulating l-citrulline in CI which correlated inversely with intestinal-Fatty Acid Binding Protein. Bacteremia was elevated post-burn on day 1 and again from day 7-14 in burn and CI groups. Microbiome analysis showed phylogenetic shifts and differential abundance across groups with CI animals exhibiting distinct microbial signatures linked to intestinal dysfunction and liver injury. Liver RNA-seq revealed group-specific gene expression changes, with CI-altered pathways implicating immune responses and lipid metabolism, which were correlated with gut microbiota such as Bacteroidaceae and Lachnospiraceae. Taken together, we present a first-of-its kind large animal model of radiation combined injury to highlight the interplay between gut-liver axis disruptions and systemic injury responses.},
}

Animals
*Burns/metabolism/pathology/genetics/microbiology/complications
Swine
*Liver/metabolism/radiation effects/pathology
Swine, Miniature
*Gastrointestinal Microbiome/radiation effects
Disease Models, Animal
Transcriptome
*Radiation Exposure/adverse effects
*Radiation Injuries, Experimental
Multiomics

@article {pmid41266339,
year = {2025},
author = {Muletz-Wolz, CR and Urrutia-Carter, J and Osborne, O and Kutos, S and Meneses Montano, J and Madison, JD and Gratwicke, B and Racharaks, R and Roncal, NE and Jimenez, RR and Ellison, A and Cleland, TP},
title = {Novel antimicrobial peptides and peptide-microbiome crosstalk in Appalachian salamander skin.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {213},
pmid = {41266339},
issn = {2055-5008},
support = {IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; BB/W013517/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/W013517/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MI210200//Walter Reed Army Institute of Research/ ; MI210200//Walter Reed Army Institute of Research/ ; },
mesh = {Animals ; *Skin/microbiology ; *Caudata/microbiology ; *Microbiota ; *Antimicrobial Peptides/pharmacology/metabolism/genetics ; Bacteria/drug effects/classification/genetics ; Proteomics ; Batrachochytrium/drug effects ; Humans ; *Antimicrobial Cationic Peptides/pharmacology ; Gene Expression Profiling ; },
abstract = {Using multi-omics tools, we discovered new antimicrobial peptides (AMPs) and examined AMP-microbial interactions in three Appalachian salamander species (Plethodon cinereus, Eurycea bislineata and Notophthalmus viridescens). We conducted skin transcriptomics (n = 13) and proteomics (n = 91) to identify 200+ candidate AMPs. With candidate AMPs, we identified correlations with skin microbiomes and synthesized 20 peptides to challenge against pathogens of amphibians (Batrachochytrium dendrobatidis: Bd) and humans (ESKAPEE). Using transcriptomics, candidate AMPs were detected in all individuals with Cathelidicins being most common. Using proteomics, AMPs were found in 34% of individuals (31/91)-predominately E. bislineata-with Kinin-like peptides being most common. Candidate AMP composition generally predicted skin bacterial composition, suggesting that AMPs influence host-microbial symbioses. Crude and synthesized peptides showed limited activity against Bd. Two synthesized Cathelicidins (Pcin-CATH3 and Pcin-CATH5) inhibited human pathogens, Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli. Our findings inform the potential usage of AMPs in conservation and translational applications.},
}

Animals
*Skin/microbiology
*Caudata/microbiology
*Microbiota
*Antimicrobial Peptides/pharmacology/metabolism/genetics
Bacteria/drug effects/classification/genetics
Proteomics
Batrachochytrium/drug effects
Humans
*Antimicrobial Cationic Peptides/pharmacology
Gene Expression Profiling

@article {pmid41266305,
year = {2025},
author = {Fouladi, F and Chen, Y and Bera, S and Jarmusch, AK and Van Tyne, D and Palella, FJ and Margolick, JB and Chew, KW and Sun, J and Martinson, J and Rinaldo, CR and Peddada, SD},
title = {A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10204},
pmid = {41266305},
issn = {2041-1723},
support = {ZIA ES103400/ImNIH/Intramural NIH HHS/United States ; ZIA ES103389/ImNIH/Intramural NIH HHS/United States ; ZIA ES 103400//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; ZIA ES 103389//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; },
mesh = {Humans ; *HIV Infections/microbiology/metabolism ; Male ; *HIV-1 ; *Dysbiosis/microbiology/metabolism ; Adult ; Feces/microbiology ; *Metabolome ; *Microbiota ; Homosexuality, Male ; Gastrointestinal Microbiome ; Purines/metabolism ; Middle Aged ; },
abstract = {The microbiome plays an important role in immune responses and inflammation in HIV-1 infection. Hence, a deeper understanding of the changes in the microbiome, its function and metabolites, and their interactions prior to HIV-1 infection is potentially important for HIV-1 prevention strategies. Using stool, oral washes, and plasma biospecimens obtained from men who have sex with men (MSM) and who were without HIV-1, we found several differences in microbial ecologies, gene functions, and metabolites between MSM who became HIV-1 infected (Pre-HIV) within six months and those who remained HIV-1 uninfected (Non-HIV). The Pre-HIV group had an enrichment of enzymes involved in purine metabolism, lower amino acid metabolism, and higher oxidative stress before the infection compared to the Non-HIV group. We also introduced a novel and broadly applicable taxon-specific measure of DISruption in COrrelations (DISCO) with other features, such as microbial taxa and metabolites in a given group (e.g., Pre-HIV group) relative to a reference group (e.g., Non-HIV group). Using DISCO, we identified several gut and oral species with disrupted correlations prior to HIV-1 infection. Application of DISCO to external datasets revealed that Prevotella spp. are consistently disrupted in their correlations across multiple cohorts prior to or following HIV-1 infection.},
}

Humans
*HIV Infections/microbiology/metabolism
Male
*HIV-1
*Dysbiosis/microbiology/metabolism
Adult
Feces/microbiology
*Metabolome
*Microbiota
Homosexuality, Male
Gastrointestinal Microbiome
Purines/metabolism
Middle Aged

@article {pmid41266190,
year = {2025},
author = {Wang, Y and Li, J and Lian, Z and Hao, H and Zheng, X},
title = {Tryptophan metabolites at the service of neuroimmune sensing of microbes.},
journal = {Trends in molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmed.2025.10.009},
pmid = {41266190},
issn = {1471-499X},
abstract = {Hosts have evolved multifaceted, intricate mechanisms to sense and respond to the microbes they coexist with, and these mechanisms play an important role in health and disease. The co-metabolism of dietary components by hosts and their microbiomes produces a myriad of signaling molecules, which are increasingly recognized in pathophysiology regulation via their engagement with the neuro-immune network. In this review, we focus on the emerging role of tryptophan (Trp) metabolites in host-microbe crosstalk through the lens of neuroimmune sensing in the gut and beyond. We highlight how Trp metabolites orchestrate the immune and neural networks to mediate the local and trans-organ effects of the microbiome. We also consider how a neuroimmunometabolic perspective could offer valuable insights into the pathogenesis of, and treatment strategies for, chronic diseases.},
}

