@article {pmid41704312,
year = {2026},
author = {Zhang, X and Sha, L and Mai, Y and Xu, J and Nizamani, MM and Fang, F},
title = {Coastal gradients and human disturbance shape bacterial and fungal rhizosphere microbiomes of Heliotropium arboreum in Hainan, China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1774048},
pmid = {41704312},
issn = {1664-302X},
abstract = {Coastal ecosystems in Hainan exhibit steep sea-land gradients in salinity and nutrient availability, yet the rhizosphere microbiome of the pioneer shrub Heliotropium arboreum remains poorly understood. We investigated bacterial and fungal communities across seven coastal sites using replicated transects from seaward to shrub-belt to inland zones, and linked community patterns to soil physicochemical properties and human disturbance. Bacterial communities consistently showed higher richness, evenness, and compositional stability than fungal communities. Alpha diversity increased from seaward to inland zones for both groups, with a stronger gradient in fungi. Community composition was dominated by Proteobacteria and Planctomycetota in bacteria and Ascomycota in fungi, with distinct dominant genera across zones and sites. β-diversity analyses revealed clear differentiation of microbial communities among zones and locations, with fungi showing stronger turnover and site separation than bacteria, indicating higher sensitivity to environmental filtering and disturbance. Redundancy analysis indicated that fungal communities were primarily structured by available potassium, total nitrogen, and soil organic carbon, whereas bacterial communities were most strongly associated with soil pH (7.468-9.613 across sites) and nitrate concentrations. Functional profiling suggested complementary roles in decomposition and nitrogen cycling, and human-disturbed sites showed higher predicted pathogenic potential. Overall, H. arboreum hosts an environmentally filtered rhizosphere microbiome shaped jointly by coastal gradients and disturbance, with fungi responding more strongly than bacteria to spatial and environmental variation.},
}

@article {pmid41704310,
year = {2026},
author = {Romero-Rivera, M and Fernández-de-Bobadilla, MD and Beltrán, M and Del Campo, R and Avendaño-Ortiz, J and Herencias, C},
title = {Genome assembly and functional predation analysis of novel Bdellovibrio isolates from human gut microbiota.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1752098},
pmid = {41704310},
issn = {1664-302X},
abstract = {INTRODUCTION: Predatory bacteria of the Bdellovibrio and like organisms (BALOs) have long been postulated as living antimicrobials, yet their occurrence and ecological roles within human-associated microbiota have remained uncertain due to the absence of culturable human-derived isolates. Here, we report the first successful isolation and comprehensive characterization of viable Bdellovibrio bacteriovorus from human fecal samples.

METHODS: Targeted enrichment was applied to five pooled fecal samples to facilitate predator recovery. We performed whole-genome sequencing on the isolates and conducted comparative genomics across 162 publicly available Bdellovibrio genomes. Additionally, pangenome analysis of 22 high-quality genomes and phenotypic assays against clinical pathogens were conducted to assess genomic diversity, prey specificity, and biosafety profiles.

RESULTS: Despite extremely low natural abundance, targeted enrichment recovered predators in two of five pooled samples, which produced characteristic lytic plaques. Sequencing revealed >99% average nucleotide identity to reference strain HD100 with only 26 core single-nucleotide polymorphisms across both isolates, indicating minimal divergence between human-associated and environmental lineages. Comparative genomics showed that only 10.4% of public genomes fulfill criteria for B. bacteriovorus sensu stricto. Pangenome analysis revealed a stable, highly conserved core (~2,500-2,650 genes) and an expanding accessory genome. Phenotypically, the human-derived isolates displayed narrower prey ranges concentrated on Pseudomonas spp., including multidrug-resistant clinical strains, and no acquired virulence factors were detected.

DISCUSSION: Collectively, these findings suggest predation in the human gut and that viable Bdellovibrio could be natural, genomically conserved members of the intestinal ecosystem. This work advances a testable keystone-predator framework for human microbiome ecology and opens an ecologically informed therapeutic pathway in which human-associated Bdellovibrio may help control multidrug-resistant pathogens while supporting microbiota homeostasis.},
}

@article {pmid41704005,
year = {2026},
author = {Shi, W and Xie, R and Zhang, H and Su, S and Tan, J and Sun, Y and Guo, J},
title = {Additive effects of nitrogen deficiency and water stress on reassembly of the rhizosphere microbiome.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71010},
pmid = {41704005},
issn = {1469-8137},
support = {32372808//National Natural Science Foundation of China/ ; 32202468//National Natural Science Foundation of China/ ; 32102401//National Natural Science Foundation of China/ ; JCYJ20220530145216037//Shenzhen Science and Technology Program/ ; JCYJ20230807111217035//Shenzhen Science and Technology Program/ ; JCYJ20250604174526034//Shenzhen Science and Technology Program/ ; JCYJ20250604174524032//Shenzhen Science and Technology Program/ ; 2024SKLBC-KF05//State Key Laboratory of Biocontrol (Sun Yat-sen University)/ ; },
abstract = {Rhizosphere microbial symbioses confer advantages to host plants under environmental stress. However, the effect of multiple stressors on triggering rhizomicrobiome reassembly remains poorly understood, as stress effects can be additive, antagonistic, or synergistic. Tomato was used as a model plant to investigate the interactions between nitrogen deficiency and two contrasting water stresses (drought and waterlogging) on the reassembly of rhizosphere bacterial and fungal communities through quantitative microbiome profiling. The combination of nitrogen deficiency with drought or waterlogging increased α-diversity, except for bacteria under the combined stress of nitrogen deficiency and drought. Nitrogen deficiency generally reduced the abundance of taxonomic groups, with this reduction exacerbated under drought but reversed under waterlogging, particularly for bacteria. Similar results were observed for the abundance of bacterial functional guilds and dominant microbial taxa. The interactive effects of nitrogen deficiency and water stress on microbial α-diversity, as well as on the abundance of taxonomic groups, functional guilds, and dominant taxa were predominantly additive. Additive interactions dominated rhizomicrobiome reassembly in response to nitrogen deficiency and water stress, with distinct response patterns observed between bacterial and fungal communities. This study provides new insights into rhizomicrobiome dynamics under multiple abiotic stressors.},
}

@article {pmid41703989,
year = {2026},
author = {Wang, Q and Hu, Z and Wang, Y and Guo, S and Zhang, X and Ren, Y and Li, J and Li, X and Cui, H},
title = {Lactobacillus paragasseri LG-1 Alleviates Urticaria-Like Symptoms in Mice via Modulation of Gut Microbiota, Hypoxanthine and Uric Acid.},
journal = {Microbial biotechnology},
volume = {19},
number = {2},
pages = {e70316},
doi = {10.1111/1751-7915.70316},
pmid = {41703989},
issn = {1751-7915},
support = {202303021221224//Fundamental Research Program of Shanxi Province/ ; J202301E036//Bethune Charitable Foundation/ ; 2023RC009//The Youth Science and Technology Innovation Talent Project Four Batches of Shanxi Province/ ; 2025C02080//The Key Research and Development Plan of Zhejiang Province/ ; 2021DG700024-ZZ202210//The State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ ; },
mesh = {Animals ; *Uric Acid/blood/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Lactobacillus/growth & development/metabolism/physiology ; *Hypoxanthine/blood/metabolism ; Disease Models, Animal ; *Probiotics/administration & dosage ; RNA, Ribosomal, 16S/genetics ; Female ; DNA, Ribosomal/chemistry/genetics ; },
abstract = {Chronic Spontaneous Urticaria (CSU) is an immunoinflammatory disorder with complex pathogenesis. Emerging evidence implicates that gut microbiota dysbiosis plays a pivotal role in this pathological network. Integrated 16S rRNA sequencing and untargeted metabolomics revealed distinct CSU-associated signatures, including significant reductions in Lactobacillus abundance and elevated serum uric acid (UA) and hypoxanthine levels. Functional screening identified Lactobacillus paragasseri LG-1 from breast milk as a potent purine-metabolising strain, demonstrating significant hypoxanthine and UA degradation in vitro. In an ovalbumin (OVA)-induced urticaria murine model, LG-1 administration demonstrated marked reductions in serum UA and hypoxanthine concentrations, alleviated clinical manifestations, and suppressed inflammation via TLR4-NF-κB pathway inhibition. Moreover, it modulated gut microbial composition by promoting Lactobacillus proliferation while restraining pathogenic bacteria. These findings collectively established that LG-1 exerted dual therapeutic effects through uric acid/hypoxanthine degradation and microbiome remodelling. Our study provides compelling evidence for microbiome-targeted strategies in CSU management, highlighting LG-1 as a promising therapeutic candidate.},
}

Animals
*Uric Acid/blood/metabolism
*Gastrointestinal Microbiome
Mice
*Lactobacillus/growth & development/metabolism/physiology
*Hypoxanthine/blood/metabolism
Disease Models, Animal
*Probiotics/administration & dosage
RNA, Ribosomal, 16S/genetics
Female
DNA, Ribosomal/chemistry/genetics

@article {pmid41703963,
year = {2026},
author = {Skoog, T and Yang, Y and Olah, P and Katayama, S and Karisola, P and Smith, C and Weidinger, S and Barker, J and Lauerma, A and Andersson, B and Homey, B and Fyhrquist, N and Kere, J and Alenius, H and , },
title = {Integrated Methylome-Transcriptome Analysis Reveals Epigenomic Remodeling and Rho GTPase-Linked Immune-Epithelial Crosstalk in Atopic Dermatitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70259},
pmid = {41703963},
issn = {1398-9995},
support = {//Seventh Framework Programme/ ; //Innovative Medicines Initiative/ ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by immune dysregulation and epithelial barrier dysfunction. Although transcriptional changes in AD skin are increasingly well characterized, DNA methylation patterns remain less well understood.

METHODS: Here, we present an integrated analysis of matched DNA methylomes, transcriptomes, and microbiomes from lesional (n = 40), adjacent non-lesional (n = 38), and healthy control (n = 40) skin, using complementary cell-type-adjusted models.

RESULTS: We identified thousands of differentially methylated regions (DMRs) across all pairwise contrasts (lesional vs. healthy: n = 13,514; lesional vs. non-lesional: n = 4591; non-lesional vs. healthy: n = 1716), including both hyper- and hypo-methylated regions with balanced effect sizes. A core subset of DMRs persisted after methylation-based adjustment, whereas the extensive lesional vs. non-lesional set was largely composition-driven. Integration with transcriptomic co-expression networks linked DMRs to immune-epithelial modules, and 225 DMR-gene pairs showed significant anti-correlation (FDR < 0.05). Lesional skin with dominant Staphylococcus aureus colonization differed at 92 DMRs compared with absent-colonized skin, of which 70 also overlapped with local severity. Pathway analyses consistently highlighted Rho GTPase and actin-junctional programs across analytic layers, suggesting that Rho GTPase signaling is a central integrator of immune, epithelial, and microbial interactions in AD.

CONCLUSIONS: Our study underscores the importance of epigenomic remodeling in AD and highlights potential avenues for precision intervention in chronic inflammatory skin disease.},
}

@article {pmid41703894,
year = {2026},
author = {Kamath, S and Chan, NSL and Joyce, P},
title = {GLP-1 agonists and the gut microbiome: A bidirectional relationship.},
journal = {British journal of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bcp.70487},
pmid = {41703894},
issn = {1365-2125},
support = {2022-CF-EMCR-004-25314//Hospital Research Foundation/ ; },
abstract = {Glucagon-like peptide-1 (GLP-1) receptor agonists have transformed the management of type 2 diabetes mellitus (T2DM) and obesity, yet their interactions with the gut microbiome remain an emerging frontier in pharmacological and metabolic research. Mounting evidence suggests that the gut microbiota modulates GLP-1 secretion via microbial metabolites, including short-chain fatty acids and bile acid derivatives, while GLP-1 agonists reciprocally reshape microbial composition, influencing metabolic outcomes beyond their classical incretin functions. This bidirectional interplay has profound implications for precision medicine, as gut microbial signatures have been associated with variability in therapeutic response, raising the possibility that microbiome features could contribute to response stratification in future studies. Advances in pharmacomicrobiomics, multiomics integration and computational modelling now enable a more refined dissection of these interactions, illuminating potential microbial targets for intervention. Study discrepancies may arise from variations in host diet, baseline microbiome composition and genetic factors influencing GLP-1 signalling. Future studies should incorporate stratified analyses accounting for these confounders to understand causative mechanisms. This review collates current evidence on the microbiome-mediated modulation of GLP-1 dynamics, evaluates the pharmacomicrobiomic impact of GLP-1 agonists and outlines future research directions at the interface of gut microbiota and incretin biology. By unravelling the complexities of this host-microbe-drug axis, the field moves closer to a paradigm of personalized metabolic medicine, where future GLP-1 therapeutic strategies may consider host metabolic and microbial context, optimizing efficacy and minimizing variability in patient response.},
}

@article {pmid41703879,
year = {2026},
author = {Gialluisi, K and De Vero, L and Petruzzino, G and Verrone, L and Perrone, G and Moretti, A and Capozzi, V and Ferrara, M},
title = {Cryopreservation of fermented table olives microbiomes: an integrative case study on viability, functional stability, and biobanking applications.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118430},
doi = {10.1016/j.foodres.2026.118430},
pmid = {41703879},
issn = {1873-7145},
mesh = {*Cryopreservation/methods ; *Olea/microbiology ; *Microbiota ; Fermentation ; Biological Specimen Banks ; Cryoprotective Agents ; Microbial Viability ; *Fermented Foods/microbiology ; Glycerol ; *Food Microbiology ; Dimethyl Sulfoxide ; Food Storage ; Iridoids ; },
abstract = {Microorganisms and their assembly in composite microbiomes play a crucial role in food fermentation, significantly influencing product quality, safety, and nutritional value. Preserving these microbiomes in culture collections is essential for maintaining biodiversity and supporting bio-based innovation in sustainable food systems. However, the long-term conservation of complex microbiomes remains challenging due to microbial heterogeneity and sensitivity to preservation methods. This study evaluated the effectiveness of two cryopreservation protocols for the long-term storage of microbiomes from naturally fermented table olives (cv. Leccino), a traditional Mediterranean diet staple food. Glycerol and dimethyl sulfoxide (DMSO), both at 15% (v/v), were used as cryoprotectants and microbiome samples were stored at -140 °C. Microbial viability, taxonomic composition, and metabolic functionality were assessed over one year using culture-dependent techniques, RNA-based metabarcoding, and Biolog® EcoPlate profiling. Moreover, the oleuropein degradation was evaluated in microbiome samples recovered after one year of cryopreservation. Results indicated that the viability of the microbial consortium slightly decreased, regardless of the cryoprotectant used, and no significant changes in the metabolic profile were observed. In addition, the metabarcoding analysis revealed no significant differences in relative abundances after the storage period. The study confirmed the effectiveness of the cryopreservation method, proper maintenance of the microbial consortium viability and functionality after long-term storage. These findings support the feasibility of microbiome biobanking for fermented foods and highlight the importance of tailored preservation strategies to ensure the stability and functionality of microbial consortia. This approach contributes to the conservation of microbial resources, reproducibility in microbiome science, and the development of high-quality standardisation in fermented products.},
}

*Cryopreservation/methods
*Olea/microbiology
*Microbiota
Fermentation
Biological Specimen Banks
Cryoprotective Agents
Microbial Viability
*Fermented Foods/microbiology
Glycerol
*Food Microbiology
Dimethyl Sulfoxide
Food Storage
Iridoids

@article {pmid41703844,
year = {2026},
author = {Fang, X and Pu, Q and Qu, A and Wang, C and Shen, T and Wu, S and Li, M and Sui, M and Ji, Z and Huang, Y},
title = {Mechanisms of phenolic conversion in anaerobic fermentation of tea leaves revealed by integrating microbiome and metabolome analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118381},
doi = {10.1016/j.foodres.2026.118381},
pmid = {41703844},
issn = {1873-7145},
mesh = {*Fermentation ; *Phenols/metabolism/analysis ; *Plant Leaves/microbiology/metabolism/chemistry ; *Microbiota ; *Tea/microbiology/chemistry/metabolism ; *Metabolome ; Anaerobiosis ; Metabolomics/methods ; Bacteria/metabolism ; *Camellia sinensis/microbiology ; Flavonoids/metabolism ; },
abstract = {To systematically investigate the phenolic transformation mechanisms during tea anaerobic fermentation, the changes in phenolics and microbial communities of pickled teas under varying extrusion degrees were analyzed by combining metabolomics and microbiomics. The changes in 118 differential phenolics (p < 0.05, variable importance in projection >1.0, and fold change >1.2 or < 1/1.2) revealed that anaerobic fermentation drives the bioconversion of bound phenolics into free phenolics and their derivatives in tea leaves. Additionally, the potential metabolic pathways of tea phenolics in anaerobic fermentation were comprehensively proposed, mainly including hydrolysis of polymerized/galloylated catechins, hydrolysis of flavonoid glycosides, and hydrolysis of galloylated phenolics to release gallic acid and its further derivatization. The degree of extrusion significantly influenced microbial community succession: high-extrusion enriched Enterobacter, Cladosporium, Setophoma, and Vishniacozyma, enhancing the hydrolysis of flavonoid glycosides and depsides, while light-extrusion promoted Candida, Cyberlindnera, Lactobacillus, and Pantoea, favoring the accumulation of free phenolics and their derivatives. These findings establish a mechanistic link between microbial ecology and phenolic biotransformation, providing a foundation for precision fermentation in tea processing.},
}

*Fermentation
*Phenols/metabolism/analysis
*Plant Leaves/microbiology/metabolism/chemistry
*Microbiota
*Tea/microbiology/chemistry/metabolism
*Metabolome
Anaerobiosis
Metabolomics/methods
Bacteria/metabolism
*Camellia sinensis/microbiology
Flavonoids/metabolism

@article {pmid41703840,
year = {2026},
author = {Mo, Q and Qin, M and Liang, H and Wei, L and Li, Y and Qin, Y and Tang, L and Liang, J and Qian, C and Liang, Y and Luo, S and Wei, Y and Kong, L and Cheng, J},
title = {Lactiplantibacillus pentosus JWN01 and Lactiplantibacillus plantarum JWN02 attenuate renal fibrosis and pathological autophagy in hyperuricemic nephropathy via gut-kidney axis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118376},
doi = {10.1016/j.foodres.2026.118376},
pmid = {41703840},
issn = {1873-7145},
mesh = {Animals ; *Probiotics/pharmacology ; *Hyperuricemia/complications ; *Autophagy/drug effects ; Gastrointestinal Microbiome ; Fibrosis ; Mice ; *Kidney Diseases/pathology ; *Kidney/pathology ; Male ; Uric Acid/blood ; Humans ; *Lactiplantibacillus plantarum ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {Hyperuricemic nephropathy (HN) is a worldwide metabolic disorder marked by uric acid (UA) imbalance and renal tubulointerstitial fibrosis, yet therapies that both lower UA and prevent fibrosis remain limited. Targeting the gut-kidney axis with probiotics is a promising strategy, but most candidates are food-derived and not human-adapted. We isolated two Lactiplantibacillus strains, Lactiplantibacillus pentosus JWN01 and Lactiplantibacillus plantarum JWN02, from the healthy newborn skin representing a relatively unperturbed, early-life human microbiome. In vitro, these two human-derived probiotic strains showed robust survival under simulated gastrointestinal conditions and efficiently degraded UA precursors (inosine, guanosine). In Uox[-]/[-] mice, oral supplementation with these probiotics for 12 weeks significantly reduced serum UA levels, improved renal function, and regulated key urate transporters, such as ABCG2, GLUT9, and OAT1, in kidney and ileum. The treatment also reinforced intestinal barrier integrity by upregulating tight junction proteins (Claudin-1, Occludin, ZO-1) and alleviated renal fibrosis by inhibiting the TGF-β1/SMAD3 signaling pathway. Gut microbiome analysis showed that JWN01 and JWN02 administration reshaped the microbial composition by decreasing potentially harmful genera (Mammaliicoccus, Staphylococcus, Corynebacterium) and enriching beneficial taxa (Muribaculaceae, Lactiplantibacillus, Akkermansia). This microbial shift was accompanied by partial restoration of disturbed gut metabolites, including Coenzyme Q10 and p-cresol sulfate. Proteomic profiling of proximal tubules, along with subsequent validation, demonstrated that intervention with JWN01 and JWN02 suppressed pathological autophagy-evidenced by reduced ULK1, LC3A/B, and Beclin-1 expression, and increased P62 levels. Notably, the potential inflammation-related biomarkers MSP and IBA1, elevated in HN, were reversed following probiotic treatment. Together, these findings indicate that L. pentosus JWN01 and L. plantarum JWN02 confer protective effects against HN through modulation of the gut-kidney axis, supporting their potential as functional probiotics for dietary management of hyperuricemia.},
}

Animals
*Probiotics/pharmacology
*Hyperuricemia/complications
*Autophagy/drug effects
Gastrointestinal Microbiome
Fibrosis
Mice
*Kidney Diseases/pathology
*Kidney/pathology
Male
Uric Acid/blood
Humans
*Lactiplantibacillus plantarum
Mice, Inbred C57BL
Disease Models, Animal

@article {pmid41703759,
year = {2026},
author = {Gigl, F and Abdullahi, M and Benkwitz-Bedford, S and Eastwood, N and Zhou, J and Hollert, H and Orsini, L},
title = {Challenging Evolutionary Paradigms: Daphnia Populations Resurrected From Unpolluted Environments Show Enhanced Detoxification Ability to Aromatic Pollutants.},
journal = {Molecular ecology},
volume = {35},
number = {4},
pages = {e70272},
doi = {10.1111/mec.70272},
pmid = {41703759},
issn = {1365-294X},
support = {101112877//Horizon Europe HORIZON-IA/ ; 101057014//Horizon Europe Partnership for the assessment of Risk of Chemicals/ ; //Goethe University Academy for Early Career Researchers/ ; //RobustNature Excellence Cluster Initiative/ ; },
mesh = {Animals ; *Daphnia/genetics/drug effects/microbiology ; *Water Pollutants, Chemical/toxicity ; Gastrointestinal Microbiome/drug effects/genetics ; *Polycyclic Aromatic Hydrocarbons/toxicity ; Transcriptome ; Phenanthrenes/toxicity ; Inactivation, Metabolic/genetics ; *Biological Evolution ; },
abstract = {Understanding how organisms respond to chemical stress requires disentangling genetically encoded (constitutive) adaptations from environmentally induced (plastic) responses. This challenge is particularly acute for polycyclic aromatic hydrocarbons (PAHs), widespread aquatic pollutants with well-documented toxicity, where mechanisms of tolerance, including host-microbiome interactions, are unexplored. We used Daphnia magna, a keystone freshwater species with clonal reproduction and dormant egg banks to test population-specific (constitutive) responses to phenanthrene (PHE), a common PAH. Populations resurrected from contrasting historical environments were exposed to sub-lethal PHE concentrations, and both host transcriptomes and gut microbiomes were profiled to assess induced responses. Transcriptomic analysis revealed distinct, population-specific responses in detoxification, stress signalling, and endocrine regulation. Unexpectedly, the semi-pristine (pollution-naïve) population showed higher tolerance, with robust induction of cytochrome P450 and hormonal pathways, while populations historically exposed to pollution exhibited chronic stress signatures and reduced plasticity. Gut microbiome profiling revealed PHE-induced functional shifts across populations, with the pollution-naïve population showing broader stress-associated responses and historically exposed populations to pollutants exhibiting more detoxification-focused microbiome profiles. Both host and microbial datasets consistently showed enrichment in pyruvate and carbon metabolism, indicating coordinated energy mobilisation and detoxification responses. Our results show that historical exposure to chemical stress and wider pollution does not necessarily confer enhanced physiological tolerance to PHE. Instead, hydrocarbon stress elicits coordinated, functionally linked responses across the host and its associated microbiome. By leveraging Daphnia's unique ecology and evolutionary history, we disentangle constitutive from plastic responses and show that microbiome functional reconfiguration under PHE exposure is coordinated with host responses, contributing to population-specific profiles.},
}

Animals
*Daphnia/genetics/drug effects/microbiology
*Water Pollutants, Chemical/toxicity
Gastrointestinal Microbiome/drug effects/genetics
*Polycyclic Aromatic Hydrocarbons/toxicity
Transcriptome
Phenanthrenes/toxicity
Inactivation, Metabolic/genetics
*Biological Evolution

@article {pmid41703668,
year = {2026},
author = {Rezaei Somee, M and González-Rosales, C and Gralka, M and Turner, S and Bertilsson, S and Dopson, M and Mehrshad, M},
title = {Cross-feeding options define genome evolution and community assembly of deep groundwater microbiome.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00865-z},
pmid = {41703668},
issn = {2524-6372},
abstract = {BACKGROUND: Deep groundwaters populated by diverse and active microbes are among the most energy and nutrient-limited ecosystems. Characteristics of this ecosystem (including nutrient and dispersal limitations, low cell densities, and an episodic growth strategy) interactively underpin the so far elusive eco-evolutionary dynamics of its microbiome. Here, we used genome-resolved modular metabolic analyses of disconnected deep groundwater sites in the Fennoscandian Shield to test how eco-evolutionary constraints in these deep groundwater ecosystems shape microbial genome architecture, metabolic versatility, and community assembly at different depths.

