@article {pmid42943597,
year = {2026},
author = {Atuahene, PY and Stevenson, B and Sang, Y},
title = {AI-Facilitated Discovery of Microbiome-Originated Antimicrobial Peptides: A Perspective on Combating Antibiotic Resistance Within Public Health and Food Safety Frameworks.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943597},
issn = {2076-2607},
support = {Evans-Allen-1013186//USDA NIFA/ ; 2020-67016-31347//NIFA AFRI/ ; 2025-38821-45500//NIFA AFRI/ ; },
abstract = {The escalating crisis of antimicrobial resistance (AMR) demands innovative therapeutic strategies beyond conventional antibiotics. Antimicrobial peptides (AMPs), particularly those originating from the human, animal, and environmental microbiome, represent a promising frontier within public health microbiology and microbial food safety. Recent advances in artificial intelligence (AI) and machine learning (ML) have revolutionized the discovery pipeline, enabling high-throughput mining of metagenomic data and de novo generation of novel peptide sequences. This perspective review synthesizes recent breakthroughs in AI-driven discovery of microbiome-originated AMPs, examines their preclinical efficacy against multidrug-resistant (MDR) pathogens under One Health and climate-sensitive frameworks and application in infectious disease treatment and discusses translational challenges including pharmacokinetics, toxicity, manufacturing scalability, and applications in food preservation and water safety. We argue that the convergence of microbiome science, deep learning, and synthetic biology positions AI-discovered AMPs as viable next-generation interventions against antibiotic resistance across human, animal, and environmental domains.},
}

@article {pmid42943608,
year = {2026},
author = {Xie, M and Shang, H and Wang, F and Yang, J and Geer, N and Zhang, Q and Xu, X and Baolige, D},
title = {Exploratory Shotgun Metagenomic Analysis of the Fecal Microbiome and Antimicrobial-Resistance Potential in Simmental Calves with Different Diarrheal Statuses.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943608},
issn = {2076-2607},
support = {2025ZY0147//Central Government Guiding Local Science and Technology Development Fund Project/ ; 2025YFDZ0091//Inner Mongolia Autonomous Region Science and Technology Plan/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Project/ ; },
abstract = {Calf diarrhea is frequently accompanied by disruption of the gastrointestinal microbiota, but the relationships between clinical status and microbial community composition, gene-content functional potential, and antimicrobial-resistance-associated features remain incompletely characterized. This exploratory study aimed to characterize these features in calves with different diarrheal statuses using shotgun metagenomics. Six approximately 2-month-old Simmental calves from Chahar Right Middle Banner, Inner Mongolia, were included, comprising two healthy calves, two calves with mild diarrhea, and two calves with severe diarrhea. Read-based taxonomic profiling was complemented by gene-abundance-weighted taxonomic annotation, and microbial functional potential was characterized using eggNOG/COG, KEGG, and CAZy annotations, together with conservatively screened CARD-associated sequence-homology candidates. The two severe-diarrhea samples exhibited lower bacterial richness and Shannon diversity, although PCoA did not show clear separation according to clinical severity. These two samples showed high representation of Proteobacteria and Enterobacteriaceae-related taxa, particularly Escherichia-related assignments, together with lower representation of Ruminococcaceae, Faecalibacterium, and Prevotella. Gene-content profiles showed higher representation of selected functions related to transport, environmental sensing, motility, secretion, and bacterial cell-envelope processes, whereas several glycan- and complex-carbohydrate-associated functions showed lower representation. Selected CARD-associated candidates were also more abundant in the severe-diarrhea samples. Within this small exploratory cohort, the two severe-diarrhea samples therefore showed concordant taxonomic and gene-content differences; however, these observations should not be interpreted as a general severity-specific microbiome signature and require validation in larger longitudinal cohorts.},
}

@article {pmid42943642,
year = {2026},
author = {Chen, S and Li, S and Li, Y and Zhang, Y and Duan, X and Xu, C and Qian, W and Si, H and Liu, H and Li, Z},
title = {Comparison of Fecal Microbiome of Wild Red Deer in Different Regions Reveals Geographic Differentiation.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943642},
issn = {2076-2607},
support = {20240101012JJ//Natural Science Foundation of Jilin provinces/ ; 2023YFD1302000//National Key Research and Development Program of China/ ; CARS-43//earmarked fund/ ; JLARS-2026-080204//Jilin Agricultural Research System/ ; },
abstract = {The gut microbiome plays critical roles in nutrient metabolism and host adaptation in ruminants, yet genome-level functional differences in the fecal microbiomes across geographic populations of wild red deer remain underexplored. Here, we integrated 16S rRNA gene sequencing and shotgun metagenomics to characterize the fecal microbiome of wild red deer populations in Inner Mongolia (NMG, n = 16) and Gansu Province (GS, n = 16), China. The NMG population exhibited significantly higher α-diversity and a distinct microbial community compared to GS (adjusted p < 0.05). NMG was enriched in Clostridium, Eubacterium, and Bacillus, while GS harbored higher abundances of Ruminococcus, Oscillospira, and Faecalibacterium (adjusted p < 0.05). Functional profiling revealed that the fecal microbiome in NMG showed greater functional potential associated with amino acid, pyruvate, and butanoate metabolism pathways, whereas the fecal microbiome in GS was enriched in the genetic potential of starch/sucrose metabolism, glycan degradation, and bile acid biotransformation (adjusted p < 0.05). CAZyme analysis demonstrated that GS was enriched in glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases, while NMG showed higher auxiliary activity family abundance (adjusted p < 0.05). Genome-resolved metagenomics recovered 456 species-level genome bins (SGBs), revealing that GS-enriched SGBs (Rikenellaceae, Oscillospirales CAG-272) contained CAZyme genes associated with pectin degradation, whereas NMG-enriched SGBs contained genes associated with lignin modification and chitin degradation. These findings demonstrate the significant differences in the fecal microbiomes between the two geographically distinct wild red deer populations.},
}

@article {pmid42943644,
year = {2026},
author = {Shankar, V and Paliy, O},
title = {Light Penetration, Dissolved Oxygen, and Riparian Zone Extent Are Associated with the Structure, Gene Expression, and Lipid Production of Riverbed Microbial Communities.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943644},
issn = {2076-2607},
support = {DBI-1335772//U.S. National Science Foundation/ ; },
abstract = {We analyzed riverbed microbiota structure, gene expression, and fatty acid production across several sites along Little Miami River in Ohio, United States. The sites varied in stream width, shading, surrounding land use, and the size of the riparian zone. Within each site, we observed strong concordance among microbial community composition, functional gene expression, and fatty acid signature. All microbial communities were dominated by the members of phylum Proteobacteria, class Planctomycetacia, and by algal and cyanobacterial cells. The measured concentrations of chlorophyll a, dissolved oxygen, and soluble phosphorus were the main environmental determinants of microbial community structure. These were in turn dependent on the level of penetrating sunlight and, to a lesser degree, on the width of the riparian zone. The level of sunlight affected the expression of light-harvesting complexes, methanogenesis genes, anaerobic respiratory reductases and fermentation pathways, as well as functions of denitrification, ammonification, and sulfate reduction. The expression of phosphorus scavenging and antibiotic resistance genes was highest at the site lacking a riparian zone and surrounded by farmland. Overall, our findings demonstrate that riverbed microbiota exhibit consistent structural and functional responses to interacting geochemical and anthropogenic gradients. Our data also provide support for the hypothesis that phototrophic microorganisms act as central organizers of benthic community metabolism.},
}

@article {pmid42943648,
year = {2026},
author = {He, Y and Zhu, X and Huang, Z and Yang, X and Yi, B},
title = {Ecological Editing: Decoupling Microbial Signals from Metabolic Noise to Reprogram the Gut Ecosystem.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943648},
issn = {2076-2607},
support = {82404050//National Natural Science Foundation of China/ ; 82560565//National Natural Science Foundation of China/ ; 20252BAC250152//Key Project of the Natural Science Foundation of Jiangxi Province/ ; 20252BAC250125//Key Project of the Natural Science Foundation of Jiangxi Province/ ; 20252BAC200530//Youth Project of the Natural Science Foundation of Jiangxi Province/ ; GJJ2403619//Scientific and Technological Research Project of the Jiangxi Provincial Department of Education/ ; GJJ2503436//Scientific and Technological Research Project of the Jiangxi Provincial Department of Education/ ; SKJP1320242247//Jiangxi Provincial Health Commission Science and Technology Program/ ; },
abstract = {The translation of microbiome therapeutics is hampered by the stochasticity of faecal microbiota transplantation (FMT), an empirical transfer of undefined biomass confounded by donor heterogeneity, procedural variability, and immunogenic debris. As the field moves towards precision medicine, microbiome engineering is diverging into two philosophies: the subtractive paradigm, which purifies the native ecosystem by removing deleterious metabolites, and the additive paradigm, which assembles functional guilds de novo. In this review, we propose that density-based ecological purification, termed quantitative fractionated microbiota (QFM), may act as an immunological sieve, using washed microbiota transplantation (WMT) as its best-characterised clinical exemplar, to separate therapeutic signals (viable microbiota and bacteriophages) from metabolic noise (for example, pro-inflammatory lipid mediators and glucocorticoid metabolites). We explicitly frame this separation as a conceptual working model rather than an established mechanism: the quantitative assays, cut-off values, and units required to operationalise a signal-to-noise distinction do not yet exist, and we set out what would be needed to develop them. Conversely, live biotherapeutic products (LBPs) offer compositional precision but face a critical bottleneck, namely engraftment failure in colonisation-resistant hosts. We propose that the future lies less in competition between these modalities than in their convergence, which we term the soil-and-seed framework. In this framework, subtractive ecological priming (QFM/WMT) may transiently lower colonisation resistance by liberating niche space and by reducing soluble inflammatory exposure, thereby preparing the mucosa for subsequent engraftment of additive consortia. We describe this hybrid strategy as a hypothesis with an explicit validation roadmap. If it holds, this shift would move microbiome therapy from stochastic biomass transfer towards predictable ecosystem engineering.},
}

@article {pmid42943735,
year = {2026},
author = {Zhu, H and Tang, M and Li, M and Zhang, Z and Kang, L and Wang, Q and Wang, R and Hua, C and Zhou, H and Zhou, W and Wu, Y and Wang, Z},
title = {Oleanolic Acid-Loaded Cyclodextrin Metal-Organic Framework Ameliorates NAFLD via Modulation of Gut Microbiota and Liver Metabolism.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {20},
pages = {},
pmid = {42943735},
issn = {1420-3049},
support = {32372452//National Natural Science Foundation of China/ ; WJ202510R02//State Administration for Market Regulation/ ; PAPD//Jiangsu Higher Education Institutions/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/etiology/microbiology ; *Liver/metabolism/drug effects ; *Oleanolic Acid/pharmacology/chemistry ; Mice ; *Metal-Organic Frameworks/chemistry/pharmacology ; Male ; Diet, High-Fat/adverse effects ; *Cyclodextrins/chemistry ; Disease Models, Animal ; Metabolomics/methods ; Mice, Inbred C57BL ; },
abstract = {Oleanolic acid (OA) possesses hepatoprotective properties, but its clinical application is hampered by poor aqueous solubility. This study aimed to enhance OA solubility and investigate its therapeutic mechanism for NAFLD by encapsulating it in a γ-cyclodextrin metal-organic framework (OA@CDMOF). The OA@CDMOF complex was synthesized and characterized. Its effects on a high-fat diet (HFD)-induced NAFLD mouse model (MOD) were evaluated by combined liver metabolomics and 16S rRNA amplicon sequencing analyses. When encapsulated into CDMOF to yield an OA@CDMOF complex, the solubility of OA significantly improved. OA@CDMOF administration ameliorated HFD-induced metabolic alterations and liver injury. It modulated the gut microbiota composition, notably enriching the phylum Firmicutes while decreasing the abundance of Bacteroidota. Liver metabolomic analysis revealed that OA@CDMOF was associated with changes in metabolites related to glycerophospholipid, purine, glutathione, and vitamin B6 metabolism. Furthermore, it was associated with changes in metabolites related to lipolysis in adipocytes, pentose and glucuronate interconversions, and key signaling pathways, including AMPK, FoxO, and cGMP-PKG. Importantly, OA@CDMOF showed protective effects comparable to those of free OA, with no statistically significant difference between the two groups. This study elucidates the mechanism by which OA@CDMOF alleviates NAFLD through modulation of the gut microbiome and host metabolism. Our findings provide novel insights into the hepatoprotective role of OA@CDMOF and suggest a promising nanostrategy for NAFLD intervention.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/etiology/microbiology
*Liver/metabolism/drug effects
*Oleanolic Acid/pharmacology/chemistry
Mice
*Metal-Organic Frameworks/chemistry/pharmacology
Male
Diet, High-Fat/adverse effects
*Cyclodextrins/chemistry
Disease Models, Animal
Metabolomics/methods
Mice, Inbred C57BL

@article {pmid42943823,
year = {2026},
author = {Awlqadr, FH and Saeed, MN and Ramddan, AB and Sdiq, AFH and Hama, HK and Hossain, MS and Noreen, S and Raza, H and Kiss, AP},
title = {Next-Generation Functional Nanoplatforms: Engineering Plant-Derived Extracellular Vesicles for Targeted Bioactive Delivery and Health Applications.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {20},
pages = {},
pmid = {42943823},
issn = {1420-3049},
mesh = {*Extracellular Vesicles/chemistry/metabolism ; Humans ; *Plants/chemistry/metabolism ; *Drug Delivery Systems ; Phytochemicals/chemistry ; Animals ; },
abstract = {Plant-derived extracellular vesicles (PDEVs) are being recognized as a capable novel class of natural nanocarriers that have important uses in delivering bioactives and facilitating innovations in functional foods and precision health technologies. PDEVs are lipid-bilayer-enclosed vesicular structures that commonly occur at the nanoscale, although their reported sizes vary depending on the plant source, isolation procedure, and measurement method. They contain diverse biomolecules, including lipids, proteins, microRNAs, and phytochemicals, and have been investigated for their potential roles in interspecies communication and the delivery of bioactive compounds. Compared with some conventional nanocarriers, PDEVs have shown favorable biocompatibility and stability under certain experimental conditions; however, these properties are dependent on the plant source, isolation method, cargo, formulation, and experimental model; therefore, they are uniquely positioned for oral delivery systems. This review presents a complete picture of the process of PDEV biogenesis, the molecular architecture of PDEVs, and their cargo. We evaluate and compare the source materials of PDEVs to determine whether they will influence how effectively the bioactive agent is delivered to its intended target and produce the therapeutic effect. Additionally, we present a review of the advances in technology for the analysis of PDEVs: methods of extraction, purification, and characterization of PDEV; current and future techniques for loading cargo into PDEVs; methods of modifying the surfaces of PDEVs; and methods of developing, producing, and delivering hybrid systems of PDEVs. Finally, a comprehensive review of the use of PDEVs in delivering nutraceuticals, modulating the gut microbiome, delivering probiotic systems, and exhibiting anti-inflammatory, antioxidant, and anti-cancer effects. Even as these positive advancements occur, challenges related to scalability, standardization, and purity remain significant barriers to industrial translation. PDEVs are well-positioned to serve as a sustainable, next-generation nanoplatform at the intersection of nanotechnology, food science, and biomedicine. PDEVs also provide unprecedented opportunities to advance functional foods and precision nutrition.},
}

*Extracellular Vesicles/chemistry/metabolism
Humans
*Plants/chemistry/metabolism
*Drug Delivery Systems
Phytochemicals/chemistry
Animals