@article {pmid41266021,
year = {2026},
author = {Rutledge, S and Brown, RS},
title = {Acute Alcoholic Hepatitis: New and Experimental Medications.},
journal = {Clinics in liver disease},
volume = {30},
number = {1},
pages = {71-92},
doi = {10.1016/j.cld.2025.09.005},
pmid = {41266021},
issn = {1557-8224},
mesh = {Humans ; *Hepatitis, Alcoholic/therapy/drug therapy/genetics ; Liver Regeneration/drug effects ; Interleukins/therapeutic use ; Granulocyte Colony-Stimulating Factor/therapeutic use ; Interleukin-22 ; Acute Disease ; Acyltransferases ; Phospholipases A2, Calcium-Independent ; },
abstract = {Severe alcohol-associated hepatitis (AH) is associated with high mortality and is rising in incidence but there are limited treatment options. Therapies being studied for AH include those targeting systemic cytokine-mediated inflammation, hepatic regeneration, reactive oxygen species, the microbiome, and genetics. Regenerative agents (such as granulocyte colony-stimulating factor, interleukin-22, and stem cell therapies) and therapies targeting the dysregulated microbiome hold the most promise and warrant larger trials. Manipulating the underlying genetics (eg, by gene editing of PNPLA3 or HSD17B13) is a lofty goal in personalized targeted therapy for AH but is many years from primetime.},
}

Humans
*Hepatitis, Alcoholic/therapy/drug therapy/genetics
Liver Regeneration/drug effects
Interleukins/therapeutic use
Granulocyte Colony-Stimulating Factor/therapeutic use
Interleukin-22
Acute Disease
Acyltransferases
Phospholipases A2, Calcium-Independent

@article {pmid41266019,
year = {2026},
author = {Maddur, H and Flamm, S},
title = {Alcohol-Related Liver Disease: Novel Insights into Mechanism.},
journal = {Clinics in liver disease},
volume = {30},
number = {1},
pages = {45-54},
doi = {10.1016/j.cld.2025.08.004},
pmid = {41266019},
issn = {1557-8224},
mesh = {Humans ; *Liver Diseases, Alcoholic/metabolism/etiology/genetics ; Oxidative Stress ; Gastrointestinal Microbiome ; MicroRNAs/metabolism ; Epigenesis, Genetic ; Lipid Metabolism ; Receptors, G-Protein-Coupled/metabolism ; },
abstract = {Alcohol-related liver injury is complex and remains poorly understood. Research to date has pinpointed the role of oxidative stress, hepatic inflammation, and derangements in lipid metabolism as drivers of disease pathogenesis. More recent research has identified alterations in the gut microbiome, epigenetics, G protein-coupled receptors, and microRNA's as possible drivers of disease pathogenesis and may serve as potential new treatment targets.},
}

Humans
*Liver Diseases, Alcoholic/metabolism/etiology/genetics
Oxidative Stress
Gastrointestinal Microbiome
MicroRNAs/metabolism
Epigenesis, Genetic
Lipid Metabolism
Receptors, G-Protein-Coupled/metabolism

@article {pmid41265701,
year = {2025},
author = {Wijesundara, SH and Weeraratne, TC and Noordeen, F and de Silva, WAPP},
title = {Microbiome and physicochemical properties of breeding waters of Aedes albopictus mosquitoes in Sri Lanka.},
journal = {Parasitology international},
volume = {},
number = {},
pages = {103199},
doi = {10.1016/j.parint.2025.103199},
pmid = {41265701},
issn = {1873-0329},
abstract = {Aedes albopictus is a key vector of arboviral transmission, and its widespread adaptability to diverse breeding habitats makes control efforts challenging. This study aimed to evaluate the bacterial communities and physicochemical characteristics of Ae. albopictus breeding sites across selected localities in Sri Lanka and to assess their potential influence on adult mosquito fitness using adult body size as an indicator. A total of 133 positive breeding sites were surveyed across eight districts. Breeding sites were categorized by premise type, container type, nature (natural or artificial), and as indoor or outdoor. From a subset of 73 representing breeding sites, microbial cultures were isolated, and bacterial diversities were assessed. Adult emergence rate was recorded under standardized rearing conditions, and female body size was estimated using wing length measurements. Physicochemical parameters, including temperature, pH, dissolved oxygen, electrical conductivity, and total dissolved solids, were reported for each breeding site. Each breeding site consisted of 2-6 distinct bacterial morphotypes, with Aeromonas hydrophila, Acinetobacter proteolyticus, and Bacillus subtilis as the most frequently reported species. The physicochemical properties of the breeding water (temperature, conductivity, TDS, and DO) were significantly different between sites (P < 0.05). There was a strong correlation between the diversity of bacteria and the wing length of mosquitoes. A relatively weak correlation was noted between the body size measurements and the bacterial abundance. A moderate explanatory power was present between water quality parameters, microbial composition, and the adult Ae. albopictus body size (R[2] = 27.7 %).},
}

@article {pmid41256617,
year = {2025},
author = {Surve, SV and Valls, RA and Barrack, KE and Gwilt, LL and Gardner, TB and O'Toole, GA},
title = {The Regional Landscape of the Human Colon Culturome in Health and Cystic Fibrosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41256617},
issn = {2692-8205},
abstract = {Cystic fibrosis (CF) alters gut physiology, yet its impact on microbial communities across colonic regions (ascending, transverse, descending colon) and microhabitats (lumen, mucosa) remains incompletely understood. Here, we applied culturomics to characterize gut microbiota in 32 individuals (22 nonCF, 10 CF). Persons with CF (pwCF) exhibited significantly higher viable bacterial loads than nonCF individuals, particularly in mucosal samples. Anaerobes predominated overall, with relative enrichment of aerobes in the mucosa of pwCF. Alpha diversity was reduced in mucosal samples and aerobic cultures for pwCF, whereas beta diversity was influenced by all the tested variables except the colonic region. Phylum-level analyses revealed enrichment of Proteobacteria and depletion of Actinobacteria, Bacteroidota, and Firmicutes in samples from pwCF, consistent with stool analysis. Random forest models identified selected oral-associated microbes as key predictive taxa and accurately classified polyp status with very high accuracy. Whole-genome sequencing of Bacteroides fragilis (n=21) and Escherichia coli (n=15) isolates, representing a subset of 109 gut bacterial genomes sequenced from this cohort, revealed minimal genomic variation across colonic regions and sample types, indicating intra-individual strain stability. The understandings from this pilot culturome study may help in developing targeted microbial therapeutic approaches to address the gut dysbiosis of CF.},
}

@article {pmid41265504,
year = {2025},
author = {McKee, KS and Bassis, CM and Golob, J and Palazzolo, B and Comstock, SS and Rosas-Salazar, C and Stanford, JB and Ananda, S and O'Connor, T and Gern, JE and Paneth, N and Dunlop, AL and , },
title = {Vaginal microbiome structure in pregnancy and host factors predict preterm birth: Results from the ECHO Cohort.},
journal = {Annals of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.annepidem.2025.11.003},
pmid = {41265504},
issn = {1873-2585},
abstract = {PURPOSE: The vaginal microbiome is dynamic, typically shifting during pregnancy toward enrichment of Lactobacillus. However, proliferation of Lactobacillus may be absent among women with preterm births (PTBs). We sought to identify robust vaginal microbiota signatures along with host factors that predicted PTB across diverse U.S. cohorts.