RESULTS: The analysis revealed that lineages with larger genomes (≥ 2.6 Mb) maintained higher population sizes in the deepest and most oligotrophic groundwaters, whereas lineages with known metabolic dependencies, such as and DPANN, declined in relative abundance with depth. This pattern was interpreted as consistent with limited opportunities for sustained metabolic cross-feeding in these ecosystems. Moreover, while similar ecological niches based on cross-feeding interactions and potential primary production were available across different boreholes, distinct microbial lineages appeared to occupy these niches at each site.

CONCLUSION: The findings provided new insights into the role of metabolic cross-feeding in genome evolution and community assembly of deep groundwater microbiomes. By extending the streamlining theory, this study underscores the critical influence of ecological interactions, particularly metabolic exchanges, in shaping microbial life under severe nutrient limitation, offering new insights into subsurface microbial communities.},
}

@article {pmid41703218,
year = {2026},
author = {Warp, PV and Bilik, SM and Ferrari, LM and Keri, JE},
title = {Prebiotics, Probiotics, and Postbiotics for Acne Vulgaris: A Systematic Review.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {41703218},
issn = {2193-8210},
abstract = {INTRODUCTION: Microbiome-modulating therapies including prebiotics, probiotics, and postbiotics have been increasingly investigated as adjuncts or alternatives for managing acne vulgaris through effects on the gut-skin axis, inflammation, and barrier function. The objective of this systematic review is to characterize the safety and efficacy of oral and topical prebiotics, probiotics, and postbiotics in managing acne vulgaris.

METHODS: We conducted a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)-guided systematic review of randomized controlled trials, cohort studies, and case-control studies evaluating oral and topical prebiotics, probiotics, and postbiotics for acne vulgaris from inception to August 2025 in PubMed, Embase, Web of Science, and Cochrane. Inclusion criteria comprised clinical studies reporting on safety and/or efficacy of topical and/or oral prebiotic, probiotic, and postbiotic therapy in patients with acne vulgaris.

RESULTS: In total, 33 studies evaluating 2112 total patients were included, with treatment durations of 4-25 weeks; 5 prebiotic, 24 probiotic, and 7 postbiotic studies were included, with 2 studies comparing prebiotics and probiotics and 1 study comparing prebiotics and postbiotics against each other. Safety was favorable across all modalities with no serious adverse events reported. Pooled mean total lesion reductions were -37.2% for prebiotics, -45.2% for probiotics, and -49.5% for postbiotics, versus -37% for controls.

CONCLUSIONS: Prebiotic, probiotic, and postbiotic therapies appear to be safe and associated with clinically meaningful lesion reductions in acne. They may increase tolerability and add additional efficacy to standard acne treatments including topical and oral antibiotics and retinoids. Probiotics currently have the strongest evidence base, while prebiotics and postbiotics are promising adjuncts. Larger, standardized randomized trials are needed to clarify comparative efficacy, optimal formulations, and durability.},
}

@article {pmid41703109,
year = {2026},
author = {Preissner, R and Yang, Z and Preissner, S and Thöne-Reineke, C},
title = {Contact with dogs is associated with improved survival in cancer patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39952-z},
pmid = {41703109},
issn = {2045-2322},
abstract = {For cardiovascular diseases, diabetes, and asthma, the positive effects of dog ownership are shown. Cancer is a leading cause of death, but the influence of dogs on cancer incidence and survival is not well examined. As modifiable lifestyle factors gain importance in cancer survivorship research, the potential protective role of dog ownership warrants systematic investigation. We retrospectively analyzed clinical data from a federated global health research network, focusing on patients diagnosed with cancer (International Classification of Diseases (ICD-10): C00-D49). From these, we generated two cohorts with contact with dogs (cohort 1) and one without (cohort 2). After propensity score matching for age and sex, a total of about 55,000 patients were included. Analysis of the matched cohort demonstrated that dog ownership was significantly associated with reduced 5-year all-cause mortality in cancer patients compared to non-owners (RR = 0.44). Survival analysis revealed a significantly higher 5-year cumulative survival rate among dog-owning patients versus non-owners, with a hazard ratio (HR) of 0.36. Contact with dogs is associated with a 64% relative risk reduction in cancer mortality, potentially mediated by increased physical activity, psychosocial support, and microbiome modulation. While retrospective design precludes causal inference, this first large-scale matched cohort study provides compelling epidemiological evidence warranting prospective validation.},
}

@article {pmid41702954,
year = {2026},
author = {Maranha, A and Leal, EC and Alarico, S and Tiago, I and Pereira, SG and Empadinhas, N and Carvalho, E},
title = {Neuropeptides neurotensin and substance P accelerate diabetic wound healing by modulating immunity and the skin microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30723-w},
pmid = {41702954},
issn = {2045-2322},
support = {PTDC/BIA-MIC/0122/2021//Fundação para a Ciência e a Tecnologia/ ; DL57/2016/CP1448/CT0024//Fundação para a Ciência e a Tecnologia/ ; 10.54499/DL57/2016/CP1448/CT0017//Fundação para a Ciência e a Tecnologia/ ; CEECINST/00051/2018//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-MIC/0122/2021//Fundação para a Ciência e a Tecnologia/ ; UIDB/04539/2020//Fundação para a Ciência e a Tecnologia/ ; FIS-2015-01_DIA_20150630-144//INFARMED - National Authority for Medicines and Health Products/ ; },
}

@article {pmid41702871,
year = {2026},
author = {Wen, M and Ma, X and Chen, J and Wu, J and Wu, F and Ma, R and Peng, R},
title = {Composition, Structure, and Diversity of Rhizosphere Soil Microbial Community in Saffron (Crocus sativus) Affected by Root Bulb Rot.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-07-25-1456-RE},
pmid = {41702871},
issn = {0191-2917},
abstract = {Fusarium oxysporum, first identified in Yunnan Province as the causal agent of saffron corm rot, causes a destructive soil-borne disease that has become a devastating threat to saffron cultivation in Shangri-La, causing over 50% mortality. This pathogen infects saffron corms, leading to vascular browning and rot, ultimately causing plant death and severe production losses. Given the crucial role of the rhizosphere microbiome in plant immunity and soil ecology, deciphering pathogen-microbiome interactions is essential for developing sustainable disease-control strategies. High-throughput sequencing of ITS/16S rRNA (Illumina MiSeq) was combined with arbuscular mycorrhizal fungi (AMF) analysis to compare the community structures of fungi, bacteria, and AMF in the rhizosphere of healthy and diseased saffron. The effects of soil physicochemical factors on microbiome assembly were systematically evaluated. The rhizosphere microbiome of diseased plants was significantly dysregulated: (1) pathogen-related taxa (e.g., Lauriomyces) proliferated, while saprotrophic functional taxa (e.g., Mortierella elongata) underwent community restructuring; (2) disease-suppressive taxa (e.g., fususidium) were enriched, while symbiotic mycorrhizal fungi (AMF) essential for nutrient acquisition sharply declined; (3) the soil parameter-microbiome relationship changed under different health conditions:available phosphorus (AP) and available potassium (AK) drove the aggregation of pathogenic soil fungi, while pH/organic matter (OM) dominated the aggregation of healthy soil fungi; (4) Knufia and Phomopsis were important taxa regulating soil ammonia oxidation and plant vitality. Fusarium infection disrupts the rhizosphere balance by inhibiting beneficial symbionts and promoting the colonization of pathogenic or saprotrophic microorganisms, ultimately compromising the innate resistance of saffron. Our findings reveal the rhizosphere ecological mechanism underlying corm rot progression and provide a microbiome informatics framework for the selection of biocontrol agents and rhizosphere engineering. Moreover, the worker safety benefits from the reductions in psychic emanations mandate industry adoption.},
}

@article {pmid41702355,
year = {2026},
author = {Katayama, Y and Fukuda, A and Inoue, R and Kawachi, H and Sawada, R and Harada, T and Yoshimura, A and Okada, A and Shiotsu, S and Chihara, Y and Takemura, Y and Yamada, T and Nishioka, N and Iwasaku, M and Tokuda, S and Takagi, T and Kumagai, S and Koyama, S and Takayama, K and Yamada, T},
title = {Gut microbiome-driven modulation of the tumor immune microenvironment optimizes dual checkpoint blockade in advanced non-small-cell lung cancer.},
journal = {ESMO open},
volume = {11},
number = {3},
pages = {106077},
doi = {10.1016/j.esmoop.2026.106077},
pmid = {41702355},
issn = {2059-7029},
abstract = {BACKGROUND: Dual checkpoint blockade with ipilimumab plus nivolumab (I-N), with or without chemotherapy, has shown clinical efficacy for treating advanced non-small-cell lung cancer (NSCLC); however, its benefits are limited to a subset of patients. The gut microbiome influences immune responses and may impact the efficacy of immune checkpoint inhibitors, thus warranting further investigation.

MATERIALS AND METHODS: This prospective study enrolled 50 patients with NSCLC who were treated with I-N, with and without chemotherapy. Gut microbiota diversity and composition were assessed from fecal samples collected before treatment initiation, and tumor-infiltrating lymphocytes (TILs) were evaluated using multiplex immunofluorescence staining. Progression-free survival (PFS), overall survival (OS), and objective response rate were analyzed alongside gut microbiota characteristics and treatment regimens.

RESULTS: High gut microbiota diversity was associated with improved outcomes in patients receiving I-N alone and with greater CD8+ TIL infiltration, particularly PD-1+CD8+ TILs. Responders receiving I-N alone showed enrichment of short-chain fatty acid (SCFA)-producing bacteria, which were linked to favorable metabolic pathways associated with antitumor immune responses. In contrast, the association between gut microbiota diversity and treatment efficacy was not observed in patients treated with I-N plus chemotherapy. Antibiotic use before treatment was independently associated with shorter PFS and OS across all treatment regimens.

CONCLUSIONS: Gut microbiota diversity and SCFA-producing bacteria are associated with improved efficacy of I-N. Baseline gut microbiota diversity may help identify patients who are more likely to have improved outcomes with I-N plus chemotherapy than with I-N alone. These findings highlight the potential of gut microbiota as a novel biomarker for dual checkpoint blockade in NSCLC may contribute to advancing personalized medicine.},
}

@article {pmid41702202,
year = {2026},
author = {Zhang, Z and Chen, H and Fu, Y},
title = {Deciphering antibiotic resistome characteristics and dissemination risks in fertilized and irrigated agricultural soils.},
journal = {Waste management (New York, N.Y.)},
volume = {214},
number = {},
pages = {115409},
doi = {10.1016/j.wasman.2026.115409},
pmid = {41702202},
issn = {1879-2456},
abstract = {While applying animal manure remain widespread agricultural practices for resources recycling, it risks unintentionally transferring antibiotic-resistant bacteria and antibiotic resistance genes (ARGs) from manure to soils. Despite the recognized environmental implications, limited research has systematically investigated the risk characteristics of ARGs linked to the combined application of manure as base fertilizer and routine irrigation practices. The question of which practice, fertilization or irrigation, more significantly contributes to the spread of ARGs remains unresolved. To bridge the gap, this study comprehensively investigates the characteristics and dissemination risks of ARGs in agricultural soils treated with chicken/cattle manure fertilization alongside groundwater irrigation. The characteristics, differences, and interactions among the resistome, microbiome, mobilome, and virulome across irrigation systems are systematically analyzed and compared. A novel non-negative matrix factorization-based microbial source tracking approach, NMF-SourceID, with superior accuracy in tracking low-abundance sources is used to quantify the source-sink relationship of ARGs in irrigated agroecosystems. The results revealed that combined fertilization and irrigation significantly enhanced both the abundance and diversity of ARGs in agricultural soils (p < 0.05). Importantly, these practices increased environmental risks by introducing emerging ARGs, mobile genetic elements, opportunistic human pathogens, virulence factors, and promoting their ecological co-occurrence. Comparative analysis showed no significant difference (p > 0.05) in ARG levels between chicken manure-treated strawberry soils and cattle manure-amended wheat cultivation soils. Source apportionment indicated that irrigation contributed 16-26% of ARGs while manure contributed 2.7-3.8%, suggesting the impact of base fertilizer on the dissemination of ARGs is much smaller than that of irrigation. The findings of this study provide essential theoretical groundwork for guiding agricultural fertilization and irrigation practices to mitigate environmental risks associated with antibiotic resistance dissemination in agroecosystems.},
}

@article {pmid41702193,
year = {2026},
author = {Liu, J and Ugwah-Oguejiofor, CJ and Zhu, L},
title = {Granulocytic myeloid derived suppressor cells derived extracellular vesicles ameliorate DSS-induced colitis via modulation of Th17/Treg balance.},
journal = {Pathology, research and practice},
volume = {281},
number = {},
pages = {156405},
doi = {10.1016/j.prp.2026.156405},
pmid = {41702193},
issn = {1618-0631},
abstract = {Colitis is closely associated with immune system dysregulation in the gastrointestinal tract. The present study aimed to evaluate the impact of Granulocytic Myeloid-Derived Suppressor Cells (G-MDSCs)-derived extracellular vesicles (EVs) on disease activity and the immunologic profile in a murine model of colitis. G-MDSCs-EVs were administered to colitis-bearing mice and were evaluated for changes in body weight, disease activity index, colon histopathology, frequencies of Th17 and Tregs, and cytokine release from lymphocytes. The impact of G-MDSCs-EVs was also evaluated on the expression of immune-response-related genes and the intestinal microbiome. G-MDSCs-EVs prevented body weight loss and controlled the disease activity index on day 10. This treatment improved the Treg population along with a decrease in the release of IL-6, IL-17A, and IFN-γ from lymphocytes. Treatment with G-MDSCs-EVs modulated immune-response-related gene expression and influenced the gut microbiota and colon histopathology. G-MDSCs-EVs demonstrated a preliminary potential in expanding the Treg population and upregulating immunoregulatory cytokines, which contributed to improvements in disease activity index and histopathology of the affected tissue.},
}

@article {pmid41702132,
year = {2026},
author = {Maji, C and Kokiwar, PR and Biradar, A and Jauhari, R},
title = {Comment on 'Feasibility Study Exploring the Effect of Pelvic Radiotherapy on the Intestinal Microbiome and Metabolome to Improve the Detection and Management of Gastrointestinal Toxicity'.},
journal = {Clinical oncology (Royal College of Radiologists (Great Britain))},
volume = {52},
number = {},
pages = {104060},
doi = {10.1016/j.clon.2026.104060},
pmid = {41702132},
issn = {1433-2981},
}

@article {pmid41702067,
year = {2026},
author = {Guo, X and Peng, L and Zhu, Z and Fan, S and Feng, J and Fang, X and Guo, D and Yang, P},
title = {Combined effects of polystyrene micro-/nano-plastics and imidacloprid on Gut-Brain axis and neurotoxicity in juvenile Carassius auratus.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128998},
doi = {10.1016/j.jenvman.2026.128998},
pmid = {41702067},
issn = {1095-8630},
abstract = {Polystyrene micro/nanoplastics (PS-MPs/NPs) and the neonicotinoid imidacloprid (IMI) frequently co-occur in freshwater ecosystems, yet their combined toxicity profiles remain distinct and unresolved. Here, we exposed juvenile crucian carp (Carassius auratus) to PS-MPs (5 μm), PS-NPs (60-100 nm), and IMI, alone or in combination, to unravel their interactive mechanisms via a multi-omics approach. Results revealed a clear size-dependent toxicity pattern: while PS-NPs (especially with IMI) preferentially targeted the brain, PS-MPs (with or without IMI) induced the most severe intestinal histological injury, characterized by extensive intestinal fold atrophy and goblet cell depletion. In the brain, co-exposure to PS-NPs and IMI elicited potentiated neurotoxicity, manifesting as blood-brain barrier (BBB) breakdown, neuroinflammation, and a specific disruption of the glutamate-glutamine-γ-aminobutyric acid (Glu-Gln-GABA) metabolic cycle, which coincided with hyperactive and asocial behaviors. Microbiome analysis highlighted distinct dysbiotic signatures. Integrated network analyses further linked these gut microbial shifts to central neurochemical imbalances, implicating the microbiota-gut-brain axis as a potential pathway involved in systemic toxicity. In summary, this study differentiated between gastrointestinal damage caused by MPs and systemic combined toxicity caused by the penetration of NPs and IMI across biological barriers. It emphasizes the importance of size-specific assessment in understanding the complex risks of combined exposure to plastics and pesticides, providing insights for pollution management in agricultural hotspots.},
}

@article {pmid41701663,
year = {2026},
author = {Zhou, H and Chen, J and Zhang, X},
title = {Correction: BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data.},
journal = {PLoS computational biology},
volume = {22},
number = {2},
pages = {e1013974},
pmid = {41701663},
issn = {1553-7358},
abstract = {[This corrects the article DOI: 10.1371/journal.pcbi.1013124.].},
}

@article {pmid41701630,
year = {2026},
author = {Wang, G and Luo, Y and Song, S and Li, X and Pan, Y and Zhao, Z and Wang, B and Yang, Q and Yang, F and Fang, T},
title = {Role of the Gut Microbiome in Modulating Interactions Between β-Lactam Antibiotics and Statins in Coronary Heart Disease.},
journal = {Journal of cardiovascular pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1097/FJC.0000000000001805},
pmid = {41701630},
issn = {1533-4023},
abstract = {Clinical evidence suggests that the lipid-lowering efficacy of statins may be diminished by concurrent β-lactam administration in patients with coronary heart disease (CHD), yet the mechanisms driving this potential drug-drug interaction, particularly the role of gut microbiota as a mediator, remain undefined. To address this gap, we conducted a retrospective analysis of data from a tertiary hospital spanning 5 years, enrolling 436 CHD patients on statin therapy who had two hospital admissions within a 3-month window. Patients were stratified into β-lactam-treated and antibiotic-free cohorts to assess the correlation between β-lactam exposure and statin efficacy. Additionally, 16S ribosomal RNA gene sequencing was employed to characterize and compare gut microbiota profiles between CHD patients receiving combined rosuvastatin and β-lactam therapy versus those on rosuvastatin monotherapy. Our findings demonstrated that β-lactam exposure was associated with elevated low-density lipoprotein cholesterol and total cholesterol levels. Both rosuvastatin and β-lactams induced significant alterations in gut microbiota composition, with distinct shifts in bacterial taxa abundances: rosuvastatin increased the relative abundance of Faecalibacterium and Dysosmobacter, whereas β-lactams disrupted the abundance of Faecalibacterium, Roseburia, and Dysosmobacter. Collectively, these results indicate that concomitant β-lactam use impairs rosuvastatin efficacy in CHD patients, likely via perturbation of gut microbiota composition. Rosuvastatin may exert a portion of its cardioprotective effects through modulation of gut microbiota, and β-lactams may abrogate this benefit by depleting key bacterial taxa linked to statin-mediated lipid regulation. Notably, Dysosmobacter emerges as a potential mediating species in this interaction, supporting a microbiome-dependent mechanism underlying the reduced lipid-lowering efficacy of rosuvastatin during β-lactam co-administration.},
}

@article {pmid41701442,
year = {2026},
author = {Zhang, R and Zhu, J and Qu, S and Chen, X and Wang, Y and Sun, L and Zhang, X and Lu, Z and Wang, X},
title = {S1P2 Reduces Mast Cell Activation and Colonic Inflammation of L-Arginine-Induced Acute Pancreatitis.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41701442},
issn = {1573-2568},
support = {82371241, 82171232, 31900716//the National Natural Science Foundation of China/ ; 82274171//the National Natural Science Foundation of China/ ; 22XD1404900//the Program of Shanghai Academic/Technology Research Leader/ ; 20204Y0047//the Shanghai Municipal Health Commission/ ; },
abstract = {BACKGROUND: Acute pancreatitis (AP) is a serious pancreatic disorder and colonic inflammation is involved in the progression of AP. However, the role of mast cells in the regulation of colonic inflammation in AP has been less studied; thus, we explored the role of mast cells in the regulation of colonic inflammation.

METHODS: An AP model was established by intraperitoneal injection of L-arginine or caerulein. Colonic inflammation in AP was tested using H&E staining. The mRNA levels were quantified using qRT-PCR. The protein level of sphingosine-1-phosphate receptor 2 (S1P2) was quantified using western blotting or immunohistochemistry. The gut microbiota was analyzed using 16S rRNA sequencing.

RESULTS: The Western blot analysis revealed that S1P2 expression was decreased by 0.63-fold in L-arginine-AP-induced colonic inflammation. Ketotifen, a second-generation H1-antihistamine and mast cell stabilizer, increased the survival rate (90%) in the L-arginine-AP model and increased the mRNA level of S1P2 by 1.33-fold and protein expression by 1.47-fold, suggesting that ketotifen inhibited mast cell activation through the S1P2 pathway. Similarly, treatment with the S1P2 agonist CYM-5520 in the L-arginine-AP model did not result in death and decreased the proportion of mast cells in the spleen by 1.58-fold. Moreover, gut microbiome analysis revealed that the abundance of proteobacteria decreased in L-arginine-AP mice pretreated with CYM-5520. In vitro experiments revealed a 2.1-fold decrease in S1P2 expression following mast cell stimulation, and the absence of S1P2 promoted mast cell degranulation.

CONCLUSION: This study provides evidence that S1P2 can ameliorate colonic inflammation in an L-arginine-induced AP mouse model by inhibiting mast cell activation.},
}

@article {pmid41701340,
year = {2026},
author = {Li, H and Yang, Z and Li, M and Yang, H and Liu, D and Bi, Y and Dai, X and Chen, X and Miao, L and Yang, F and Chen, Z},
title = {Causal association between gut microbiota and osteonecrosis in European populations: a two-sample Mendelian randomization analysis.},
journal = {Journal of bone and mineral metabolism},
volume = {},
number = {},
pages = {},
pmid = {41701340},
issn = {1435-5604},
support = {XDYC-QNRC-2024-163//Yunnan Revitalization Talent Support Program/ ; 2024SCP001//Spring City Plan: The High-level Talent Promotion and Training Project of Kunming Yunnan Revitalization Talent Support Programme Young Talent Project/ ; 82360480//National Natural Science Foundation of China/ ; 202301AU070104//Applied Basic Research Foundation of Yunnan Province/ ; 202301AY070001-180//Applied Basic Research Foundation of Yunnan Province and Kunming Medical University/ ; 202401AY070001-330//Applied Basic Research Foundation of Yunnan Province and Kunming Medical University/ ; 2023-SW-65//Kunming Health Commission Health Science and Technology Talent Project/ ; },
abstract = {INTRODUCTION: Recent studies have linked gut microbiota composition to osteonecrosis, but the causal relationship remains unclear. Clarifying this relationship is clinically important because osteonecrosis currently lacks early biomarkers and etiology-targeted therapies; if causal, the gut microbiome would offer a readily modifiable intervention target.

METHODS: We conducted a two-sample Mendelian randomization analysis to explore this relationship. Exposure data were sourced from the MiBioGen consortium (N = 18,340), while outcome data on osteonecrosis were obtained from FinnGen (N = 392,580). The Inverse Variance Weighted method was used as the primary analytical approach, supplemented by comprehensive sensitivity analyses to assess the robustness of our findings.

RESULTS: Our analysis screened 196 microbial taxa and identified seven taxa associated with osteonecrosis risk in European populations. Protective effects were noted for the genus Odoribacter (OR = 0.579; P = 0.027) and family Alcaligenaceae (OR = 0.703; P = 0.049). Conversely, increased risk was linked to the genus Eubacterium fissicatena group (OR = 1.272; P = 0.046), genus Bifidobacterium (OR = 1.372; P = 0.038), order Bifidobacteriales (OR = 1.412; P = 0.023), family Bifidobacteriaceae (OR = 1.412; P = 0.023) and phylum Actinobacteria (OR = 1.750; P = 0.001). Sensitivity analyses confirmed the robustness of these findings, with no evidence of pleiotropy or heterogeneity.