@article {pmid42944051,
year = {2026},
author = {Ghidini, M and Sberna, G and Guerrera, LP and Maggi, F and Novazzi, F},
title = {The Gut Virome in Gastrointestinal Cancers: Mechanisms, Biomarkers, and Translational Opportunities.},
journal = {Viruses},
volume = {18},
number = {10},
pages = {},
pmid = {42944051},
issn = {1999-4915},
mesh = {Humans ; *Gastrointestinal Neoplasms/virology/therapy ; *Virome ; *Gastrointestinal Microbiome ; Animals ; Bacteriophages ; Gastrointestinal Tract/virology ; Translational Research, Biomedical ; Biomarkers, Tumor ; Oncogenic Viruses ; Bacteria/virology ; },
abstract = {The gastrointestinal tract contains a dense multi-kingdom ecosystem in which bacteria, fungi, archaea, viruses, the mucosa, and the immune system interact. Although cancer microbiome research has focused mainly on bacteria, the gut virome dominated by bacteriophages may influence gastrointestinal carcinogenesis by reshaping bacterial communities, transferring functional genes, modulating inflammation, and altering treatment response. The strongest evidence comes from colorectal cancer, where multiple cohorts show altered phage diversity, temperate-phage enrichment, disrupted phage-bacteria networks, and reproducible stool-based diagnostic signals. Emerging studies in pancreatic cancer, esophageal adenocarcinoma, hepatocellular carcinoma, and precursor lesions suggest that virome disruption extends beyond colorectal cancer, although evidence remains uneven. Classic oncogenic viruses, including Epstein-Barr virus and hepatitis viruses, provide complementary examples of direct viral carcinogenesis in digestive organs. Anelloviruses are widespread in healthy individuals and are not established causes of cancer, but their abundance and composition may reflect immune status, inflammation, tissue injury, and altered host viral ecology. Virome-related interventions remain clinically immature: fecal microbiota transplantation has reached small phase I/II studies in gastrointestinal cancers, whereas phage, fecal-filtrate, and fecal virome approaches remain preclinical or non-oncology; direct oncolytic viruses have reached late-phase testing. Major barriers include viral dark matter, specimen and assay heterogeneity, disease-related confounding, limited external validation, and weak causal evidence. Standardized, mechanistically anchored, multi-kingdom studies are needed to establish clinical utility.},
}

Humans
*Gastrointestinal Neoplasms/virology/therapy
*Virome
*Gastrointestinal Microbiome
Animals
Bacteriophages
Gastrointestinal Tract/virology
Translational Research, Biomedical
Biomarkers, Tumor
Oncogenic Viruses
Bacteria/virology

@article {pmid42944108,
year = {2026},
author = {Hang, L and Xu, H and Ding, Y and Chen, P and Song, X and Shi, D and Chen, Z},
title = {Red Tide Algal Toxin-Induced Intestinal Injury in Marine Fish: Mechanisms, Gut Microecology, and Aquaculture Health Risk Assessment.},
journal = {Veterinary sciences},
volume = {13},
number = {10},
pages = {},
pmid = {42944108},
issn = {2306-7381},
abstract = {Harmful algal blooms (HABs) can cause rapid, extensive mortality in exposed marine fish, often before fish-level diagnostic sampling can guide an emergency response. This review compares the toxin-specific evidence for intestinal injury caused by paralytic shellfish toxins, okadaic acid and Dinophysistoxins, brevetoxins, and fish-killing blooms, while distinguishing direct evidence in marine fish from evidence in other models. Intestinal barrier disruption, inflammation, and microbiome changes are valuable for explaining sublethal exposure, survivor recovery, and post-event attribution. They are not proposed as operational triggers during an acute fish kill. Practical management instead depends chiefly on site-specific environmental surveillance before exposure, predefined emergency actions when a bloom approaches, and longer-term reduction in avoidable nutrient and waste inputs where these contribute to local bloom risk. A four-stage framework links environmental hazard, fish exposure, biological effects, and production or food-safety outcomes with quantitative indicators and explicit uncertainty at each transition. This revised scope places mechanistic intestinal toxicology within the ecological time scale and operational limits of marine aquaculture.},
}

@article {pmid42944112,
year = {2026},
author = {Pizauro, LJL and Gualberto, NGS and Santos, KC and Pirovani, CP and Santana, JO and Castro, LMC and Dias, RPM and Nunes, MSC and Carlos, RSA},
title = {Descriptive, Exploratory Analysis of Microbial Community Composition Across Stages of Canine Periodontal Disease Revealed by 16S rRNA Sequencing in Dogs.},
journal = {Veterinary sciences},
volume = {13},
number = {10},
pages = {},
pmid = {42944112},
issn = {2306-7381},
abstract = {Periodontal disease (PD) is one of the most prevalent oral conditions in dogs, yet the microbial dynamics underlying its progression remain incompletely understood. This exploratory study aimed to describe the canine oral microbiome across four clinical stages using 16S rRNA gene sequencing. Dogs were categorized as Healthy (Stage 0), Gingivitis (Stage 1), Early Periodontitis (Stage 2), and Moderate-Advanced Periodontitis (Stages 3-4) according to American Veterinary Dental College (AVDC) criteria. Pooled subgingival plaque samples from the groups were analyzed for microbial diversity, taxonomic composition, and ecological patterns. Alpha diversity differed among the four pooled profiles, with the highest observed richness in the Early Periodontitis (Stage 2) pool and the lowest in the Moderate-Advanced Periodontitis (Stages 3-4) pool. Beta diversity analyses showed separation among the pooled profiles, particularly between the healthy and severe groups. Taxonomic profiling identified higher relative abundances of sequences assigned to Porphyromonas gingivalis and Treponema denticola in the more advanced disease stage pools, while Fusobacterium nucleatum reached its highest relative abundance in the Early Periodontitis (Stage 2) pool. Visualization of abundance profiles across the four pooled libraries revealed concordant trends among selected treponeme taxa and Fusobacterium nucleatum, as well as inverse trends for other taxa. These findings provide a descriptive, group-level characterization of microbial community differences across AVDC-defined stages of canine periodontal disease based on pooled samples and generate hypotheses for future individual-level studies.},
}

@article {pmid42944114,
year = {2026},
author = {Ma, Q and Tharwat, M and Ullah, A and Liu, J and Alkheraif, AA and Khan, MZ},
title = {Integrating Host Transcriptomics and Metagenomics in the Periparturient Dairy Cow: From Molecular Signatures to Host-Microbiome Interfaces.},
journal = {Veterinary sciences},
volume = {13},
number = {10},
pages = {},
pmid = {42944114},
issn = {2306-7381},
support = {QU-APC-2026//Qassim University/ ; },
abstract = {The periparturient or transition period-roughly three weeks before to three weeks after calving-compresses the most severe metabolic, endocrine and immunological demands of the production cycle into a few weeks and accounts for most clinical disease and involuntary culling in dairy herds. Conventional surveillance relies on downstream indicators-non-esterified fatty acids, β-hydroxybutyrate, calcium and acute-phase proteins-that document failed adaptation without resolving its regulatory origins. Two omics platforms now close that gap. Transcriptomics shows that the liver, adipose tissue, mammary gland, endometrium, rumen epithelium and circulating leukocytes each execute a distinct, temporally ordered program organized around lipid mobilization, gluconeogenesis, endoplasmic reticulum stress, redox defense and inflammatory resolution, layered over a regulatory tier of non-coding RNAs. Metagenomics shows in parallel that rumen, hindgut, uterine, vaginal, teat-apex and colostrum communities are restructured by parturition and by the dietary shift into lactation, with reproducible dysbiotic signatures accompanying ketosis, fatty liver, metritis, endometritis and intramammary infection. Critically, the two layers are mechanistically coupled: microbial short-chain fatty acids, secondary bile acids, purine derivatives and amino acids reprogram hepatic and immune cell transcription, while host lipolysis, inflammation and mineral demand reshape community structure. This review synthesizes both groups of literature within a single framework, formalizes five host-microbiome interfaces supported by paired measurements and identifies the biomarker, nutritional and genetic-selection opportunities that emerge only when host and microbial evidence are read together.},
}

@article {pmid42944140,
year = {2026},
author = {Ma, H and Yao, Y and Wei, Y},
title = {Effects of Eucommia ulmoides Leaf-Astragalus membranaceus Complex on Antioxidant Capacity, Immune Function, Gut Microbiota and Serum Metabolome of Yellow-Feather Broilers.},
journal = {Veterinary sciences},
volume = {13},
number = {10},
pages = {},
pmid = {42944140},
issn = {2306-7381},
support = {YCKJ-2022057//Yuncheng Science and Technology Program/ ; },
abstract = {Background: Phytogenic feed additives may provide sustainable alternatives for improving poultry productivity and health. This study evaluated the chemical composition, antioxidant activity, and in vivo effects of a 1:1 Eucommia ulmoides leaf-Astragalus membranaceus complex (EG) in yellow-feathered broilers. Methods: The nutritional composition, bioactive compounds, and antioxidant activity of EG were characterized. A total of 200 one-day-old yellow-feathered broilers were randomly allocated into four dietary treatments with five replicates per group and 10 birds per replicate: the control group (CG) receiving a basal diet and three EG supplementation groups receiving diets supplemented with 0.5% (EG (0.5%)), 1.0% (EG (1.0%)), 2.0% (EG (2.0%)) Eucommia ulmoides leaf-Astragalus membranaceus complex for 42 days. Growth performance, serum antioxidant and immune indicators, intestinal microbiota composition, and serum metabolomic profiles were analyzed. Results: EG contained 46.53% polysaccharides and exhibited concentration-dependent radical-scavenging activity. Supplementation with EG (0.5%) consistently increased body weight and average daily gain and reduced the feed conversion ratio without affecting feed intake. EG increased serum antioxidant enzyme activities and immunoglobulin concentrations but did not affect routine biochemical parameters. The EG (0.5%) group was therefore selected for microbiome and metabolome analyses. EG altered jejunal and cecal microbial composition without significantly affecting α-diversity and increased cecal Faecalibacterium and Blautia at day 21 and Faecalibacterium and Parabacteroides at day 42. Metabolomics identified 103 differential metabolites associated mainly with amino acid, glycerophospholipid, and energy metabolism. Spearman's analysis further associated Bacteroidota, Bacillota, Enterococcus, and Blautia with amino acid, carbohydrate, and lipid-related metabolites. Conclusions: These findings indicate that EG (0.5%) may improve growth and feed efficiency while modulating antioxidant status, humoral immune indices, intestinal microbial composition, and systemic metabolism in yellow-feathered broilers.},
}

@article {pmid42944158,
year = {2026},
author = {Li, D and Zhang, J and Zhang, L and Liu, X and Chen, P},
title = {A Systematic Comparison of Differential Metabolites and Functional Pathways in the Gut Contents of Yaks and Plateau Yellow Cattle Across Altitudinal Gradients.},
journal = {Veterinary sciences},
volume = {13},
number = {10},
pages = {},
pmid = {42944158},
issn = {2306-7381},
support = {QY-HS-2025A-01//The 2025 County-Level Science and Technology Plan Project of the East-West Collaboration Financial Assistance Fund/ ; 26CXNA042//The 2026 Provincial Science and Technology Program of the Gansu Provincial Department of Science and Technology/ ; },
abstract = {The yak (Bos grunniens) is a crucial species adapted to the extreme high-altitude environment of the Tibetan Plateau. However, a systematic understanding of how gut metabolic homeostasis contributes to this adaptation, particularly across altitudinal gradients and in comparison with sympatric species, remains limited. This study employed untargeted metabolomics to profile the intestinal contents of high-altitude yaks (HYs, 3800 m), low-altitude yaks (LYs, 2500 m), and plateau yellow cattle (PC, 3500 m) from the Gannan region. Multivariate analysis revealed distinct clustering of the three groups, with PLS-DA model validation parameters (R2Y(cum) > 0.997, Q2(cum) > 0.990), confirming significant species-specific and altitude-adaptive differentiation in the gut metabolome. A suite of differentially abundant metabolites (DAMs) was identified: HYs were enriched with stress- and inflammation-related molecules (e.g., prostaglandin E2, uric acid-indicative of oxidative stress and inflammatory responses) and steroid metabolites; LYs showed a profile oriented towards basic anabolism and antioxidant defense (e.g., L-galactono-1,4-lactone, allantoin); PC were characterized by unique lipid derivatives (e.g., 5-hexyl-2-furanhexanoic acid) and fungal-origin metabolites. Pathway enrichment analysis pinpointed Linoleic acid metabolism as one of the most significantly enriched pathways, with key hydroxyoctadecadienoic acids (HODEs) and related oxylipins significantly upregulated in HYs. Other significantly enriched pathways included Tryptophan metabolism, ABC transporters, and Protein digestion and absorption. Our findings suggest that high-altitude adaptation in yaks is associated with remodeling of the intestinal metabolic network. The identified signature metabolites and consistently enriched candidate pathways provide novel insights into potential host-microbiome-associated mechanisms and establish a metabolic foundation for the conservation of plateau livestock genetic resources and the development of precision husbandry strategies. However, these findings should be interpreted as hypothesis-generating because altitude, species, diet, and environment were not fully decoupled.},
}

@article {pmid42944202,
year = {2026},
author = {Ahmad, K and Islam, T and Jamal, QMS and Srivastava, S and Rabbee, MF},
title = {The Gut-Mammary Axis in Dairy Cattle: A Review of Gut Microbiota-Driven Influences on Lactation.},
journal = {Veterinary sciences},
volume = {13},
number = {10},
pages = {},
pmid = {42944202},
issn = {2306-7381},
support = {QU-APC-2026//Qassim University/ ; },
abstract = {The gut microbiota is increasingly recognized as an important regulator of cattle health and productivity, particularly in shaping lactation performance. This review synthesizes current research on how gut microbial communities influence milk yield, composition, and lactational physiology. The diverse microbial populations in the ruminant gastrointestinal tract produce key metabolites, including short-chain fatty acids, microbial amino acids, and vitamins, that support host energy balance and nutrient utilization during lactation. We discuss the role of the gut microbiota in the gut-mammary axis and how microbial fermentation influences immune modulation, mastitis, and nutrient metabolism, all of which affect mammary gland development and milk synthesis. The review also examines how factors such as diet composition, feed additives (e.g., prebiotics, probiotics, and postbiotics), antimicrobial use, and environmental stressors alter microbiota structure and function. These changes can promote microbial resilience or dysbiosis, thereby affecting lactation either positively or negatively. Understanding these complex interactions offers promising avenues for microbiome-targeted interventions to enhance dairy performance and animal well-being. Future research should emphasize integrated multi-omics approaches to identify causal pathways and inform precision strategies for improving lactation efficiency in cattle.},
}

@article {pmid42944216,
year = {2026},
author = {Huang, W and Yu, X and Xia, Y and Li, W and Zhao, X},
title = {Machine Learning in Mammals' Health: Integrating Multi-Omics Data for Precision Nutrition and Sustainable Production.},
journal = {Veterinary sciences},
volume = {13},
number = {10},
pages = {},
pmid = {42944216},
issn = {2306-7381},
support = {CSTB2023NSCQ-MSX0786//Natural Science Foundation of Chongqing/ ; KJQN202500214//Chongqing Municipality Education Commission/ ; NW-CSTB2025NYKJGGXM-DPJSLXMX0003//Agricultural Science and Technology R&D Program of Chongqing/ ; },
abstract = {Precision nutrition in modern mammalian production aims to transition from static feeding regimens toward dynamic and customized strategies by unraveling complex interactions among genetics, environment, the gut microbiome, and host physiology. Machine learning provides a powerful analytical framework to navigate high-dimensional multi-omics datasets. However, existing applications frequently lack systematic criteria for algorithm selection and remain largely confined to observational statistical associations without progressing toward causal verification. This perspective delineates a coherent translational chain spanning three interconnected operational scenarios: key functional microbiota screening to identify whom to intervene on, multi-omics biomarker identification to define when to intervene, and host pathway characterization to reveal how the animal responds. We critically examine the operational boundaries, interpretability trade-offs, and failure modes of classical algorithms including LASSO, support vector machines, random forest, and graph neural networks across these domains. Furthermore, we address critical field bottlenecks such as high dimensionality, small-sample overfitting, batch effects, and black-box opacity, while highlighting emerging paradigms including multimodal data fusion, transfer learning, and causal machine learning to bridge the gap between data-driven screening and actionable nutritional interventions. Ultimately, transforming machine learning from an auxiliary predictive tool into an autonomous precision nutrition engine requires shifting the research focus from isolated model accuracy to reproducible and causally validated biological targets.},
}