METHODS: We meta-analyzed 16S rRNA gene amplicon sequence data from the Environmental influences on Child Health Outcomes Cohort. We classified community state types (CSTs) and employed penalized logistic regression models to assess the association between vaginal CST and PTB. We generated supervised random forest models and validated them using a train-and-test approach to identify the most predictive vaginal taxa and host factors.

RESULTS: Of 683 births, 12% were preterm. Overall, 26% had a non- L. iners Lactobacillus-dominant CST (I, II, V), 43% had a L. iners-dominant CST (III), and 30% had a diverse, non-Lactobacillus-dominant (IV-B, IV-C) CST. Vaginal CST was strongly associated with PTB (adjusted odds ratio [aOR], 3.86, 95% confidence interval [CI], 1.57-11.3 for diverse, non-Lactobacillus-dominant communities and aOR, 3.03, 95% CI, 1.25-8.78 for L. iners-dominant compared to L. crispatus-dominant communities). The model with the highest area under the curve (AUC=.77) included Gardnerella vaginalis, age, Prevotella timonensis, and L. crispatus.

CONCLUSIONS: Along with host factors, vaginal microbiota could be used for predictive risk scoring for PTB across different U.S. cohorts.},
}

@article {pmid41265489,
year = {2025},
author = {Akhirini, N and Suprayogi, WPS and Saraswati, PN and Ratriyanto, A and Irawan, A},
title = {Fermented soybean meal using Bacillus subtilis and Aspergillus oryzae positively enhances cecal microbial composition and broiler performance.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.250400},
pmid = {41265489},
issn = {2765-0189},
abstract = {OBJECTIVE: This study investigated the effect of fermented SBM (FSBM) prepared through solid-state fermentation using Bacillus subtilis (BS) and Aspergillus oryzae (AO) to replace SBM in broiler chickens' diets on production, digestibility, and cecal microbial profile.

METHODS: In total, 160 sex-mixed day-old chicks of Cobb 500 broiler chickens were randomly assigned to four groups, four pens (replicates; 10 birds each pen), and were raised for 35 days under tropical conditions. The treatments were control (basal diet; CON) or SBM replaced by FSBM produced using AO (AO group), BS (BS group), and their combination (AO+BS group).

RESULTS: Birds fed AO+BS diet resulted in higher (p=0.003) BW while BS diet tended (p=0.063) to have higher final BW than CON or AO. Similarly, birds fed FSBM prepared under either BS or AO+BS had higher feed intake (p<0.01) than the CON group. No difference was found on feed conversion ratio (FCR). Relative organ weights including heart, liver, abdominal fat, and total inner organs were lower (p<0.01) on birds fed AO+BS diet than CON, but relative carcass weight was unaffected (p>0.05). Treatments with BS or AO+BS increased dry matter (DM) (p=0.032), organic matter (OM) (p=0.016), and crude protein (CP) (p=0.044) digestibility, while AO did not affect DM and CP digestibility. Broilers fed AO+BS diet showed greater abundance of Firmicutes phylum and Bacteroides genus than CON group. Several microbial taxa biomarkers were identified via LEfSE analysis, including higher abundance of Enterococcus and Bacillus in AO+BS group but lower abundance of Erysipelatoclostridium, Odoribacter, Ruminococcaceae bacterium, Staphylococcus, and Clostridium methylpentosum group in CON group.

CONCLUSION: B. subtilis and A. oryzae could synergistically enhance the nutritional quality of SBM, positively alter cecal microbiota, and improve the production performance of broiler chickens.},
}

@article {pmid41265441,
year = {2025},
author = {Xu, Y and Wang, Z and Wu, J and Yue, Y and Ren, Y and Pan, Y and Li, J and Liu, C and Borriss, R and Liu, X and Qiao, J and Lee, YW and Wu, H and Dini-Andreote, F and Shen, Q and Xiong, W and Gao, X and Berendsen, RL and Gu, Q},
title = {Keystone Pseudomonas species in the wheat phyllosphere microbiome mitigate Fusarium head blight by altering host pH.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.016},
pmid = {41265441},
issn = {1934-6069},
abstract = {Phyllosphere microbiota play crucial roles in supporting host performance. However, the dynamic changes of phyllosphere-associated microbiome during pathogen infections and their impacts on plant health remain unknown. Here, we found phyllosphere microbes can mitigate wheat Fusarium head blight (FHB), a severe disease caused by Fusarium graminearum (F. graminearum) pathogen that promotes infection by inducing host alkalinization. Using wheat head microbial community profiling and metatranscriptomics, we found Pseudomonas spp. significantly enriched on infected wheat heads. Through isolating 595 bacterial strains from infected wheat heads-including 196 Pseudomonas isolates-we identified certain enriched Pseudomonas isolates capable of producing organic acids that counteract pathogen-induced pH upshift. In vitro experiments confirm the selective promotion of specific host-acidifying Pseudomonas in wheat heads. Field trials confirmed that host-acidifying Pseudomonas strains effectively controlled FHB. These findings highlight the pivotal role of plant-beneficial microbes in host pH regulation and offer innovative avenues for sustainable plant disease control.},
}

@article {pmid41265342,
year = {2025},
author = {Uyeda, KS and Borovik, AS},
title = {Forged in O2: Transition metal ions and the rise of aerobic life.},
journal = {Journal of inorganic biochemistry},
volume = {275},
number = {},
pages = {113147},
doi = {10.1016/j.jinorgbio.2025.113147},
pmid = {41265342},
issn = {1873-3344},
abstract = {The evolution of oxidative metabolism has shaped life on Earth, from ancient anaerobic microorganisms to modern eukaryotes. Central to aerobic life is the ability of metalloproteins to regulate and utilize dioxygen through tightly controlled biochemical processes. Beginning with the emergence of oxygenic photosynthesis and aerobic respiration, the pivotal roles of metalloenzymes in dioxygen activation, utilization and detoxification are then highlighted. Bridging perspectives from bioinorganic chemistry, enzymology, synthetic biology and microbiome science, we discuss how studies of biomimetic molecular complexes and natural and artificial metalloproteins illuminate the structural and functional strategies used to manage dioxygen reactivity. We further consider the systemic roles of metal ions in maintaining redox balance, shaping host-microbe interactions, and contributing to pathological outcomes when misregulated. A foundation is established for understanding the critical roles that metal ions play in dioxygen chemistry that underpins both healthy metabolism and oxidative stress related diseases.},
}

@article {pmid41265278,
year = {2025},
author = {Tian, Y and Hao, F and Xu, G and Qian, Y and Liu, J and Pan, N and Yang, T},
title = {Causal effects of gut microbiome on aortic dissection: A mendelian randomization study.},
journal = {Clinics (Sao Paulo, Brazil)},
volume = {80},
number = {},
pages = {100811},
doi = {10.1016/j.clinsp.2025.100811},
pmid = {41265278},
issn = {1980-5322},
abstract = {INTRODUCTION: Aortic Dissection (AD) is a severe vascular disease with high mortality. While its progression is rapid, the development of AD is a chronic disease process. The gut microbiome may play a crucial role in this process. This study aims to explore the potential causal association between gut microbiome and AD using Mendelian Randomization (MR).