CONCLUSION: This study establishes a causal link between gut microbiota composition and osteonecrosis, suggesting that gut microbiota may be a modifiable factor in its pathogenesis. Further research is needed to elucidate underlying mechanisms and evaluate microbiota-targeted interventions for prevention and treatment.},
}

@article {pmid41700933,
year = {2026},
author = {Liu, X and Gao, JB and Li, WX and Xu, CY and Zhang, ZY and Yang, X and Ni, M},
title = {Electroacupuncture at Baliao Points Alleviates Ulcerative Colitis via α7nAChR-Mediated Macrophage Polarization and Gut Microbiota Modulation.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf321},
pmid = {41700933},
issn = {1536-4844},
support = {No. BE2022673//Jiangsu Provincial Key Research and Development Program/ ; No.ZYX22053//Nanjing Health Science and Technology Development Foundation/ ; No.BK20231132//Natural Science Foundation of Jiangsu Province/ ; },
abstract = {Ulcerative colitis (UC) is a chronic inflammatory disorder characterized by a significant unmet clinical need for more effective and tolerable therapies. This study explores the therapeutic potential and underlying mechanisms of electroacupuncture (EA) at the Baliao acupoints in a dextran sulfate sodium (DSS)-induced UC rat model. EA treatment significantly alleviated colitis symptoms, restored colon length, and enhanced gut barrier integrity by upregulating tight junction proteins (ZO-1/occludin). Mechanistically, EA activated cholinergic neurons in the dorsal root ganglion (DRG), increased the prevalence of α7nAChR (alpha 7 nicotinic acetylcholine receptor)-positive M2 macrophages in the colon, and elevated local acetylcholine levels. These effects were abolished by the α7nAChR antagonist methyllycaconitine (MLA), confirming the critical role of α7nAChR-mediated cholinergic signaling. Additionally, EA modulated gut microbiota composition, promoting beneficial bacteria (eg Lactobacillus) and suppressing pathogenic species. Heart rate variability analysis indicated enhanced vagal activity post-EA. Collectively, these findings demonstrate that EA at the Baliao acupoints alleviates experimental UC via α7nAChR-dependent facilitation of M2 macrophage polarization and restoration of a healthy gut microbiota, highlighting a promising neuromodulation-based approach for UC treatment.},
}

@article {pmid41700874,
year = {2026},
author = {Liechty, Z and Stamps, B and Babagana, M and Kupchak, B and Decicco, J and Baldwin, A and Schaeublin, NM and Pitsch, R and Strayer, K and Halford, J and Goodson, M and McNeal, N},
title = {The interactions of diet, mood, and the gut microbiome during an eight-week submarine deployment.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0305925},
doi = {10.1128/spectrum.03059-25},
pmid = {41700874},
issn = {2165-0497},
abstract = {Disruption of the gut microbiome has been linked to ill health, including impaired cognitive performance and mental health issues. Various aspects of a prolonged submarine deployment environment are known to disrupt the microbiome when they occur in other circumstances, including limited diet, altered circadian rhythm, poor sleep, and stress. In this study, we (i) characterize the changes of diet, mood, and the composition of the gut microbiome during a prolonged submarine deployment and (ii) determine whether any of these factors interact and affect submariner health and performance. Thirty-four U.S. Navy submariners, serving on a ballistic missile submarine (SSBN), provided fecal and blood samples and completed questionnaires relating to their diet and mood. Samples and questionnaires were collected at six time periods covering before, during, and after an 8-week deployment. Fecal samples were analyzed by 16S rRNA gene sequencing. Blood samples were analyzed to identify biomarkers with established links to stress, neurocognitive function, immune function, and gut barrier function. The dietary and mood questionnaires were analyzed to identify any changes over the course of the deployment. Results indicated that baseline gut microbial diversity was highly variable between individuals, although certain microbes had deployment-related changes to their composition. Changes in microbiota composition within individuals over the course of the deployment were correlated with changes in diet and mood, suggesting a link between microbiome composition and feelings of fatigue. Identification of microbial communities that confer resiliency to deployment stressors will enable future development of targeted interventions.IMPORTANCESubmariners operate in a unique deployment environment, but their experiences may shed light on how the human body responds to extended duration missions in other confined spaces, such as spaceflight. Our study is the first to show how the human gut microbiome changes during an extended submarine deployment while also tracking dietary intake and mood.},
}

@article {pmid41700857,
year = {2026},
author = {Williams, SE and Stennett, HL and Devine, AJ and Song, Z and Back, CR and Wang, L and Mantell, J and Neal, C and Jepson, MA and Essex-Lopresti, AE and Sellars, JD and Stach, JEM and Willis, CL and Curnow, P and Race, PR},
title = {OSMAC guided bioprospecting of Atlantic sponges reveals novel bacterial species and evidence for the antimicrobial thiazole alkaloid agrochelin II.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0187725},
doi = {10.1128/aem.01877-25},
pmid = {41700857},
issn = {1098-5336},
abstract = {The deep sea remains a major reservoir of underexplored microbial diversity and biosynthetic novelty. Here, we describe three bacterial species isolated from Atlantic sponges, including Stappia quadratibracata sp. nov., Bacillus crepusculi sp. nov., and Psychrobacter noctis sp. nov. Genome sequencing, phylogenomics, and phenotypic characterization confirmed their novelty and biosynthetic potential. A targeted 'One Strain Many Active Compounds' (OSMAC) screen revealed previously silent antibacterial activity from Stappia quadratibracata sp. nov., only when grown with the carbon source succinate. Metabolomics and molecular networking analysis indicated that this activity was attributable to an unstable thiazole alkaloid with spectral data closely related to, but distinct from, the epimeric siderophores agrochelin and massiliachelin. Spectroscopic studies, in tandem with comparative analysis of the biosynthetic gene cluster for this metabolite, are consistent with agrochelin II, a previously unreported thiazole alkaloid diastereoisomer. Agrochelin II exhibits iron-enhanced antibacterial activity against Staphylococcus aureus, underscoring the ecological role of iron acquisition in microbial competition. Our findings highlight the value of OSMAC-guided bioprospecting in uncovering antimicrobial metabolites from sponge-associated bacteria.IMPORTANCEBioactive microbial natural products remain the preeminent source of new lead compounds for drug development. Due to the increasingly high levels of strain and compound rediscovery from terrestrial environments, the deep-ocean is increasingly considered an attractive starting point for bioprospecting programs, which seek to isolate and characterize novel chemical scaffolds. Here, we use a combination of genomics, metabolomics, and chemical analysis, to establish the biosynthetic potential of three bacterial species isolated from deep-ocean Atlantic sponges and report the discovery and characterization of a new antimicrobial thiazole alkaloid, agrochelin II. Our findings demonstrate the usefulness of integrated cultivation-screening-metabolomics-genomics pipelines for microbial metabolite discovery and identify the genus Stappia as a hitherto neglected source of bioactive natural products.},
}

@article {pmid41700855,
year = {2026},
author = {Rojas Calderón, D and Sandholm, RM and Samskott, T and Mjøs, MT and Lorentsen, ED and Røhr, ÅK and Bakke, I and La Rosa, SL},
title = {Genotypic characterization of gut isolates from Atlantic salmon fry reveals beneficial microbes with biotechnological potential.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0240925},
doi = {10.1128/aem.02409-25},
pmid = {41700855},
issn = {1098-5336},
abstract = {Aquaculture is a rapidly growing industry, with Atlantic salmon being one of the most intensively farmed food-producing fish in the world. While the gut microbiota is recognized to play an important role in the health and performance of various fish, knowledge of its functional capacities in salmon is gradually expanding, facilitating a better understanding of host-microbiome interactions. Nevertheless, data on the gut microbiota of juvenile salmon remain limited. Here, we isolated and genotypically characterized 11 bacteria obtained from the gut content of Atlantic salmon fry. Whole-genome sequencing using long-read Nanopore technology and functional annotation revealed their extensive metabolic versatility, including a broad array of carbohydrate-active enzymes, proteases, lipases, and (poly)phenol-degrading enzymes potentially contributing to the metabolism of feed-derived components. Additionally, all isolates possessed genomic potential for producing beneficial metabolites, including the short-chain fatty acids acetate and propionate, as well as several B vitamins and vitamin K2. Genes encoding bacteriocins and other secondary metabolites were identified, suggesting niche competitiveness against intestinal pathogens. Among the isolates, we further show that Lactococcus raffinolactis ASF-5 has the potential to selectively remove indigestible oligosaccharides from plant-based feeds. Indeed, this isolate grew on raffinose, an oligosaccharide associated with anti-nutritional effects in salmon. Using AlphaFold 3 models, we show that this capability is supported by a GH36 α-galactosidase and two GH32 sucrases, which can act cooperatively in the complete hydrolysis of raffinose. Finally, L. raffinolactis ASF-5 had a favorable safety profile for use as a feed supplement, showing susceptibility to all tested antibiotics and lacking hemolytic activity.IMPORTANCEAlthough metataxonomy studies have enhanced our knowledge of the salmon gut microbiota, the functional potential of bacteria from this ecosystem remains underexplored. Well-characterized bacterial isolates are crucial to advance the growing salmon aquaculture field, allowing insights into nutrient metabolism, informing the development of beneficial interventions, and helping in identifying enzymes to improve feed digestibility. This study highlights the functional capacity of 11 bacteria isolated from the gut of salmon fry in contributing to the metabolism of carbohydrates, proteins, lipids, fatty acids, and (poly)phenols from feed, potentially increasing nutrient availability for the host or providing beneficial metabolites, including short-chain fatty acids, vitamins, and bacteriocins. Importantly, Lactococcus raffinolactis ASF-5 could be used to remove indigestible sugars like raffinose from plant meals. Identifying such beneficial, host-specific bacteria opens new opportunities for developing customized feed supplements or enzymes that enhance feed digestibility, to promote the health and welfare of Atlantic salmon, and enhance the economic sustainability of aquaculture.},
}

@article {pmid41700827,
year = {2026},
author = {Stanley, D and Kim, Y and Haas, E and Mohamed, A and Eleftherianos, I},
title = {On the Significance of Amino Acids in Insects.},
journal = {Archives of insect biochemistry and physiology},
volume = {121},
number = {2},
pages = {e70134},
doi = {10.1002/arch.70134},
pmid = {41700827},
issn = {1520-6327},
support = {//Glocal Project of Gyeongkuk National University/ ; },
mesh = {Animals ; *Insecta/physiology/metabolism/microbiology ; *Amino Acids/metabolism ; Microbiota ; },
abstract = {While there are many amino acids in nature, all biological proteins are made of the 20 standard amino acids, which occur in virtually all organisms, including viruses. Here, we move beyond proteins to consider the broader biological significance of amino acids in insects. Some amino acids, particularly glycine, act in insect mating systems. We note that insects have biological requirements for essential amino acids, compounds that are required by many species, but must be acquired by consumption or donated by microbiome components. Dietary amino acid requirements differ among insect groups and species. Some insect species rely on tasting and recalling amino acid tastes in their natural foraging areas. An unknown number of microbiome components provide essential amino acids to their hosts. Together, sensory detection, transport systems, and microbial provisioning position amino acids as multifunctional regulators that connect molecular physiology to behavior and ecology. We conclude by highlighting research priorities-mechanistic studies of transport and sensing, life-stage comparative analyses, and integrative metabolomic approaches-to resolve how amino acids shape insect fitness and to translate these insights for pollinator health, pest management, and edible-insect nutrition.},
}

Animals
*Insecta/physiology/metabolism/microbiology
*Amino Acids/metabolism
Microbiota

@article {pmid41700755,
year = {2026},
author = {You, C and Ren, P and Guan, Y and Gong, K and Hua, Z and Zhou, W and Mei, X and Wang, Y and Wang, X and Xu, Y and Shen, Q and Wei, Z},
title = {Forecasting Root Rot Disease through Predictive Microbial Functional Profiling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e22628},
doi = {10.1002/advs.202522628},
pmid = {41700755},
issn = {2198-3844},
support = {2022YFC3501501//National Key Research and Development Program of China/ ; GuiKe AA24010003//Guangxi Science and Technology Program/ ; KJYQ2025034//Fundamental Research Funds for the Central Universities/ ; BK20240194//Natural Science Foundation of Jiangsu Province/ ; 42377118//National Natural Science Foundation of China/ ; 42277113//National Natural Science Foundation of China/ ; BE2022423//Jiangsu Carbon Peak & Carbon Neutrality Science and Technology Innovation Special Fund/ ; 2024M760612//China Postdoctoral Science Foundation/ ; },
abstract = {Early diagnosis of soil-borne diseases like root rot is a long-standing challenge in agriculture. While microbial functional genes are recognized as potent indicators of soil healthy, their application has been primarily limited to current or past soil conditions. Here, we demonstrate that microbial functional genes can transition from descriptive indicators to reliable predictive biomarkers. By analyzing 199 paired metagenomes from healthy and diseased medicinal plants rhizosphere soil samples, we identified a conserved core set of functional genes, specifically those governing biofilm formation, stress response, and plant-microbe mutualism that are robustly associated with root rot disease. To bridge the gap between discovery and field application, we developed a framework that integrates cost-effective qPCR assay for these key genes and fused their abundance data with machine learning. This model achieved over 80% accuracy in predicting disease onset from independent, pre-symptomatic soil samples, identifying risks long before visible symptoms of infection appeared. Our findings suggest a practical path for moving beyond simple microbial correlations toward an active forecasting tool. By positioning microbial functional genes at the core of disease management, this framework provides a targeted approach for mitigating soil-borne risks and supporting sustainable agricultural practices.},
}

@article {pmid41700712,
year = {2026},
author = {Accetto, T and Strašek Smrdel, K and Taskovska, M and Starčič Erjavec, M and Smrkolj, T and Seme, K and Kreft, ME},
title = {Negative-control-anchored urinary microbiome profiling with absolute 16S quantification: a pilot study in newly diagnosed, treatment-naive bladder cancer and healthy individuals.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag020},
pmid = {41700712},
issn = {1574-6968},
abstract = {Recent studies utilizing 16S rRNA amplicon sequencing have challenged the notion of urine sterility, yet urine is a low-biomass specimen in which apparent community profiles can be strongly influenced by background signal from reagents and processing. To address this interpretability gap, we integrate culture-independent absolute 16S rRNA gene quantification with urinary 16S amplicon sequencing in a negative-control-anchored workflow. Bacterial load provides a biomass-aware quality control gate that defines interpretable low-biomass thresholds and objective exclusion criteria. As a pilot application, we compared midstream urine collected prior to instrumentation from healthy volunteers and newly diagnosed bladder cancer (BC) patients, quality filtering retained 29 controls and 5 BC cases. Samples > 106 copies/mL typically produced > 10 000 reads; near 105 copies/mL read counts dropped sharply yet remained distinguishable from background. Thirteen negative controls (V3-V4 PCR and stabilization buffer; median 90, mean 124 reads) supported excluding samples with < 1 000 reads. Median bacterial load was lower in BC than in controls (7.0×103 vs 1.07 × 106 copies/mL), although not significant in this underpowered cohort (p = 0.07). This cohort-size-independent framework enables load-based triage for sequencing, reduces background-driven over-interpretation in low-biomass urine datasets, and supports modelling bacterial load as a covariate or stratifier in future studies of the bladder cancer microbiome.},
}

@article {pmid41700473,
year = {2026},
author = {Wang, K and Tong, Z and Shen, Y and Liu, Y and Wang, M and Fang, Q},
title = {Field-Aged Shade Nets Residues Disrupt Rhizosphere Microbiota and Nitrogen Metabolism in Tea (Camellia sinensis).},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15486},
pmid = {41700473},
issn = {1520-5851},
abstract = {Plastic residues in agricultural production pose escalating risks to soil health and food security, yet the impacts of shade nets (SNs) residues in soil have received little attention. Here, we compared the effects of pristine and field-aged polyethylene SNs through a year-long exposure experiment with tea plants (Camellia sinensis). Both pristine and aged SNs impaired soil and plant health, but the adverse effects of aged SNs were more pronounced. Pristine SNs decreased soil pH and increased chromium content, while aged SNs further depleted soil available nitrogen, promoted stronger rhizosphere microbial restructuring, and induced ferroptosis-like lipid peroxidation in roots, leading to deterioration of tea quality. Beneficial rhizosphere groups such as Proteobacteria and Rozellomycota declined, while denitrifiers bacteria and saprotrophic fungi were enriched, aggravating nitrogen loss. These shifts disrupted the soil-plant C-N balance, impairing tea plant nitrogen metabolism, which in turn suppressed glutamate and theanine biosynthesis, reallocating metabolism toward bitter ester-type catechins, and ultimately reduced tea flavor and quality. Our findings show that aged SNs act as emerging agricultural pollutants, disrupting nitrogen metabolism across soil-root-leaf scales. Recognizing aged SNs as part of global plastic pollution highlights their dual agronomic and environmental risks, underscoring the need for sustainable management and recycling in high-value agriculture.},
}

@article {pmid41700076,
year = {2026},
author = {Xu, X and Zhou, X and Zhang, M and Fang, J and Yan, Z and Zhu, X and Yu, Y and Zhu, J},
title = {Resolving cognitive heterogeneity in white matter hyperintensities through integrated analyses of microbiome, metabolome, and brain glymphatic function.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {2},
pages = {e71201},
pmid = {41700076},
issn = {1552-5279},
support = {82471952//National Natural Science Foundation of China/ ; 82371928//National Natural Science Foundation of China/ ; 2308085MH277//Anhui Provincial Natural Science Foundation/ ; 2022AH051135//Scientific Research Key Project of Anhui Province Universities/ ; 2022xkj143//Scientific Research Foundation of Anhui Medical University/ ; },
mesh = {Humans ; Male ; *Metabolome/physiology ; Female ; Aged ; *Cognitive Dysfunction/diagnostic imaging/metabolism ; *White Matter/diagnostic imaging/pathology/metabolism ; Magnetic Resonance Imaging ; *Glymphatic System/diagnostic imaging/metabolism ; *Gastrointestinal Microbiome/physiology ; *Brain/diagnostic imaging/metabolism ; Middle Aged ; *Cognition/physiology ; },
abstract = {INTRODUCTION: Individuals with similar white matter hyperintensities (WMH) burden show heterogeneous cognitive outcomes, yet the biological mechanisms underlying this variability remain incompletely understood.

METHODS: We integrated 16S rDNA sequencing, untargeted metabolomics, and multi-modal magnetic resonance imaging (MRI) to comprehensively characterize gut microbiome, plasma metabolome, and brain glymphatic function in 56 healthy controls, 40 WMH with normal cognition (WMH-NC), and 49 WMH with cognitive impairment (WMH-CI).

RESULTS: Group comparisons revealed differences in six bacterial genera, three plasma metabolites, and five glymphatic markers across three groups, with Acetivibrio, 1,5-naphthalenediamine, beta-uridine, free water fraction within the white matter, and index of diffusivity along the perivascular spaces (ALPS index) showing differences between WMH-CI and WMH-NC. Correlation and mediation analyses demonstrated associations between microbiota and cognition, mediated by tetradecyldiethanolamine and ALPS index.

DISCUSSION: These findings provide preliminary insights into plausible microbiota-metabolites-glymphatic function-cognition associations in WMH, potentially informing more targeted interventions for vascular cognitive impairment.},
}

Humans
Male
*Metabolome/physiology
Female
Aged
*Cognitive Dysfunction/diagnostic imaging/metabolism
*White Matter/diagnostic imaging/pathology/metabolism
Magnetic Resonance Imaging
*Glymphatic System/diagnostic imaging/metabolism
*Gastrointestinal Microbiome/physiology
*Brain/diagnostic imaging/metabolism
Middle Aged
*Cognition/physiology

@article {pmid41699965,
year = {2026},
author = {Williams, CE and Gopal, AC and Wang, WW and Chen, JS and Cheung, HY and Strickler, A and Logan, ML and Gunderson, AR},
title = {Composition and stability of the gut microbiome is associated with thermal tolerance and its plasticity in Anolis lizards.},
journal = {The Journal of experimental biology},
volume = {},
number = {},
pages = {},
doi = {10.1242/jeb.251650},
pmid = {41699965},
issn = {1477-9145},
support = {//Tulane University/ ; },
abstract = {Ectotherms are thought to be particularly vulnerable to climate change as they rely directly on environmental temperatures to regulate their physiology. One of the pathways by which ectotherms can alter their physiology in a warming environment is through phenotypic plasticity, which is usually treated as resulting from interactions between the organisms' genetics and the environment. However, ectotherms also host communities of microbes which can change quickly within the host and affect host physiology. To date, little is known about the extent to which gut microbes affect thermal plasticity in the non-model host organisms that will be the most affected by climate change. We investigated relationships between gut microbiome composition and host heat tolerance plasticity in three species of Anolis lizards: Anolis cristatellus, A. sagrei, and A. carolinensis. We brought wild-caught lizards into the lab and tested for 1) effects of experimental warming on gut microbiomes, and 2) associations between microbiome composition and compositional dynamics with heat tolerance and its plasticity across host individuals and species. We found that each anole species hosted a distinct gut microbial community, but that all host species had microbiomes that were largely resilient to temperature increases. However, several key aspects of microbiome composition were correlated with baseline host heat tolerance. Finally, microbiome composition and its stability was associated with the magnitude of plasticity in host heat tolerance. Our results indicate that gut microbes may play a role in the ability of ectotherms to mount plastic responses to rapidly changing thermal environments.},
}

@article {pmid41699716,
year = {2026},
author = {Song, JS and Jung, YK and Kweon, S and Kang, SH and Yim, HJ and Shin, SK and Choi, GH and Jang, ES and Lee, HL and Lee, SW and Yu, JH and Han, JE and Kim, SS and Kim, SG and Kim, YS and Kim, MJ and Yoo, JJ},
title = {Enhanced pathogen detection and gut microbiome alterations in pyogenic liver abscess: insights from next-generation sequencing.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00799-4},
pmid = {41699716},
issn = {1757-4749},
support = {2020IF0005//Asan Medical Center fund/ ; },
abstract = {OBJECTIVES: Pyogenic liver abscess (PLA) is a life-threatening infection with high mortality in Asia. Although Klebsiella pneumoniae is commonly implicated, emerging data suggest a more diverse microbial spectrum. This study investigated pathogen detection using conventional culture and next-generation sequencing (NGS) and characterized gut microbiome alterations in PLA patients compared to healthy controls.

METHOD: This was a prospective, multicenter cohort study conducted across eight tertiary hospitals. We enrolled 100 PLA patients who underwent percutaneous aspiration. Abscess aspirates underwent both conventional culture and 16 S rRNA-based NGS. Stool samples from PLA patients and 100 healthy controls were analyzed for gut microbiome composition using NGS.

RESULTS: Culture positivity was 82%, with abscess cultures positive in 77 cases and blood cultures in 32. K. pneumoniae was the most frequently isolated pathogen (67%), and polymicrobial infections were identified in only 3% of cases by culture. NGS of abscess aspirates was available in 92% of patients, including 15 culture-negative cases. NGS identified polymicrobial infections in 16.3% of patients-more than fivefold higher than culture. Among 77 patients who underwent both culture and NGS, 13 (16.9%) showed discordance, mostly due to polymicrobial or anaerobic organisms identified by NGS. Stool NGS analysis revealed significantly reduced alpha diversity in PLA patients compared to healthy controls (Shannon index 2.9 vs. 3.5, p < 0.001), increased abundance of Enterococcus species (27.1% vs. 8.6%, p < 0.001), and depletion of SCFA-producing genera including Faecalibacterium, Roseburia, and Lachnospira species. Despite K. pneumoniae dominance in abscesses, its stool abundance did not significantly differ between PLA patients and controls.

CONCLUSION: NGS improves the detection of anaerobes and mixed infections in PLA. The gut microbiota of PLA patients shows marked dysbiosis, suggesting a potential role in disease pathogenesis and future therapeutic targets.},
}

@article {pmid41699710,
year = {2026},
author = {Nejadrostam, S and Shadvar, P and Jameie, SB and Jameie, M and Farhadi, M},
title = {Gut microbiota and glioblastoma: composition, mechanisms, and therapeutic interventions.},
journal = {Infectious agents and cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13027-026-00740-z},
pmid = {41699710},
issn = {1750-9378},
abstract = {BACKGROUND: Glioblastoma (GBM) is the most common and aggressive primary malignant brain tumor, associated with an exceedingly poor prognosis. The gut microbiota, a complex community of microorganisms, critically regulates host physiological homeostasis and communicates bidirectionally with the central nervous system via the gut-brain axis. Emerging evidence suggests that dysbiosis within this axis may profoundly influence GBM pathophysiology through inflammatory and immune-modulatory mechanisms, but a comprehensive synthesis of this complex interplay and its clinical implications remains vital for therapeutic advancement.