@article {pmid42944802,
year = {2026},
author = {Ma, JY and Chen, AN and Yao, Y and Wang, H},
title = {Local Microenvironment in Adenoid Hypertrophy and Its Clinical Relevance.},
journal = {Current medical science},
volume = {},
number = {},
pages = {},
pmid = {42944802},
issn = {2523-899X},
support = {81873694//National Natural Science Foundation of China/ ; 81873694//National Natural Science Foundation of China/ ; 81873694//National Natural Science Foundation of China/ ; 2022BCA005//the key Research and Development Program of Hubei Province/ ; },
abstract = {Adenoid hypertrophy (AH) is among the most common otolaryngologic disorders in childhood, and its development cannot be adequately explained by a single inflammatory process. Increasing evidence suggests that the adenoid functions not only as an important component of upper airway mucosal immunity but also as a critical site for persistent microbial colonization and local immune remodeling. This review examines AH from structural, immunologic, and microecological perspectives, offering an integrated analytical framework to better understand coordinated imbalance within the adenoidal microenvironment. Furthermore, we investigate the relationships between distinct microenvironmental patterns and clinical phenotypes and discuss both current therapeutic strategies and emerging precision intervention approaches. Collectively, existing evidence indicates that AH is a multifaceted disorder closely associated with microenvironmental reprogramming, and its clinical heterogeneity appears to be attributed to diverse underlying biological processes.},
}

@article {pmid42944993,
year = {2026},
author = {Sansavini, M and Pieretto, G and Samra, M and Bacci, C},
title = {Periodontitis Beyond ASCVD: Emerging Cardiovascular Phenotypes in Perio-Medicine.},
journal = {Clinical oral investigations},
volume = {30},
number = {11},
pages = {},
pmid = {42944993},
issn = {1436-3771},
mesh = {Humans ; Phenotype ; *Periodontitis/complications ; *Cardiovascular Diseases/etiology ; *Atherosclerosis/etiology ; },
abstract = {BACKGROUND: Periodontitis is increasingly recognized as a chronic inflammatory disease with systemic implications beyond the oral cavity. Within perio-medicine, its association with cardiovascular disease has been extensively investigated, particularly in relation to atherosclerotic cardiovascular disease (ASCVD). However, the field is now expanding toward a broader and more phenotype-specific cardiovascular framework.

OBJECTIVE: This narrative review critically examines how the periodontitis-cardiovascular field has evolved from a predominantly ASCVD-centered model toward a broader spectrum of cardiovascular phenotypes, with particular emphasis on differences in evidence maturity, contemporary mechanistic concepts, and unresolved translational questions.

METHODS: A structured literature search was conducted in PubMed/MEDLINE, Scopus, Web of Science, and the Cochrane Library. Evidence from mechanistic, observational, and interventional studies was qualitatively synthesized according to its contribution to established clinical associations, supportive mechanistic evidence, emerging cardiovascular phenotypes, and unresolved questions regarding causality and clinical translation.

RESULTS: The association between periodontitis and coronary atherosclerotic disease represents the most mature component of the literature, with substantial observational and meta-analytic support, while ischemic cerebrovascular disease is also supported by consistent but more heterogeneous evidence. Beyond ASCVD, atrial fibrillation and heart failure currently represent the most developed emerging cardiovascular phenotypes, whereas evidence concerning abdominal aortic aneurysm and venous thromboembolism remains more preliminary and hypothesis-generating. Contemporary mechanistic models extend beyond bacteremia and systemic inflammation to include endothelial dysfunction, thrombo-inflammatory signaling, trained immunity, immune-cell trafficking, functional dysregulation of the oral microbiome, and shared biological vulnerabilities. However, these pathways differ markedly in cardiovascular-specific evidentiary maturity and should not be interpreted as equivalent evidence of human causality. Periodontal therapy can improve inflammatory biomarkers, endothelial function, selected metabolic parameters, and blood pressure in specific populations, but a persistent translational gap remains between surrogate-marker improvement and demonstrated reduction in major adverse cardiovascular events. Periodontitis may also contribute to chronic systemic inflammatory burden in susceptible individuals, although its role within cardiovascular residual inflammatory risk remains an emerging hypothesis.

CONCLUSIONS: The periodontal-cardiovascular field is evolving from a predominantly ASCVD-centered model toward a phenotype-specific continuum of evidence maturity. Periodontitis is best interpreted as a potential modifier of cardiovascular vulnerability rather than as an established causal determinant. Future research should prioritize adequately powered cardiovascular-outcome trials, standardized periodontal phenotyping, and prospective validation of emerging phenotypes and mechanistic frameworks before periodontal information can be considered clinically actionable for cardiovascular prevention.},
}

Humans
Phenotype
*Periodontitis/complications
*Cardiovascular Diseases/etiology
*Atherosclerosis/etiology

@article {pmid42945143,
year = {2026},
author = {Tariq, A and Sagheer, M and Kertz, NC and Seekford, ZK and de Bari, MAT and Macay, GA and Pandey, S and Zhai, Y and Jeong, KC and Dahl, GE and Bromfield, JJ},
title = {Prepartum Heat Stress Dysregulates Immune Resilience in Postpartum Dairy Cows.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {20},
pages = {},
pmid = {42945143},
issn = {1530-6860},
support = {2020-67015-31015//USDA | National Institute of Food and Agriculture (NIFA)/ ; //Higher Education Commission, Pakistan (HEC)/ ; },
mesh = {Animals ; Female ; Cattle ; *Postpartum Period/immunology ; *Heat-Shock Response/immunology ; Pregnancy ; *Heat Stress Disorders/immunology/veterinary ; Lipopolysaccharides ; Hot Temperature ; },
abstract = {Increasing environmental temperatures pose a major challenge to animal welfare by inducing heat stress and increasing the incidence of disease. Immune resilience is essential for maintaining animal health; however, the mechanisms linking heat stress to immune dysfunction and disease remain unclear. We hypothesized that prepartum heat stress would result in persistent disruption of immune resilience after calving when cows were no longer heat stressed. During summer, non-lactating, pregnant cows were subjected to either prepartum cooling (fans, water soakers, and shade; n = 31) or heat stress (shade only; n = 31) for the last 46 days of gestation. After calving, all cows received cooling. Postpartum health, peripheral blood, and endometrial samples were evaluated up to 21 days postpartum. Prepartum heat stress increased the incidence of postpartum diseases compared to cooled cows, with little change to the uterine microbiome. Prepartum heat stress increased postpartum white blood cell counts and mean platelet volume, while lipopolysaccharide-stimulated expression of CXCL8, IL1B, and TNF tended to be attenuated in whole blood. Interestingly, prepartum heat stress increased lipopolysaccharide-stimulated secretion of IL-6 and IL-8 in whole blood. In parallel, prepartum heat stress induced mild but persistent changes to the postpartum endometrial transcriptome associated with immunological pathways. Furthermore, prepartum heat stress attenuated basal expression of CXCL8, IL6, and TNF in cultured endometrial cells. Collectively, these findings demonstrate that prepartum heat stress increases disease incidence and disrupts peripheral and endometrial immune resilience independent of changes to the microbiome in postpartum cows.},
}

Animals
Female
Cattle
*Postpartum Period/immunology
*Heat-Shock Response/immunology
Pregnancy
*Heat Stress Disorders/immunology/veterinary
Lipopolysaccharides
Hot Temperature

@article {pmid42945300,
year = {2026},
author = {Andrade, B and Ramírez, M and Reyes, G},
title = {Microbial community structure of Penaeus vannamei post-larvae naturally infected with multiple viruses in hatchery tanks.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0361576},
pmid = {42945300},
issn = {1932-6203},
mesh = {Animals ; *Penaeidae/virology/microbiology ; Larva/virology/microbiology ; Aquaculture ; *Microbiota ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This study offers an observational evaluation of how viral and bacterial infections co-occur with alterations in the microbiome and survival of Penaeus vannamei post-larvae, one of the most economically important species in global aquaculture.

METHODS: Eleven commercial larval production tanks were classified into three distinct infection scenarios using histology and PCR: Baculovirus penaei (BP) monoinfection, mixed infections (BP, white spot syndrome virus [WSSV], and acute hepatopancreatic necrosis disease [AHPND]-causing bacteria), and non-infected controls. High-molecular-weight DNA was subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform, followed by evaluation of microbial diversity, community structure, and infection-associated microbial signatures.

RESULTS: Although BP was the most abundant viral genus across infected groups, severe mortality was observed only under mixed-infection conditions, which were closely associated with AHPND-causing bacteria presence and microbiome disruption rather than with BP alone. Deep metagenomic sequencing revealed reduced, distinct microbiome structures in shrimp infected with BP and in those with mixed infections, compared to non-infected individuals. Non-infected post-larvae maintained complex and well-balanced bacterial communities, predominantly composed of Donghicola and Muricauda. Nudiviridae and Oscillospiraceae showed comparable relative abundances in BP-only and mixed-infection groups. In contrast, mixed infections were characterized by a relative increase in Vibrio, together with the PCR-detection of PirAB toxin genes, whereas WSSV remained detectable in the metagenomic dataset despite its comparatively low relative abundance, while the infection remained thermally suppressed and asymptomatic in the larvae. Functionally, infected larval microbiomes were enriched for transposases, retrotransposons, and virulence-factor genes. The near-complete BP-GR25 genome (119,245 bp) was assembled and annotated from larval metagenomes.

CONCLUSION: These results highlight the value of high-throughput sequencing in the early detection of pathogens in aquaculture, where subtle microbial shifts during postlarval stages can be valuable indicators of health status for production.},
}

Animals
*Penaeidae/virology/microbiology
Larva/virology/microbiology
Aquaculture
*Microbiota
Metagenomics
Metagenome

@article {pmid42945345,
year = {2026},
author = {Zang, C and Tang, L and Deek, RA},
title = {Supervised and covariate-adjusted dimension reduction for prediction and visualization using microbiome data.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
pmid = {42945345},
issn = {1477-4054},
support = {R56LM014522/LM/NLM NIH HHS/United States ; S10OD028483/OD/NIH HHS/United States ; //University of Pittsburgh's CTSI Trans-disciplinary Collaboration Pilot Award/ ; RRID:SCR_022735//University of Pittsburgh Center for Research Computing and Data/ ; },
mesh = {Humans ; Principal Component Analysis ; Algorithms ; *Microbiota ; Dimensionality Reduction ; *Gastrointestinal Microbiome ; *Computational Biology/methods ; Prediction Algorithms ; },
abstract = {Given that the gut microbiome has been shown to play a critical role in human health, discerning the relationship between microbial taxa and disease outcomes or phenotypes is of interest. Often, this involves association testing, predictive modeling, and visualizing trends in the data. Principal coordinates analysis (PCoA) is a commonly used dimension reduction technique in microbiome studies. PCoA relies on pairwise distances between samples and serves as a nonlinear alternative to the classic principal component analysis when non-Euclidean distances are used. Its low-dimensional embeddings provide intuitive visualizations but do not incorporate outcome-related information. Therefore, the low-dimensional principal coordinates may have poor performance in visualizing outcome differences, as well as in downstream disease prediction tasks. Additionally, covariates, such as demographics, lifestyle factors, and technical artifacts, can obscure true biological signals, leading to masked or spurious associations and limited generalizability. To address these limitations, we propose a supervised and covariate adjusted PCoA algorithm. By utilizing outcome information, while simultaneously minimizing the influence of nuisance variables, our method produces low-dimensional embeddings that better separate disease outcomes in visualizations and result in improved accuracy in downstream regression and classification tasks. We demonstrate the effectiveness of the proposed method and highlight its ability to extract important associations between the microbiome and disease outcomes while mitigating nuisance variation through simulations and application to real microbiome profiling studies.},
}

Humans
Principal Component Analysis
Algorithms
*Microbiota
Dimensionality Reduction
*Gastrointestinal Microbiome
*Computational Biology/methods
Prediction Algorithms

@article {pmid42945712,
year = {2026},
author = {Schenck, CH},
title = {Introduction to the special issue on RBD 40 years old: Perspectives on extensive clinical and research intersections.},
journal = {Sleep medicine},
volume = {149},
number = {},
pages = {109330},
doi = {10.1016/j.sleep.2026.109330},
pmid = {42945712},
issn = {1878-5506},
abstract = {This Introduction to the special issue in Sleep Medicine marking the 40th anniversary of the first publication on REM sleep behavior disorder (RBD) in 1986 provides a brief historical background with early timelines, followed by current RBD and REM-without-atonia diagnostic considerations; and updates on RBD global epidemiology, RBD in younger populations, and the spectrum of RBD comorbidities and biomarkers. Other topics covered include RBD gut microbiome dysbiosis, proteome abnormalities, and neuroinflammation; RBD international research consortia; RBD economic burden and adverse quality of life; and neurodegeneration risk disclosure for newly diagnosed idiopathic/isolated RBD patients. Thirty-four RBD clinical and research intersections are depicted in a figure. Two recent review articles are cited that identified more than 4200 peer-reviewed journal articles published to date on RBD. The six articles contained in this special RBD issue cover animal models and basic science; genetics; pathogenesis; measurement and diagnosis; neurodegeneration, neuroimaging, and phenoconversion biomarkers; and cognition. RBD epitomizes the close collaboration and cross-fertilization of clinical and basic science research.},
}

@article {pmid42945960,
year = {2026},
author = {Porcari, S and Bolte, LA and Björk, JR and Elkrief, A and Derosa, L and Ferrari, M and Pezzullo, AM and Severino, A and Fusco, W and Messaoudene, M and Costa Silva, CA and Fidelle, M and Routy, B and Mählmann, L and Thomas, AM and Ciccarese, C and Nero, C and Fagotti, A and Tortora, G and Gasbarrini, A and Iacovelli, R and Bria, E and Futreal, A and McQuade, J and Kroemer, G and Hospers, GAP and de Haan, JJ and Wargo, J and Segata, N and Weersma, RK and Ianiro, G and Zitvogel, L and , },
title = {Antibiotics and outcomes of cancer immunotherapy: An updated meta-analysis and clinical applications.},
journal = {Cancer cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ccell.2026.09.012},
pmid = {42945960},
issn = {1878-3686},
abstract = {The gut microbiome is a modifiable determinant of response to immune checkpoint inhibitors (ICI), positioning antibiotic exposure as a critical yet under-recognized risk factor for worse survival outcomes in immuno-oncology. As nearly 30% of ICI-treated patients receive antibiotics and indications of cancer immunotherapy are expanding, this issue represents a global challenge in oncology. Here, we paint an updated and comprehensive landscape of antibiotic exposure in immuno-oncology, provide actionable clinical recommendations, and envision future avenues for improvement. First, we describe the biological mechanisms by which antibiotic-induced dysbiosis contributes to ICI resistance. Next, through an updated meta-analysis of 116 cohorts and 97,850 cancer patients treated with ICI, we found a significant association between antibiotic exposure and survival outcomes (overall survival, hazard ratio [HR]: 1.49, 95% confidence interval [CI]: 1.34-1.65; progression-free survival, HR: 1.44, 95% CI: 1.31-1.58). Finally, we discuss antibiotics stewardship and microbiome-centered strategies to prevent, diagnose, and/or repair dysbiosis.},
}