METHODS: This study employed a two-sample MR approach using Genome-Wide Association Study (GWAS) data from the Finnish population to investigate the causal association between gut microbiota and AD. Single Nucleotide Polymorphisms (SNPs) associated with 473 gut microbiota taxa were selected as instrumental variables, and various MR methods were applied to evaluate the causal effects. Sensitivity analyses were conducted to assess the robustness of the results, and a reverse MR analysis was performed to validate the directionality of the associations.

RESULTS: The MR analysis confirmed that Actinomycetales, Bacillales A, Lawsonibacter sp002161175, Prevotella sp002933775, Saccharomonospora, Acidaminococcus fermentans, CAG-110, CAG-177 sp002451755, CAG-177 sp003514385, and Eisenbergiella sp900066775 may exert protective effects, whereas koll11, Magnetospirillum A, Poseidoniaceae, Pseudomonas aeruginosa, Bacteroides eggerthii, CAG-269 sp002372935, and Dorea phocaeense may increase the risk of AD. Sensitivity analyses confirmed the robustness of these findings.

CONCLUSION: This study provides new insights into the role of gut microbiome in AD, identifying specific taxa that may serve as protective or risk factors. Further research is needed to validate these findings in broader populations.},
}

@article {pmid41265274,
year = {2025},
author = {Eichinger, J and Seifert, J and Sáenz, JS and Amin, N and Lorenz, S and Eckel, F and Zollfrank, C and Windisch, W and Brugger, D},
title = {The interaction of microplastics with the ruminal ecosystem in vitro.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140481},
doi = {10.1016/j.jhazmat.2025.140481},
pmid = {41265274},
issn = {1873-3336},
abstract = {Mismanaged plastic waste contaminates marine and terrestrial environments, so farm animals are increasingly exposed to microplastics (MP) in feed. Yet their interactions with the rumen microbiome are largely unknown. We evaluated these interactions in vitro with the Hohenheim Gas Test. Five MP chemical species - polylactide, polyhydroxybutyrate, high‑density polyethylene, polyvinyl chloride and polypropylene - were tested in two particle‑size classes (<125 µm and 125-500 µm) and six doses (0-70 mg per incubation cylinder). Each MP variant was incubated with rumen fluid plus hay or barley. We recorded cumulative gas production, pH and dry‑matter (DM) disappearance, followed by volatile‑fatty‑acid profiling, metaproteomics and metabolomics. MP consistently reduced cumulative gas output independent of polymer type, particle size or dose, but enhanced total DM degradation dose-dependently. In barley incubations, metaproteomics revealed a shift from Bacteroidetes toward Firmicutes and higher abundance of protein categories "replication & repair" and "translation", while "carbohydrate metabolism & transport" and "amino‑acid metabolism" declined. The results show that MPs interact with, and are at least partly degraded by, the ruminal microbiota. Progressive size reduction in the rumen could facilitate MP translocation into animal tissues, underscoring the need for in‑vivo studies on animal health and food‑safety implications.},
}

@article {pmid41265266,
year = {2025},
author = {Fernández-Triana, I and Rubilar, O and Fincheira, P and Fernández-Baldo, MA and Saldivar-Diaz, M and Lora-Peña, OA and Benavides-Mendoza, A and Schoebitz, M and Tighe-Neira, R and Leiva, S and Tortella, GR},
title = {Abiotic multi-stressor co-exposure to hazardous pollutants reveals drought as the primary driver of soil microbiome shifts.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140515},
doi = {10.1016/j.jhazmat.2025.140515},
pmid = {41265266},
issn = {1873-3336},
abstract = {Soil microbial communities are essential for ecosystem functioning, yet their responses to combined abiotic stressors remain unclear, as most studies focus on single-stressor effects. In this work, the combined effects of different drought levels and co-contamination with copper nanoparticles and the fungicide carbendazim on microbial community structure and function in an agricultural soil over 120 days were evaluated. Enzymatic activities, potential nitrification rate, and functional gene abundances (16S and amoB) were measured. Moreover, 16S rRNA metabarcoding was applied to explore microbial diversity and community dynamics comprehensively. Pesticide dissipation kinetics were also assessed. General metabolic and nutrient-cycling enzymes were susceptible to combined stress under SD and ED. Although alpha and beta diversity showed limited differences at the end of the experiment, co-occurrence networks revealed progressive increases in microbial connectivity and negative correlations, indicating structural reorganization. Functional predictions highlighted a shift from nitrogen and phosphorus cycling toward carbon-degradation pathways, suggesting stress-induced trade-offs. Significantly, pesticide dissipation was markedly reduced under SD, with prolonged half-lives and higher residues, reflecting impaired microbial degradation capacity. Collectively, our results demonstrate that drought is the dominant driver of microbial reorganization, amplifying the effects of emerging contaminants on microbial interactions, functional potential, and pollutant fate.},
}

@article {pmid41265168,
year = {2025},
author = {Jiang, Y and Xie, Y and Liu, F and Qin, Y and Zhang, Y and Tang, L and Dong, X and Li, L and Chen, S and Yuan, B and You, Y and Qiu, R},
title = {Biological Validation of the PSC-MCAT: Analyzing Dental Plaque Microbiota Across Caries Risk Levels in Preschoolers.},
journal = {International dental journal},
volume = {76},
number = {1},
pages = {104007},
doi = {10.1016/j.identj.2025.104007},
pmid = {41265168},
issn = {1875-595X},
abstract = {OBJECTIVE: Although Caries Risk Assessment (CRA) tools are widely recognised in preventive dentistry for predicting dental caries risk in children, there is a notable lack of studies addressing CRA within the Chinese population. This study aimed to evaluate the biological validity of the modified caries-risk assessment tool for preschool children (PSC-MCAT) by analysing the oral microbiome of children stratified by caries risk.

MATERIALS AND METHODS: A comprehensive analysis of the oral microbiome was conducted on 72 preschool children categorised into low- (L), moderate- (M), and high-risk (H) groups based on the PSC-MCAT criteria. Next-generation sequencing was employed to assess microbial diversity and structure. Statistical analyses were performed to identify significant differences among the risk groups.

RESULTS: The analysis revealed statistically significant differences in microbial diversity and structure among the caries risk groups (P < .05). Specific caries risk biomarkers, including Scardovia, Prevotella, and Megasphaera, were significantly enriched in the H group (P < .05). Co-occurrence network analysis showed that the M group exhibited a more complex microbial network compared to the H group, while the L group displayed sparse ecological interactions. KEGG pathway analysis identified 8 differentially abundant metabolic pathways among the risk groups. Furthermore, certain biomarkers in the H group, such as Scardovia and Megasphaera, were associated with D-arginine and D-ornithine metabolic pathways (P < .05) and were closely linked to children's oral health behaviours, including sweet food intake frequency and regular fluoride application (P < .05).