MAIN BODY: This narrative review systematically synthesizes the existing literature from MEDLINE (via PubMed), Scopus, and Web of Science, covering publications up to September 26, 2025, to elucidate the multifaceted role of the gut microbiota-brain axis in GBM. Our study focuses on three critical domains: microbial composition alterations, mechanistic insights, and therapeutic interventions. The review confirms significant alterations in the gut microbial community in GBM across both clinical and preclinical models, with consistent enrichment or depletion of specific bacterial taxa that may affect tumor pathogenesis and prognosis. Mechanistically, gut microbiota-derived metabolites and receptor interactions are shown to modulate GBM progression by influencing tumor-promoting hallmarks, including metabolic reprogramming, immune evasion, and sustained proliferative signaling. Furthermore, the efficacy of standard treatments, including temozolomide chemotherapy and immune checkpoint inhibitors, is actively modulated by the patient's gut microbiota composition. Dietary approaches and traditional medicines further demonstrate microbiota-dependent effects on tumor progression and immune regulation.

CONCLUSION: This review underscores the critical and intricate role of the gut microbiota-brain axis in GBM biology, affecting both tumor progression and therapeutic responsiveness. The compiled evidence establishes a clear rationale for advancing microbiota-targeted strategies as novel adjunctive interventions to enhance clinical outcomes for individuals with GBM.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid41699655,
year = {2026},
author = {Wang, X and Si, C and Kong, C and Qiao, J and Li, Y and Chang, B and Tang, X and Zhang, J and Yang, B},
title = {Polyphenolic nanodot-integrated spindle nanoplatform heals oral mucositis via microbiota restoration and glycolysis inhibition.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04119-5},
pmid = {41699655},
issn = {1477-3155},
support = {jcsz2023481-32//Science and Technology Project of Jilin Provincial Department of Finance/ ; jcsz2023481-1//Healthcare Talent Development Project of the Jilin Provincial Department of Finance/ ; 82470941//National Natural Science Foundation of China/ ; 82301044//National Natural Science Foundation of China/ ; 2024QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; },
abstract = {Oral mucositis (OM) is a debilitating complication occuring in most patients receiving chemotherapy. Through correlation analysis of oral microbiota sequencing data with host metabolomics data, we confirmed that disruption of the oral microbiota (dysbiosis) could lead to changes in metabolic activity in mucosal tissues, characterized by increased glycolysis in epithelial cells. Here, on the basis of the three-level microbiota-microenvironment-host metabolism regulatory network of in OM, we propose an integrated biofunctional nanoplatform (CP@ZS-NDs) that consists of a spindle-shaped zinc silicate core with polyphenol chlorogenic acid nanodots adsorbed on its outer surface, is delivered via a gel delivery system and has wet tissue surface adhesion and antioxidant capabilities. CP@ZS-NDs influence carbohydrate metabolism in host oral epithelial cells through regulation of the oral microenvironment by improving the microbiome composition. Moreover, we preliminary proved that CP@ZS-NDs promote the healing of OM by inhibiting the UDP-galactose-related metabolic pathway and regulating the Integrin α3β1-Fak-Rac1 axis. These findings demonstrate the effectiveness of CP@ZS-NDs in maintaining oral microbiota homeostasis, which is crucial for the treatment of OM and provide new insights for clinical treatment strategies.},
}

@article {pmid41699406,
year = {2026},
author = {Yang, Y and van Schaik, W and McNally, A and Zong, Z},
title = {Microbiome-mediated colonization resistance to and countermeasures of Klebsiella pneumoniae.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1761},
pmid = {41699406},
issn = {2041-1723},
support = {2024YFE0106200//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; MR/S013660/1//RCUK | MRC | Medical Research Foundation/ ; MR/S013660/1//RCUK | Medical Research Council (MRC)/ ; },
}

@article {pmid41699270,
year = {2026},
author = {Bashiardes, S and Heinemann, M and Adlung, L and Valdés-Mas, R and Mahdi, JA and Nobs, SP and Tuganbaev, T and Yamada, T and Horn, M and Mor, U and Cohen, Y and Israel, S and Korem, M and Oster, Y and Olshtain-Pops, K and Orenbuch-Harroch, E and Arslan, MD and Molina, S and Zur, M and Eliyahu-Miller, S and Bukimer, A and Federici, S and Dori-Bachash, M and Amar, N and Elbirt, D and Cohen-Poradosu, R and Turner, D and Hershcovici, T and Vainer, E and Stettner, N and Harmelin, A and Gebremeskel, H and Kebede, Y and Schmidt, S and Zmora, N and Dhamodaran, A and Puschhof, J and Bentwich, Z and Shapiro, H and Amit, I and Elinav, H and Elinav, E},
title = {Human immunodeficiency virus-associated gut microbiome impacts systemic immunodeficiency and susceptibility to opportunistic gut infection.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41699270},
issn = {2058-5276},
abstract = {The gut microbiome of people living with human immunodeficiency virus (PLWH) has been characterized, but its role in influencing host immunity and associated clinical features are unclear. Here we used shotgun metagenomics to characterize the faecal microbiome of two geographically distinct cohorts of PLWH and healthy controls in Israel and Ethiopia. We uncovered disease-specific, geographically divergent microbial patterns including a shift from Bacteroides to Prevotella species in an Israeli cohort and multiple Enterobacteriaceae species including Escherichia coli and Klebsiella quasivariicola in an Ethiopian cohort. We identified correlations between human immunodeficiency virus-related dysbiosis and the extent of systemic immunodeficiency, as proxied by peripheral CD4[+] T cell counts. Faecal microbiome transplantation from PLWH with high peripheral CD4[+] T cell counts induced colonic epithelium-associated CD4[+] T cells in germ-free or antibiotic-treated recipient mice. Impaired epithelium-associated lymphocyte induction in recipients of faecal microbiome transplantation from severely immunodeficient PLWH donors was associated with altered protection from Cryptosporidium parvum infection. Collectively, our results suggest a link between systemic immunodeficiency and associated intestinal dysbiosis in PLWH, resulting in impaired gut mucosal immunity.},
}

@article {pmid41699248,
year = {2026},
author = {Żurek, M and Czesak, M and Pietruczuk-Padzik, A and Stefańska, J and Stępień, K and Rzepakowska, A},
title = {Microbial colonization of tracheostoma region in patients with voice prostheses - double-blind randomized clinical trial.},
journal = {European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery},
volume = {},
number = {},
pages = {},
pmid = {41699248},
issn = {1434-4726},
}

@article {pmid41699149,
year = {2026},
author = {Merenstein, D and Grant-Beurmann, S and Sanders, ME and Tan, T and Burke, B and Kumar, A and Herbin-Smith, K and Sparenborg, J and D'Amico, F and Roberts, B and Fraser, C},
title = {Probiotic intervention not beneficial to prevent antibiotic-associated diarrhea in absence of antibiotic-induced microbiome disruption.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39826-4},
pmid = {41699149},
issn = {2045-2322},
support = {Award Number 7772608, IND #13691//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; Award Number 7772608, IND #13691//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; },
}

@article {pmid41699141,
year = {2026},
author = {Yang, H and Zhang, Y and Ma, Z and Li, L and Zheng, G and Chang, Q and Ji, C and Xia, Y and Zhao, Y},
title = {Sulfur microbial diet, genetical predisposition, and the risk of chronic kidney disease: a cohort study.},
journal = {European journal of clinical nutrition},
volume = {},
number = {},
pages = {},
pmid = {41699141},
issn = {1476-5640},
abstract = {BACKGROUND/OBJECTIVES: Our study evaluated the prospective association between the sulfur microbial diet (SMD), a diet associated with sulfur-metabolizing bacteria in stool, and the chronic kidney disease (CKD) risk, and further investigated whether genetic risk modified this association.

METHODS: This study involved 98,491 UK Biobank participants who had completed at least two 24-hour dietary recall measurements. SMD scores were computed by summing the product of β-coefficients for each food group and their corresponding intake values. Incident CKD was identified using UK Biobank algorithms. The polygenic risk score (PRS) for CKD was constructed based on 263 single-nucleotide polymorphisms. Hazard ratios (HRs) with 95% confidence intervals (CIs) and population attributable fractions (PAFs) were calculated using Cox proportional hazard regression models.

RESULTS: During a median follow-up of 9.38 years, we documented 2,032 incident CKD cases. We observed a dose-response association between the SMD score and increased CKD risk (P for non-linearity = 0.78). Participants in the highest tertile of the SMD score had a significantly higher risk of developing CKD compared to those in the lowest tertile (HR: 1.24, 95% CI: 1.11-1.39, PAF: 6.81, 95% CI: 3.29-10.34). No significant multiplicative or additive interactions between PRS and the SMD score were found (all P > 0.05). The positive associations between the SMD and the CKD risk were similar across low or high genetic risk groups.

CONCLUSION: Higher adherence to SMD was associated with an increased risk of CKD, regardless of genetic risk. Future studies are needed to validate our findings.},
}

@article {pmid41699131,
year = {2026},
author = {Flierl, E and Lutz, R and Heller, K and Schiffer, M and Wirtz, S and Backhaus, J and Weber, M and Kesting, MR and Moest, T},
title = {Impact of drug-induced immunosuppression following kidney transplantation on periodontal health and the periodontal microbiome: a longitudinal controlled study.},
journal = {Clinical oral investigations},
volume = {30},
number = {2},
pages = {79},
pmid = {41699131},
issn = {1436-3771},
}

@article {pmid41699104,
year = {2026},
author = {Li, F and Yang, Y and Fu, Y and Zhang, S and Wu, P and Wang, J and Dong, Y and Wu, N and He, X and Wang, T and Yang, S and Li, J and Li, S and Lai, Y and Yuan, J and Ren, J and Dai, X and Liang, G and Liu, G and Hu, Y and Dennis, CL and Zheng, JS and Pan, A and Pan, XF},
title = {Dynamic interactions between gut microbiome and host lipidome in antenatal depression: a large longitudinal study.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {41699104},
issn = {1476-5578},
abstract = {Temporal alterations in the host lipidome and gut microbiome, and their dynamic interactions, in the progression of antenatal depression remain poorly understood. Here, we characterized the maternal lipidome and gut microbiome in 1086 Chinese pregnant women from the Tongji-Huaxi-Shuangliu Birth Cohort using 2954 serum and 2812 fecal samples collected longitudinally across early, mid, and late pregnancy. Our analyses identified 95 host lipids, and seven gut microbial genera associated with antenatal depression. Period-specific and longitudinal analyses indicated that lysophosphatidylethanolamines (LPEs) exhibited concordant associations with antenatal depression. In addition, temporal analyses suggested that decreases in the abundances of gut microbial genera [Ruminococcus]_gnavus_group and Enterococcus preceded the onset of antenatal depression and demonstrated extensive associations with LPEs and acylcarnitines (CARs). Integrative analyses revealed bidirectional concurrent and temporal crosstalk between microbiota-lipid axis and antenatal depression, with LPEs and medium- and long-chain CARs constituting key molecules of this axis. Collectively, this study offers valuable insights into the interplay between host lipidome and gut microbiome in the development of antenatal depression, laying a foundation for future investigations into the microbiota-lipid axis during pregnancy.},
}

@article {pmid41698880,
year = {2026},
author = {Huang, T and Yang, H and Zhang, L and Wang, X and Chen, Y and Dai, H and Hashimoto, K and Luo, Y and Pu, Y and Liu, Y},
title = {HLA-B27-associated gut microbiota and amino acid perturbations promote ankylosing spondylitis through M1 macrophage activation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630561},
doi = {10.1080/19490976.2026.2630561},
pmid = {41698880},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *HLA-B27 Antigen/genetics/immunology/metabolism ; *Spondylitis, Ankylosing/microbiology/immunology/metabolism/genetics ; Animals ; Mice ; Male ; Female ; *Amino Acids/metabolism ; *Macrophage Activation ; Fecal Microbiota Transplantation ; Adult ; Middle Aged ; *Macrophages/immunology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; Metabolomics ; Dysbiosis ; },
abstract = {Ankylosing spondylitis (AS) is strongly associated with the human leukocyte antigen B27 (HLA-B27), yet how this genetic risk factor interacts with the gut microbiome remains unclear. We integrated fecal gut microbiota analysis, untargeted metabolomics, and clinical phenotyping in 88 participants, including HLA-B27-positive patients with AS (n = 28), HLA-B27-positive healthy controls (n = 30), and HLA-B27-negative healthy controls (n = 30). HLA-B27 positivity, particularly in AS, was associated with marked alterations in gut microbial composition and metabolic profiles, with forty bacterial species showing progressive disease-related shifts across cohorts. Integrated pathway and metabolomic analyses identified three amino acid-related pathways consistently disrupted in AS: tryptophan metabolism, cysteine metabolism, and pyruvate-centered biosynthesis of branched-chain amino acids, ornithine, and lysine. Correlation network analyses linking differential taxa, metabolites, and clinical indices revealed previously unrecognized microbial and metabolic signatures that robustly distinguished AS from both control groups. To explore causality, fecal microbiota transplantation (FMT) from clinical donors into antibiotic-treated mice recapitulated key disease-relevant features, including impaired intestinal barrier function, systemic inflammation, trabecular bone loss, and polarization of macrophages toward a proinflammatory M1 phenotype. Mechanistic validation identified cinnabarinic acid as a critical microbial-derived metabolite that suppresses M1 macrophage polarization via activation of the aryl hydrocarbon receptor (AhR) pathway and confers protection in the FMT model. Together, these findings support a model in which HLA-B27-associated gut dysbiosis and metabolic reprogramming promote AS pathogenesis through macrophage-mediated inflammation and osteocatabolic signaling, highlighting microbial-metabolic pathways as potential therapeutic targets.},
}

*Gastrointestinal Microbiome
Humans
*HLA-B27 Antigen/genetics/immunology/metabolism
*Spondylitis, Ankylosing/microbiology/immunology/metabolism/genetics
Animals
Mice
Male
Female
*Amino Acids/metabolism
*Macrophage Activation
Fecal Microbiota Transplantation
Adult
Middle Aged
*Macrophages/immunology
Bacteria/classification/genetics/isolation & purification/metabolism
Feces/microbiology
Metabolomics
Dysbiosis

@article {pmid41698855,
year = {2026},
author = {Simani, L and Hooshmandi, E and Hajisoltani, R and Hooshmandi, S},
title = {Probiotics and seizure susceptibility in preclinical epilepsy models: mechanistic insights from a systematic review and meta-analysis.},
journal = {Reviews in the neurosciences},
volume = {},
number = {},
pages = {},
pmid = {41698855},
issn = {2191-0200},
abstract = {The gut microbiota can affect neuronal excitability, inflammation, and oxidative balance via the gut-brain axis, shaping seizure susceptibility. To translate these findings into clinical approaches, a synthesis of preclinical microbiome-based evidence is needed. This systematic review and meta-analysis examined the putative anticonvulsant, anti-inflammatory, antioxidant, and neuroprotective effects of probiotics in rodent models. An extensive systematic search up to July 2025 identified eligible animal studies in which probiotics were administered in seizure models. Reported outcomes included seizure latency, duration, severity, and frequency, as well as inflammation, oxidative stress, and behavioral measures. Of the 24 studies that met the inclusion criteria, 19 provided sufficient data to be included in the meta-analysis. The most frequently used strains belonged to the Lactobacillus (e.g., acidophilus, casei, fermentum) and Bifidobacterium genera (e.g., bifidum, longum), with occasional synbiotic combinations. Probiotics significantly increased seizure latency (MD = 22.09; 95 % CI: 10.52 to 33.67) and reduced seizure severity (MD = -1.08; 95 % CI: -1.39 to -0.76) and duration (MD = -23.19; 95 % CI: -35.56 to -10.82). Probiotics significantly reduced IL-1β, IL-6, and TNF-α levels while MDA showed a nonsignificant trend toward reduction (p = 0.076). Behaviorally, improvements in spatial learning (p < 0.05) and reduced anxiety-like behavior (p < 0.001) were observed. Probiotic supplementation appears to exert anticonvulsant, anti-inflammatory, antioxidant, and behavioral benefits in preclinical epilepsy models, although the evidence is heterogeneous and limited to animal studies. Mechanistic evidence indicates modulation of the gut-brain axis, enhanced GABAergic signaling, and improved mitochondrial function. These findings support further investigation of specific probiotic formulations as promising adjunct candidates in well-designed, mechanism-driven clinical trials.},
}

@article {pmid41698723,
year = {2026},
author = {Salako, AO and Ogbeh, JI and Adekola, HA and Odubela, O and Akinsolu, F and Jimoh, R and Musari-Martins, TE and Luka, S and Oba, A and Ayegbeso, D and Odubela, OO and Gbaja-Biamila, TA and Musa, AZ and Salako, BL},
title = {Gut microbiome profile among children and adolescents living with sickle cell disease: a protocol for systematic review and meta-analysis.},
journal = {BMJ open},
volume = {16},
number = {2},
pages = {e111353},
pmid = {41698723},
issn = {2044-6055},
mesh = {Humans ; Systematic Reviews as Topic ; *Anemia, Sickle Cell/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects ; Child ; Meta-Analysis as Topic ; Adolescent ; Research Design ; Anti-Bacterial Agents/therapeutic use ; Analgesics/therapeutic use ; },
abstract = {INTRODUCTION: This systematic review aims to synthesise current evidence on gut microbiome profiles among children with sickle cell disease (SCD), assess the influence of analgesic and antibiotic use, and explore the contributions of environmental factors on their gut microbiota diversity. Through identification of consistent microbial patterns and gaps in the existing literature, this review will provide vital insight into potential microbiome-targeted strategies for improving health outcomes in paediatric SCD care.

METHODS AND ANALYSIS: Studies describing the gut microbiota among paediatric SCD human subjects (<18 years) will be identified by searching PubMed, Cochrane Library, Web of Science, Google Scholar and Scopus from inception to November 2025. Two independent reviewers will complete title and abstract screening, full-text review and data extraction. The grading of recommendations assessment, development and evaluation tool will be employed to assess the strength of evidence for each outcome. Extracted data will be presented in tables, and a meta-analysis will be conducted if appropriate.

ETHICS AND DISSEMINATION: Ethical approval will not be required as this is a systematic review of published data. The findings will be disseminated through publications in peer-reviewed journals and presentations at relevant scientific conferences.

PROSPERO REGISTRATION NUMBER: CRD420251102736.},
}

Humans
Systematic Reviews as Topic
*Anemia, Sickle Cell/microbiology/drug therapy
*Gastrointestinal Microbiome/drug effects
Child
Meta-Analysis as Topic
Adolescent
Research Design
Anti-Bacterial Agents/therapeutic use
Analgesics/therapeutic use

@article {pmid41698695,
year = {2026},
author = {Lawrie, RD and Ponnusamy, L and Deguenon, JM and Travanty, NV and Reisig, D and Roe, RM},
title = {Transmission of the internal microbiota of cotton field-collected bollworms (Lepidoptera: Noctuidae), from larvae to pupae and adults.},
journal = {Environmental entomology},
volume = {55},
number = {1},
pages = {},
doi = {10.1093/ee/nvag007},
pmid = {41698695},
issn = {1938-2936},
support = {02853//Research Capacity Fund/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; Pupa/microbiology/growth & development ; *Moths/microbiology/growth & development ; RNA, Ribosomal, 16S/analysis ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Gossypium ; *Gastrointestinal Microbiome ; },
abstract = {Caterpillar pests and their microbiota are of growing interest in relation to pest control, including any future use of living wild-type or genetically modified microbes for pest suppression and risk assessment. This study investigated whether bacteria associated with field-collected larval bollworms, Helicoverpa zea, persist through metamorphosis to the adult, potentially enabling the insects to transport microbes over long distances as the moths disperse. Fifth stadium, fully fed larvae were collected from non-Bt cotton in the field and allowed to pupate without additional feeding and emerge as adults in the laboratory. Bacterial community composition and diversity were assessed at each stage using Illumina sequencing of the 16S rRNA gene. Analysis of the internal bacterial communities revealed that alpha and beta diversity differed significantly between larvae, pupae, and adults. Despite this difference, 79 amplicon sequence variants were retained from the larval to the adult stage. The 5 most abundant taxa shared between larvae, pupae, and adults were Enterobacter, Klebsiella, an undefined Enterobacteriaceae species, Enterococcus casseliflavus, and Klebsiella oxytoca. Some of these bacteria are typical gut microbes. Further research is needed to characterize the composition and functional roles of these bacteria in H. zea, to evaluate their influence across generations, and to determine whether bacteria can be acquired by the larvae from their environment and persist into the adult stage. The role of the caterpillar microbiome in the context of modern cotton agroecosystems remains a largely understudied area of insect-microbe ecology.},
}

Animals
Larva/microbiology/growth & development
Pupa/microbiology/growth & development
*Moths/microbiology/growth & development
RNA, Ribosomal, 16S/analysis
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Gossypium
*Gastrointestinal Microbiome

@article {pmid41698575,
year = {2026},
author = {Du, Y and Zhao, S and Hu, Y and Wang, X and Zhang, L and Lin, B and Wang, M and Xu, Q},
title = {Dietary selection of starters drives changes of growth performance, fermentation, hindgut microbiome, and metabolism in preweaning calves.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27473},
pmid = {41698575},
issn = {1525-3198},
abstract = {Early feeding of starter is an effective strategy for modulating gastrointestinal microbiota in newborn calves. However, the effects of starter nutrient composition on calf gut microbiota vary significantly. Although both fiber and starch are essential for early calf nutrition, each has distinct advantages and disadvantages. This study investigated how high-starch and high-fiber diets influence growth performance, hindgut health, and microbiota in calves. Two groups of calves were fed experimental starters with distinct nutrient compositions: a high-starch (HS, n = 8) diet containing 40.4% starch and 13.3% NDF, and a high-fiber (HF, n = 7) diet containing 18.8% starch and 30.5% NDF (DM basis). The experiment spanned calf ages 14 to 63 d, with weekly BW and body size measurements using calibrated scales and measuring tape. Serum was collected via jugular venipuncture for metabolic marker analysis. At trial end, animals were slaughtered to collect hindgut tissues and contents for immunoblotting, metagenomic sequencing, and metabolite analysis. We identified a fundamental trade-off that HS feeding shaped a Bifidobacterium-dominated enterotype, correlating with superior growth performance. In contrast, HF feeding selected for a Bacteroides-dominated, more mature microbiota and significantly enhanced gut barrier integrity by upregulating key tight junction proteins (ZO-1, Claudin-1, and E-cadherin). Multiomics integration revealed that this trade-off was underpinned by different microbial metabolic pathways. The HS hindgut was enriched in enzymes and metabolites for carbohydrate and AA fermentation, driving growth. Conversely, the HF hindgut exhibited enhanced enzymatic capacity for fiber degradation (e.g., starch phosphorylase) and a metabolic profile favoring arginine biosynthesis and acetate production, which supported barrier function. This functional divergence was further evidenced in distinct short-chain fatty acid (SCFA) profiles. The HF group exhibited significantly elevated acetate and a trend for higher total SCFA concentration, whereas the HS group showed increased branched-chain fatty acids (isovalerate) and a trend toward higher butyrate and valerate proportions. Our findings provide a mechanistic model linking dietary carbohydrate source to a fundamental choice between growth optimization and gastrointestinal health in preweaning calves, offering novel insights for targeted nutritional strategies.},
}

@article {pmid41698473,
year = {2026},
author = {Grover, M and Barbara, G and Chey, W and Chumpitazi, BP and Feinle-Bisset, C and Schellekens, H and Quigley, EMM},
title = {The Intestinal microenvironment and Disorders of Gut-Brain Interactions.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.02.015},
pmid = {41698473},
issn = {1528-0012},
abstract = {The past decade has witnessed a tremendous profusion of data on the luminal contents of the gastrointestinal tract and their interactions with the host, many of which have been implicated in the pathophysiology of Disorders of Gut-Brain Interaction (DGBI). The role of food in DGBI-related symptoms has attracted much attention and while many alterations in gut microbiome composition have been described, the multitude of factors that confound study design and interpretation in DGBI has precluded the discovery of a specific microbial "signature". The complexities of the gut barrier, its immune and enteroendocrine systems, so critical to the transmission of signals from lumen to host, continue to be revealed. Along the way, concepts such as the microbiome-gut-brain axis have emerged to explain symptom generation in DGBI, forming the basis for novel diagnostic approaches and therapeutic interventions. Taken together, recent research findings have renewed interest in luminal and enteric phenomena in DGBI.},
}

@article {pmid41698463,
year = {2026},
author = {Henderickx, JGE and Smits, WK and Zeller, GF and Kuijper, EJ},
title = {How to set up and manage a microbiome research facility.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.02.007},
pmid = {41698463},
issn = {1469-0691},
abstract = {BACKGROUND: The increasing number of therapeutic intervention studies in the microbiome field has sparked broad interest among clinicians and scientists to incorporate microbiome analyses in their research. However, microbiome study design, data generation, bioinformatics and statistical data analysis is typically of a complexity that requires specific domain expertise to avoid biases, spurious findings, and other analysis pitfalls. As such, academic hospitals and research institutes are increasingly recognising the need for a dedicated microbiome research facilities that support every step in human microbiome research to a high standard.