@article {pmid42946056,
year = {2026},
author = {Geurts, J and Pot, B and Knipping, K and Braat, M and Peters, S},
title = {Lactose, Lactose Maldigestion and Lactose Intolerance: Definitions, Misunderstandings, Mechanisms, and Public Health Implications.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100760},
doi = {10.1016/j.advnut.2026.100760},
pmid = {42946056},
issn = {2156-5376},
abstract = {Lactose is the principal carbohydrate in milk, serving a critical role in infant energy metabolism as well as contributing to neurodevelopment, and the establishment of a healthy gut microbiota. Later in life, lactose digestion capacity varies widely across human populations owing to the genetically determined decline of intestinal lactase expression after weaning-a condition termed 'lactase non-persistence'. Approximately two-thirds of the global adult population exhibits reduced lactase activity, yet the clinical consequences of this enzymatic reduction are far less uniform than commonly assumed. This review provides a comprehensive examination of lactose functionality, the physiology of lactose digestion, and the consequences of lactase persistence and non-persistence. We present formal definitions for the spectrum of terms used in lactose research-including lactase persistence, lactase non-persistence, lactose maldigestion, and lactose intolerance-and argue that the critical distinction between lactose maldigestion (a physiological state) and lactose intolerance (a clinical syndrome) is frequently overlooked in both research and public health. Drawing on evidence from double-blind randomised controlled trials , microbiome intervention studies, and global epidemiological data, the evidence indicates that the majority of individuals with lactose maldigestion do not develop clinically meaningful symptoms at moderate intake levels of most dairy products. We further discuss the mechanism of colonic adaptation, whereby gradual lactose exposure selectively enriches Bifidobacterium populations capable of fermenting lactose without excessive gas production resulting in greater lactose tolerance. Finally, we examine the public health implications of these findings, noting that food-based dietary guidelines worldwide-including those in populations with high prevalence of lactase non-persistence-consistently recommend dairy consumption owing to its established associations with reduced risk of type 2 diabetes, colorectal cancer, and improved bone health.},
}

@article {pmid42946473,
year = {2026},
author = {Pradhan, M and Molinaro, A and Ginanni Corradini, S and Silecchia, G and Ferri, F and Capoccia, D and Lv, B and Wu, H and Huber-Schönauer, U and Völkerer, A and Mischitelli, M and Parlati, L and Bergström, G and Datz, C and Leonetti, F and Tilg, H and Tremaroli, V and Bäckhed, F},
title = {Gut microbiome profiles associated with simple liver steatosis in MASLD.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337572},
pmid = {42946473},
issn = {1468-3288},
}

@article {pmid42946695,
year = {2026},
author = {Dahal, A and Chang, WC and Grashel, B and Morgan, D and Spagna, D and Kim, DH and Sachdeva, S and Phelan, KJ and Satish, L and Biagini, JM and Haslam, DB and Ollberding, NJ and Khurana Hershey, GK},
title = {Longitudinal Skin Bacterial Cluster Associated With Protection Against Allergic Co-Morbidity in Pediatric Atopic Dermatitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70554},
pmid = {42946695},
issn = {1398-9995},
support = {U19AI070235//National Institute of Allergy and Infectious Diseases/ ; F30AI181481//National Institute of Allergy and Infectious Diseases/ ; T32GM149200/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is an inflammatory skin condition that often portends the development of allergic comorbidities. Despite evidence supporting the role of the skin microbiome in AD, its temporal patterns and associations with risk or protection for allergic co-morbidity remain unclear. Our objective is to characterize core species of the pediatric AD bacterial microbiome, assess microbial networks and clusters, and identify global microbial changes relevant to AD and the atopic march.

METHODS: We performed metagenomic shotgun sequencing on 353 non-lesional skin samples from children in the Mechanisms of Progression of Atopic Dermatitis to Asthma in Children (MPAACH) cohort across 5 annual visits. We assessed taxonomic composition and analyzed longitudinal skin microbial patterns with progression to allergic co-morbidities.

RESULTS: We identified 436 distinct species. Shannon diversity and richness declined with age, and socioeconomic factors explained the variance in species composition. Staphylococcus aureus (SA) was more abundant in severe AD. Cluster 5, comprised of typically gut-associated microbes, was more abundant in non-sensitized children who did not develop allergic co-morbidities over time.

CONCLUSIONS: Our analyses revealed key patterns in core taxa, diversity and abundance of the skin microbiome over time in early life and highlighted previously unexplored factors such as socioeconomic status as key contributors to the variability in species composition. Abundance of SA confers risk, while gut-associated microbes may offer protection, influencing the clinical trajectory of AD and the atopic march. Thus, these results provide a novel and comprehensive understanding of the temporal dynamics of the skin microbiota in pediatric AD.},
}

@article {pmid42946700,
year = {2026},
author = {Han, J and Zhang, Y and Zhang, H and Zhou, K and Chen, X and Ning, K},
title = {mHolmes improves cross anatomical cadaveric microbiome forecasting for postmortem interval estimation.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42946700},
issn = {2041-1723},
mesh = {Humans ; *Microbiota ; *Postmortem Changes ; Cadaver ; *Forensic Microbiology/methods ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {Forensic microbiology leverages postmortem microbiome succession as a promising biomarker for estimating the postmortem interval (PMI). However, current methods are constrained by sparse sampling (typically 3-5 time points) and limited cross-anatomical generalizability, leading to imprecise PMI estimates with errors often exceeding ±3 days, particularly in cases of dismembered remains. To address these limitations, we developed mHolmes, a Transformer-based transfer learning framework for forecasting cadaveric microbiome dynamics. Trained on daily longitudinal data from 34 cadavers over 21 days, mHolmes achieves daily predictions of microbial dynamics, with reduced error (MAE < 2 days) in cross-anatomical forecasting tasks (e.g., hip to face). Shapley Additive exPlanations (SHAP) analysis supports interpretability by identifying seven bacterial classes as candidate PMI-associated features. This study supports mHolmes as a robust forecasting framework that addresses key limitations in sparse and cross anatomical microbiome data, improves PMI estimation from incomplete observations, and has potential forensic applications in body part matching and higher resolution timeline reconstruction.},
}

Humans
*Microbiota
*Postmortem Changes
Cadaver
*Forensic Microbiology/methods
Bacteria/classification/isolation & purification/genetics

@article {pmid42946867,
year = {2026},
author = {Vaishally, and Shukla, SP},
title = {An Antimicrobial Oosporein Pigment-producing Fungus Associated with the Lac Insect.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42946867},
issn = {1432-184X},
support = {Ramalingaswami Fellowship//Department of Biotechnology, Ministry of Science and Technology, India/ ; SRG/2021/000600//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Pigments, Biological/metabolism/pharmacology/biosynthesis ; *Hemiptera/microbiology ; Female ; *Acremonium/metabolism/isolation & purification/genetics ; *Anti-Infective Agents/metabolism/pharmacology ; *Hypocreales/isolation & purification/metabolism/genetics ; Bacteria/drug effects ; Nymph/microbiology ; },
abstract = {Insects host diverse fungal communities that produce biologically active secondary metabolites. Here, we use culture-dependent and culture-independent methods to characterise fungi associated with the lac insect Kerria lacca - a species well known for its natural red lac pigment. We isolated several fungi from the external surface of the insects. Of these, only Acremonium sp. 'ALR' was found to produce a red pigment under laboratory conditions. We therefore investigated this pigment in relation to the insect's lac pigment. The pigment from Acremonium sp. ALR was identified as oosporein. In vitro bioassays demonstrated that the fungus exhibits broad-spectrum antimicrobial activity, inhibiting the growth of bacteria and fungi, including sooty moulds associated with the lac insect's honeydew. The fungus belongs to the order Hypocreales, which includes the lac insect's yeast-like symbiont and many entomopathogenic fungi that produce toxins and chemically reactive pigments. We detected the fungus on the cuticle of K. lacca nymphs and adult females, as well as in the wax deposits near the site of emergence of crawler nymphs. We hypothesise that the fungus may adhere to the nymphs' cuticles during their emergence and can get passively transmitted during the host's life stages. However, oosporein was detected in neither the lac insects nor their resin, based on liquid chromatography mass spectrometry analysis. Conversely, lac pigments were not detected in the pigment extracts of Acremonium sp. ALR, demonstrating that the two pigments are chemically distinct and that the Acremonium sp. ALR did not impact the lac insect's own pigment synthesis.},
}

Animals
*Pigments, Biological/metabolism/pharmacology/biosynthesis
*Hemiptera/microbiology
Female
*Acremonium/metabolism/isolation & purification/genetics
*Anti-Infective Agents/metabolism/pharmacology
*Hypocreales/isolation & purification/metabolism/genetics
Bacteria/drug effects
Nymph/microbiology

@article {pmid42947086,
year = {2026},
author = {Kunkli, A and Rátonyi, D and Kozma, B and Farkas, B and Majoros, L and Póka, R and Sipos, AG and Takacs, P and Krasznai, ZT and Kozma, B},
title = {Cervicovaginal zinc and copper profiles across vaginitis phenotypes and hydrogel assignment: an exploratory pilot study.},
journal = {BMC women's health},
volume = {26},
number = {1},
pages = {},
pmid = {42947086},
issn = {1472-6874},
mesh = {Female ; Humans ; Pilot Projects ; *Zinc/analysis/metabolism ; *Copper/analysis ; Adult ; Phenotype ; *Cervix Uteri/chemistry/metabolism/microbiology ; Candida albicans/isolation & purification ; *Vagina/microbiology/chemistry/metabolism ; Fluconazole/therapeutic use ; Hydrogels ; Middle Aged ; *Vaginitis/microbiology/metabolism/drug therapy ; Antifungal Agents/therapeutic use ; Prospective Studies ; Candidiasis, Vulvovaginal/drug therapy ; Hydrogel, Polyethylene Glycol Dimethacrylate ; },
abstract = {Zinc (Zn) and copper (Cu) support epithelial integrity, nutritional immunity, and host-microbiome interactions, yet cervicovaginal trace-metal dynamics across vaginitis phenotypes remain poorly defined. We prospectively quantified cervicovaginal lavage (CVL) Zn and Cu by ICP-OES in an exploratory secondary analysis nested within a single-center randomized trial involving 56 symptomatic women and asymptomatic controls (mean age, 36.0 ± 11.8 years; mean BMI, 23.1 ± 4.9 kg/m[2]). We examined whether CVL trace-element concentrations varied according to culture-defined phenotype and randomized hydrogel exposure. CVL Zn concentrations were higher in the Candida albicans-positive (120.2 ± 95.6 µg/L) and symptomatic culture-positive bacterial phenotypes (83.8 ± 55.2 µg/L) than in controls (58.6 ± 27.2 µg/L), whereas Cu showed less consistent variation. Among participants assigned to hydrogel, phenotype-specific differences from controls were not statistically significant. In the fluconazole-only group, higher Zn concentrations were observed in the C. albicans-positive phenotype (154.3 ± 113.5 vs. 54.2 ± 23.8 µg/L), accompanied by higher Cu concentrations (12.13 ± 4.76 vs. 5.76 ± 2.86 µg/L). These exploratory findings indicate that cervicovaginal trace-element profiles may vary across symptomatic culture-defined phenotypes and treatment groups. Our findings should be interpreted as hypothesis-generating. Biological and clinical relevance remains uncertain and warrants confirmation in adequately powered, longitudinal studies using dilution-normalized CVL measurements. Trial registration: The study protocol was approved by the Hungarian National Institutional Review Medical Research Council (approval No. 3282-7/2023/EUIG). The parent trial is registered at ClinicalTrials.gov (NCT05895162; 2023-05-15). Each participant signed a written informed consent form. All procedures performed in studies involving human participants were under the ethical standards of the Hungarian National Institutional Review Medical Research Council and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. This article does not contain any studies with animals performed by any of the authors.},
}

Female
Humans
Pilot Projects
*Zinc/analysis/metabolism
*Copper/analysis
Adult
Phenotype
*Cervix Uteri/chemistry/metabolism/microbiology
Candida albicans/isolation & purification
*Vagina/microbiology/chemistry/metabolism
Fluconazole/therapeutic use
Hydrogels
Middle Aged
*Vaginitis/microbiology/metabolism/drug therapy
Antifungal Agents/therapeutic use
Prospective Studies
Candidiasis, Vulvovaginal/drug therapy
Hydrogel, Polyethylene Glycol Dimethacrylate

@article {pmid42947171,
year = {2026},
author = {Etesami, E and Kamrani, F and Nikparast, A and Sepehrinia, M and Homayounfar, R and Razzaz, JM},
title = {Dietary index for gut microbiota and risk of metabolic syndrome: the mediating role of hepatic steatosis in a prospective cohort study.},
journal = {Diabetology & metabolic syndrome},
volume = {18},
number = {1},
pages = {},
pmid = {42947171},
issn = {1758-5996},
abstract = {BACKGROUND: Metabolic syndrome (MetS) is a growing public health concern, with emerging evidence implicating that gut microbiota plays a role in MetS pathogenesis. The Dietary Index for Gut Microbiota (DI-GM) quantifies diet quality in relation to microbial diversity. This study examined the association between DI-GM and MetS risk, evaluating hepatic steatosis as a potential mediator.

METHODS: This prospective cohort included 4,503 adults (20-70 years) from the Monitoring of Metabolic Diseases Risk Factors in Tehran (MMRT) study, followed over five years. Dietary intake was assessed using a validated 125-item food frequency questionnaire to calculate DI-GM scores. Hepatic steatosis was quantified via controlled attenuation parameter (CAP) using transient elastography. MetS was defined according to Adult Treatment Panel III criteria. Multivariable logistic regression and mediation analyses evaluated associations.

RESULTS: Higher DI‑GM scores were associated with lower MetS incidence. In the fully adjusted model (Model 2), participants in the highest DI‑GM quartile had a 66% lower odds of MetS compared with the lowest quartile (OR = 0.34; 95% CI: 0.27-0.43; P‑trend < 0.001). Each one‑unit increase in the DI‑GM score was associated with an 18% decrease in the odds of MetS (OR = 0.82; 95% CI: 0.78-0.85; P < 0.001). All five MetS components showed significant inverse associations, with the strongest effects observed for elevated waist circumference, hypertriglyceridemia, and low high‑density lipoprotein cholesterol. In mediation analysis, hepatic steatosis accounted for approximately 65% of the DI‑GM-MetS association (indirect effect: -0.0263; P < 0.01), although causal interpretation is limited by the observational design.

CONCLUSION: Greater adherence to a gut microbiota-supportive diet, as measured by DI-GM, is associated with a reduced risk of MetS, largely mediated by reductions in hepatic fat. These findings highlight the potential of microbiome-oriented dietary interventions for MetS prevention.},
}

@article {pmid42947191,
year = {2026},
author = {Samuthpongtorn, C and Vimonsuntirungsri, T and Tangkijvanich, P and Pittayanon, R},
title = {Comparative pilot study using mucosal brushing and mucosal biopsy for detecting duodenal microbiome in functional dyspepsia.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
pmid = {42947191},
issn = {1757-4749},
support = {GA68/053//the Ratchadapiseksompotch Fund, Faculty of Medicine/ ; },
abstract = {BACKGROUND: Functional dyspepsia (FD) is a prevalent gastrointestinal disorder affecting quality of life, with recent studies suggesting a role of the duodenal microbiome in its pathogenesis via the gut-brain axis. The optimal specimen sampling collection method and the specific microbial features associated with FD remain unclear.