CONCLUSION: This study provides the first biological validation of the PSC-MCAT's risk stratification capacity, establishing a mechanistic link between clinical risk tiers and the dynamics of acidogenic pathobionts as well as host-microbe metabolic interactions. These findings offer valuable insights for prognostic predictions and targeted caries management strategies.},
}

@article {pmid41264973,
year = {2025},
author = {See, MS and Ching, XL and Razali, N and Asri, IS and Abdullah, MM and Bidai, J and Rusli, MU and Ma, NL},
title = {Blood heavy metals content and gut microbiota profile in immature and nesting wild green turtles (Chelonia mydas).},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107688},
doi = {10.1016/j.marenvres.2025.107688},
pmid = {41264973},
issn = {1879-0291},
abstract = {Sea turtles live in habitats where they experience chronic exposure to pollutants, such as heavy metals, over the course of their long lifespan. This makes them valuable model organisms for studying the long-term biological impacts of persistent environmental contaminants. Morphological changes are often insufficient to capture the impacts of low-dose exposures, whereas gut microbiota profiling can offer critical insights into host health and adaptive responses to environmental stressors. This study investigated the relationship between heavy metal exposure and gut microbiota composition in green turtles (Chelonia mydas) at immature (IM, n = 10) and nesting (NT, n = 9) stages. Metal concentrations in whole blood were measured using inductively coupled plasma mass spectrometry (ICP-MS), while gut microbiota were characterized via 16S rRNA gene sequencing. The blood of immature turtles exhibited significantly higher concentrations of manganese (Mn), whereas nesting turtles had elevated arsenic (As), lead (Pb), barium (Ba), and strontium (Sr). Analysis of gut microbiota revealed significant differences in both α-Shannon and β-diversity associated with different pollutants, indicate restructuring of microbial communities. PICRUSt2 revealed alteration of carbohydrate, nucleotide, vitamin, and xenobiotic metabolisms among growth stages. Correlation analysis (LEfSe and CCA) further showed that bacterial genera such as Methylophaga and Thermomonas were positively associated with Cd, Pb, and Sr, whereas Lactobacillus and Rodentibacter displayed negative correlations with these metals. Collectively, this highlights the potential of pollutants to compromise host health through microbiome-mediated mechanisms.},
}

@article {pmid41264968,
year = {2025},
author = {Yang, C and Bao, L and Shi, Z and Xv, X and Li, J and Jiang, D and You, L},
title = {Jingning formula alleviates ADHD by restoring gut microbiota dysbiosis and tryptophan metabolic dysfunction.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {269},
number = {},
pages = {117256},
doi = {10.1016/j.jpba.2025.117256},
pmid = {41264968},
issn = {1873-264X},
abstract = {Jingning Fang (JNF), a clinically used herbal medicine for attention deficit hyperactivity disorder (ADHD), demonstrates significant efficacy in alleviating core symptoms such as hyperactivity and impulsivity in pediatric patients. To systematically investigate its therapeutic mechanisms, we implemented an integrated approach encompassing UPLC-Q-TOF/MS-based untargeted metabolomics profiling of brain, serum, and fecal specimens, targeted quantification of tryptophan pathway metabolites across these biological compartments, and gut microbiome characterization via 16S rRNA sequencing. Our analysis revealed a prominently dysregulated metabolic pathway in ADHD, characterized by perturbations in tryptophan metabolism that were particularly pronounced in feces (P < 0.05). Notably, the kynurenic acid (KYNA)/quinolinic acid (QUINA) ratio, a pivotal indicator of kynurenine pathway homeostasis, exhibited robust correlations with both behavioral manifestations and gut microbial ecology. These findings provide a mechanistic basis for JNF's clinical efficacy in ADHD management by highlighting its role in restoring gut microbiome balance and tryptophan metabolic homeostasis.},
}

@article {pmid41264233,
year = {2025},
author = {Yun, Y and Duan, C and He, X and Tang, R and Lan, Y and Lu, M and Liu, T and Fan, X and Fan, Z and Ran, J},
title = {Gut microbiome plasticity explains the altitudinal distribution pattern and adaptability in a small mammal species (Apodemus draco).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0238825},
doi = {10.1128/spectrum.02388-25},
pmid = {41264233},
issn = {2165-0497},
abstract = {Altitudinal distribution patterns of species, a central focus of ecology, predominantly focus on environmental factors and only rarely on the host's intrinsic adaptive capacity. Particularly, the role of gut microbiota has not yet been studied. Here, we used the wild South China Field Mouse (Apodemus draco), a widely distributed small mammal species, as the study subject to investigate the altitudinal distribution pattern of the species and assess how gut microbiota contributes to the formation of this pattern. A total of 219 wild samples were captured in the middle section of the Qionglai Mountains, China, and 121 adult individuals were selected for metagenomic sequencing (e.g., gut microbial diversity, network topology, composition, and functional profiles). Vegetation cover of each sampling quadrat was assessed using Normalized Difference Vegetation Index. Our results indicate that A. draco exhibited a hump-shaped altitudinal distribution, but the peak abundance of A. draco corresponds to lower vegetation cover of habitats. Gut microbial diversity, complexity, robustness, energy harvesting ability, and carbohydrate utilization capacity all peaked at the mid-altitude zone, matching the host's spatial distribution pattern. Furthermore, the gut microbiome in high-altitude A. draco populations facilitates host acclimatization in extreme high-altitude niches by enhancing energy harvesting, hypoxia tolerance, and pathogen resistance.IMPORTANCEWe propose for the first time that the gut microbiome serves as a pivotal factor in structuring the altitudinal distribution pattern of species and further reveal a gut microbiota-mediated adaptive strategy underlying mammalian high-altitude adaptation. These results demonstrate that the gut microbiome fundamentally facilitates host adaptation to ecological niches. The study provides a novel insight into the factors of species' spatial distribution from a gut microbiota perspective.},
}