OBJECTIVES: We aim to offer an experience-based approach on what we consider essential aspects of such a microbiome research facility.

SOURCES: Insights and recommendations are based on our experiences with establishing and running a microbiome research facility at the Leiden University Medical Center (LUMC, Leiden, the Netherlands), which was initiated in 2017.

CONTENT: This review uses an existing microbiome research facility as an example to provide information on its advantages, structure, and financial and legal frameworks. Additionally, key portfolio items of such an expertise centre are discussed.

IMPLICATIONS: A dedicated microbiome research facility can support microbiome research in clinical studies, and provides opportunities to centralise activities, innovate and validate analytical and computational methodology, foster industrial collaborations, and supports competitive funding applications through a dedicated infrastructure. Central facilities to support clinicians and scientists in the design, execution and interpretation of microbiome analyses constitutes a key step towards conducting high-quality gut microbiome research and education.},
}

@article {pmid41698451,
year = {2026},
author = {Maxan, ME and Moens, F and Marzorati, M and Mohamad, M and Yue, C and Said, J and Basit, AW and Gaisford, S and Patel, VC},
title = {A multi-strain probiotic modulates gut microbiome composition, intestinal barrier integrity and inflammation in a multi-compartmental in vitro gut model of decompensated alcohol-related advanced chronic liver disease.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {126678},
doi = {10.1016/j.ijpharm.2026.126678},
pmid = {41698451},
issn = {1873-3476},
abstract = {Decompensated advanced chronic liver disease (dACLD), which is defined by the onset and worsening of clinical complications that require hospitalisation and can lead to organ dysfunction, is patho-biologically characterised by an altered gut microbiome composition and function, intestinal barrier failure, immune dysfunction and systemic inflammation. The gut microbiome represents a promising therapeutic target in dACLD to prevent the onset of such life-threatening clinical complications. We investigated the effect of a live, multi-strain, aqueous probiotic suspension (Symprove™) on faecal material from three people with alcohol-related dACLD utilising an advanced in vitro gut model. We evaluated the impact of Symprove™ on mucosal and luminal bacterial microbiome diversity after 48 h by 16S rRNA gene sequencing. The effect on epithelial tight-junction (TJ) integrity was estimated using transepithelial electrical resistance measurement. We quantified metabolites, anti-inflammatory markers, chemokines and epithelial wound healing pre- and post-treatment in cell culture models. The relative proportions of the main bacterial phyla differed from those of healthy subjects studied previously: levels of Firmicutes decreased and Bacteroidetes increased. Dosing with Symprove™ resulted in faecal microbiome modulation over a 48-h period. Several other surrogate indicators of gut barrier integrity and mucosal immunity improved with Symprove™ exposure; estimated TJ integrity and epithelial wound healing improved. Short chain fatty acids and anti-inflammatory cytokine production (IL-6 and IL-10) increased, whilst pro-inflammatory chemokines (MCP-1 and IL-8) decreased. These data support Symprove[TM] as a potential microbiome-targeting therapeutic for patients with dACLD, to prevent clinical complications, and warrants further investigation.},
}

@article {pmid41698031,
year = {2026},
author = {Meng, Q and An, X and Hu, W and Ma, M and Chen, Z and Wei, G and Chen, C},
title = {Nanopriming with Silicon Quantum Dots Strengthens Wheat Drought Tolerance through Physiological Regulation and Microbial Functions.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11900},
pmid = {41698031},
issn = {1520-5118},
abstract = {Seed priming offers a promising approach to strengthening drought resilience in wheat. In this study, seeds were primed with silicon quantum dots (SiQDs) at concentrations of 0, 250, 500, 750, and 1000 mg L[-1]. Under drought stress induced by 15% PEG-6000, 500 mg L[-1] SiQDs increased the level of germination by 18.2%. In a 30 day pot experiment conducted under drought conditions at 40% field capacity, 500 mg L[-1] SiQDs significantly enhanced shoot biomass (157.1%) and the relative water content (26.7%), reduced root malondialdehyde (24.7%), and increased root proline (76.7%) and soluble sugar (68.7%). 16S rRNA gene and metagenomic sequencing analyses revealed that SiQDs enriched Proteobacteria in the rhizosphere, including the genera Sphingomonas, Lysobacter, and Variovorax, and activated functional pathways associated with biofilm formation and bacterial colonization. These results demonstrate that SiQD priming enhances drought tolerance by improving plant physiological responses and modulating rhizosphere microbial communities.},
}

@article {pmid41697847,
year = {2026},
author = {Wang, D},
title = {How gut microbiota modulate anesthetic drug response and perioperative outcomes.},
journal = {Drug metabolism reviews},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/03602532.2026.2630851},
pmid = {41697847},
issn = {1097-9883},
abstract = {The pursuit of precision in anesthesiology is persistently challenged by profound and unpredictable inter-patient variability in drug response. While pharmacogenomics has provided critical insights, a significant portion of this variability remains unexplained. Emerging evidence now positions the gut microbiota as a central, dynamic regulator of perioperative pharmacology. This review introduces and explores the concept, used here as a working label, of the anesthetic pharmacomicrobiome, defined as the set of microbial-host interactions that may influence perioperative drug disposition and effect. We adopt this descriptive shorthand for clarity. We synthesize evidence demonstrating how gut microbes clearly directly metabolize some perioperative drugs (for example opioids), and how other agents (for example propofol) have biologically plausible microbe-related interactions (propofol glucuronidation and potential microbial β-glucuronidase-mediated reactivation) that remain to be demonstrated in direct clinical studies; hypothesis-driven statements are labeled as 'Hypothesis/Speculative'. Furthermore, we detail how the perioperative period itself, through fasting, antibiotics, opioids, and surgical stress, assaults this microbial ecosystem, creating a vicious cycle of dysbiosis that amplifies risk for adverse outcomes like prolonged sedation, postoperative delirium, and chronic pain. Finally, we outline a translational roadmap, advocating for microbiome-based diagnostics, targeted therapeutic interventions, and integrated dosing models to usher in a new era of precision, microbiome-informed perioperative care.},
}

@article {pmid41697467,
year = {2026},
author = {Mickens, KL and Dillon, SM and Guo, K and Wilson, CC and Santiago, ML},
title = {Cytotoxic CD4 T Cells: Dual Agents in HIV-1 Pathogenesis and Persistence.},
journal = {Current HIV/AIDS reports},
volume = {23},
number = {1},
pages = {5},
pmid = {41697467},
issn = {1548-3576},
support = {T32 AI052066/AI/NIAID NIH HHS/United States ; NIH R01 AI145428, AI108404 and AI134220//National Institute of Allergy and Infectious Diseases/ ; NIH R01 AI145428, AI108404 and AI134220//National Institute of Allergy and Infectious Diseases/ ; T32 TR004367/TR/NCATS NIH HHS/United States ; },
abstract = {PURPOSE OF REVIEW: Cytotoxic CD4 T cells (CD4 CTL) have long been recognized for their potentially protective role in people with HIV, but only recently have their contributions in HIV-1 pathogenesis and viral persistence been appreciated. This review summarizes evidence highlighting their critical role in HIV-1-mediated CD4 T cell depletion and in maintaining the viral reservoir, with special consideration for their abundance and development in the gut.

RECENT FINDINGS: CD4 CTL are increased in frequency in people with HIV (PWH). Granzyme B activity in CD4 CTL promotes HIV-1 mediated death of gut CD4 T cells. CD4 CTL that express survival markers such as BCL-2, TNFR2/CD120b, and OX40 appear to resist HIV-1 mediated cell death, potentially contributing to the viral reservoir. Multiple cytokine (IL-2, IL-15) and transcriptional (BACH2, EOMES) pathways were implicated in CD4 CTL differentiation and maintenance. In the gut, CD4 CTL activity appears to be intricately linked to the microbiome, as cytotoxic protein expression can develop in response to bacterial exposure. CD4 CTL from the gut, induced by the presence of bacteria in vitro, are highly infectable by HIV-1.

SUMMARY: CD4 CTL may act as dual agents in HIV-1 infection, amplifying tissue damage and serving as resilient cellular reservoirs. Understanding the mechanisms regulating their differentiation, cytotoxicity, and survival could inform new therapeutic strategies aimed at restoring gut mucosal integrity, resolving chronic inflammation, and targeting the persistent HIV-1 reservoir.},
}

@article {pmid41697448,
year = {2026},
author = {Kumar, A and Patel, R and Yadav, S and Prajapati, B and Sharma, S and Batta, K and Kaushik, R and Kumar, S and Dudhat, K and Rustagi, S},
title = {Psyllium Husk: A Comprehensive Review of its Functional Properties, Health Benefits, Mechanisms of Action, and Potential Adverse Effects.},
journal = {Current nutrition reports},
volume = {15},
number = {1},
pages = {13},
pmid = {41697448},
issn = {2161-3311},
}

@article {pmid41697419,
year = {2026},
author = {Ni, W and Huang, H and Wang, X and Yu, A and Ren, J and Li, H},
title = {Metagenomic Analysis Reveals Alterations in the Gut Microbiome of Preterm Infants with Extrauterine Growth Restriction.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {177},
pmid = {41697419},
issn = {1432-0991},
support = {No. 82101811//National Natural Science Foundation of China/ ; No. RCJC20231211085923029//Shenzhen Science and Technology Program/ ; No. SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; Guangdong High-level Hospital Construction Fund//Guangdong High-level Hospital Construction Fund/ ; Clinical key specialty construction project of Guangdong Province//Clinical key specialty construction project of Guangdong Province/ ; No. 20232011//Project of Guangdong Provincial Administration of Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature/growth & development ; Infant, Newborn ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Female ; Feces/microbiology ; Male ; },
abstract = {Extrauterine growth restriction (EUGR) is a pervasive clinical issue in preterm infants, affecting neonatal development and their long-term health. This study aimed to characterize the gut microbiome and its derived genes in preterm neonates with EUGR using metagenomic sequencing. Sixty-two preterm infants hospitalized in the neonatal intensive care unit at Guangdong Women and Children Hospital were enrolled in this study. Participants were divided into two groups: the EUGR group (n = 34) and the normal growth group (AGA, n = 28). Fecal samples were collected at one month postnatally. Total bacterial DNA was extracted and sequenced using the Illumina HiSeq X Ten system. Significant differences in the gut microbial community between the EUGR and AGA groups were observed, as evidenced by the Bray-Curtis dissimilarity index. The EUGR group exhibited a notable increase in Klebsiella pneumoniae and Enterococcus faecalis, along with a significant decrease in Streptococcus raffinosi, Rothia mucilaginosa, Parabacteroides merdae and Eggerthella lenta compared to the AGA group. Functional annotation of metagenomic genes identified 415 genes with significantly different relative abundances between the groups. A classification model incorporating five discriminatory genes achieved effective separation of EUGR from AGA infants. Additionally, the EUGR group exhibited a higher relative abundance of antibiotic resistance genes. This study elucidates the alterations in the gut microbiome and its derived genes in preterm neonates with EUGR. These findings provide new insights into the potential microbial signatures associated with impaired growth, although further mechanistic studies are needed to clarify causal relationships.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Infant, Premature/growth & development
Infant, Newborn
Metagenomics
*Bacteria/genetics/classification/isolation & purification
Female
Feces/microbiology
Male

@article {pmid41697396,
year = {2026},
author = {Wang, Y and Liu, J and Wang, W and Xu, G and Lin, Y and Song, P and Zhou, X and Zheng, K},
title = {Identification of fecal microbiome signatures associated with longevity through 16S rRNA sequencing in different age groups in China.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {65},
pmid = {41697396},
issn = {1432-0614},
support = {2023K200//Quzhou Science and Technology Research Project/ ; },
mesh = {Humans ; Middle Aged ; *Feces/microbiology ; China ; RNA, Ribosomal, 16S/genetics ; Aged ; *Longevity ; *Gastrointestinal Microbiome/genetics ; Aged, 80 and over ; Male ; *Bacteria/classification/genetics/isolation & purification ; Female ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; Age Factors ; Phylogeny ; Adult ; },
abstract = {The gut microbiota plays a key role in aging and longevity. Therefore, identifying longevity-associated microbes in healthy and long-lived individuals and elucidating the molecular mechanisms through which they influence longevity are essential steps toward developing effective anti-aging interventions. In this study, we performed 16S rRNA sequencing on 301 fecal samples collected across three age groups. Long-lived individuals (≥ 90 years) had more diverse gut microbiota than typical older individuals (60-89 years), with diversity comparable to that of younger adults (45-59 years). Compared with typical older individuals, long-lived individuals exhibited a marked increase in the relative abundance of Bacteroidota and Akkermansia, accompanied by a decreased abundance of Prevotella_9 and Megamonas. Additionally, the microbiota from this age group showed significant enrichment in unsaturated fatty acid metabolism, ketone body synthesis and degradation, and tryptophan metabolism, suggesting that differences in microbiota composition and function may contribute to longevity. Finally, we developed a qPCR-based method to detect differentially abundant microbiota and established a classification model capable of distinguishing between age groups. In conclusion, the unique composition and function of the gut microbiota in long-lived individuals offer insights for identifying methods and targets for anti-aging interventions. KEY POINTS: • Long-lived individuals exhibited a marked increase in Bacteroidota and Akkermansia • Long-lived individuals exhibited enrichment in unsaturated fatty acid metabolism • We developed a qPCR-based method to detect differentially abundant microbiota.},
}

Humans
Middle Aged
*Feces/microbiology
China
RNA, Ribosomal, 16S/genetics
Aged
*Longevity
*Gastrointestinal Microbiome/genetics
Aged, 80 and over
Male
*Bacteria/classification/genetics/isolation & purification
Female
Sequence Analysis, DNA
DNA, Bacterial/genetics/chemistry
Age Factors
Phylogeny
Adult

@article {pmid41697143,
year = {2025},
author = {Faraon, B and Cohn, SM and Kreiswirth, B and Mediavilla, JR and Perdomo, T and Rhee, P and Ramirez, A and Jardine, R and Rollins, B and Hiraldo, L and Wong, K and Chidiebere, N and Pollock, BH},
title = {Is the Vermiform Appendix a "Safe House"?: A Preliminary Examination of the Appendix Microbiome.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002774},
pmid = {41697143},
issn = {1540-0514},
}

@article {pmid41697036,
year = {2026},
author = {Reva, ON and Sifuna, A and Orata, F and Omolo, C and Iramiot, JS and Enright, MC and Mutshembele, A and Zhou, J and Shivoga, WA},
title = {From Lake Victoria to the Tap: Antibiotic Resistance and Pathogenic Contamination of Kisumu City Water Supply and Wastewater Network.},
journal = {Tropical medicine & international health : TM & IH},
volume = {},
number = {},
pages = {},
doi = {10.1111/tmi.70105},
pmid = {41697036},
issn = {1365-3156},
support = {GCRFNGR8\1143//UK Global Challenges Research Fund Networking/ ; NIHR163838//UK National Institute for Health and Care Research/ ; },
abstract = {Waterborne diseases and antimicrobial resistance (AMR) pose mounting public health threats across sub-Saharan Africa, particularly in rapidly urbanising regions dependent on untreated or poorly treated surface waters. This study applied shotgun metagenomic sequencing to characterise microbial communities, virulence factors and antibiotic resistance genes (ARGs) in water samples collected from Lake Victoria, River Wigwa, Dunga Water Treatment Plant, Nyalenda Wastewater Stabilisation Ponds and the tap water outlet in post-treatment supply pipe in Kisumu city (Kenya). Bacterial taxa dominated all metagenomes, with 121 classes represented. Cyanobacteria, particularly Planktothrix, were highly abundant in lake and tap water, whereas wastewater and river samples exhibited greater taxonomic diversity. Major human pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii and Bacillus cereus/anthracis, were detected in nearly all samples, with unexpectedly high prevalence in tap water. Viral indicators of faecal contamination (adenoviruses, enteroviruses and torque teno viruses) corroborated widespread wastewater influence. Functional gene profiling revealed a rich resistome comprising aminoglycoside-modifying enzymes, β-lactamases, vancomycin-resistance operons and disinfectant-resistance determinants. The highest ARG and virulence gene frequencies occurred in tap and treatment-plant water, suggesting that incomplete disinfection and biofilm persistence promote the proliferation and exchange of ARGs between environmental and pathogenic taxa. In contrast, Lake Victoria water exhibited lower ARG abundance, reflecting natural self-purification processes. These findings underscore the inadequate water treatment and open wastewater systems create ecological 'hotspots' for ARG selection and horizontal gene transfer. Metagenomic surveillance integrated into One Health frameworks can enhance risk forecasting and guide interventions to mitigate AMR emergence and dissemination in freshwater systems serving over 35 million people across the Lake Victoria basin.},
}

@article {pmid41696869,
year = {2026},
author = {Ju, Y and Lin, S and Hu, S and Jin, X and Xiao, L and Zhang, T and Zhang, Y and Zhang, L and Ma, X and Zhu, F and Guo, R},
title = {GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630563},
doi = {10.1080/19490976.2026.2630563},
pmid = {41696869},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Machine Learning ; *Mental Disorders/microbiology ; *Brain ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Male ; Metagenomics ; Female ; *Brain-Gut Axis ; Biomarkers ; },
abstract = {Emerging evidence underscores bidirectional communication along the microbiota-gut-brain axis in neuropsychiatric disorders. However, the field lacks dedicated metagenomic resources with standardized phenotyping for these conditions. Existing single-cohort studies face inherent limitations due to restricted sample sizes, confounding heterogeneity, and methodological fragmentation, compromising reproducibility and mechanistic insights. To overcome these challenges, we constructed the Gut Microbiome in Multinational Integrated Neuropsychiatric Disorders (GutMIND) database, a comprehensive resource integrating shotgun metagenomic data with harmonized metadata. Adhering to a standardized preprocessing protocol and rigorous quality control workflow, this dataset represents the largest gut-brain microbiome repository to date, encompassing 31 studies across 12 countries (n = 3,492) spanning 14 neuropsychiatric conditions. Utilizing this dataset, we characterized microbial community heterogeneity, which was significantly elevated in patients compared to healthy controls. Subsequently, we developed a computational framework, MetaClassifier, enabling the diagnosis of neuropsychiatric disorders and the identification of microbial biomarkers. Employing a comprehensive two-stage validation strategy, we first assessed the model utilizing taxonomic abundance profiles via nested cross-validation in the high-quality discovery cohort (n = 2,734), achieving a mean AUROC of 0.69 (range: 0.55-0.78) across 8 disorders. Its robustness was further confirmed in an independent platform-extended validation cohort (n = 400), yielding a mean AUROC of 0.71 (range: 0.60-0.76). We also developed the Microbial Gut-Brain Axis Health Index (MGBA-HI), which effectively distinguished neuropsychiatric status in both the high-quality cohort and the platform-extended cohort. Furthermore, integrative analysis of health-abundant species, index-derived biomarkers, and ecological prevalence, we identified 9 core neuropsychiatric-protective microbiota. These species predominantly exhibited metabolic capacities linked to glutamate synthesis and acetate production. Building upon this, the GutMIND framework ensures robust cross-cohort comparability while minimizing technical heterogeneity, thereby enhancing inferential rigor in gut microbiome-neuropsychiatry research. Notably, the MetaClassifier, MGBA-HI, and core microbiota hold translational potential for developing microbiome-based prognostic tools and personalized therapeutic strategies in neuropsychiatric disorders. The source code and usage instructions for MetaClassifier are accessible at https://github.com/juyanmei/MetaClassifier.},
}

Humans
*Gastrointestinal Microbiome
*Machine Learning
*Mental Disorders/microbiology
*Brain
Cohort Studies
Bacteria/classification/genetics/isolation & purification
Male
Metagenomics
Female
*Brain-Gut Axis
Biomarkers

@article {pmid41696642,
year = {2025},
author = {Meeusen, H and Lohr, J and van Eijndthoven, T and Kalf, RS and Roeselers, G and van Helvoort, A and Gorter, JA and van Vliet, EA and Tims, S and Silva, JP and Aronica, E},
title = {A novel ketogenic diet that reduces seizures and prevents liver steatosis leads to related gut microbiome changes and restores cecal short-chain fatty acid levels in the rapid kindling rat model of epileptogenesis.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2567677},
pmid = {41696642},
issn = {2993-3935},
abstract = {We recently introduced an innovative ketogenic diet (KD) demonstrating superior antiseizure efficacy in a rat kindling model of epileptogenesis without inducing hepatic steatosis compared to a classic KD. This new diet features reduced fat content, lower plasma ketosis levels, and incorporates new ingredients, including a novel fermentable fiber blend, omega-3 polyunsaturated fatty acids (PUFAs) that partially replace omega-6 PUFAs, and medium-chain fatty acids that partially substitute for stearic acid. In the present study, we conducted gut microbiota analyses on cecum samples to elucidate its contribution to these effects. The analysis revealed distinctive features compared to the classic KD and control diet: higher weighted alpha diversity, distinct beta diversity, increased Bifidobacterium and Clostridium sensu stricto 1 abundances, and altered genera abundances correlated with seizure scores and liver triglyceride content. Furthermore, these genera abundances were linked to stearic acid and omega-3 PUFA plasma levels. Notably, the novel KD restored short-chain fatty acid levels and the butyrate-to-propionate ratio in the cecum, possibly driving lipid oxidation and ketone production while preventing liver steatosis. These findings suggest the involvement of the gut microbiome in mediating the antiseizure efficacy and reducing the adverse metabolic effects of a KD, thereby enhancing its utility for epilepsy treatment.},
}

@article {pmid41696351,
year = {2026},
author = {Singh, MG and Wahengbam, R},
title = {Optimization of DADA2 in QIIME2 for improving fidelity in 16S rRNA V4 amplicon data analysis.},
journal = {Biology methods & protocols},
volume = {11},
number = {1},
pages = {bpag002},
pmid = {41696351},
issn = {2396-8923},
abstract = {High-throughput sequencing generates vast data, often containing low-quality bases, chimeras, and artifacts that can mislead taxonomic classification and diversity assessments. Divisive amplicon denoising algorithm 2 (DADA2) enhances taxonomic resolution by excluding low-quality bases and optimizing amplicon sequence variant inference. Proper truncation reduces computational load while maintaining key hypervariable regions for accurate classification. In this study, we examine the effect of various truncation lengths during the DADA2 analysis in ensuring statistical robustness and improving the reliability of microbial community profiling in ecological and environmental studies. Truncation of read length from 175 to 185 bp improves the quality read recovery rate, and preserves microbial diversity in the V4 hypervariable region of the Illumina paired-end reads. Incorporating the optimal truncation length strategy optimizes read recovery and preserves the richness and evenness of microbial communities.},
}

@article {pmid41696101,
year = {2026},
author = {Vasudevan, D},
title = {Gut microbiota dysbiosis, circulating microbial genetic traces, and their role in gestational diabetes.},
journal = {World journal of diabetes},
volume = {17},
number = {2},
pages = {114124},
pmid = {41696101},
issn = {1948-9358},
abstract = {Diabetes mellitus is a leading metabolic and non-communicable disease, affecting nearly 537 million adults worldwide. Recent research highlights the gut microbiota as a crucial factor in the onset and progression of diabetes. Gut microbial dysbiosis, an imbalance in microbial composition, has been increasingly recognized as a contributor to diabetes pathogenesis during pregnancy. The gut microbiome is influenced by multiple internal and external factors, which can worsen diabetes-related complications. A higher abundance of pathogenic microbes may lead to the release of microbial metabolites or DNA into circulation, contributing to metabolic disorders such as obesity, cardiovascular disease, and liver dysfunction. Microbial nucleic acids have been identified in the bloodstream of individuals with diabetes and in pregnant women, suggesting the existence of a circulating or blood microbiome. Various physiological and pathological conditions may permit gut microbes or their components to enter the bloodstream. This review introduces the concept that the blood microbiome may play a critical role during pregnancy, potentially increasing susceptibility to diabetes. It emphasizes the mechanistic link between gut dysbiosis, microbial translocation, and pregnancy-associated metabolic disturbances. Exploring gut and blood microbiome interactions in pregnancy could reveal early biomarkers and therapeutic targets for gestational diabetes mellitus. Future studies should focus on longitudinal microbiome analyses and interventions to restore microbial balance, offering new preventive strategies against diabetes during pregnancy.},
}