OBJECTIVES: This pilot study compared mucosal brushing and biopsy for duodenal microbiome sampling, with an exploratory secondary aim of assessing microbial differences between FD and non-FD controls.

METHODS: Patients undergoing esophago-gastro-duodenoscopy (EGD) were recruited from February 2024 to May 2025. FD patients were identified using the Rome IV criteria, and non-FD controls without upper GI symptoms were included. Duodenal samples were collected via mucosal brushing and biopsy, followed by DNA extraction and 16 S rRNA sequencing of the V1-V2 region. α-diversity (richness, Shannon, Simpson) and β-diversity (Bray-Curtis dissimilarity) were assessed between FD and non-FD controls and between sampling methods. Paired Wilcoxon signed-rank tests compared sampling methods, while linear regression models adjusted for age, sex, and BMI compared FD and non-FD controls within each method. Microbial associations with FD were examined using generalized linear models, adjusting for age, sex, and BMI, with Benjamini-Hochberg FDR correction.

RESULTS: Forty participants (FD n = 20; non-FD controls n = 20) were included, yielding 80 paired samples. Brushing showed higher retention of non-chimeric reads and lower filtering losses than biopsy (all p < 0.0001). Brushing also yielded greater alpha diversity-genus richness (81[33] vs. 19[17]), Shannon (3.68[0.46] vs. 2.60[0.89]), and Simpson (0.96[0.03] vs. 0.89[0.08]); all p < 0.0001-and a distinct community structure (PERMANOVA R²=0.16, p = 0.001). Within each sampling method, FD and non-FD controls did not differ in alpha or beta diversity after adjustment. Exploratory differential abundance modeling identified Streptococcus as numerically higher in FD across both methods, although no genus survived FDR correction (all q > 0.05).

CONCLUSION: Mucosal brushing collects luminal/mucus-associated microbiota and therefore yielded higher bacterial biomass and greater microbial diversity than mucosal biopsy. No significant differences in alpha or beta diversity were detected between FD and non-FD controls within either method, although the study was not powered to exclude such differences. Exploratory analyses suggested numerically higher Streptococcus abundance in FD that did not survive FDR correction. This hypothesis-generating finding requires validation in larger studies.

GOV IDENTIFIER: NCT06326918.},
}

@article {pmid42947200,
year = {2026},
author = {Todó-Llorens, M and Rooney, N and Peachey, L},
title = {Colobine gut microbiome vulnerability to captivity: a meta-analysis of herbivorous primates.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42947200},
issn = {2524-4671},
abstract = {BACKGROUND: Colobine monkey species have a multi-cavity forestomach adapted to a folivorous diet and foregut fermentation, making their gut microbiome essential for efficient digestion of plant fibre. In captivity, these species frequently experience gastrointestinal disorders associated with dietary changes and microbial dysbiosis. Understanding how their microbiome differs from that of other primates is therefore critical for improving health and husbandry. This study used a meta-analysis of global primate microbiome data to compare the faecal microbiome of colobines with those of other herbivorous primates, focusing on the effects of captivity.

RESULTS: Data from 16 studies involving 35 primate species and 7 primate families/subfamilies, comprising 1,690 faecal samples generated using 16 S rRNA amplicon sequencing, were re-analysed using standardised bioinformatic and compositional-statistical pipelines. Significant differences in microbial diversity and composition were observed among wild primates across families/subfamilies, diets, and fermentation strategies. Colobinae had a distinctive microbiome characterised by low Shannon diversity and high relative abundance of Firmicutes, particularly Ruminococcaceae and Lachnospiraceae, which were also prominent members of the wild colobinae core microbiome. Across all families/subfamilies and within colobinae, observed Shannon diversity was lower in captivity; however, multivariable mixed-effects models showed that alpha-diversity estimates were highly sensitive to study identity, species representation and methodological covariates. In contrast, beta-diversity and ALDEx2 analyses provided consistent evidence of captivity-associated compositional restructuring. Captive colobinae were enriched in Bacteroidetes and Spirochaetes, and families such as Prevotellaceae, Rikenellaceae, Methanobacteriaceae, Spirochaetaceae and Bacteroidaceae, whereas wild colobines were enriched in fibre-associated taxa, including Ruminococcaceae and Lachnospiraceae.

CONCLUSIONS: Captivity alters the gut microbiota of colobine primates, affecting microbial diversity and core fibre-fermenting taxa important for gastrointestinal health. However, adjusted alpha-diversity models revealed substantial confounding by study, species, and methodological variables, indicating that diversity effects should be interpreted cautiously. Their specialised folivorous diet and foregut-fermenting physiology appear to produce a highly efficient yet fragile microbial ecosystem poorly adapted to ex-situ conditions. The strongest evidence for captivity-associated disruption was consistent alterations in faecal microbial composition, highlighting the need for diet formulations and microbiome-based health monitoring tailored to the unique digestive ecology of colobines to mitigate the high prevalence of gastrointestinal disorders in captivity.},
}

@article {pmid42947211,
year = {2026},
author = {Zhang, F and Zhang, X and Zhang, Z},
title = {Role of Intestinal Stem Cells in the Pathogenesis and Repair of Necrotizing Enterocolitis.},
journal = {Expert reviews in molecular medicine},
volume = {28},
number = {},
pages = {e51},
doi = {10.1017/erm.2026.10084},
pmid = {42947211},
issn = {1462-3994},
mesh = {Humans ; *Enterocolitis, Necrotizing/pathology/etiology/metabolism/therapy ; *Stem Cells/metabolism/cytology ; Animals ; *Intestinal Mucosa/metabolism/pathology ; *Intestines/pathology/cytology ; Regeneration ; Signal Transduction ; },
abstract = {BACKGROUND: Necrotizing enterocolitis (NEC) is a leading gastrointestinal emergency in preterm infants, characterized by severe epithelial injury, dysregulated inflammation, and defective mucosal repair. Intestinal stem cells (ISCs) at the crypt base are essential for epithelial renewal and barrier restoration after injury.

METHODS: We summarized recent advances in the molecular and cellular mechanisms governing ISC injury and regeneration in NEC, emphasizing canonical repair pathways, niche-derived regulatory circuits, and emerging ISC-targeted therapies.

RESULTS: NEC disrupts ISC survival, proliferation, and differentiation through aberrant innate immune activation, microbial dysbiosis, and impairment of Wnt, Notch, and epidermal growth factor (EGF) signalling. ISC function is also shaped by interactions with Paneth cells, mesenchymal niche components, immune cells, and microbial metabolites. Disruption of this niche compromises crypt regeneration, perpetuates barrier dysfunction, and amplifies intestinal inflammation. Restoring ISC activity and niche integrity has therefore prompted interest in growth factor supplementation, microbiota modulation, immune-based interventions, and stem cell-oriented approaches.

CONCLUSIONS: ISC-centred regenerative failure provides an integrated framework linking epithelial biology, immunology, and microbiome research in NEC. Restoring ISC function and niche integrity represents a promising therapeutic direction with experimental and translational relevance.},
}

Humans
*Enterocolitis, Necrotizing/pathology/etiology/metabolism/therapy
*Stem Cells/metabolism/cytology
Animals
*Intestinal Mucosa/metabolism/pathology
*Intestines/pathology/cytology
Regeneration
Signal Transduction

@article {pmid42947250,
year = {2026},
author = {Kronsten, VT and Ntuli, Y and Paintsil, EK and Woodhouse, CA and Tranah, TH and Cheung, S and Hagan, D and Merrick, B and Cape, A and Maher, F and Sultana, K and Prossomariti, D and Rodrigues, S and Masterson, C and Hebditch, V and Zamalloa, A and Mullish, BH and Singanayagam, A and Patel, VC and Thursz, MR and , and Goldenberg, SD and Carter, B and Edwards, LA and Shawcross, DL},
title = {PROMISE: a PROspective randomised double-blind parallel group placebo-controlled multicentre trial of faecal MIcrobiota tranSplantation to improve outcomEs in patients with cirrhosis over 24 months-study protocol for a clinical trial.},
journal = {Trials},
volume = {27},
number = {1},
pages = {},
pmid = {42947250},
issn = {1745-6215},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods/adverse effects ; Double-Blind Method ; Multicenter Studies as Topic ; Randomized Controlled Trials as Topic ; Treatment Outcome ; *Liver Cirrhosis/therapy/microbiology ; Prospective Studies ; *Gastrointestinal Microbiome ; Time Factors ; Clinical Trials, Phase III as Topic ; },
abstract = {BACKGROUND: Patients with cirrhosis have reduced gut bacterial diversity and a gut microbiota dominated by pathobionts. These changes, coupled with increased gut permeability and bacterial translocation, increase susceptibility to infection and death. There is also considerable concern that high antimicrobial exposure in the cirrhotic population drives the development of antimicrobial resistance (AMR). We previously performed a randomised feasibility trial of endoscopically administered jejunal faecal microbiota transplant (FMT) slurry derived from stringently screened donors, and showed it to be safe and well-tolerated in patients with cirrhosis (PROFIT Trial: NCT02862249). FMT was associated with reduced enteropathogenic bacteria in the gut, augmented ammonia excretion, ameliorated systemic inflammation, and enhanced innate immune responses to pathogen challenge. The trial was not powered to detect differences in clinical outcomes. The PROMISE study will evaluate the efficacy of lyophilised encapsulated FMT to reduce infection, decompensating events and mortality in patients with cirrhosis secondary to alcohol-related liver disease (ALD), metabolic dysfunction-associated steatotic liver disease (MASLD) cirrhosis and metabolic dysfunction and alcohol-related liver disease (MetALD).

METHODS: The PROMISE study is a phase 3 multicentre, randomised, double-blinded, placebo-controlled trial that will evaluate encapsulated lyophilised FMT in 300 participants with ALD, MetALD or MASLD cirrhosis (Model for End-Stage Liver Disease Sodium (MELD-Na) score 8-16). Participants will be randomly allocated (1:1) to receive FMT or matched placebo capsules every 91 days for 21 months, with 24-month follow-up. The primary endpoint is time-to-infection or decompensating event resulting in presentation to the emergency department or hospitalisation. Secondary endpoints include all hepatic decompensation, all-cause infection, antibiotic usage, incidence of AMR, hospitalisation rates, liver disease severity scores, quality of life scores, Hospital Anxiety and Depression Scale score (HADS), alcohol use, and mortality. Mechanistic endpoints include quantification of plasma bacterial DNA, plasma and faecal cytokines/biomarkers, plasma and faecal metabolome, faecal proteome, faecal microbiome composition and diversity (including resistome) and monocyte and mucosal-associated invariant T (MAIT) cell frequency, phenotype and function. Recruitment commenced in June 2023. Results will be disseminated via peer-reviewed journals, international conferences and patient support groups.

DISCUSSION: The PROMISE study will assess the efficacy and evaluate the mechanisms of action of FMT in patients with ALD, MASLD and MetALD cirrhosis. FMT may provide an alternative non-antibiotic treatment for these patients through ecological reconstitution of microbial balance.

TRIAL REGISTRATION: ISRCTN, ISRCTN17863382. Registered on 25th March 2022, https://www.isrctn.com/ISRCTNISRCTN17863382 .

CLINICALTRIALS: gov NCT06461208. Registered on 4th June 2024, https://clinicaltrials.gov/study/NCT06461208#study-overview .},
}

Humans
*Fecal Microbiota Transplantation/methods/adverse effects
Double-Blind Method
Multicenter Studies as Topic
Randomized Controlled Trials as Topic
Treatment Outcome
*Liver Cirrhosis/therapy/microbiology
Prospective Studies
*Gastrointestinal Microbiome
Time Factors
Clinical Trials, Phase III as Topic

@article {pmid42947262,
year = {2026},
author = {Baxter, N and Plata, G and Bown, L and Shields, J and Augspurger, N and Kumar, A and Susanti, D},
title = {Bacillus probiotic blend modulates ileal microbiome to improve growth performance and prevent necrotic enteritis in broiler chickens.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42947262},
issn = {2524-4671},
abstract = {The intensification of poultry production has led to an increased prevalence of necrotic enteritis (NE), a costly disease caused by Clostridium perfringens, traditionally managed through antibiotic use. However, concerns over antibiotic resistance have driven the search for alternative solutions. This study evaluates the efficacy of a three-strain Bacillus probiotic blend as an alternative for preventing NE in broiler chickens. The three Bacillus strains, Bacillus subtilis ATCC PTA126786, B. velezensis ATCC PTA127064, and B. velezensis ATCC PTA 127065, were selected based on their probiotic attributes, especially their ability to inhibit the growth of C. perfringens and other poultry pathogens. Our results from in vivo experiments showed that dietary supplementation with the probiotic blend significantly reduced NE-associated mortality and improved growth performance metrics such as average daily gain and feed conversion ratio. Metagenomic analyses of ileal contents of chickens supplemented with the Bacillus blend revealed a significant reduction in the abundances of C. perfringens, Enterococcus cecorum, and Eimeria acervulina following NE challenge, despite modest changes in overall microbiome composition. Importantly, the observed probiotic efficacy was strongly associated with the Bacillus strains colonization in the gut, as measured by the Bacillus genome recovery in ileal content samples. These findings highlight the potential of Bacillus-based probiotics as an effective alternative to antibiotics in poultry production, contributing to improved animal health and sustainability.},
}

@article {pmid42947314,
year = {2026},
author = {López, RC and Bonachela, JA and Dominguez-Bello, MG and Manhart, M and Levin, SA and Blaser, MJ and Muñoz, MA},
title = {Towards precision microbiome medicine through ecological network balance.},
journal = {Clinical and translational medicine},
volume = {16},
number = {11},
pages = {},
doi = {10.1002/ctm2.70875},
pmid = {42947314},
issn = {2001-1326},
support = {PID2023-149174NB-I00//Spanish Ministry and Agencia Estatal de Investigación MICIU/AEI/10.13039/501100011033/ ; DMS-2052616//National Science Foundation/ ; },
}

@article {pmid42947318,
year = {2026},
author = {Klištincová, N and Farkas, Z and Bučková, M and Puškárová, A and Kválová, K and Planý, M and Pavlović, J and Koreňová, J and Kuchta, T and Pangallo, D},
title = {Comprehensive Microbiome Profiling of Cheese Production Environments Using Long-Read Sequencing.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {},
doi = {10.1111/1462-2920.70461},
pmid = {42947318},
issn = {1462-2920},
support = {APVV-20-0001//Slovak Research and Development Agency/ ; },
mesh = {*Cheese/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Air Microbiology ; RNA, Ribosomal, 28S/genetics ; },
abstract = {Environmental microbiota in cheese-production facilities can influence both product quality and hygienic conditions. This study characterised airborne and surface-associated microbial communities in production and ripening rooms of eight Slovak bryndza cheese facilities using culture-dependent methods and long-amplicon Nanopore sequencing. Air samples were collected with PBS-filled impingers and surface-swab suspensions were processed for DNA extraction. Bacterial 16S rRNA and fungal 28S rRNA gene amplicons were sequenced and taxonomically classified using Kraken2 and EMU. Community analyses included alpha-diversity estimates, Bray-Curtis ordination, PERMANOVA and supplementary ALDEx2 comparisons. Microbial loads varied among facilities and rooms, with elevated bacterial or fungal counts detected in several ripening environments. Sequencing revealed diverse bacterial and fungal communities comprising ripening-associated microorganisms, environmental contaminants, potential spoilage organisms and low-abundance taxa of hygienic relevance. Surface material had limited effects on overall bacterial and fungal community composition, although selected differences in fungal richness were observed among materials and individual facilities showed distinct microbial profiles. To our knowledge, this is among the first studies applying long-amplicon Nanopore sequencing to jointly characterise airborne and surface-associated bacterial and fungal communities in dairy-production environments. These findings support integrated environmental monitoring that considers microbial load, community diversity and facility-specific production conditions.},
}