@article {pmid41264189,
year = {2025},
author = {Mohamad Zain, N and Mohd Amin, I and Abdul Razak, F and Abu Hassan, MI},
title = {Preliminary screening of pomegranate-derived compounds for antimicrobial and anti-virulence effects against cariogenic streptococci.},
journal = {The Saudi dental journal},
volume = {37},
number = {10-12},
pages = {84},
pmid = {41264189},
issn = {1013-9052},
abstract = {As a biofilm-mediated disease, dental caries is primarily attributed to the activity of Streptococcus mutans and Streptococcus sobrinus, key contributors to enamel mineral loss under acidic conditions. Current broad-spectrum antimicrobials disrupt the oral microbiota and carry undesirable side effects, prompting interest in targeted, microbiome-friendly alternatives. This study evaluated the antimicrobial, anti-cariogenic, and cytotoxic properties of pomegranate (Punica granatum) derived compounds, corilagin, ellagic acid, gallocatechin, kaempferol-7-O-glucoside, punicalagin, punicalin, and rutin against cariogenic S. mutans and S. sobrinus, and the commensal S. gordonii. Antibacterial activity was assessed using disc diffusion, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) methods. Anti-virulence effects were evaluated through glycolytic pH drop and cell surface hydrophobicity assays. Cytotoxicity was determined using the brine shrimp lethality assay. Punicalagin, punicalin, and ellagic acid showed strong, selective bactericidal activity against S. mutans and S. sobrinus, with low MICs and MBC/MIC ratios, while sparing S. gordonii. These compounds significantly suppressed acid production, maintaining pH above the critical demineralisation threshold, and reduced surface hydrophobicity in cariogenic strains without affecting the commensal. Most compounds exhibited low toxicity (LC50 > 500 µg/mL), indicating a favourable safety profile. Overall, punicalagin and punicalin demonstrated dual antimicrobial and anti-virulence activity with selective targeting of cariogenic pathogens. These findings support the potential inclusion of punicalagin and punicalin in oral care formulations aimed at preventing dental caries while preserving beneficial oral microbiota. As this is a preliminary screening study, the results should be interpreted cautiously, and further biofilm and host-cell assays are needed to confirm translational potential.},
}

@article {pmid41264167,
year = {2025},
author = {Baek, KW and Yun, K and He, MT and Kim, NK and Kim, JS and Ahn, K and Kim, JH},
title = {Integrated transcriptomic and 16S rRNA analyses reveal colon and brain barrier-preserving effects of red radish (Raphanus sativus L.) sprout supplementation in high-fat diet-fed mice.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41264167},
issn = {2092-9293},
abstract = {BACKGROUND: Radish sprouts (Raphanus sativus L.) are rich in dietary fibers and phytochemicals with antioxidant and anti-inflammatory activities. However, their whole-food effects on the gut-brain axis remain poorly defined.

OBJECTIVE: This study examined the preventive potential of whole-food red radish sprout (RS) powder against high-fat diet (HFD)-induced obesity and cognitive decline in mice, focusing on its effects on barrier integrity, inflammation, oxidative stress, and gut microbiota.

METHODS: Male C57BL/6 mice were fed an HFD for 16 weeks with or without RS powder (low or high dose). Assessments included body and tissue indices, oral glucose tolerance, serum leptin, cognitive performance, oxidative stress in brain, gene expression of tight junction and inflammatory markers in colon and brain, and fecal microbiota profiling using 16S rRNA sequencing.

RESULTS: RS supplementation attenuated HFD-induced weight gain, improved glucose tolerance, and reduced leptin levels, with stronger effects at the higher dose. Cognitive deficits were rescued by RS, accompanied by alleviation of brain oxidative stress and reduced expression of neuroinflammatory genes (Tnf, Il6, Il1b, Aif1, Gfap). RS restored tight-junction genes (Tjp1, Ocln, Cldn1, Jam2, Cdh5) while simultaneously decreasing Cldn2 and pro-inflammatory transcripts, and upregulating Il10. Although alpha diversity was unchanged, beta diversity differed significantly; RS reduced the Firmicutes/Bacteroidota ratio, enriched Akkermansia and Lactobacillus, and suppressed Oscillibacter and Desulfovibrio.

CONCLUSION: Whole-food RS powder prevents HFD-induced obesity and cognitive decline by reinforcing barrier integrity, reducing inflammation and oxidative stress, and reshaping gut microbiota. These findings support RS as a practical functional food for early obesity intervention via gut-brain axis regulation.},
}

@article {pmid41263968,
year = {2025},
author = {Brennan, AA and Renshaw, CP and Tata, SC and Campanella, A and Hartman, R and Carlotz, R and Downs, M and Yurtola, A and Baum, J and Rodriguez, KM and Bertucci, MA and Tal-Gan, Y},
title = {The Quorum Sensing-Controlled Competence Regulon Drives H2O2 Production in Streptococcus gordonii.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00926},
pmid = {41263968},
issn = {2373-8227},
abstract = {Streptococcus gordonii sp. firmicutes is an early colonizer of the oral microbiome and contributes positively to oral health. While this species has been found to produce hydrogen peroxide by spxB expression, the relationship of this expression to the competence regulon has not yet been explored. To this end, this study sought to investigate the connection of the S. gordonii competence regulon quorum sensing (QS) circuitry with downstream proliferative phenotypic expression resulting from competence-stimulating peptide (CSP) exposure, with specific attention to peroxide formation. Following confirmation of the native CSP, RNA-seq was completed to gain insights into transcriptomic variations resulting from CSP incubation. Later, structure-activity relationship (SAR) analyses of the native CSP were completed. The results revealed residues integral to CSP:ComD binding and activation, while indicating which residues were considered dispensable to this process. Phenotypic assessment revealed that peroxide formation was modulated via the competence regulon. Finally, interspecies competition assays were carried out to understand the interactions between S. gordonii and S. mutans, with S. gordonii demonstrating a profound capability of antagonizing S. mutans growth and proliferation. Our results support that this antagonism is mainly attributed to hydrogen peroxide production by S. gordonii. This finding suggests that S. gordonii may be exploited for its beneficial proliferative phenotypes downstream of the competence regulon.},
}

@article {pmid41263913,
year = {2025},
author = {Merrick, B and Prossomariti, D and Kertanegara, M and Wyatt, D and Goldenberg, S},
title = {Facilitators and barriers to recruitment and retention in a feasibility trial of encapsulated faecal microbiota transplant to eradicate carriage of antibiotic-resistant bacteria at an academic hospital in central London: a nested qualitative study.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e104783},
doi = {10.1136/bmjopen-2025-104783},
pmid = {41263913},
issn = {2044-6055},
mesh = {Humans ; London ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Feasibility Studies ; Middle Aged ; Qualitative Research ; Adult ; Focus Groups ; *Patient Selection ; COVID-19/epidemiology ; Aged ; *Carrier State/therapy ; },
abstract = {OBJECTIVES: This nested qualitative study (NQS) aimed to identify facilitators and barriers to the delivery of a substantive randomised controlled trial investigating the eradication of gastrointestinal tract carriage of antibiotic-resistant organisms using encapsulated faecal microbiota transplant (FMT).

DESIGN: NQS within a participant-blinded, randomised, placebo-controlled, single-centre, feasibility trial (RCT)-Feasibility of ERadicating gastrointestinal carriage of Antibiotic-Resistant Organisms (FERARO) (ISRCTN reg. no. 34 467 677)-with data collected via focus groups and analysed using thematic analysis.

SETTING: RCT participants were recruited from a large academic tertiary referral hospital in central London. Focus groups were held at the hospital or via videoconferencing for those unable to travel.

PARTICIPANTS: This study included 13 FERARO study participants across two focus groups. 11 participants were under RCT follow-up and unaware of their treatment allocation, two participants had completed 6-month follow-up and knew whether they had received FMT or matched placebo. Additional data were opportunistically collected on reasons for declining RCT participation.