@article {pmid41696071,
year = {2025},
author = {Forbrigger, Z and MacDonald, T and Kulkarni, K and Stadnyk, AW},
title = {Investigating diet to control asparagine uptake as an adjunct to asparaginase treatment.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1634113},
pmid = {41696071},
issn = {2234-943X},
abstract = {Ongoing refinements of multidrug regimens, and particularly the addition of L-asparaginase, resulted in an immediate gain in survival for pediatric acute lymphoblastic leukemia patients. Yet L-asparaginase has substantial side effects which may require dose reductions or delays in subsequent doses. There are at least 3 possible sources of L-asparagine to consider when balancing blood levels with asparaginase dosing, diet, cell synthesis and bacterial synthesis. To date, there is one precedent, in mice, in which blood L-asparagine levels are reduced as a consequence of reducing consumed levels. We build on that approach in experiments aimed at testing whether long-term dietary restriction of L-asparagine and possibly gut bacteria can impact blood levels. In our experiment, 2 groups of mice received food pellets with either 4% or 0% L-asparagine. Blood and fecal metabolites and fecal bacteria were sampled over 72 days. After this accommodation period, all mice continued their diet and received a single injection of pegylated E. coli recombinant L-asparaginase. Samples for bacteria and metabolites were collected 4 and 5 days later, respectively. Neither diet had adverse effects on the general health of the mice nor did diet alone change blood L-asparagine levels. Both diets led to changes in gut bacteria. L-asparaginase depleted blood L-asparagine in mice consuming either diet. Bacteria identified in fecal pellets revealed that the microbiomes of mice in the 2 cages were different (cage effect) and remained different although metagenomic analyses of day 72 feces indicated there were no diet-dependent differences in bacterial asparaginase or asparagine synthetase. These outcomes indicate that mice recover from any short-term down regulation of blood L-asparagine due to diet and consequently the metabolic controls become complex, and the gut microbes seem to not be a great influence. Further research should include approaches to determine the source of L-asparagine in the blood while ingesting diets with no/low or high amounts of L-asparagine.},
}

@article {pmid41696022,
year = {2026},
author = {Thobor, BM and Hill, CEL and Custer, GF and Garcias-Bonet, N and Fox, MD and El-Khaled, YC and Aylagas, E and Dini-Andreote, F and Struck, U and Tilstra, A and Peixoto, R and Carvalho, S and Wild, C and Mueller, B},
title = {Contrasting physiological adaptation strategies to natural environmental change in two Red Sea coral holobionts.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag008},
pmid = {41696022},
issn = {2730-6151},
abstract = {Coral holobionts acquire energy and nutrients from heterotrophic feeding, Symbiodiniaceae symbiosis, and additional metabolic functions (e.g. nitrogen (N) fixation) from associated bacterial communities. Since symbioses often require stable environmental conditions, corals in environments with seasonal variability have likely evolved adaptation strategies by either maintaining (i.e. regulating) or shifting (i.e. conforming) key functional traits, but empirical data is needed. We investigated carbon (C) and N elemental and stable isotope ratios alongside bacterial community composition in the hydrocoral Millepora dichotoma and the scleractinian coral Stylophora pistillata every two months over one year. These data were integrated with environmental parameters to investigate potential adaptation strategies of the coral holobionts over a seasonal cycle. S. pistillata showed temporal changes in δ[13]C, δ[15]N and C:N ratios in both host and Symbiodiniaceae tissues (indicating stable host-Symbiodiniaceae C/N cycling), in combination with stable bacterial communities. M. dichotoma, did not exhibit temporal changes in elemental and stable isotope ratios, but higher δ[15]N and C:N variability, and 61% higher C:N ratios in Symbiodiniaceae compared to host tissue. Temporal shifts in bacterial communities resulted in significantly enriched predicted metabolic functions for C, N, and sulfur cycling in winter. Stable C/N cycling and bacterial community composition suggest a regulator-like life history strategy of S. pistillata, whereas variable C/N cycling and flexible bacterial communities indicate a conformer-like life history strategy for M. dichotoma. Both contrasting adaptation strategies enable these organisms to succeed amid current environmental change, yet to what extent this can be maintained under future climate scenarios remains to be investigated.},
}

@article {pmid41696020,
year = {2026},
author = {Kim, J and Murakami, T and Toyoda, A and Mori, H},
title = {Behavioural phase transitions in the migratory locust, Locusta migratoria, are related to changes in the gut bacterial composition.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag009},
pmid = {41696020},
issn = {2730-6151},
abstract = {Locusta migratoria is a grasshopper species that can change its behaviour from solitary to gregarious. Previous studies have implicated metabolites such as serotonin and dopamine in the regulation of behavioural transition in this species. While many studies using cultured microbes have demonstrated that some microbes harbor the neuroactive metabolic potential of these neurotransmitters, the association between microbial community composition and phase transition remains poorly understood. Here, we employed 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing analyses to compare the composition of gut microbial communities of L. migratoria in different behavioural phases. We found that Serratia ureilytica was enriched in the gut of gregarious individuals in contrast to the decreased presence of Klebsiella aerogenes, one of the most abundant taxa in wild individuals. The gut microbiome of gregarious individuals was functionally characterised by enriched kynurenine and tryptophan synthesis pathways, and by reduced representation of GABA, indole, and dopamine metabolism pathways compared with that of solitary individuals. These compositional changes were consistent with the enrichment of S. ureilytica and depletion of K. aerogenes, which possess the corresponding genes. In particular, the genes for kynurenine synthesis encoded by S. ureilytica specific to the gregarious phase, are known to be involved in the tryptophan production and are associated with reduced serotonin synthesis. These results highlight a distinct shift in both the taxonomic and functional composition of the gut microbiome across behavioural phases and suggest a potential microbial contribution to the behavioural changes of L. migratoria.},
}

@article {pmid41696005,
year = {2026},
author = {Ito, K and Adachi, M and Scheftgen, AJ and Suen, G and Hiyama, R and Seki, K and Nakai, S and Yano, R and Nishida, T and Hanada, M and Fukuma, N},
title = {In vitro comparative analysis of steamed wood and other lignocellulosic substrates on ruminal fermentation and microbiota.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1750760},
pmid = {41696005},
issn = {2297-1769},
abstract = {Lignocellulosic biomass such as wood is increasingly recognized as a promising low-opportunity-cost feed (LCF) that does not compete with human-edible food. In this study, we evaluated rumen fermentation characteristics and microbial community responses using an in vitro batch culture system with a diverse set of substrates, including steamed and untreated woods, xylo-oligosaccharides, spent mushroom substrates, and conventional feeds. Hierarchical clustering based on bacterial community composition revealed five distinct microbial clusters. Certain steamed woods and xylo-oligosaccharides formed separate clusters from untreated woods and conventional feeds, and were associated with the dominance of specific genera such as Succinivibrio and Selenomonas. These microbial shifts may reflect differences in substrate characteristics, potentially related to hemicellulose- and oligosaccharide-derived components. The results suggest that both steamed wood and xylo-oligosaccharides enhance fermentability and are associated with distinct microbial community structures under in vitro conditions. These substrates show promise as sustainable feed ingredients, and further in vivo studies are needed to evaluate their efficacy and long-term impacts on animal health and productivity.},
}

@article {pmid41695956,
year = {2026},
author = {Ali, A and AlHussaini, KI},
title = {Diagnostic challenges and treatment approaches for Clostridioides difficile infection in IBD patients.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1740387},
pmid = {41695956},
issn = {1664-302X},
abstract = {BACKGROUND: Clostridioides difficile infection (CDI) poses a major clinical challenge in patients with inflammatory bowel disease (IBD) due to overlapping symptoms, diagnostic complexities, and distinct therapeutic considerations. The interaction between CDI and IBD involves disrupted gut microbiota, immune dysregulation, and disease-specific risk factors.

METHODS: This review critically examines the current evidence on the diagnosis and management of CDI in patients with IBD. Literature sources discussing diagnostic methodologies, therapeutic strategies, and preventive interventions were analyzed, with a focus on recent advances and their clinical applicability.

RESULTS: Diagnosing CDI in IBD remains difficult due to similar clinical presentations between infectious colitis and IBD flares, alongside limitations of stool assays, molecular tests, and endoscopic evaluations. Emerging diagnostic tools may enhance the accuracy and timeliness of detection. Standard therapies, antibiotics, and fecal microbiota transplantation (FMT) remain essential; however, their application requires individualization, taking into account immunosuppressive therapy, drug interactions, and the risk of recurrence. Treatment outcomes are further influenced by disease severity and patterns of antimicrobial resistance. Preventive strategies, including antimicrobial stewardship, probiotics, and vaccination, may help reduce the incidence of CDI among patients with IBD.

CONCLUSION: CDI in IBD necessitates a personalized management approach that incorporates accurate diagnostics, targeted therapy, and preventive measures. Despite therapeutic advances, significant knowledge gaps persist regarding host microbiome interactions and the optimization of individualized treatment. Future research should focus on improving diagnostic precision and developing personalized medicine strategies to enhance outcomes for IBD patients affected by CDI.},
}

@article {pmid41695944,
year = {2026},
author = {Fascio, CJ and Rubio Molina, AC and Marin-Gallego, BJ and de Cristóbal, RE and Espinosa-Urgel, M and Vincent, PA and Farizano, JV and Adler, C},
title = {Interspecies interactions among sugarcane-associated bacteria and their impact on plant growth promotion traits.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1714037},
pmid = {41695944},
issn = {1664-302X},
abstract = {Microbes associated with plants have proven to play a fundamental role in their growth and phytosanitary status. Microbial community architecture and function results from interactions with the host and with each other. Therefore, microbial diversity and the array of possible interspecies interactions should be considered as key elements for the development of future biocontrol and crop improvement strategies. To gain some insight into this potential, we isolated 16 rhizospheric and 16 endophytic bacteria from sugarcane and tested their ability to interact with each other. To this end, we performed 120 pairwise interaction assays within each group. Although most interactions were neutral in both rhizospheric and endophytic communities, negative interactions were more frequent between rhizospheric isolates. In contrast, positive ones predominated among endophytic isolates. After determining the interaction phenotypes between isolates, we tested their impact on plant growth promoting (PGP) traits and biocontrol against Xanthomonas albilineans. Our results demonstrate that interspecies interactions among sugarcane-associated bacteria can modulate key PGP traits regardless of their interaction phenotype, highlighting a potentially overlooked layer of functional regulation within the microbiome. Accordingly, social behavior of microorganisms might set the basis for a rational design of performance-improved bioinoculants for agriculture, particularly consortia-based inoculants.},
}

@article {pmid41572191,
year = {2026},
author = {Khan, S and Sultan, MT and Abbas, A and Kausar, T and Sidrah, and Shabbir, H and Hussain, A and Elkhedir, AE},
title = {The interplay between malnutrition, persistent diarrhea, lactose intolerance, and food associated gut dysbiosis in children; a comprehensive review.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {113},
pmid = {41572191},
issn = {1471-2431},
abstract = {BACKGROUND: Persistent diarrhea, lactose intolerance, and gut dysbiosis are major gastrointestinal conditions that worsen malnutrition in children, especially in low and middle-income countries. Due to these factors, there is a vicious cycle in which diarrhea worsens malnutrition by reducing the gut’s capacity to absorb nutrients. Persistent diarrhea is defined by WHO, diarrhea (≥ 3 loose/watery stools daily) lasting 14 days or longer posing higher risk of malnutrition than acute diarrhea.

METHODS: This review explores the interconnected nature of these conditions and their cumulative impact on child health and development. A comprehensive literature review was conducted using databases such as Google Scholar, PubMed, Web of Science and Scopus, focusing on studies examining the pathophysiology, clinical manifestations, and management strategies in malnourished children. This review explores current evidences on etiology (E. coli, Cryptosporidium, sequential infections), pathophysiology (malabsorption, villus atrophy, enteric inflammation), dietary interventions (zinc, vitamin A, glucose-polymer ORS) and microbiome-based (probiotics, dysbiosis, correction) strategies of persistent diarrhea.

RESULTS: Findings show that persistent diarrhea causes mucosal damage and nutrient malabsorption, while secondary lactose intolerance leads to osmotic diarrhea and further caloric loss. Gut dysbiosis, marked by the depletion of beneficial bacteria and overgrowth of pathogens, impairs digestion, disrupts immune function, and sustains chronic inflammation. Together, these conditions create a vicious cycle that perpetuates malnutrition and stunting. Recommended interventions include oral rehydration therapy, lactose-restricted diets, micronutrient supplementation (particularly zinc and vitamin A), and microbiota-based therapies such as probiotics and prebiotics.

CONCLUSION: The review concludes that integrated approaches—combining nutritional support, microbiome restoration, and improved hygiene—are essential for breaking the cycle of malnutrition and gastrointestinal disease. Addressing these issues through targeted public health policies and personalized interventions can significantly improve outcomes for vulnerable pediatric populations.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12887-026-06529-8.},
}

@article {pmid41695942,
year = {2026},
author = {Guo, Y and Zou, S and Yang, X and Li, R and Fu, W and Xu, C and Zhang, F and Yang, X},
title = {Enterococcus faecium secreted the NlpC/P60 family protein to enhance host immunity and indirectly increases Akkermansia muciniphila for slowing aging.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1680593},
pmid = {41695942},
issn = {1664-302X},
abstract = {While probiotics like Enterococcus faecium are known for gut health benefits, their potential anti-aging effects are poorly understood. This study investigated whether E. faecium fermentation broth delays aging and explored its mechanisms. Using a mouse model, lifespan assays suggested that the E. faecium fermentation broth may contribute to lifespan extension, indicating anti-aging properties. Microbiome analysis showed it modulated gut microbiota, increasing beneficial Akkermansia abundance. Key active components identified included myo-inositol (promoting hair follicle growth), D-ribose, and secreted proteins. While myo-inositol increased the abundance of Lactobacillus reuteri and Lactobacillus johnsonii, it did not increase Akkermansia. A high-content secreted protein, NlpC/P60, present in E. faecium fermentation broth, may enhance host immunity through the NOD-like receptor signaling pathway, thereby restricting pathogen colonization and reshaping the gut microbiota. This immune boost indirectly elevated levels of beneficial bacteria like Akkermansia muciniphila and L. johnsonii, improving overall microbiota composition and mitigating age-related diseases. The findings demonstrate that E. faecium fermentation broth combats aging through multiple pathways, primarily microbiota modulation and immune enhancement. The identification of NlpC/P60 as a key mediator provides crucial mechanistic insight. This study elucidates the material basis and pathways by which E. faecium fermentation broth delays aging, offering experimental support for developing novel microecological therapies against age-related diseases.},
}

@article {pmid41695773,
year = {2026},
author = {Fan, J and Xu, Y},
title = {Molecular mechanisms underlying the lifespan and healthspan benefits of dietary restriction across species.},
journal = {Frontiers in genetics},
volume = {17},
number = {},
pages = {1771707},
pmid = {41695773},
issn = {1664-8021},
abstract = {Dietary restriction (DR), defined as reduced caloric intake or selective limitation of specific nutrients without malnutrition, is one of the most robust interventions known to extend lifespan and healthspan across species. Studies from yeast to mammals demonstrate that DR elicits conserved genetic, transcriptional, and epigenetic programs that promote cellular maintenance and stress resistance. At the molecular level, DR engages evolutionarily conserved nutrient-sensing pathways, including insulin/IGF-1 signaling (IIS), the mechanistic target of rapamycin (mTOR), AMP-activated protein kinase (AMPK), and NAD[+]-dependent sirtuins, which converge on key transcription factors (TFs) and transcriptional coactivators (TCs) to coordinate metabolic and longevity-associated gene expression. Downstream, these pathways enhance autophagy and proteostasis, remodel mitochondrial function and redox balance, reshape immune and inflammatory networks, and induce epigenetic and transcriptional reprogramming. Recent work further highlights amino acid-specific sensing mechanisms, endocrine mediators such as fibroblast growth factor 21 (FGF21), the gut microbiome, circadian regulators, and nuclear pore-associated transcriptional plasticity as integral components of DR responses. Importantly, the physiological outcomes of DR are context dependent and influenced by genetic background, sex, age at intervention, and the type and duration of restriction. In this review, we summarize current knowledge on the genetic and molecular architecture underlying DR-induced longevity and health benefits across species, discuss implications for aging-related diseases, and outline future directions toward precision nutrition and safe translational strategies.},
}

@article {pmid41695675,
year = {2026},
author = {Keum, GB and Doo, H and Kwak, J and Sun, X and Cho, J and Kim, HB},
title = {Effects of phytobiotics on intestinal barrier function and gut microbiome in weaned piglets challenged with enterotoxigenic Escherichia coli.},
journal = {Journal of animal science and technology},
volume = {68},
number = {1},
pages = {181-196},
pmid = {41695675},
issn = {2055-0391},
abstract = {Weaned piglets are highly susceptible to infections caused by enterotoxigenic Escherichia coli (ETEC), and phytobiotic supplementation has been explored as a potential strategy to prevent or mitigate such infections during the weaning period. However, comprehensive studies on the specific effects of phytobiotics on pig gut health and microbiota composition remains limited. Therefore, this study aimed to investigate the effects of various phytogenic feed additives (PFAs) on intestinal barrier function and gut microbiota composition in weaned piglets challenged with ETEC. A total of 63 weaned piglets ([Yorkshire × Landrace] × Duroc), 28 days old with an initial body weight of 8.03 ± 0.43 kg, were used in a 21-day trial. Piglets were randomly assigned to one of seven treatment groups: NC, negative control (basal diets without E. coli challenge); PC, positive control (basal diets + E. coli challenge); T1, PC + 0.04 % P1; T2, PC + 0.01 % P2; T3, PC + 0.10 % P3; T4, PC + 0.04 % P4; T5, PC + 0.10 % P5. The five phytobiotic materials were as follows: a bitter citrus extract rich in flavonoids (P1), a microencapsulated blend of thymol and carvacrol (P2), a composite of P1 and P2 (P3), a grape polyphenol-based mixture containing green tea and hops (P4), and a fenugreek seed powder rich in saponins (P5). Piglets in challenged groups were orally inoculated with ETEC at a concentration of 1.2 × 10[10] CFU/mL from days 8 to 10. The results showed that PFA supplementation upregulated the expression of tight junction and mucin-related genes including ZO-1 and MUC3. Based on 16S rRNA gene sequencing, distinct microbial shifts were observed depending on the specific PFA composition. The relative abundances of beneficial genera such as Lactobacillus, Olsenella, and Collinsella increased following PFA supplementation. These genera are known to be associated with short-chain fatty acid production, improved gut health, and increased resistance to pathogens. Additionally, increases in Acinetobacter and Medioterraneibacter, which may be involved in the metabolism of plant-derived compounds, were observed. Collectively, our results suggest that PFAs may enhance gut health and contribute to the stabilization of the intestinal microbiota in weaned piglets.},
}

@article {pmid41695535,
year = {2025},
author = {Deng, J and Zhang, Z and Wang, Y and Ai, J and Zhao, Y and Li, B and Li, H and Deng, Y and Zhang, F},
title = {Organic fertilizer-mediated assembly of rhizosphere core microbiota contributes to increased sugarcane productivity.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1689397},
pmid = {41695535},
issn = {1664-462X},
abstract = {Optimizing fertilization strategies to enhance crop yield remains a critical challenge in sustainable agriculture. In this study, two field experiments were conducted in Yunnan Province, China, to evaluate the effects of three fertilization regimes-no fertilization (CK), chemical fertilization (F), and combined chemical and organic fertilization (FM)-on sugarcane yield, soil biochemical properties, and rhizosphere bacterial communities. The results showed that the FM treatment significantly increased sugarcane yield at both sites compared to CK and F. This yield improvement was accompanied by increased soil nutrient availability, enhanced enzyme activities, and significant changes in microbial community structure. High-throughput 16S rRNA sequencing results indicated that the FM treatment selectively enriched specific taxa, such as Actinobacteriota and Proteobacteria, and promoted the development of a more modular and stable microbial co-occurrence network. Correlation analysis and structural equation modeling further revealed that the FM treatment improved sugarcane yield primarily through microbiome-driven pathways that indirectly enhanced soil biochemical functions. Overall, this study unveils the mechanistic links between integrated fertilization strategies, rhizosphere microbial network stability, and sugarcane yield, providing scientific evidence for sustainable fertilization management in sugarcane production systems.},
}

@article {pmid41695353,
year = {2026},
author = {Fiordaliso, M and Pala, B and Marincola, G and Piscione, M and Savino, L and Mazzone, M and Di Marcantonio, MC and Mincione, G},
title = {Biliary stents can modify the microbiota and promote the progression of pancreatic cancer.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1633611},
pmid = {41695353},
issn = {2234-943X},
abstract = {Pancreatic cancer (PC), the fourth cause of cancer-related deaths, is an aggressive disease with an increased worldwide incidence. Pancreatic ductal adenocarcinoma (PDAC), ~90% of pancreatic malignancies, arises from pancreatic ducts. PC has a unique microenvironment hosting a heterogenous combination of cell populations, including immune cells and microbes. Microorganisms appear involved in every step of PC's natural history, from creating a predisposing environment for in situ carcinogenesis to cell migration and metastasis. Biliary stent placement through endoscopic retrograde cholangiopancreatography (ERCP) can mitigate jaundice in PC patients but may alter the intestinal microbiota and contribute to tumor initiation and progression. Disruption of the antimicrobial barrier of the sphincter of Oddi, due to endoscopic sphincterotomy and stent insertion, promotes duodenal reflux, permitting bacterial colonization and biofilm formation. Although ERCP is the preferred drainage route, studies reported lower complication rate and reduced dysbiosis with percutaneous transhepatic biliary drainage (PTBD). The biliary microbiome in stented patients undergoing pancreaticoduodenectomy is altered, exhibiting higher levels of Enterococci, Klebsiella, and Candida species. The decision to place a biliary stent in PC patients should be carefully considered, given the potential for dysbiosis and its impact on therapeutic resistance. This underscores the need for further research into interventions that could modulate the microbiota, such as PTBD, probiotics or targeted microbial therapies.},
}

@article {pmid41695280,
year = {2026},
author = {Wang, YP and Dai, JL and Li, L and Wen, B},
title = {Insights into the influencing factors of fecal gut microbiota in hepatocellular carcinoma.},
journal = {World journal of gastroenterology},
volume = {32},
number = {6},
pages = {115217},
pmid = {41695280},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Liver Neoplasms/microbiology/diagnosis/virology/pathology ; *Carcinoma, Hepatocellular/microbiology/diagnosis/virology ; *Feces/microbiology ; Antiviral Agents/therapeutic use/pharmacology ; Metabolome ; Hepatitis B/drug therapy/complications/virology ; Hepatitis B virus ; Dysbiosis ; Biomarkers, Tumor/metabolism ; },
abstract = {Recently, Feng et al published a significant study. Through multi-omics analysis, their research team revealed associations between fecal metabolome, gut bacteria, and serum indicators in patients with hepatocellular carcinoma (HCC). These results suggest that the composition of the metabolome and gut bacteria in fecal samples hold promise as potential biomarkers for the diagnosis of HCC. After carefully reviewing their work, we offer two points of insight: (1) The influence of different factors on gut microbiota changes in HCC; and (2) The impact of the hepatitis B virus and antiviral drugs on the gut microbiota of patients with HCC.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Liver Neoplasms/microbiology/diagnosis/virology/pathology
*Carcinoma, Hepatocellular/microbiology/diagnosis/virology
*Feces/microbiology
Antiviral Agents/therapeutic use/pharmacology
Metabolome
Hepatitis B/drug therapy/complications/virology
Hepatitis B virus
Dysbiosis
Biomarkers, Tumor/metabolism