*Cheese/microbiology
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Air Microbiology
RNA, Ribosomal, 28S/genetics

@article {pmid42947561,
year = {2026},
author = {Morffe, J and Guiglielmoni, N and Wassey, N and Gueddach, K and Schuster, A and Becker, K and Bast, J and Schiffer, P and Holovachov, O},
title = {Morphogenomic description of Cranifera cranifera (Chitwood, 1932) Kloss, 1960 from captive Blaptica dubia Serville, 1838 cockroach.},
journal = {Journal of helminthology},
volume = {100},
number = {},
pages = {e151},
doi = {10.1017/S0022149X26102569},
pmid = {42947561},
issn = {1475-2697},
support = {dha.2024.4.3-192//Artdatabanken, Sveriges Lantbruksuniversitet/ ; BA 58004-1//Deutsche Forschungsgemeinschaft/ ; BA 58004-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Male ; Phylogeny ; *Cockroaches/parasitology ; Genome, Mitochondrial ; *Genome, Helminth ; *Rhabditida/genetics/anatomy & histology/classification ; Sequence Analysis, DNA ; },
abstract = {Nematodes of the superfamily Thelastomatoidea are found in the digestive system of various arthropods, feeding on their host microbiome. They are sometimes considered to be ecologically intermediate forms between free-living rhabditids and parasitic Spirurina, while phylogenetically they are nested within the latter. In addition to new morphological data on the male morphology, this manuscript presents the first nuclear genome assembly of a thelastomatid species, Cranifera cranifera, using a long-read sequencing approach, making a total of three nuclear genomes available for superfamily Thelastomatoidea. The C. cranifera nuclear genome assembly presented here is 243 Mb long, consists of 7563 contigs, has an N50 of 43 kb, and includes 94% of the BUSCO nematoda_odb12 genes. The mitochondrial genome is 24644 bases long, includes a complete set of protein-coding, rRNA, and tRNA genes, and a repetitive region 9731 bases long, which includes multiple copies of tRNA-Asn(gtt) and tRNA-Lys(ttt). The nuclear assembly also contained two sequence variants of the 28S rRNA and two of the 18S rRNA genes, highlighting the presence of intragenomic variation within the rRNA operon. The newly generated assemblies (nuclear and organelle) will add to a growing body of genomic resources for underrepresented and understudied animal parasitic nematodes from Clade 3, enabling comprehensive studies in their phylogeny and trait evolution in the future.},
}

Animals
Male
Phylogeny
*Cockroaches/parasitology
Genome, Mitochondrial
*Genome, Helminth
*Rhabditida/genetics/anatomy & histology/classification
Sequence Analysis, DNA

@article {pmid42947608,
year = {2026},
author = {Wang, C and Zheng, G and Chen, Y and Zhang, L and Li, X and Ning, P and Quan, M and Wang, D and Xie, Z},
title = {Supraoptimal Mycorrhizal Colonisation Elicits Defence and Depletes Rhizosphere Inhabiting Massilia in Mild Salt‑Stressed Maize: A Split‑Root Comparison of Locally Colonised Roots.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.71000},
pmid = {42947608},
issn = {1365-3040},
support = {KF2024-6//the Open Research Fund Program of State Key Laboratory of Nutrient Use and Management/ ; ZR2024QD021//Shandong Provincial Natural Science Foundation/ ; 32270065//the National Natural Science Foundation of China/ ; tscy20251061//Taishan Industrial Experts Programme/ ; },
abstract = {Environmental conditions, such as light availability, affect the growth‑promoting effects of arbuscular mycorrhizal (AM) symbiosis. However, how the root‑rhizosphere continuum responds when mycorrhizal structures become unsuitable due to environmental deterioration remains unresolved. Using a split‑root system under mild salinity and low light, we generated two AM colonisation states (moderate and supraoptimal) and focused on roots with similar colonisation rates to compare local responses under different whole‑plant symbiotic backgrounds. Supraoptimal colonisation reduced the mycorrhizal growth response compared with moderate colonisation, and this reduction was uncoupled from ion homoeostasis. Root transcriptomics and rhizosphere exudates revealed that supraoptimal colonisation induced jasmonate/ethylene‑mediated defence responses, downregulated carbon transporter genes, and shifted exudation from symbiosis‑supporting lipids/terpenoids toward defence‑related amino acid derivatives. Consequently, supraoptimal colonisation reduced beneficial bacteria, notably Massilia, and simplified co‑occurrence networks. We propose a model in which salt stress and low light drive a host‑mediated "defence‑symbiosis" trade‑off, reducing the mycorrhizal growth response under supraoptimal AM colonisation. These findings provide a mechanistic framework for optimising AM applications in saline systems.},
}

@article {pmid42947638,
year = {2026},
author = {Hofseth, LJ and Bailey, AM and Pine, SR and Giovannucci, EL},
title = {The Modern Exposome in Early-Onset Carcinogenesis.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgag078},
pmid = {42947638},
issn = {1460-2180},
}

@article {pmid42947647,
year = {2026},
author = {Jani, N and Hinsch, V and Joseph, M and Ball, R and Johnson, K and Sikirzzhytski, V and Gowda, V and Ebel, L and Ganesh Babu, S and Hasnie, I and Villanueva, H and Baird, M and Hogan, K and Hofseth, L and Kubinak, J and Peña, MMO},
title = {Multiple Exposures to Antibiotics Affect Tumor Development in a Mouse Model of Early-Onset Colorectal Cancer.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgag077},
pmid = {42947647},
issn = {1460-2180},
abstract = {Early-onset colorectal cancer (EOCRC), defined as colorectal cancer in individuals under 50 years old, is a growing global epidemic, with incidence and mortality rates steadily increasing over the past several decades. Although EOCRC has been linked to established colorectal cancer risk factors, its underlying causes remain poorly understood. We propose that EOCRC may result from exposure to environmental factors, collectively known as the exposome, that have increased globally across EOCRC birth cohorts. Based on our current knowledge of EOCRC, the use of antibiotics is a potential exposome that may increase the risk for EOCRC. We hypothesized that exposure to antibiotics alters the gut microbiota resulting in dysbiosis that promotes inflammation in the distal colon and rectum, leading to increased risk of developing EOCRC. To test this, we examined the effects of repeated exposure to two commonly prescribed classes of pediatric antibiotics on gut microbiome composition, colonic inflammation, and tumor development following exposure to a carcinogen in a mouse model of EOCRC. A/J mice were subjected to multiple rounds of antibiotics followed by treatment with azoxymethane (AOM) to initiate tumor development, and assessment of colon tumor development. Antibiotic treatment induced dysbiosis and both local and systemic inflammation. Subsequent exposure to AOM showed that the two classes of antibiotics had different effects on tumor development in the distal colon and influenced the risk for EOCRC development in different ways.},
}

@article {pmid42947750,
year = {2026},
author = {Jang, YS and Na, H and Lee, HJ and Bang, Y and Ryu, JS and Kim, H and Seo, D and Sim, I and Suh, DH and Jung, ES and Ji, Y and Kim, DH and Choi, HJ and Shin, JU},
title = {Preventive administration of Bifidobacterium animalis subsp. lactis HEM20-01 attenuates the development of atopic dermatitis-like inflammation in mice, along with gut microbial and succinate alterations.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1915780},
pmid = {42947750},
issn = {1664-3224},
mesh = {Animals ; *Dermatitis, Atopic/prevention & control/microbiology/metabolism/immunology ; *Succinic Acid/metabolism ; Mice ; *Gastrointestinal Microbiome/immunology ; Disease Models, Animal ; *Probiotics/administration & dosage ; Male ; Inflammation ; *Bifidobacterium ; Skin/pathology/metabolism/immunology ; Cytokines/metabolism ; Pyroglyphidae ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disorder frequently accompanied by gut dysbiosis and neurobehavioral comorbidities, but the microbial metabolites mediating gut-skin crosstalk remain unclear. We investigated whether preventive administration of Bifidobacterium animalis subsp. lactis HEM20-01 attenuates the development of AD-like phenotypes and characterized the accompanying gut microbiome, succinate, intestinal, and behavioral alterations.

METHODS: HEM20-01 was orally administered to NC/Nga mice beginning 2 weeks before house dust mite (HDM) induction and continued throughout the 4-week induction period. Cutaneous and intestinal inflammation were assessed by histology, gene expression, and multiplex cytokine analysis, and behavior by the open field test. Fecal microbiota composition and metabolite profiles were analyzed by 16S rRNA gene sequencing and gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS)-based metabolomics. Exogenous succinate was administered in an independent MC903-induced dermatitis model to test whether succinate can aggravate these responses.

RESULTS: HDM-induced AD-like mice showed activation of the intestinal succinate receptor 1 (SUCNR1)-tuft cell-IL-25 axis and enrichment of the putative succinate-associated family Rikenellaceae and its genus Alistipes, together with elevated fecal and plasma succinate. Preventive HEM20-01 administration attenuated the development of cutaneous and intestinal inflammatory phenotypes. HEM20-01-treated mice also showed a lower relative abundance of putative succinate-associated taxa (Bacteroidaceae, Rikenellaceae, Christensenellaceae, Bacteroides, and Alistipes), lower circulating succinate levels, reduced activation of SUCNR1-tuft cell-IL-25-related signaling, and attenuated behavioral and hippocampal serotonergic alterations compared with untreated AD-like mice. In a separate MC903-induced dermatitis model, succinate supplementation exacerbated cutaneous and intestinal inflammation.

CONCLUSIONS: Preventive HEM20-01 administration attenuates the development of AD-like phenotypes and associated behavioral alterations, accompanied by changes in gut microbiome composition, lower circulating succinate, and intestinal inflammatory signaling.},
}

Animals
*Dermatitis, Atopic/prevention & control/microbiology/metabolism/immunology
*Succinic Acid/metabolism
Mice
*Gastrointestinal Microbiome/immunology
Disease Models, Animal
*Probiotics/administration & dosage
Male
Inflammation
*Bifidobacterium
Skin/pathology/metabolism/immunology
Cytokines/metabolism
Pyroglyphidae

@article {pmid42947758,
year = {2026},
author = {Kim, J and Carr, KM and Alqudah, S and Bacik, KA and Park, H and Fulmer, CG and Awoniyi, M and Claesen, J and Nemet, I},
title = {Gut microbially produced phenolic acids have differential and sex-dependent effects on host metabolic health.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.12.757096},
pmid = {42947758},
issn = {2692-8205},
abstract = {Gut microbiota-derived metabolites are increasingly recognized as important regulators of host metabolism, but the specific functions of individual metabolites remain poorly understood. We therefore investigated the metabolic effects of two structurally related, phenylalanine-derived microbial metabolites, phenylacetic acid (PAA) and phenylpropionic acid (PPA), in a mouse model of diet-induced obesity. Although clinical studies have linked PAA and its downstream product phenylacetylglutamine to metabolic disease, PAA did not alter body mass or adiposity in this model. Instead, it improved glucose tolerance selectively in male mice and markedly remodeled lipid metabolism in both sexes, reducing circulating triglycerides and acylcarnitines and activating hepatic PPAR-α-associated transcriptional programs associated with fatty acid ω-hydroxylation and peroxisomal lipid metabolism. Despite this extensive metabolic remodeling, PAA did not worsen hepatic steatosis, fibrosis, or markers of liver injury. By contrast, PPA had minimal effects on hepatic metabolic pathways but produced pronounced sex-dependent physiological responses, increasing adiposity in female mice and improving glucose tolerance in male mice. These findings show that structurally related microbial metabolites can have distinct, sex-dependent metabolic effects and highlight the need to define the actions of individual microbiome-derived metabolites when developing targeted therapies for metabolic disease.},
}

@article {pmid42947790,
year = {2026},
author = {Elashi, AA and Hedaya, L and Maggio, V and Naja, K and Rizzo, M and Elrayess, MA},
title = {Insights from multi-omics on GLP-1 receptor agonists in type 2 diabetes and obesity.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1812193},
pmid = {42947790},
issn = {1663-9812},
abstract = {Glucagon like peptide-1 receptor agonists (GLP-1RAs) have revolutionized the management of T2D and obesity. T2D clustering highlights distinct phenotypes that differ in GLP-1RA benefit. While they have markedly improved quality of life for many individuals, converging evidence indicates that genetic variation, metabolomic remodeling, and gut microbiota composition contribute to substantial inter-individual variability in GLP-1RA efficacy and tolerability. GLP-1RAs, in return, can variably affect the metabolome and microbiome composition in treated individuals. This review focuses on human multi-omics GLP-1RA intervention studies, complemented by relevant mechanistic preclinical evidence. Genetic variation in GLP1R, TCF7L2, and other loci has been associated with differences in glycaemic and weight outcomes, although most findings remain preliminary, inconsistent across populations, or not yet replicated. Pharmacometabolomic studies show recurrent of lipid-related pathways including, glycerophospholipids, sphingolipids, ceramides, amino acids, and bile acids, with drug-specific signatures. GLP-1RAs are also associated with changes in gut microbial composition, including taxa such as Akkermansia and Bacteroides, although the direction and clinical significance of these changes vary across studies due to methodological and population heterogeneity. Multi-omics and AI-based models show promise for predicting treatment response by integrating genetic, metabolic, microbial, and clinical data to supporting more effective and individualized therapy and advancing precision medicine.},
}

@article {pmid42947793,
year = {2026},
author = {Çapaş, M and Yavuz Bedir, E and Ergan, K and Arı Gedik, B and Dener, B and Agagündüz, D},
title = {Beyond associations: methodological and conceptual challenges in diet-microbiome research for cardiometabolic risk.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1913324},
pmid = {42947793},
issn = {2296-861X},
}

@article {pmid42947889,
year = {2026},
author = {Tauekelova, A and Katkenov, N and Kozhakhmetov, S and Jarmukhanov, Z and Vinogradova, E and Abdrakhmanov, A and Sailybayeva, A and Bekbossynova, M and Kushugulova, A},
title = {Gut microbiome taxonomic and functional capacity alterations in CHD and HFpEF.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1875692},
pmid = {42947889},
issn = {1664-302X},
abstract = {The gut microbiome is known to modulate metabolic health, yet its role in coronary heart disease (CHD) and heart failure with preserved ejection fraction (HFpEF) remains unclear. In the present study, we profiled the gut microbiome of 234 participants using shotgun metagenomic sequencing across controls (n = 43), individuals with low-risk atherosclerosis (LRAS, n = 23), and patients with CHD + HFpEF (n = 168). Species richness was significantly increased in CHD + HFpEF, with no disruption in taxonomic evenness. LRAS did not diverge significantly in alpha metrics. In contrast, beta diversity analysis demonstrated significant divergence of both LRAS and CHD + HFpEF taxonomic structure from controls, with the greatest divergence in CHD + HFpEF, particularly in older patients. Notably, all differences were attenuated when comparing obese controls and disease groups. However, significant heterogeneity in multivariate dispersion was observed, and a contribution of differences in variation cannot be excluded. Further differential analysis, adjusting for age, BMI, sex, and glucose and lipid profiles, revealed significant associations between specific taxa and CHD + HFpEF, including depletion of the saccharolytic fermenter Bifidobacterium and enrichment of taxa linked to proteolytic or inflammatory metabolism (notably Prevotella and Bilophila), regardless of age and BMI. Subsequent analysis of inferred functional features indicated increased potential for L-citrulline, L-glutamate, L-lysine, and pyrimidine metabolism in CHD + HFpEF. Collectively, the present analysis suggests that CHD + HFpEF is associated with distinct compositional and functional shifts in the gut microbiome. Further longitudinal and interventional research is required to determine which of these microbial features contribute to disease progression and to better characterize underlying mechanisms.},
}