RESULTS: Participants found FMT to be an acceptable and holistic management strategy and noted positive impacts from RCT participation including enhanced personal health awareness and valuable support from the research team. The time and travel commitment presented the most substantial barrier to RCT participation. Many participants were motivated by a desire to give something back to the UK National Health Service and/or research. Patients' current health status also influenced the decision-making process, and, while infrequently cited, the COVID-19 pandemic added extra complexity likely impacting individuals' willingness to participate.

CONCLUSIONS: While FMT is generally acceptable to participants, logistical barriers such as the time and travel commitment associated with RCT participation need consideration. Effective communication, personal connections and participant education on antimicrobial resistance are likely to be crucial for enhancing recruitment and retention in future trials.

TRIAL REGISTRATION NUMBER: ISRCTN registration number 34 467 677 and EudraCT number 2019-001618-41.},
}

Humans
London
*Fecal Microbiota Transplantation/methods
Male
Female
Feasibility Studies
Middle Aged
Qualitative Research
Adult
Focus Groups
*Patient Selection
COVID-19/epidemiology
Aged
*Carrier State/therapy

@article {pmid41263680,
year = {2025},
author = {Jakubczyk-Słabicka, A and Kasprzak, J and Skonieczna-Żydecka, K and Sławek, J and Górska-Ponikowska, M},
title = {Gut and skin microbiome profiles as promising biomarkers in Parkinson's disease - preliminary results.},
journal = {Neurologia i neurochirurgia polska},
volume = {},
number = {},
pages = {},
doi = {10.5603/pjnns.108273},
pmid = {41263680},
issn = {0028-3843},
}

@article {pmid41263597,
year = {2025},
author = {Ku, M and Taibi, A and Wu, D and Chen, YT and Lopez-Dominguez, L and Yang, Y and Chen, S and Liang, F and Liu, R and Tsao, R and Power, KA and Thompson, LU and Comelli, EM},
title = {Altered mouse cecal microbiome-serum enterolignans relationships in response to dietary lignans ingested through whole flaxseed or flaxseed hull.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03558a},
pmid = {41263597},
issn = {2042-650X},
abstract = {Flaxseed (FS) is rich in bioactive compounds, including fiber and lignans, which provide health benefits largely mediated by gut microbial metabolism. However, gut microbiota responses, including their relationship with fiber- and lignan-derived microbial metabolites (short chain fatty acids (SCFA) and enterolignans enterodiol and enterolactone), remain unclear. We addressed this through administration of an isocaloric flaxseed (FS) or flaxseed hull (FH) diet to female mice, where FH provided a higher amount of fiber and lignan secoisolariciresinol diglucoside compared to FS. Both diets increased cecal SCFA and serum enterolignans concentrations compared to the basal control diet (BD). Compared to FS, FH increased serum secoisolariciresinol, enterodiol, and total lignans, but not SCFA concentrations. FS and FH increased α- and β-diversity and altered microbiota composition and functional potential compared to BD, but no differences were observed between FS and FH, except for altered abundance of select taxa and a limited number of functions. However, the two diets altered the microbial network structure, including keystone species shifts from Intestinimonas in FS to Carnobacterium in FH, and taxa relationships with enterolignans and SCFA. Our findings suggest that while intestinal microbiota composition responses to whole flaxseed result in increased circulating enterolignans and intestinal SCFA production, FH can further elevate serum enterolignans via reorganization of interactions among taxa.},
}

@article {pmid41263574,
year = {2025},
author = {Tang, L and Xie, P and Wang, H and Hong, X and Gong, Z and Zhao, G and Yue, M},
title = {The sex hormone-gut microbiome axis: mechanistic drivers of sex-disparate bacterial infection outcomes and precision clinical interventions.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0023625},
doi = {10.1128/cmr.00236-25},
pmid = {41263574},
issn = {1098-6618},
abstract = {SUMMARYSex disparities in bacterial infections pose significant challenges in clinical microbiology, influencing diagnostic approaches, antimicrobial stewardship, and patient outcomes. Males frequently exhibit heightened severity in conditions like Helicobacter pylori-associated gastritis and Vibrio cholerae outbreaks, whereas females face amplified risks during reproductive phases for pathogens, such as Listeria monocytogenes and Salmonella spp. Beyond genetic and behavioral factors, the bidirectional sex hormone-gut microbiome axis emerges as a key mechanistic driver: estrogens bolster innate immunity and microbial diversity (e.g., enriching short-chain fatty acid-producing taxa like Bifidobacterium), while androgens and progesterone impose immunosuppressive effects, altering colonization resistance and virulence modulation. Microbial contributions-via β-glucuronidase-mediated hormone deconjugation, bile acid biotransformations, and metabolite signaling-further calibrate host responses, as evidenced in Clostridioides difficile recurrence and enterohemorrhagic Escherichia coli virulence upregulation. This review synthesizes epidemiological, preclinical, and emerging clinical data, highlighting the axis's role in pathogen-specific immune evasion and dysbiosis-driven exacerbations. Clinically, these insights advocate for sex-stratified microbiome diagnostics (e.g., 16S rRNA sequencing for risk profiling) and targeted therapies, including hormone-modulated probiotics to restore barrier function, fecal microbiota transplantation to curb antibiotic-associated vulnerabilities, and selective estrogen receptor modulators to enhance clearance in high-risk cohorts. Despite advances, gaps in human longitudinal studies and pathogen-strain interactions limit translation. Future research integrating multi-omics with clinical trials could refine precision interventions, optimizing infection management in diverse populations and aligning with evolving demands for personalized microbiology.},
}

@article {pmid41263569,
year = {2025},
author = {Ding, W and Ling, Z and Liu, X and Zhang, J and Cheng, Y and Zhu, Z and Wu, L and Xu, X and Gao, Y and Hu, X},
title = {Impact of carbapenem-resistant Klebsiella pneumoniae infection on gut microbiota and host immunity: a case-control study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297525},
doi = {10.1128/spectrum.02975-25},
pmid = {41263569},
issn = {2165-0497},
abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a critical global health threat with limited treatment options. While the gut microbiota is a reservoir for opportunistic pathogens and a regulator of host immunity, the reciprocal impact of systemic CRKP infection on gut microbial ecology and immune responses remains poorly defined. In a prospective case-control study, 38 patients with confirmed CRKP infection and 38 matched hospitalized controls without CRKP were enrolled. Fecal samples underwent 16S rRNA gene sequencing to characterize microbial profiles, and serum cytokine levels were quantified using multiplex immunoassays. CRKP infection was associated with significantly reduced microbial diversity and a distinct shift in community structure, characterized by depletion of beneficial commensals (Bacteroides, Faecalibacterium, Roseburia) and enrichment of pathobionts (Klebsiella, Enterococcus). Enterotype analysis revealed a predominance of a Klebsiella/Enterococcus-dominated enterotype in CRKP patients. Functional predictions indicated impaired carbohydrate and butyrate metabolism alongside increased virulence- and resistance-associated pathways. Systemically, patients exhibited elevated pro-inflammatory cytokines (IL-6, TNF-α, IFN-γ) and chemokines (IP-10, MCP-1, RANTES). Correlation analyses linked opportunistic taxa with heightened inflammatory markers, while beneficial short-chain fatty acid producers showed inverse associations. Systemic CRKP infection is associated with profound gut dysbiosis and a hyper-inflammatory immune response. The strong microbiota-immune correlations suggest that the gut microbiota may serve as a biomarker and a potential therapeutic target for mitigating CRKP-associated immune dysfunction, though the directional relationship (cause vs. consequence) between dysbiosis and CRKP infection remains to be elucidated.IMPORTANCECarbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical global threat with limited therapeutic options. This study reveals that systemic CRKP infection is associated with profound gut dysbiosis-characterized by loss of beneficial commensals (e.g., Faecalibacterium) and expansion of pathobionts (e.g., Klebsiella, Enterococcus)-as well as a hyperinflammatory immune response. We demonstrate strong correlations between specific microbial taxa and host cytokines, suggesting that the gut microbiome may hold potential as a biomarker and therapeutic target. These findings enhance our understanding of host-microbe interactions in CRKP infection and support the exploration of microbiota-based therapies. However, further studies, including longitudinal and animal models, are needed to clarify whether gut dysbiosis directly influences CRKP outcomes or is a secondary consequence.},
}