@article {pmid41695278,
year = {2026},
author = {Lu, JG and Gao, YZ},
title = {Dyspepsia following Helicobacter pylori eradication: Shifts in etiology and clinical challenges.},
journal = {World journal of gastroenterology},
volume = {32},
number = {6},
pages = {115699},
pmid = {41695278},
issn = {2219-2840},
mesh = {Humans ; *Dyspepsia/microbiology/epidemiology/etiology/diagnosis ; *Helicobacter Infections/drug therapy/complications/microbiology/epidemiology ; *Helicobacter pylori/drug effects/isolation & purification ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Stomach Neoplasms/epidemiology/microbiology ; Japan/epidemiology ; Prevalence ; Gastrointestinal Microbiome/drug effects ; Retrospective Studies ; },
abstract = {This editorial discusses a landmark 2025 retrospective cohort study by Suzuki et al using > 23000 endoscopic records from Japan's Helicobacter pylori (H. pylori) eradication program. The study addressed the clinically significant phenomenon of persistent dyspeptic symptoms after successful bacterial eradication. Comprehensive analysis revealed that 28.7% of the patients continued to experience functional dyspepsia (defined as self-reported upper abdominal pain or bloating) after eradication, a prevalence rate indistinguishable from that of the never-infected control groups. Notably, Suzuki et al demonstrated no significant epidemiological association between dyspepsia and the risk of gastric cancer. These findings suggest that persistent symptoms may originate from multifactorial mechanisms, including post-eradication alterations in gastric acid secretion, visceral hypersensitivity, and potential gastric microbiome changes. These evidence-based insights support the implementation of stratified management approaches based on individual symptom patterns and sociodemographic characteristics, moving beyond uniform eradication protocols. This study recommends reducing emphasis on dyspepsia symptoms in revising endoscopic screening guidelines to minimize unnecessary interventions and improve medical resource efficiency. This research contributes significantly to mitigating public health anxiety regarding H. pylori infection, prevents indiscriminate antibacterial overuse, and provides a robust scientific foundation for developing more rational, evidence-based clinical decision-making frameworks for H. pylori-associated dyspepsia management.},
}

Humans
*Dyspepsia/microbiology/epidemiology/etiology/diagnosis
*Helicobacter Infections/drug therapy/complications/microbiology/epidemiology
*Helicobacter pylori/drug effects/isolation & purification
*Anti-Bacterial Agents/therapeutic use/adverse effects
Stomach Neoplasms/epidemiology/microbiology
Japan/epidemiology
Prevalence
Gastrointestinal Microbiome/drug effects
Retrospective Studies

@article {pmid41695277,
year = {2026},
author = {Yin, HY and You, QH and Zhang, WJ and Ji, G and Dang, YQ},
title = {High-protein diets and metabolic dysfunction-associated steatotic liver disease: A double-edged sword in liver health.},
journal = {World journal of gastroenterology},
volume = {32},
number = {6},
pages = {113804},
pmid = {41695277},
issn = {2219-2840},
mesh = {Humans ; Gastrointestinal Microbiome ; *Diet, High-Protein/adverse effects ; *Liver/metabolism/pathology/immunology ; *Non-alcoholic Fatty Liver Disease/epidemiology/metabolism/diet therapy ; *Fatty Liver/epidemiology/etiology/metabolism ; Animals ; Plant Proteins, Dietary ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is among the most prevalent chronic liver conditions globally and is closely linked with a range of metabolic disorders. Recently, the high-protein diet (HPD) has garnered attention for its potential benefits in weight management and metabolic health; however, its impact on MASLD remains a subject of debate. This article provided a systematic review of epidemiological studies, clinical trials, and foundational research concerning the role of HPD in MASLD. It examined the mechanisms by which HPD influences liver metabolism, inflammatory responses, and gut microbiota in patients with MASLD and assessed their clinical efficacy. The review revealed that HPD exerts dual effects on MASLD, contingent upon the protein source and consumption levels, and plant-based proteins conferred metabolic advantages. Therefore, it is advised that patients with MASLD prioritize plant-based proteins while moderating animal protein intake. Future research should aim to elucidate the mechanisms underlying HPDs and deploy personalized nutrition approaches that integrate genomic, proteomic, metabolomic, and microbiome profiles to predict individual responsiveness to specific protein sources, thereby enabling precision dietary algorithms for MASLD prevention and treatment.},
}

Humans
Gastrointestinal Microbiome
*Diet, High-Protein/adverse effects
*Liver/metabolism/pathology/immunology
*Non-alcoholic Fatty Liver Disease/epidemiology/metabolism/diet therapy
*Fatty Liver/epidemiology/etiology/metabolism
Animals
Plant Proteins, Dietary

@article {pmid41695142,
year = {2025},
author = {Wang, J and Liu, L and Sheng, J and Zhang, L and Li, Q and Gao, T and Liu, X},
title = {Effects of different doses of oregano essential oil on growth performance, health parameters, and the gut microbiome-metabolome profile in heat-stressed Pinan cattle (Piedmontese × Nanyang).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1712904},
pmid = {41695142},
issn = {1664-302X},
abstract = {INTRODUCTION: This study investigated the dose-response efficacy of dietary oregano essential oil (OEO) in mitigating severe heat stress (THI ≈ 86) in beef cattle.

METHODS: Thirty-six Pinan bulls were fed a basal diet alone (control) or supplemented with 7 (L-OEO) or 14 g/d (H-OEO) of OEO for 60 days.

RESULTS: The low-dose OEO (7 g/d) significantly improved hepatic function (reduced ALT, AST; increased ALB, TP), enhanced immune (increased IgA, IgM) and antioxidant status (decreased MDA, increased SOD, CAT), and increased the ruminal abundance of Bacteroidota and Prevotella, which correlated negatively with acyl-glycine metabolites. In contrast, the high dose (14 g/d) only increased GSH-Px and T4, resulted in higher MDA than L-OEO, and did not significantly affect the rumen microbiota.

CONCLUSION: Supplementation with 7 g/d OEO optimally improved overall health and metabolic function in heat-stressed bulls, whereas a 14 g/d dose offered no additional benefits.},
}

@article {pmid41695140,
year = {2025},
author = {Fu, Y and Chen, S and Cui, L and Cao, Y and Dong, Y and Duan, Y and Wu, C},
title = {Lactobacillus paracasei WIS43 alleviates DSS-induced colitis by modulating gut microbiota and suppressing inflammation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721585},
pmid = {41695140},
issn = {1664-302X},
abstract = {INTRODUCTION: Ulcerative colitis (UC) is a chronic inflammatory disorder of the colon with rising incidence and limited therapeutic options. Probiotics are increasingly recognized as potential interventions, but strain-specific differences remain insufficiently defined.

METHODS: We conducted a meta-analysis of publicly available microbiome datasets to characterize disease-associated dysbiosis, focusing on the genus Lactobacillus. We then evaluated Lactobacillus paracasei WIS43, a novel strain isolated from the breast milk of a healthy volunteer, in a dextran sulfate sodium (DSS)-induced murine colitis model, using mesalazine and the commercial strain Lactobacillus paracasei LPC-37 as comparators. Disease severity, histopathology, inflammatory cytokines, and gut microbiota composition were systematically assessed.

RESULTS: Meta-analysis confirmed a significant depletion of Lactobacillus in UC patients. In vivo, WIS43 treatment reduced body weight loss, disease activity index scores, and colon shortening. Histological analysis revealed preserved epithelial integrity and reduced inflammatory infiltration. WIS43 significantly decreased serum and colonic TNF-α, IL-6, and IL-1β levels, demonstrating stronger anti-inflammatory activity than LPC-37 and comparable efficacy to mesalazine. 16S rRNA sequencing further showed that WIS43 restored beneficial taxa, including Lactobacillus johnsonii and Lactobacillus taiwanensis, while reducing potentially pathogenic bacteria.

CONCLUSION: These findings identify WIS43 as a promising probiotic candidate for the prevention and treatment of UC, supporting its therapeutic potential through coordinated modulation of host immunity and gut microbiota.},
}

@article {pmid41695138,
year = {2025},
author = {Atterbury, RJ and Gigante, AM and Jalasvuori, M and Lavigne, R and Schouler, C and Mariano, V and Barrow, P},
title = {The application of bacteriophage to veterinary and One-Health medicine-a road map.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1725071},
pmid = {41695138},
issn = {1664-302X},
abstract = {The STAR-IDAZ international research consortium established a working group on Alternatives to Antimicrobials to explore various approaches for reducing our reliance on antimicrobials. These included bacteriophages, activating the immune system and manipulating the microbiome. The sub-group investigating bacteriophages have developed a road map for the application of phages in a One Health context. We present this roadmap here, in review format, along with a discussion of how phages may be combined with other therapies.},
}

@article {pmid41695029,
year = {2026},
author = {Qin, H and Zhang, L and Rao, Z and Wei, X and Táncsics, A and Sheng, R and Liu, Y and Chen, A and Fang, C and Huang, F and Long, P and Zhu, B},
title = {Decoding endophytic microbiome dynamics: engineering antagonistic synthetic consortia for targeted fusarium suppression in monoculture regimes.},
journal = {Horticulture research},
volume = {13},
number = {2},
pages = {uhaf286},
pmid = {41695029},
issn = {2662-6810},
abstract = {Biological control leveraging endophytic microbes represents a promising eco-friendly strategy to mitigate soil-borne diseases, yet the efficacy and mechanistic underpinnings of synthetic microbial communities (SynComs) derived from plant endophytes remain poorly understood. This study employed a holistic approach-integrating field sampling, microbial profiling, and functional validation-to investigate the dynamics of edible lily (Lilium) microbiomes under continuous cropping and develop targeted SynComs against Fusarium oxysporum. Metacommunity analysis revealed that prolonged monoculture co-enriched both potentially beneficial taxa (e.g. Pseudomonas, Bacillus) and pathogenic Fusarium, reflecting a dynamic equilibrium where naturally recruited antagonists were insufficient to prevent pathogen dominance, while increasing the complexity of endophytic co-occurrence networks. Keystone bacterial lineages, including Burkholderiaceae and Pseudomonas, emerged as critical stabilizers of the endosphere microbiome. Notably, 50% of endogenous bacterial taxa exhibited rhizospheric origins, contrasting with fungal communities where <10% derived from soil-a finding underscoring host-specific filtering mechanisms. Through systematic isolation and combinatorial testing, we engineered SynComs combining core antagonistic strains (Rhizobium, Methylobacterium, Talaromyces) with auxiliary microbes. Fungal-integrated SynComs outperformed bacteria-only consortia in plant growth promotion and pathogen suppression. By bridging fundamental microbial ecology with translational agriculture, our findings establish SynComs as scalable tools for sustainable soil health management, reducing reliance on synthetic fungicides while addressing the yield-limiting challenges in continuous cropping systems.},
}

@article {pmid41694821,
year = {2026},
author = {Giridharan, S and Pandiyan, B and Kumar, NV and Godbole, M and Soumian, S},
title = {Effects of Isha Yoga Practices on Health Outcomes: A Systematic Review of Controlled Studies.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e101478},
pmid = {41694821},
issn = {2168-8184},
abstract = {The global burden of chronic diseases and mental health disorders has intensified the need for holistic interventions such as yoga. Isha Yoga, a comprehensive system integrating physical postures, breathwork, and meditation, has demonstrated preliminary benefits in stress reduction and physiological regulation. This systematic review evaluates the effects of Isha Yoga practices on mental and physical health outcomes in controlled studies. In accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, systematic searches were conducted in PubMed, Scopus, Web of Science, and the Cochrane Library from database inception to July 2025. Eligible studies employed controlled designs, including randomised controlled trials (RCTs), non-randomised controlled studies, and cross-sectional comparative studies that evaluated the effects of Isha Yoga practices on health-related outcomes with comparators. Methodological quality and risk of bias were assessed using the Cochrane Risk of Bias 2 tool for RCTs and the Risk Of Bias In Non-randomized Studies - of Interventions (ROBINS-I) tool for non-randomised studies. Due to heterogeneity, a narrative synthesis was performed, grouped by outcomes with subgroups for expertise and dosage. Nine studies were included: three RCTs, four non-RCTs, and two cross-sectional studies. Mental health benefits were consistent, with moderate-to-large reductions in stress (four studies; d=0.27-0.94), anxiety and depression (three studies; d=0.48-1.88), and improvements in well-being and resilience (four studies; d=0.32-0.78). Physiological outcomes demonstrated enhanced heart rate variability (one study; p=0.01-0.02), reduced inflammation and metabolic markers (two studies; p<0.02), and microbiome shifts (one study; padj=0.001). Effects were dose-dependent (≥3-4 days per week) and stronger amongst experienced practitioners. Risk of bias was moderate overall; sensitivity analyses confirmed findings. Isha Yoga demonstrates promising mental health benefits and preliminary physical health benefits, with stronger effects observed in sustained practice. Methodological limitations warrant caution. Future large-scale RCTs with active comparators and biomarkers are recommended to confirm efficacy and elucidate underlying mechanisms.},
}

@article {pmid41694675,
year = {2025},
author = {Generalova, A and Hodzhev, Y and Tsafarova, B and Panaiotov, S},
title = {Targeting the mycobiome in sarcoidosis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1747685},
pmid = {41694675},
issn = {2296-858X},
abstract = {INTRODUCTION: Sacoidosis is a multisystem granulomatous disorder characterized by the formation of non-caseating granulomas in affected organs, predominantly the lungs and lymph nodes. Despite extensive research, its etiology remains elusive. Recent evidence suggests fungi may play a role in disease pathogenesis through immune modulation and chronic inflammation.

METHODS: We conducted a comprehensive fungal profiling study using samples from thirteen patients with confirmed sarcoidosis and five controls with other pulmonary diseases. Multiple specimen types were analyzed, including bronchoalveolar lavage fluid, lung tissue biopsies, and blood (both cultured and non-cultured). Fungal communities were characterized using ITS (Internal Transcribed Spacer) targeted sequencing followed by bioinformatic analysis.

RESULTS: Distinctive taxonomic patterns emerged in sarcoidosis samples. Several genera previously implicated in the pathogenesis of sarcoidosis were detected, including Penicillium, Mucor, Saccharomyces, and Yarrowia, which are regarded as potential pathogens. Sample type and processing method significantly influenced community composition, with cultured samples showing reduced diversity dominated by fast-growing taxa.

CONCLUSIONS: This study provides evidence of diverse fungal communities in sarcoidosis patients' blood and respiratory specimens, with potential immunomodulatory implications. Our findings integrate with existing epidemiologic and immunologic evidence highlighting fungi as credible antigenic drivers in sarcoidosis and suggest directions for future functional studies exploring fungal-host interactions in disease pathogenesis.},
}

@article {pmid41694576,
year = {2026},
author = {Hu, Z and Dan, W and Xi, M and Fang, Z and Feng, K and Mei, J and Ting, Z and Liu, B and Luo, Z},
title = {Reprogrammed Fibrotic Niche Fuels Lung Cancer Initiation and Reciprocal Remodeling.},
journal = {International journal of biological sciences},
volume = {22},
number = {4},
pages = {1920-1949},
pmid = {41694576},
issn = {1449-2288},
mesh = {*Lung Neoplasms/metabolism/pathology ; Humans ; *Pulmonary Fibrosis/metabolism/pathology ; Animals ; Extracellular Matrix/metabolism ; Tumor Microenvironment ; },
abstract = {Pulmonary Fibrosis (PF), an end-stage manifestation of interstitial lung diseases, is associated with largely unfavorable prognoses. Lung cancer (LC), a leading cause of nationally cancer-related mortality with progressively increasing incidence, exhibits pathological interconnections with PF. The chronic remodeling of the pulmonary microenvironment-including cellular components, extracellular matrix (ECM), inflammatory cytokine networks, and metabolic reprogramming-represents the core pathogenic mechanism underlying PF-LC comorbidity. This review systematically elaborates how the fibrotic microenvironment promotes malignant transformation of lung cancer via chronic inflammation, increased matrix stiffness, immunosuppressive regulation, and epigenetic modulation. Furthermore, we investigate the bidirectional crosstalk by which LC progression reciprocally modulates fibrotic processes. Finally, we integrate current clinical challenges and propose novel therapeutic strategies targeting the fibrotic microenvironment to address this lethal pathophysiological synergy.},
}

*Lung Neoplasms/metabolism/pathology
Humans
*Pulmonary Fibrosis/metabolism/pathology
Animals
Extracellular Matrix/metabolism
Tumor Microenvironment

@article {pmid41694562,
year = {2026},
author = {Jiang, R and Zheng, L and Fang, J and Guan, Q and Yuan, H and Liang, J and Zhang, J and Han, Q and Liu, M},
title = {Targeting the gut microbiome for type 2 diabetes management: a scoping review of systematic reviews and meta-analyses.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1682174},
pmid = {41694562},
issn = {1664-2392},
mesh = {*Diabetes Mellitus, Type 2/microbiology/therapy ; *Gastrointestinal Microbiome/physiology/drug effects ; Humans ; Meta-Analysis as Topic ; Systematic Reviews as Topic ; *Probiotics/therapeutic use ; },
abstract = {BACKGROUND: The Gut Microbiome (GM) is now a novel target for the treatment of Type 2 Diabetes Mellitus (T2DM), and several systematic reviews and Meta-analyses have provided evidence on the efficacy and safety of modulating GM in T2DM, but this evidence has not been consolidated.

OBJECTIVE: The purpose of this scoping review was to summarize the currently available evidence and to assess the breadth and quality of these systematic reviews and Meta-analyses.

METHODS: This study was guided by the PRISMA Extension for Scoping Reviews (PRISMA ScR) and the Arksey and O'Malley methodological framework. Electronic searches were conducted in multiple databases from the time of construction to May 1, 2025. Systematic reviews and Meta-analyses of regulatory GM to improve T2DM were included. 2 researchers independently screened full text, extracted review characteristics, and assessed methodological quality using the AMSTAR2 scale tool.

RESULT: A total of 23 systematic reviews and Meta-analyses were included, which were published in 2015-2024.Probiotics/synbiotics were the most commonly used interventions; the included studies were generally of low methodological quality (only 1 was of high quality); most of the studies reported an improvement in some glycemic and lipid markers by modulating the microbiota, but there was heterogeneity in the results; and there was insufficient attention to adverse events.

CONCLUSION: The available evidence suggests that regulating GM may be beneficial, but is limited by the quality of the studies, and future studies with large samples, long-term follow-up, and standardized adverse event reporting are needed to demonstrate its safety and long-term effectiveness conclusively.

https://doi.org/10.17605/OSF.IO/PW28U.},
}

*Diabetes Mellitus, Type 2/microbiology/therapy
*Gastrointestinal Microbiome/physiology/drug effects
Humans
Meta-Analysis as Topic
Systematic Reviews as Topic
*Probiotics/therapeutic use

@article {pmid41694529,
year = {2026},
author = {Vivarelli, S and De Francesco, C and Paba, E and Giambò, F and Fenga, C},
title = {The resistome bridge between livestock and workers: novel frameworks for early detection and monitoring of antimicrobial resistance.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1746385},
pmid = {41694529},
issn = {2296-2565},
mesh = {Animals ; *Livestock/microbiology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Occupational Exposure ; One Health ; },
abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, driven by the extensive use of antibiotics in both human medicine and livestock production. In the context of the One Health framework, this review investigates the role of the gut microbiome and resistome, which represents the collection of antimicrobial resistance genes (ARGs), within livestock and among occupationally exposed workers. Intensive farming practices often involve routine, subtherapeutic antibiotic use, fostering antibiotic-resistant bacteria (ARB) in the gastrointestinal tract of animals. These ARB and ARGs are excreted into the environment, contributing to resistance spread through mobile genetic elements. From a Planetary Health perspective, this environmental dissemination reflects how human-driven livestock practices can perturb ecosystems, creating global health risks that link animal, human, and environmental well-being. Human exposure, particularly among farm workers and veterinarians, raises significant concerns about zoonotic transmission of pathogens and, potentially, ARB. Novel advances in metagenomic and metatranscriptomic technologies enhanced our understanding of gut microbial communities and their resistomes, revealing overlaps in ARG profiles between animals and livestock workers. These technologies also support the development of novel microbiome-targeted strategies, including prebiotics, probiotics, food supplementation and workplace-improvement strategies, aimed at reducing antimicrobial use and restoring healthy microbiome balance. The review also highlights the importance of integrated surveillance and cross-sectoral collaboration to monitor and control AMR transmission. Understanding the ecological dynamics of the gut resistome in livestock systems is essential for designing effective interventions that safeguard both animal and human health.},
}

Animals
*Livestock/microbiology
Humans
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Occupational Exposure
One Health

@article {pmid41694266,
year = {2026},
author = {Ovadia, C and McIlvride, S and Schoonejans, JM and Spagou, K and Gómez-Romero, M and Smith, A and Papacleovoulou, G and Nikolova, V and Dixon, PH and Holmes, E and Marchesi, JR and Williamson, C},
title = {Maternal diet-induced hypercholanemia alters gut microbiota and metabolome in adult female Western diet-fed offspring.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {251},
number = {},
pages = {10810},
pmid = {41694266},
issn = {1535-3699},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; *Diet, Western/adverse effects ; Pregnancy ; *Metabolome ; Mice ; Bile Acids and Salts/metabolism ; Cholic Acid ; *Prenatal Exposure Delayed Effects/metabolism ; *Cholestasis, Intrahepatic/metabolism/microbiology ; Mice, Inbred C57BL ; *Pregnancy Complications/metabolism ; },
abstract = {Children of mothers with intrahepatic cholestasis of pregnancy (ICP) are more likely to develop metabolic disease later in life. Using a mouse model of gestational cholestasis, we previously found that 18-week-old offspring had metabolic alterations that were exacerbated in female offspring when challenged with a Western diet (WD). Microbiota changes are emerging as a potential mechanism for developmental programming, and the maternal gut microbiota is known to be altered in pregnancy and in ICP. We hypothesized that, in our model, the offspring gut microbiota is altered by maternal gestational disease, potentially impacting future offspring metabolic health. Female mice were fed a cholic acid (CA)-supplemented diet for 1 week preceding and throughout pregnancy to mimic gestational hypercholanemia. Female offspring were challenged with a WD from 12 to 18 weeks of age and cecal contents were collected for metataxonomics and metabolomic profiling. Maternal CA dietary supplementation was associated with markedly increased cecal sulfated bile acid species (up to 387-fold increase). Whilst WD-feeding of offspring was associated with a greater proportion of primary to secondary bile acids, and more tauro-conjugated bile acids than for offspring fed a normal diet, this adaptation to WD-feeding was not evident for those whose mothers were fed a CA-supplemented diet. Indeed, WD-fed offspring of CA-supplemented mothers had a >2-fold reduction in CA and dehydrocholic acid levels compared to those from NC-fed mothers. This corresponded with an altered profile of cecal microbiota, with clear separation of microbiotal profiles according to maternal diet in the WD-fed, but not NC-fed, offspring. This observational mouse study has shown that exposure to maternal hypercholanemia can significantly impact the effects of an obesogenic diet on offspring intestinal bile acid metabolism and gut microbiota, likely increasing their vulnerability to metabolic dysfunction when exposed to the "second hit" of an unhealthy postnatal environment.},
}

Animals
Female
*Gastrointestinal Microbiome/physiology
*Diet, Western/adverse effects
Pregnancy
*Metabolome
Mice
Bile Acids and Salts/metabolism
Cholic Acid
*Prenatal Exposure Delayed Effects/metabolism
*Cholestasis, Intrahepatic/metabolism/microbiology
Mice, Inbred C57BL
*Pregnancy Complications/metabolism

@article {pmid41694241,
year = {2026},
author = {Bourguignon, L and Benazzouk, Y and Bokou-Gianneli, E and Zani, F and Blagih, J and Lamarche, C},
title = {Sucralose as a Way to Enhance Regulatory T Cells, the SWEET Trial: Clinical Research Protocol.},
journal = {Canadian journal of kidney health and disease},
volume = {13},
number = {},
pages = {20543581261418540},
pmid = {41694241},
issn = {2054-3581},
abstract = {BACKGROUND: Kidney transplantation is the most effective treatment for patients with end-stage kidney disease. Modern immunosuppressive treatment has prolonged graft survival and reduced transplant rejection. However, these immunosuppressive regimens are associated with multiple side effects, including increased infections and cancer risk, nephrotoxicity, and metabolic complications. Attaining transplant tolerance with minimal reliance on immunosuppressive drugs is considered the ultimate goal in transplantation. Regulatory T cells (Tregs) adoptive immunotherapy has been proposed as a strategy to achieve transplant tolerance. However, this approach is labor-intensive and expensive, limiting its large-scale applicability. There is, therefore, a need to develop methods that promote Treg-mediated tolerance in vivo. Treg function and numbers are influenced by dietary components, and dietary interventions could provide a new therapeutic opportunity. Recently, our group demonstrated that sucralose supplementation, a commonly used sugar substitute (sweetener), reduces proinflammatory T-cell function and unpublished data indicating enhanced Treg frequencies. Building on this discovery, we propose to investigate the impact of sucralose on modulating T-cell populations and function in humans.