@article {pmid42947928,
year = {2026},
author = {Penner, J and Fanella, S},
title = {La prise en charge des infections bactériennes de la peau et des tissus mous d'origine communautaire et la prévention des récurrences chez les enfants.},
journal = {Paediatrics & child health},
volume = {31},
number = {7},
pages = {828-838},
pmid = {42947928},
issn = {1205-7088},
abstract = {Les infections de la peau et des tissus mous comptent parmi les maladies infectieuses les plus fréquentes chez les enfants. Leur gravité varie entre des infections simples spontanément résolutives et de graves syndromes nécrosants qui exigent la prise d'antibiotiques par voie intraveineuse, une intervention chirurgicale et des soins intensifs. Une barrière cutanée incomplète, découlant d'affections pédiatriques courantes comme l'eczéma et les abrasions cutanées, prédispose à l'infection. Lorsqu'il faut administrer des antibiotiques, le choix et la durée du traitement devraient dépendre des organismes les plus probables en cause, des profils de sensibilité possibles et des différences épidémiologiques selon les régions. Des traitements inappropriés au moyen d'antibiotiques à trop large spectre ou d'une durée trop prolongée sont nuisibles au microbiome, accroissent les effets secondaires des antimicrobiens, perpétuent la colonisation des organismes résistants et précipitent ainsi la résistance aux antimicrobiens. Le présent document de principes fournit aux prestataires de soins une boîte à outils pour la prise en charge optimale des infections bactériennes de la peau et des tissus mous, y compris les épisodes récurrents. Il n'aborde pas les principes thérapeutiques de ce type d'infections chez les patients immunodéprimés ou brûlés, en raison de la prise en charge complexe nécessaire dans ces deux contextes.},
}

@article {pmid42947931,
year = {2026},
author = {Xie, L and Hu, Y and Du, K and Liu, K and Yang, S and Zhou, Y and Zhang, Q and Lan, C},
title = {Gut microbial immunometabolic pathways associated with cardiac arrest risk: genetic evidence and exploratory fecal microbiome profiling.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1931987},
pmid = {42947931},
issn = {2296-634X},
abstract = {BACKGROUND: Cardiac arrest remains difficult to predict, and upstream biological determinants are poorly defined. Gut microbiota can influence host metabolism, immunity and inflammation, but their relevance to cardiac arrest risk remains unclear.

METHODS: We performed bidirectional two-sample Mendelian randomization to prioritize associations between gut microbial traits and cardiac arrest. Two-step mediation analyses were then used to assess whether circulating metabolites, immune cell phenotypes and inflammatory proteins could represent candidate intermediary pathways. An independent exploratory fecal 16S rRNA cohort of patients with cardiac arrest and healthy controls was analysed to provide descriptive post-arrest microbiome context.

RESULTS: Mendelian randomization prioritized 14 candidate gut microbial taxa or microbial metabolic pathways associated with cardiac arrest risk. Mediation analyses identified 55 candidate mediation pathways involving 41 candidate mediators, including 10 pathways with comparatively stronger statistical support based on the joint-significance criterion and the Sobel test. Metabolite-related signals accounted for most candidate mediation pathways, with additional contributions from immune cell phenotypes and inflammatory factors. In the exploratory 16S cohort, diversity and ordination patterns did not show robust group separation, whereas descriptive compositional summaries showed partial taxonomic overlap with signals highlighted by the genetic analyses; these observations were not considered directional or causal validation.

CONCLUSION: These findings prioritize an immunometabolic framework linking gut microbial variation to cardiac arrest risk, with metabolic mediation representing the predominant candidate layer for follow-up study. The exploratory clinical 16S results provide descriptive post-arrest context rather than independent validation, and the genetic findings should be interpreted as candidate associations requiring larger prospective and experimental confirmation.},
}

@article {pmid42947989,
year = {2026},
author = {Sallem, OK},
title = {Phenotype-informed selection of microbiota-directed interventions in irritable bowel syndrome: current evidence and limitations.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1921349},
pmid = {42947989},
issn = {1663-9812},
abstract = {Irritable bowel syndrome (IBS) is a heterogeneous disorder of gut-brain interaction in which bowel-habit subtype, dominant symptoms, post-infectious onset, bile-acid handling, visceral sensitivity, and diet-microbiota interactions may influence the treatment response. This narrative mini-review asks whether available clinical evidence is sufficient to select or sequence microbiota-directed and microbiota-modulating interventions according to Rome bowel-habit subtype and clinically observable dominant symptoms. Literature was identified through PubMed/MEDLINE and major guidelines, systematic reviews, meta-analyses, and pivotal trials published through June 2026. Evidence was interpreted at the level of the exact intervention or product, studied population, target outcome, consistency, independent replication, safety, and guideline position. Mechanistic data support plausible links through fermentation, epithelial barrier function, mucosal immunity, bile-acid metabolism, visceral sensitivity, and gut-brain signaling, but mechanistic or microbiome changes do not establish the clinical efficacy. Rifaximin has the clearest replicated and guideline-supported role in IBS with diarrhea, while soluble fiber has guideline support for global or constipation-associated symptoms. Evidence for individual probiotics, postbiotics, partially hydrolyzed guar gum, galactooligosaccharides, and fermented matrices remains product-specific or emerging and is rarely independently replicated. Symptom improvement with a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (low-FODMAP diet) does not establish microbiota mediation. Fecal microbiota transplantation (FMT) and microbiome-guided prescribing remain investigational. Current evidence, therefore, supports only limited phenotype-informed matching and does not establish a validated treatment sequence or microbiome-defined therapeutic phenotype.},
}

@article {pmid42948109,
year = {2026},
author = {Kumar, S and Meena, KK and Sorty, AM and Wakchaure, GC and Kumar, M},
title = {Editorial: Microbiome-driven strategies for alleviation of biotic and abiotic stresses in agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {2004577},
pmid = {42948109},
issn = {1664-302X},
}

@article {pmid42948196,
year = {2026},
author = {Nguyen, LT and Lamb, HJ and Ross, EM and Mahony, TJ and Morgan, D and Hayes, BJ},
title = {Simultaneous traceability and microbiome characterisation across beef supply chains with Oxford Nanopore sequencing.},
journal = {Translational animal science},
volume = {10},
number = {},
pages = {txag160},
pmid = {42948196},
issn = {2573-2102},
abstract = {The advent of portable sequencing technologies, such as Oxford Nanopore Technologies (ONT), has created opportunities for real-time traceability across food supply chains, specifically for beef products from paddock to plate. The stability of DNA across an animal's lifespan and its presence in carcasses and beef make a DNA-based system an effective means for traceability from paddock to restaurant or supermarket, circumventing the risk of tag loss and potentially preventing cattle theft, substitution, and food fraud. In this study, we investigated whether long-read Nanopore sequencing can identify the animal of origin at different stages of the supply chain, including in the feedlot, the abattoir processing plant, and the butcher shop. Twenty-one animals were sampled at three different levels of the supply chain: (1) hair samples at the feedlot, (2) muscle samples at the abattoir and (3) unknown muscle cuts from the butcher shop. When sampled at different points across the supply chain, samples from the same animals matched with 99% to 100% identity, while samples from different animals showed good discrimination. This study also illustrated the potential of ONT to detect microorganisms in the same dataset, thereby characterising the relative abundance of bacterial communities across the supply chain. Despite the high sequencing cost, the portability of the Nanopore technologies, requiring only a sequencer of the size of a small phone, is a significant advantage and suggests that it could be deployed for traceability purposes at various points in the supply chain, such as race, processing plant, butchers, supermarkets and restaurants. Future validation of the complete extraction and sequencing workflow under field conditions will be essential to confirm practical applicability in these settings.},
}

@article {pmid42948281,
year = {2026},
author = {Zhu, L and Deng, Z and Mou, W and Deng, G and Lu, H and Xu, L and Lin, S and Huang, H and Wu, K and Liang, Q and Li, H and Zheng, Z and Lin, A and Luo, P},
title = {Rethinking the tumor microbiome: Methodological challenges and a framework for rigorous research.},
journal = {mLife},
volume = {},
number = {},
pages = {},
pmid = {42948281},
issn = {2770-100X},
abstract = {The intratumoral microbiome, as an essential component of the tumor microenvironment, has attracted increasing attention in recent years. The tumor microbiota displays an intricate interplay with its biological behaviors. However, emerging controversies, including the retraction of Poore et al.'s article, highlight significant challenges within this field. These issues extend beyond questions of reliability in this particular work to challenge fundamental theoretical assumptions and methodological validity across the entire field of tumor microbiome research, profoundly impacting its future direction. Here, we systematically summarize and discuss the current challenges and limitations in tumor microbiome research. We further propose a series of practical optimization strategies and solutions, from microbial quantification to functional experiments, providing a comprehensive framework covering the entire workflow of tumor microbiome analysis. With ongoing technical progress and standardized protocols, tumor microbiome research is poised to deliver novel insights into tumor biology and contribute to the development of improved therapeutic strategies.},
}

@article {pmid42931362,
year = {2026},
author = {Deleemans, JM and Mina, R and Spiropoulos, A and Lawal, OA and Reimer, RA and Karim, S and Richardson, B and Carlson, LE},
title = {The Chemo-Gut Probiotic Trial Protocol: A Double-Blind Randomized Controlled Trial Investigating the Effects of a Multi-Strain Probiotic on Gut Microbiota, Gastrointestinal Symptoms, and Psychosocial Health Among Cancer Survivors.},
journal = {Methods and protocols},
volume = {9},
number = {5},
pages = {},
pmid = {42931362},
issn = {2409-9279},
support = {//Alberta Cancer Foundation/ ; },
abstract = {Background: Survivors of cancer experience chronic gastrointestinal (GI) and psychosocial health symptoms and reduced gut microbial diversity. This may compromise their long-term health and wellbeing. No studies have investigated probiotics for managing both GI and psychosocial symptoms together, or their effects on the composition of the gut microbiota in post-treatment cancer survivors. Aims: To investigate the effects of a probiotic vs. placebo on (i) abdominal pain and depressive symptoms (primary outcomes); (ii) (a) GI (i.e., gas/bloating, diarrhea, and constipation), and psychosocial (i.e., anxiety, cognitive function, and fatigue) symptoms and (b) gut microbiota composition; and (iii) relationships between bacteria and GI and psychosocial symptoms. Methods: This double-blind, placebo-controlled, two-arm, randomized trial will recruit N = 66 participants allocated 1:1 to the probiotic or placebo group for a 12-week trial. Adult survivors diagnosed with a solid tumor or blood cancer who have completed chemotherapy within the last 5 years and show elevated GI or psychosocial symptoms will be included. The probiotic capsule contains a blend of Lacticaseibacillus rhamnosus, Lactobacillus helveticus, and Bifidobacterium animalis subsp. lactis strains, ingested orally once daily. Stool samples will be collected at baseline and week 12 and analyzed using 16S rRNA gene sequencing. GI and psychosocial surveys will be completed at baseline and at weeks 6 and 12. Descriptive statistics, frequencies, paired-samples t-tests, linear mixed models, and Spearman's correlational analyses will be used. Conclusions: We explore a novel, microbiota-based intervention for chronic GI and psychosocial symptoms following cancer treatment. Our findings and commitment to person-centered knowledge translation via creating informational materials will enable people to make informed decisions about their health.},
}

@article {pmid42931636,
year = {2026},
author = {Wang, Y and Yu, W and Kanda, K and Iwata, H and Guo, J},
title = {In Ovo Exposure to Phenanthrene Promotes Antimicrobial Resistance Genes and Hemolysin Virulence Factor in Guts of Chicken Embryos.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931636},
issn = {2305-6304},
support = {42571089//National Natural Science Foundation of China/ ; 2026JC-YXQN-119//Natural Science Basic Research Program of Shaanxi/ ; },
abstract = {Antimicrobial resistance genes (ARGs) are increasingly recognized as emerging environmental contaminants that threaten ecological integrity and animal health. Polycyclic aromatic hydrocarbons (PAHs) are widespread pollutants that accumulate in the environment and have been detected in wild bird eggs. Although PAHs have been shown to accelerate ARG dissemination in environmental matrices, their influence on ARG dynamics in birds is unclear. Therefore, it is hypothesized that exposure to elevated levels of PAHs promotes the propagation and enrichment of ARGs in the avian gut. In this study, chicken embryos at Hamburger-Hamilton Stage 1 (HHS 1) were exposed in ovo to phenanthrene (PHE; 1, 100, and 400 nmol/g egg), and the toxic effects were evaluated. High PHE exposure significantly reduced embryonic tarsus length by 14.81% and increased the liver somatic index (LSI) by 26.97%. Functional annotation based on the Virulence Factor Database (VFDB) showed that the relative abundance of hemolysin, a microbial virulence factor associated with gastrointestinal microorganisms, was significantly elevated in the high-PHE group. In a Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, genes involved in nucleotide excision repair (NER) and basal transcription factor (BTF) pathways showed significantly lower relative abundance following high-dose exposure. Additionally, ARGs related to polymyxin and pleuromutilin resistance were significantly enriched in the high-exposure group. Partial least squares path modeling (PLS-PM) indicated that ARG enrichment was jointly shaped by multiple factors. PHE may be directly associated with ARG proliferation or may act indirectly through mobile genetic elements (MGEs), whereas bacterial community abundance might be linked to the potential dissemination of ARGs given its significant positive association with MGEs. Collectively, these findings provide correlative evidence that PHE exposure is associated with increased ARG abundance in avian organisms and highlight the need for an integrated evaluation of PAH-associated hazards to avian health.},
}

@article {pmid42931684,
year = {2026},
author = {Miao, Z and Yuan, F and Zou, Q and Yuan, C and Zheng, Y and Wang, K and Lyu, B and Luo, Z and Jiang, M},
title = {Stage-Associated Plant-Soil-Microbiome Patterns and Rhizosphere Pb-Zn Stabilization in Indocalamus decorus at a Mining Site.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931684},
issn = {2305-6304},
support = {Grant No. 32371976//National Natural Science Foundation of China/ ; grant numbers 202611KY0005//Funding for the Construction of the Chengdu National Botanical Garden System/ ; },
abstract = {Indocalamus decorus is a perennial bamboo with potential for phytomanagement, but its Pb-Zn partitioning and associated microbiome under field co-contamination remain unclear. Parallel plantings were established at a Pb-Zn mining site and the provenance site. Plant nutrients, rhizosphere properties, Pb-Zn concentrations and soil fractions, and bacterial and fungal communities were evaluated across four developmental stages at the mining site; shoot initiation was also evaluated at the provenance site. At shoot initiation, mine-site plants had lower organ P concentrations, whereas root N was maintained. Rhizosphere nutrient availability was relatively high during shooting. Pb accumulated mainly in roots, while Zn was transferred more readily to culms; organ-specific bioconcentration factors for both metals remained below 1. Compared with bulk soil, rhizosphere soil contained lower DTPA-extractable Pb and Zn, smaller acid-soluble/exchangeable fractions, and larger residual fractions. Sample compartment explained 60.8% and 66.9% of bacterial and fungal community variation, respectively. Rhizosphere fungi were associated with a broader range of metal fractions and plant metal-distribution indices than other microbial compartments. These results indicate root-dominated Pb retention, reduced rhizosphere Pb-Zn lability, and compartment-specific microbial associations, supporting further evaluation of I. decorus as a candidate for phytostabilization-oriented management of Pb-Zn-contaminated mine soils.},
}