@article {pmid41263392,
year = {2025},
author = {Zhao, R and Lu, Y and Xu, Q and Ren, H and Li, H and Gao, J and Cui, H and Yuan, Z and Cao, B and Wei, B},
title = {Gut blautia coccoides-derived 5Z-dodecenoic acid attenuates chronic psychological stress-induced gastric cancer progression.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004080},
pmid = {41263392},
issn = {1743-9159},
abstract = {BACKGROUND: Chronic psychological stress is a critical oncogenic factor of gastric cancer (GC). However, the mechanisms underlying stress-induced malignant progression remain largely unknown. Gut microbiota dysregulation is tightly associated with cancer development and metabolism.

MATERIALS AND METHODS: Chronic unpredictable mild stress (CUMS) modeling was used to prepare mice suffering from chronic psychological stress. 16s rRNA sequencing and Q300 targeted metabolite quantification were jointly conducted to depict landscapes of gut microbiome and metabolomics of CUMS mice. Fecal microbiota transplantation was employed to investigate the functions of gut microbial communities in regulating CUMS-mediated GC growth. Drug affinity responsive target stability, surface plasmon resonance and molecular docking assays were performed to screen direct target proteins of 5Z-dodecenoic acid. The interactions between RIOK2 and BYSL were verified with co-immunoprecipitation and GST pull-down and fluorescent co-localization analysis. A series of experiments for malignant behaviors and glycolysis and subcutaneous tumor transplantation were employed to detect alterations of GC cell phenotypes ex vivo and in vivo, respectively.

RESULTS: Microbiome and metabolomics collectively demonstrated disrupted gut microbial communities and metabolic patterns. Particularly, Blautia coccoides-derived 5Z-dodecenoic acid was predominately declined by CUMS. Supplementation with Blautia coccoides or 5Z-dodecenoic acid effectively mitigated the negative effects of CUMS on glycolysis and malignancy. Mechanistically, 5Z-dodecenoic acid directly inhibits the functions of RIOK2, which maintained ectopic glycolysis and malignant behaviors. RIOK2 further interacted with BYSL and maintained its properties of potentiation of GC progression and metabolism.

CONCLUSION: Our findings advance the insights of Blautia coccoides-derived 5Z-dodecenoic acid implicated in chronic psychological stress-induced GC progression and provide novel strategies for dampening GC progression.},
}

@article {pmid41263210,
year = {2025},
author = {Zhukova, NG and Sayfitdinkhuzhaev, ZF and Israilova, GM and Bustonov, OY and Nasriddinova, NA and Gaponova, OV and Zhukova, IA and Masenko, AY},
title = {[«Brain-gut-microbiome» axis in patients with Parkinson's disease].},
journal = {Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova},
volume = {125},
number = {11. Vyp. 2},
pages = {18-23},
doi = {10.17116/jnevro202512511218},
pmid = {41263210},
issn = {1997-7298},
mesh = {Humans ; *Parkinson Disease/microbiology/metabolism/physiopathology ; *Gastrointestinal Microbiome ; *Brain/metabolism ; alpha-Synuclein/metabolism ; *Brain-Gut Axis ; },
abstract = {Parkinson's disease (PD) is one of the most common motor neurological diseases. The clinical presentation of PD includes both motor symptoms (hypokinesia, muscle rigidity, and tremor) and non-motor manifestations (asthenia, depression, hyposmia), as well as cognitive disorders. The primary link in PD pathogenesis is considered to be the accumulation of pathological α-synuclein; however, neuroinflammation, oxidative stress, mitochondrial dysfunction, and dysregulation of the Brain-gut microbiome axis also contribute to the pathological processes. This review of modern medical literature, encompassing domestic and foreign authors, summarizes recent studies on the significance of gastrointestinal tract changes in PD patients. The analysis revealed the involvement of the microbiome and specific bacterial taxonomic groups in the development of PD. In addition, the accumulation of α-synuclein, according to recent data, begins specifically in the nerve plexuses of the intestine and then spreads along the nerves upward into the central nervous system, affecting the substantia nigra, in particular.},
}

Humans
*Parkinson Disease/microbiology/metabolism/physiopathology
*Gastrointestinal Microbiome
*Brain/metabolism
alpha-Synuclein/metabolism
*Brain-Gut Axis

@article {pmid41263129,
year = {2025},
author = {Mesiha, M and Cumbermack, M and Kim, J and White, R and Lin, T and Rubin, J and Jotwani, R},
title = {How pro-inflammatory diets influence perioperative outcomes.},
journal = {Pain management},
volume = {},
number = {},
pages = {1-6},
doi = {10.1080/17581869.2025.2591598},
pmid = {41263129},
issn = {1758-1877},
abstract = {Recent evidence shows that pro-inflammatory diets-high in saturated fats, added sugars, and ultra processed foods-have been linked to elevated levels of cytokines like interleukin-6 (IL-6) and tumor necrosis factor (TNF), showing a marked increase in systemic inflammation, disrupted immune function and altered anesthetic drug metabolism. These effects have been linked to prolonged recovery, impaired wound healing, and increased complication rates. Additionally, a pro-inflammatory diet changes the gut microbiome, impacting pain perception, opioid sensitivity and stress response by the gut-brain axis. On the contrary, an anti-inflammatory diet reduces inflammatory markers and is associated with a shorter hospital stay. This review synthesizes data from randomized controlled trials (RCT), meta-analyses, and mechanistic studies from 2000-2025, emphasizing literature on omega-3 fatty acids, specialized pro-resolving mediators (SPMs), and short-chain fatty acids (SCFAs). Targeted interventions such as education on nutrition and dietary assessment risk could enhance surgical recovery. Perioperative interventions discussed include pre/probiotic supplementation, omega-3 fatty acid administration, and also dietary counseling as part of Enhanced Recovery After Surgery (ERAS) pathways.},
}