OBJECTIVE: To determine whether sucralose supplementation increases circulating Treg frequencies and alters T-cell function and populations in healthy adults.

DESIGN: This is a randomized, double-blind, placebo-controlled, crossover pilot trial.

SETTING: The study will be monocentric, at the Maisonneuve-Rosemont Hospital.

PATIENTS: Twelve healthy adult volunteers (>18 years of age), of both sexes, with no prior history of autoimmune disease or current treatments of immunomodulatory drugs. In addition, pregnant women will also be excluded from this study.

MEASUREMENTS: The primary outcome will be an alteration in circulating Treg frequency after sucralose supplementation. The secondary outcomes include modulation in the frequency of CD45[+] cells, the frequency of CD4[+] T-cell subsets, the differentiation of both CD4[+] and CD8[+] T cells, and T-cell function after antigen-specific and alloreactive challenges. Feasibility will also be evaluated, including adherence to visits, blood draw, ease of recruitment, percentage of study completion, and adherence to supplements. Exploratory outcomes in response to sucralose supplementation include changes in circulating metabolites and gut microbiome composition.

METHODS: Participants will be randomly assigned to receive either a placebo or sucralose (5-7 mg/kg/day) for four weeks, separated by a two-week washout period. This will be followed by a crossover phase, where patients receiving sucralose will receive the placebo and vice versa for an additional four weeks. Capsules will be prepared and blinded by a licensed pharmacy. Blood will be collected at baseline, after four weeks of treatment or placebo, after washout and after four weeks of crossover for Peripheral Blood Mononuclear Cell (PBMC) isolation, flow cytometry, functional assays, and metabolomics. Stool samples will be collected for microbiome sequencing.

LIMITATIONS: This will be a small, single-center, short-duration trial in healthy volunteers. Findings might not apply to transplant recipients.

CONCLUSION: The SWEET trial will provide first-in-human data on sucralose as a potential, inexpensive oral immunomodulator to promote Tregs.

TRIAL REGISTRATION: NCT06997133 (2025-06-05).},
}

@article {pmid41694172,
year = {2026},
author = {Chatzidou, P and Stratos, A and Chint, M and Niakou, A and Pissiotis, A and Kamalakidis, S},
title = {Denture-Associated Candidiasis and Mucormycosis in Post-COVID-19 Older Adults Managed Through an Integrated Prosthodontic and Infectious Disease Approach: A Narrative Review.},
journal = {Cureus},
volume = {18},
number = {2},
pages = {e103448},
pmid = {41694172},
issn = {2168-8184},
abstract = {The COVID-19 pandemic has exposed significant vulnerabilities among older adults, particularly denture wearers, to opportunistic fungal infections, including mucormycosis and oral candidiasis. This narrative review, following PRISMA-ScR (Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Narrative Reviews) guidelines, collected evidence from 2020 to 2025 to examine the connection between denture use, systemic comorbidities, and fungal complications in elderly individuals after COVID-19. A total of 21 of 104 studies were included, covering case-control, cross-sectional, cohort, and retrospective studies from India, Europe, the Middle East, and North America. Several studies have reported higher rates of oral fungal colonization among denture wearers,with Candida albicans being the most frequently isolated species, followed by resistant strains such as Candida auris. However, these observations are primarily derived from heterogeneous observational studies and should therefore be interpreted as associative rather than causal. COVID-19-related mucormycosis (CAM) was primarily reported as rhino-orbito-cerebral disease, with oral manifestations including palatal necrosis, gingival ulcers, and tooth mobility. Key risk factors identified include diabetes mellitus, corticosteroid therapy, prolonged intensive care unit (ICU) stays, and poor denture hygiene. Mortality related to CAM ranged from 18% to 56%, while candidiasis, though less deadly, significantly affected oral function, nutrition, and overall quality of life. Diagnostic methods included clinical and intraoral examinations, microbiological cultures, imaging techniques, and emerging salivary biomarkers. Treatments included systemic antifungal medications, surgical removal, and prosthesis disinfection, highlighting the important role of prosthodontists in prevention and rehabilitation. Knowledge gaps remain regarding the predictive value of oral lesions for systemic infections, the long-term effects of COVID-19 on the oral microbiome, and the need to standardize denture hygiene protocols. This review emphasizes the importance of integrated dental and medical care in reducing morbidity and mortality among denture-wearing older adults recovering from COVID-19, while recognizing that early oral findings may serve as warning indicators rather than definitive predictors of systemic infection.},
}

@article {pmid41694112,
year = {2026},
author = {Zhou, H and Yu, W and Lei, J and Chang, R and Cheng, Y and Wang, G and Lin, L},
title = {Pathophysiological mechanisms of fatigue and multidisciplinary management strategies (Review).},
journal = {Experimental and therapeutic medicine},
volume = {31},
number = {4},
pages = {91},
pmid = {41694112},
issn = {1792-1015},
abstract = {Fatigue is a common clinical symptom, and its complex pathophysiological mechanisms markedly affect the quality of life and social function of patients. With the advancement of omics technologies and artificial intelligence applications, the ability to understand the mechanisms of fatigue has been notably enhanced. Fatigue is a complex process involving the interaction of multiple systems and factors. The occurrence of fatigue involves multilevel regulation of energy metabolism, neuroendocrine and immune systems. Based on omics and molecular biology, abnormal energy metabolism, oxidative stress and mitochondrial dysfunction serve a central role in the pathogenesis of fatigue. Disorders in the neuro-endocrine-immune network and dysfunction of the microbiome-gut-brain axis constitute key systemic integration mechanisms. Clinically, numerous diseases, including chronic fatigue syndrome and endocrine, neurological and autoimmune disease, can manifest as fatigue symptoms. In terms of treatment, individualized, multidisciplinary collaborative comprehensive management models have become nursing standards. In addition, the application of telemedicine technology has markedly improved the accessibility and compliance of fatigue management. The present review aimed to examine the conceptual framework, physiological mechanisms, clinical manifestations and management strategies of fatigue to provide reference for clinical diagnosis and treatment practice. Future research should focus on strengthening the exploration and translational application of molecular mechanisms, developing novel intervention targets, establishing effective fatigue assessment models and optimizing management strategies to provide strong evidence-based support for clinical practice.},
}

@article {pmid41694087,
year = {2026},
author = {Hu, Q and Sardi, MI and Naqvi, SA and Paton, ND and Hackenhaar, L and Pluk, P and de Laat, J and Chakrabarti, A and Khafipour, E},
title = {Effects of processed soybean meal on growth performance and gut microbiome composition in pigs in regular nursery and enterotoxigenic Escherichia coli challenged conditions.},
journal = {Translational animal science},
volume = {10},
number = {},
pages = {txag004},
pmid = {41694087},
issn = {2573-2102},
abstract = {Hydrothermal-mechanical (HTM) processing of soybean meal (SBM) has been shown to enhance intestinal health and growth in post-weaning pig compared to conventional SBM. It was hypothesized that HTM processing improves protein utilization, particularly under enterotoxigenic Escherichia coli (ETEC) challenge, resulting in better growth and a more resilient hindgut microbiome. A total of 268 weaned pigs (6.82 ± 0.85 kg body weight) were allotted to regular nursery (5 pigs/pen, 10-11 pens/treatment) or ETEC challenge (3 pigs/pen, 12 pens/treatment) and fed one of three isocaloric diets with equal standardized ileal digestible lysine: SBM, HTM SBM, or enzyme-treated (Enz Trt) SBM. Test soy products replaced SBM in a wheat-barley-SBM base diet for the first 3 wk, followed by a common diet for 3 wk. On d 14 post-weaning, ileal digesta and feces were collected for crude protein (CP) digestibility, short-chain fatty acid (SCFA), and microbiome analysis. Growth performance, digestibility, and SCFA data were analyzed using general linear models and microbiome data from Nanopore shotgun sequencing were center-log-ratio transformed for statistical analysis in R. No diet × challenge interaction was observed on ADG, ADFI or BW. Pigs in regular nursery conditions had higher ADG (P < 0.01) and ADFI (P < 0.05) than ETEC challenged pigs during d 0-7. HTM SBM and Enz Trt SBM improved ADG (P < 0.05) with similar ADFI compared to SBM across conditions. From d 7-12, pigs fed HTM SBM or Enz Trt SBM had greater ADG (P < 0.05) and ADFI (P < 0.01) than SBM-fed pigs. BW remained lower (P < 0.05) in SBM-fed pigs from d 12-21 and during the final 3 wk. Under regular nursery conditions, HTM SBM improved apparent total tract digestibility of CP (P < 0.01) compared SBM, but with no difference from Enz Trt SBM. Microbiome composition was affected by diet (P < 0.01) and ETEC challenge (P < 0.01). HTM SBM and Enz Trt SBM tended to increase α-diversity (P = 0.10) of the microbiome compared to SBM, with no difference between the two treatments. HTM SBM and Enz Trt SBM increased abundance of species positively correlated with growth and beneficial SCFA, such as caproate (P < 0.05) and valerate (P < 0.05). In conclusion, HTM SBM and Enz Trt improved ADFI, ADG resulting higher BW and promoted beneficial microbes linked to performance in nursery pigs under both regular nursery and ETEC-challenged conditions.},
}

@article {pmid41693862,
year = {2025},
author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X},
title = {Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1726935},
pmid = {41693862},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Tuberculosis, Multidrug-Resistant/microbiology/diagnosis/immunology ; Mycobacterium tuberculosis/genetics ; Male ; Female ; Gene Expression Profiling ; Biomarkers/analysis ; Metagenomics ; Prospective Studies ; Middle Aged ; Adult ; Microbiota ; Transcriptome ; Bacteriophages/genetics ; Lung/microbiology ; },
abstract = {BACKGROUND: Drug-resistant tuberculosis (DR-TB) undermines global TB control, yet how resistant Mycobacterium tuberculosis strains interact with the lung microbiome, phage communities, and local host immunity remains poorly defined.

METHODS: In a prospective cohort of 130 pulmonary TB patients (49 DR-TB, 81 drug-susceptible TB [DS-TB] patients), bronchoalveolar lavage fluid (BALF) was subjected to paired metagenomic and transcriptomic profiling. Microbial and bacteriophage community structures were assessed by diversity metrics and differential abundance testing, whereas host responses were characterized by gene expression, pathway enrichment, and immune cell deconvolution. A Random Forest model was trained to evaluate the diagnostic potential of host transcriptional signatures.

RESULTS: DR-TB airways presented distinct microbial beta diversity, with enrichment of Streptococcus spp. and streptococcal-targeting phages (e.g., Javan variants, phi-Ssu5SJ28rum). Transcriptomic analysis revealed 494 differentially expressed genes, which were associated with increased oxidative phosphorylation, suppressed ion channel and transporter activity, and enrichment of extracellular matrix remodeling pathways. Immune profiling demonstrated a significant reduction in γδ T cells in DR-TB patients (P = 0.0059). An 8-gene host-derived signature (ARHGEF5, PTGES3L, GAL3ST1, RANBP17, ACTA2_AS1, CBY3, MAMSTR, and LOC102031319) discriminated DR-TB from DS-TB with high accuracy (AUC = 0.837).

CONCLUSION: This dual-omics study defines the airway niche of DR-TB as a convergence of microbial dysbiosis, phage imbalance, and host immune-metabolic dysfunction. By uncovering DR-TB-specific microbial and transcriptional signatures, and deriving a predictive host-based classifier, our findings provide mechanistic insights and highlight novel opportunities for microbiome- and host-directed interventions in drug-resistant tuberculosis.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology
*Tuberculosis, Multidrug-Resistant/microbiology/diagnosis/immunology
Mycobacterium tuberculosis/genetics
Male
Female
Gene Expression Profiling
Biomarkers/analysis
Metagenomics
Prospective Studies
Middle Aged
Adult
Microbiota
Transcriptome
Bacteriophages/genetics
Lung/microbiology

@article {pmid41693857,
year = {2025},
author = {Pan, S and Zhu, H and Yin, R and Lin, J and Wang, Z and Cui, W and Li, Z and Liu, B},
title = {Carcinogen metabolism and bladder cancer: role of gut microbiota in disease and prevention.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1727550},
pmid = {41693857},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Urinary Bladder Neoplasms/prevention & control/metabolism/microbiology/etiology ; *Carcinogens/metabolism/toxicity ; Dysbiosis ; Animals ; Carcinogenesis ; },
abstract = {Bladder cancer remains a significant global health concern, with environmental carcinogen exposure-particularly from tobacco-derived compounds such as aromatic amines, polycyclic aromatic hydrocarbons (PAHs), and nitrosamines-recognized as a primary etiological factor. These carcinogens undergo complex metabolic activation in the liver, bladder epithelium, and gut microbiota, generating reactive intermediates that initiate DNA damage, oxidative stress, and pro-tumorigenic signaling. This review synthesizes emerging evidence on how carcinogen-induced metabolic reprogramming contributes to bladder cancer initiation and progression, emphasizing the roles of key genetic pathways and metabolic enzymes involved in xenobiotic detoxification, DNA repair, and redox regulation. In parallel, we examine the influence of gut microbiota on carcinogen bioactivation and biotransformation, highlighting its dual role as both a metabolic modulator and a potential preventive target. We critically evaluate human observational data linking microbiome dysbiosis to bladder cancer risk, while addressing limitations such as small cohort sizes and confounders like diet and age. Finally, we discuss promising strategies for risk mitigation, including microbiome-directed interventions, dietary modulation, and chemopreventive agents that counteract carcinogenic effects. By integrating molecular oncology, toxicogenomics, and host-microbiome interactions, this review provides a mechanistic framework for understanding bladder cancer etiology and identifies novel opportunities for preventive and precision interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Urinary Bladder Neoplasms/prevention & control/metabolism/microbiology/etiology
*Carcinogens/metabolism/toxicity
Dysbiosis
Animals
Carcinogenesis

@article {pmid41693784,
year = {2026},
author = {Kaźmierczak-Siedlecka, K and Kucharski, R and Stachowska, E and Pelikant-Małecka, I and Marano, L and Makarewicz, W and Kalinowska, M and Dambrauskas, Ž and Kalinowski, L},
title = {Intra-tumoural microenvironment and bugs-based drug design: foreseeable future in oncology and immuno-oncology.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1732712},
pmid = {41693784},
issn = {1663-9812},
abstract = {The term tumour microenvironment (TME) encompasses the coexistence of microorganisms and different cellular elements including endothelial cells, macrophages, cancer-associated fibroblasts and a complex network of microvessels. Integration of tumour immunity and intratumoural microbiome into anti-cancer strategies represents a promising frontier in precision oncology (for instance in case of solid cancers, such as pancreatic or colorectal tumours). Characterization of the intratumoural microbial signature has emerged as a critical step in drug discovery, influencing therapeutic efficacy as well as resistance. There are several approaches, such as elimination of pathogenic microorganisms within the TME, modulation of specific microbial-immune axes, including interactions among microbial species that may enhance or suppress tumour progression, and exploitation of bacterial strains engineered to express pro-drug-converting enzymes for localized tumour therapy via intratumoural injection. Furthermore, tumour organoid-immune co-culture models, particularly when combined with 3D bioprinting technologies, offer robust experimental platforms for dissecting tumour-microbiome-immune crosstalk. The reciprocal communication between the immune system and the tumour-associated microbiome/metabolome highlights novel opportunities for therapeutic innovation in oncology and immuno-oncology.},
}

@article {pmid41501629,
year = {2026},
author = {Peng, H and Chen, J and Shao, Y and Li, J and Chen, M and He, C and Sun, J and Wang, W and Cao, X and Yang, H and Zhou, J and Wu, Z},
title = {Impact of gut microbiota on atypical endometrial hyperplasia and endometrial cancer: a comprehensive analysis of microbial composition and metabolomic profiling.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {122},
pmid = {41501629},
issn = {1471-2180},
support = {24JRRA621//the Natural Science Foundation of Gansu Province/ ; 22JR5RA718//the Natural Science Foundation of Gansu Province/ ; },
abstract = {BACKGROUND: Endometrial cancer (EC) is one of the most common malignant tumors in women, and in recent years, the role of gut microbiota in tumorigenesis has gradually gained attention. Previous studies have shown that the gut microbiome is closely related to the occurrence of various cancers, but the specific mechanisms through which gut microbiota contribute to the development of endometrial cancer (EC) remain unclear. This study aims to analyze the gut microbiome characteristics of atypical endometrial hyperplasia (AEH) and EC, and to explore key gut microbial species and metabolites, providing evidence for the etiological research and early screening of EC and AEH.

METHODS: This study selected 24 AEH or EC patients from the Gynecology Department of Gansu Provincial Maternity and Child Care Hospital between February 2023 and October 2023. The patients were divided into the AEH group (n=7) and the EC group (n=17), with 24 healthy women selected as a control group. Fecal and serum samples were collected, and 16S rRNA gene sequencing was performed using the Illumina MiSeq platform. Serum metabolomics analysis was conducted using LC-MS technology. Spearman correlation analysis was used to explore the associations between gut microbiota and metabolites, and potential gut microbial biomarkers were evaluated using ROC analysis.

RESULTS: The study found that as AEH progressed to EC, significant changes occurred in the composition of the gut microbiota, particularly in Klebsiella, whose abundance increased from 0.264% in the control group to 0.809% in the AEH group and 6.092% in the EC group, with significant differences (P<0.001, FDR=0.026). LEfSe analysis identified Megamonas, Klebsiella, Escherichia, and Akkermansia as potential biomarkers. ROC analysis showed that the AUCs of Megamonas/Klebsiella for EC were 0.864/0.838, and the AUCs of Escherichia/Akkermansia for AEH were 0.744/0.920. Metabolomics analysis revealed significant enrichment of glycerophospholipid metabolism in both the EC and AEH groups, with significant differences in lipid metabolism in the EC group. Correlation analysis indicated significant positive correlations between Enterococcus and hypoxanthine, inosine in the EC group (r=0.686, 0.637, P<0.05).

CONCLUSION: This study reveals the dynamic changes in the gut microbiome during the development of endometrial lesions, especially the increasing abundance of Klebsiella as AEH progresses to EC, suggesting that it may play a key role in the occurrence and progression of EC. Furthermore, significant changes in lipid metabolism further support the role of gut microbiota in regulating lipid metabolism in EC pathogenesis. This study provides new insights into the role of gut microbiota in endometrial cancer and offers a theoretical basis for early diagnosis and personalized treatment strategies based on gut microbiota.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04568-2.},
}

@article {pmid41693708,
year = {2025},
author = {Mudda, NS and Zhang, L and Sampelli, P},
title = {Targeting gut-brain-immune axis in amyotrophic lateral sclerosis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1637976},
pmid = {41693708},
issn = {1664-3224},
mesh = {*Amyotrophic Lateral Sclerosis/immunology/microbiology/therapy/metabolism ; Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; *Brain/immunology/metabolism ; Dysbiosis/immunology ; *Brain-Gut Axis/immunology ; Cytokines/metabolism ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron neurodegenerative disorder with a median survival of only 3-5 years. The heterogeneity of the disease and lack of effective therapies highlight the importance of identifying novel pathogenic mechanisms. We hypothesize that dysbiosis of gut microbiota enhances ALS by disrupting intestinal barrier function and altering metabolite profiles to drive systemic inflammation and neuronal stress. Precisely, the decrease in health-promoting bacteria (e.g., Akkermansia muciniphila, Bifidobacterium and Lactobacillus spp.) in ALS can reduce neuroprotective metabolite production (short-chain fatty acids, nicotinamide, GABA, precursors of serotonin) and increase gut permeability, enabling lipopolysaccharide (LPS) and pro-inflammatory cytokines into the circulation. Such changes would activate microglia and impair motor neuron homeostasis by glutamate excitotoxicity and mitochondrial dysfunction. The gut-brain axis operates through immune-mediated mechanisms, where ALS-associated microbiota changes compromise mucosal immunity and trigger peripheral Th1/Th17-biased responses with impaired Treg regulation. Elevated endotoxin levels correlate with TLR4-driven inflammation, promoting pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) that cross into the CNS and prime microglia toward a neurotoxic M1 phenotype, creating a milieu where IL-17A and other mediators directly injure motor neurons. Our hypothesis relies on establishing human and animal evidence of microbiome derangements, barrier dysfunction, and immune deregulation with ALS. We hypothesize that restoration of an "ALS-protective" microbiota consortium or its metabolic by-products can potentially slow disease progression. Testable hypotheses include improvement of ALS model motor deficits by probiotic or fecal-microbiota therapies, and normalization of inflammatory biomarkers. This paradigm recontextualizes ALS as a gut-brain disease and suggests new directions for translational research into this unmet medical indication.},
}

*Amyotrophic Lateral Sclerosis/immunology/microbiology/therapy/metabolism
Humans
*Gastrointestinal Microbiome/immunology
Animals
*Brain/immunology/metabolism
Dysbiosis/immunology
*Brain-Gut Axis/immunology
Cytokines/metabolism

@article {pmid41693434,
year = {2026},
author = {Belančić, A and Fajkić, A and Wah Lam, Y and Alić, L and Labriffe, M and Pilipović, K and Džidić-Krivić, A and Yee Sy, H and Jankovic, S},
title = {Microbiome-driven PKs: redefining drug metabolism beyond Host enzymes.},
journal = {Expert opinion on drug metabolism & toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17425255.2026.2631415},
pmid = {41693434},
issn = {1744-7607},
abstract = {INTRODUCTION: Interindividual variability in drug response remains a significant clinical challenge, leading to therapeutic failure and toxicity. Much of this variability is unexplained by classical host-centric pharmacokinetic (PK) models, highlighting a critical gap in understanding of drug disposition. This review addresses this gap by establishing the gut microbiome as an important determinant of drug fate.

AREAS COVERED: This narrative review with scoping approach examines how microbial enzymes affect therapeutics through comprehensive analysis of mechanistic and clinical studies. Key examples discussed include irinotecan, digoxin, and sulfasalazine. We highlight specific situations where the influence of gut bacteria is particularly significant, such as with low-bioavailability drugs and in patients with an ileocolonic anastomosis, where gut bacteria directly impact drug absorption and metabolism. Additionally, we address the limitations of current PK models and explore the potential of new integrated approaches.

EXPERT OPINION: We propose that the gut microbiome should be recognized as a 'fifth pillar' of PKs. This shift in perspective is crucial for advancing personalized medicine. In this new model, a 'PK profile card' integrating microbial, genomic, and clinical data will help guide dosing. We anticipate microbiome analysis to become a standard clinical tool to optimize drug efficacy and safety.},
}

@article {pmid41693429,
year = {2026},
author = {Shabbir, U and McNulty, H and Hughes, C and Ward, M and Dooley, J and Hoey, L},
title = {B-vitamins, immune function and the ageing brain: A critical review of the evidence, mechanisms and potential role of the gut microbiome.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-33},
doi = {10.1017/S0029665126102249},
pmid = {41693429},
issn = {1475-2719},
abstract = {This review aims to explore the potential role of folate and related B-vitamins (B12, B6, and riboflavin) in maintaining cognitive health in ageing, focussing particularly on their interactions with the gut microbiota and inflammation. Low B-vitamin status, common in older adults, is associated with poorer cognitive function and dementia. Furthermore, people with dementia are observed to have increased abundance of pro-inflammatory microbes and concomitant higher concentrations of cytokines in their circulation. Therefore, gut dysbiosis and chronic inflammation have been proposed as contributors of cognitive dysfunction. Although many observational studies report that low B-vitamin status, especially vitamin B6, is associated with a worse inflammatory state, the role of the gut microbiota is much less investigated. Pre-clinical evidence suggests higher B-vitamin intakes may beneficially modulate the gut bacterial profile and its metabolic activity, positively influencing inflammation. The evidence however is inconsistent and the few human intervention studies available are confined to clinical populations, or are limited by small sample size or to a single B-vitamin at high supplementation doses. Of note, one study in rats with Alzheimer's type dementia reported an association of folate and vitamin B12 deficiency with disturbed gut bacterial composition, neuroinflammation and impaired memory. In conclusion, optimising B-vitamin status may help promote cognitive health during ageing through modulation of the gut microbiota and immune function. Well-designed human studies are however required to confirm these relationships and inform evidence-based nutritional strategies for healthy ageing.},
}