@article {pmid42931886,
year = {2026},
author = {Zeber-Lubecka, N and Ciebiera, M},
title = {cFrom microbiota to microbiome - how should gynecologists interpret cervicovaginal microbial studies?.},
journal = {Ginekologia polska},
volume = {},
number = {},
pages = {},
doi = {10.5603/gpl.115313},
pmid = {42931886},
issn = {2543-6767},
}

@article {pmid42931891,
year = {2026},
author = {Zhou, Z and Zhang, C and Yin, L},
title = {IgA nephropathy: gut microbiome insights and unmet needs in pediatrics.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {42931891},
issn = {1432-198X},
abstract = {Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulopathy worldwide and a leading cause of chronic kidney disease and kidney failure in children and young adults. Well-established pathogenic pathways include genetic susceptibility, intrinsic B-cell glycosylation abnormalities, complement activation, and immune dysregulation, and accumulating evidence further places the gut microbiome at the center of IgAN pathogenesis via the gut-kidney axis. A critical evidence gap defines the field: no prospective cohort has characterized the gut microbiome in pediatric primary IgAN. This conceptual narrative review synthesizes well-validated mechanistic data from adult cohorts-most notably microbial-mediated IgA1 deglycosylation-and extrapolates these findings to pediatric populations through the lens of the developmental entanglement framework, which accounts for the synchronized maturation of the gut microbiome, mucosal immunity, and renal structure in early life. Using an adapted Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach, we separately rate evidence quality for adult and pediatric populations, explicitly mark all pediatric extrapolations as unvalidated, and cautiously appraise indirect evidence from pediatric IgA vasculitis with nephritis (IgAVN). We further evaluate the translational potential of microbiome-guided strategies, and conclude with a pragmatic, stepwise research agenda centered on foundational cohort studies and emerging technologies to address the evidence gap. Closing this deficit will enable the development of non-invasive biomarkers and safe, mechanism-targeted therapies to prevent progressive renal failure in children with IgAN.},
}

@article {pmid42932086,
year = {2026},
author = {Chawda, D and Tyagi, N and Mubashra, and Srivastava, A and Shukla, A and Srivastava, S},
title = {Gut microbiome in colorectal cancer: a dual regulator of tumor biology and therapeutic response.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42932086},
issn = {1874-9356},
abstract = {Colorectal cancer is one of the most prevalent malignancies and a major cause of cancer-related mortality worldwide. It remains a significant health concern, with an alarming rise in early-onset colorectal cancer cases in younger populations. Many factors are reported to have been responsible for its onset, progression, and metastasis, among which the gut microbiome is found to be a crucial one. Dysbiosis among these gut microbes impacts normal cellular functions and homeostasis, which may lead to cancer. Under unfavourable conditions biological processes such as cell differentiation, proliferation, migration, and apoptosis get disrupted and give rise to pathological traits such as invasion and metastasis. Emerging evidence indicates a rather significant role of the gut microbiome in this transition, influencing both onset and progression. Over the past few decades, our understanding of microbiome-cancer interaction has evolved considerably, yet effective microbiome-based therapies remain limited. This review highlights how these microbes modulate normal biological functions to pathological ones, and we further discuss current microbiome-based therapies along with their future prospects.},
}

@article {pmid42932096,
year = {2026},
author = {Latif, MZ and Deng, M and Asghar, N and Kong, L and Kousar, S and Zhang, H and Rehman, SU and Jiang, Y and Humza, M and Lu, C and Ding, X},
title = {Plant resilience: harnessing bioactive compounds for sustainable disease protection.},
journal = {Stress biology},
volume = {6},
number = {1},
pages = {},
pmid = {42932096},
issn = {2731-0450},
support = {32272557//National Natural Science Foundation of China/ ; 32072500//National Natural Science Foundation of China/ ; ZR2022ZD23//Natural Science Foundation of Shandong Province/ ; ZR2024ZD07//Natural Science Foundation of Shandong Province/ ; Y20240208//National Foreign Expert Program/ ; },
abstract = {Plants have evolved complex phytochemical and immune defense mechanisms in response to pathogen invasion. Plants deploy phytochemical defense system-signaling molecules, secondary metabolites, antimicrobial proteins and peptides-to mitigate the pathogens they encounter. Pathogens have developed strategies-effector proteins, efflux pumps and detoxification mechanisms-to manipulate or overcome plant defenses. This review offers insights into how these bioactive compounds are biosynthesized and activated following pathogen recognition. We provide an overview of the dynamic crosstalk between PTI and ETI and their role in optimizing plant defense. Additionally, we discuss the potential of advanced genetic engineering approaches, nanocarrier-mediated elicitor delivery, and microbiome engineering to enhance these natural defenses. Finally, we address the technical bottlenecks of engineering plant immunity and provide a roadmap for future research directions. This review provides a stronger mechanistic foundation for breeding crops with durable, broad-spectrum resilience for sustainable crop protection.},
}

@article {pmid42932263,
year = {2026},
author = {Mogey, R and Goodacre, R and Curtis, F and Maden, M and Edwards, KL},
title = {Metabolomics in the wild: A scoping review of non-invasive methods for understanding vertebrate wildlife health and success.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0359720},
pmid = {42932263},
issn = {1932-6203},
mesh = {Animals ; *Metabolomics/methods ; *Animals, Wild/metabolism ; *Vertebrates/metabolism ; Conservation of Natural Resources ; },
abstract = {An increase in metabolomics research over the last decade has expanded species-specific knowledge of biological processes, but has primarily focused upon humans, domesticated and model animal species. Recent advances, particularly around data management pipelines for untargeted studies, make the field more accessible to disciplines outside those embedded in analytical chemistry, including wildlife conservation. To establish the breadth of existing wild vertebrate animal metabolomic research, specifically utilising non-invasive sampling, this scoping review establishes: (1) general trends in publication numbers; (2) coverage of wildlife taxonomic groups and species; (3) subject numbers and sample size; (4) non-invasive sample types; (5) metabolomic techniques utilised; (6) the context of current literature and (7) conservation implications. This scoping review was conducted following the JBI methodology and reported in accordance with PRISMA-ScR; searches were conducted using PubMed, Scopus, Web of Science and supplemented with Google Scholar; following screening, 83 peer-reviewed original research papers were identified using predefined criteria and data extracted. The most popular areas of research were physiology and reproduction (30%) and diet and nutrition (27%). Although most publications focused on a single species, there were 11 multi-species publications, resulting in metabolomics data for 93 species. A large proportion of which, 72%, were mammalian, and of these, 52% are currently listed at risk of extinction on the IUCN Red List. With over 60% of all publications published between 2022-2025, non-invasive vertebrate wildlife metabolomics appears to be gaining traction as a tool in wildlife physiology research. However, future research would benefit from alignment with model animal metabolome research experimental design, as few studies included the consideration of metabolite extraction optimisation, storage conditions, the use of integrated omics platforms beyond microbiome analysis and consideration of statistical power, particularly in respect to intra-individual variation and the characterisation of species-specific metabolomes.},
}

Animals
*Metabolomics/methods
*Animals, Wild/metabolism
*Vertebrates/metabolism
Conservation of Natural Resources

@article {pmid42932302,
year = {2026},
author = {Hiratsuka, D and Iki, A and Kinoshita, M and Doi, Y and Kato, O and Oshima, K and Hiraoka, T and Matsuo, M and Ichinose, M and Makabe, T and Izumi, G and Harada, M and Hirota, Y and Nabeta, M},
title = {Oral versus vaginal Lactobacillus supplementation for endometrial dysbiosis: A paired pre and post-endometrial microbiome study.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0360619},
pmid = {42932302},
issn = {1932-6203},
mesh = {Female ; Humans ; *Dysbiosis/microbiology/therapy/drug therapy ; *Lactobacillus/physiology ; *Endometrium/microbiology ; Administration, Oral ; *Microbiota ; *Probiotics/administration & dosage/therapeutic use ; *Vagina/microbiology ; Retrospective Studies ; Adult ; Administration, Intravaginal ; },
abstract = {Infertility is a global health challenge, and impaired endometrial receptivity remains an important contributor to treatment failure. Endometrial dysbiosis, characterized by a low proportion of Lactobacillus in the endometrial microbiota, has been proposed as a potentially modifiable factor that may affect endometrial receptivity and fertility, and treatment with Lactobacillus-containing probiotics is emerging as a promising therapeutic approach. However, the optimal route of Lactobacillus supplementation remains unclear. We compared oral versus vaginal supplementation using the same Lactobacillus-containing formulation as an adjunct to standardized doxycycline/metronidazole therapy and continued oral lactoferrin in patients with baseline endometrial Lactobacillus <10%, based on paired microbiome profiling of endometrial samples (aspirated intrauterine fluid and endometrial tissue). In this single-center retrospective cohort study, thirty-two patients underwent paired endometrial microbiome testing before and after 30 days of supplementation (oral, n = 18; vaginal, n = 14). In the vaginal group, the median endometrial Lactobacillus proportion increased from 0.05% [0.00-0.20] to 99.15% [70.45-100.00] (p = 0.001), whereas in the oral group it increased from 0.00% [0.00-0.18] to 0.30% [0.03-66.33] (p = 0.005). The median change was greater with vaginal versus oral supplementation (+98.90% [70.45-99.80] vs + 0.25% [0.03-66.33], p < 0.001). Post-treatment Lactobacillus ≥80%, used as an exploratory marker of marked microbiota improvement, was observed in 9/14 patients (64%) in the vaginal group and 3/18 (17%) in the oral group (p = 0.010). Exploratory reproductive outcomes were limited by the small sample size and did not define a reliable clinical threshold. These findings suggest that, within this combined treatment regimen, vaginal Lactobacillus supplementation may provide a greater route-associated additional improvement in endometrial microbiota profiles than oral administration.},
}

Female
Humans
*Dysbiosis/microbiology/therapy/drug therapy
*Lactobacillus/physiology
*Endometrium/microbiology
Administration, Oral
*Microbiota
*Probiotics/administration & dosage/therapeutic use
*Vagina/microbiology
Retrospective Studies
Adult
Administration, Intravaginal

@article {pmid42932307,
year = {2026},
author = {Li, J and Özkurt, AG and Baertschi, I and Wang, J and Aeschlimann, L and Goepfert, C and Misselwitz, B and Sokollik, C and Yilmaz, B},
title = {Baseline microbial ecology encodes probiotic responsiveness through distinct metabolic and network configurations.},
journal = {Cell reports},
volume = {45},
number = {11},
pages = {118228},
doi = {10.1016/j.celrep.2026.118228},
pmid = {42932307},
issn = {2211-1247},
abstract = {Probiotic efficacy in inflammatory bowel disease varies widely between individuals, and the sources of that variability remain poorly understood. D-lactate is a microbiota-derived metabolite that accumulates during intestinal inflammation and is associated with epithelial barrier dysfunction, which motivated our use of a consortium selected to contribute none of it. Here we show that its benefit is not an intrinsic property of the administered strains but is determined by the pre-existing ecological state of the recipient microbiome. Across three independent mouse resources, preventive administration reduced disease severity and histopathological damage only where baseline communities carried higher diversity and more complex co-occurrence architecture; in those animals the consortium preserved community structure and metabolic output, restoring disease-disrupted metabolites, and selectively raising butyrate and propionate. Sustained exogenous D-lactate did not abolish protection, placing D-lactate as a tractable readout of ecological restoration rather than its effector. Responsiveness is encoded in the baseline microbiota and predictable before intervention, establishing probiotic efficacy as a stratifiable property of the host microbiome.},
}

@article {pmid42932319,
year = {2026},
author = {Perry, NS and Cavalcanti, ARO and Hayes, KA and Yeung, NW and Sischo, DR and Shizuru, SH and Antonsen, AK and Haubner, ML and Ah Cook, AN and Hee, CE and Hill, MMY and Krenteras, CT and Maruno, TMB and Nakasone, RH and Rosenbush, HK and Stiefel, SM and Sullivan, AJ and Meyer Iii, WM},
title = {Examining microbial assemblage differences on plants preferred and avoided by threatened Hawaiian land snails to identify important food resources.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0361108},
pmid = {42932319},
issn = {1932-6203},
mesh = {Animals ; *Snails/microbiology/physiology ; Hawaii ; *Endangered Species ; Fungi/classification/isolation & purification ; Feeding Behavior ; Bacteria/classification/isolation & purification ; },
abstract = {The Hawaiian Islands, an isolated oceanic archipelago in the Pacific, had one of the world's most spectacular land snail radiations. Unfortunately, only 35% of the 759 Hawaiian snail species remain, with >100 species threatened with imminent extinction. Though many extant Hawaiian snails are arboreal and are known to eat microbes on the surface of plants, our current understanding of which microbes compose arboreal Hawaiian snails' diets remains rudimentary. Here, we examined microbial assemblages (bacterial and fungal) on plants previously identified as preferred and avoided by a diverse assemblage of arboreal snails at three sites in wet and mesic forests on O'ahu, Hawai'i, USA, to identify microbes that may form the foundation of Hawaiian arboreal snails' diets. At Mt. Ka'ala, we also investigated if microbial assemblages change across years. Across sites, microbial assemblages differed on preferred and avoided plants. While differences across sites can complicate the process of identifying key microbes, microbes with elevated abundances on preferred plants across sites are likely important food resources. Using this approach, we identified bacterial and fungal OTUs that we hypothesize form important components of Hawaiian arboreal snails' diets. While we found that microbial assemblages differed among years at Mt. Ka'ala, differences between preferred and avoided plants remained consistent across years. Expanding a snail plant preference-microbiome framework across multiple forest types is a crucial step in understanding arboreal snail diets as microbial taxa enriched on preferred plants across sites may be meaningful components of snail-associated microbial resources. Microbial taxa enriched on preferred plants are not presented here as confirmed dietary components, but as experimentally tractable candidates that should be further evaluated in laboratory trials. This information is foundational to improving captive rearing of critically endangered snails and informing habitat quality assessments for the many threatened Hawaiian snails.},
}

Animals
*Snails/microbiology/physiology
Hawaii
*Endangered Species
Fungi/classification/isolation & purification
Feeding Behavior
Bacteria/classification/isolation & purification

@article {pmid42932354,
year = {2026},
author = {Otto, M and Camus, L and Busche, T and Bünte, J and Hütten, A and Persicke, M and Klages, LJ and Kalinowski, J and Heilbronner, S and Rückert-Reed, C},
title = {Characterization of Corynebacterium species isolated from nasal swabs of healthy volunteers: description of Corynebacterium nasorum sp. nov., Corynebacterium tardum sp. nov., Corynebacterium tuingiense sp. nov., Corynebacterium limaceinasi sp. nov. and Corynebacterium kefirresidentii sp. nov.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.007292},
pmid = {42932354},
issn = {1466-5034},
mesh = {*Corynebacterium/classification/genetics/isolation & purification/chemistry ; Humans ; Bacterial Typing Techniques ; *Phylogeny ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Sequence Analysis, DNA ; Fatty Acids/chemistry ; Genome, Bacterial ; Healthy Volunteers ; Base Composition ; Adult ; *Nose/microbiology ; },
abstract = {Members of the genus Corynebacterium are common constituents of the human nasal microbiota but their cultivable diversity remains incompletely represented in taxonomic and diagnostic databases. Ten coryneform strains isolated from nasal swabs of seven healthy adults were characterized using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing, phylogenomic inference, overall genome relatedness indices, phenotypic testing and chemotaxonomic analyses. MALDI-TOF MS initially assigned most strains to Corynebacterium tuberculostearicum or Corynebacterium accolens, whereas genome-based analyses resolved the strains into five distinct species-level lineages. The lineages represented by strains LaCa116[T], LaCa142[T] and LaCa191[T] were clearly differentiated from their closest related type strains by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below accepted species-level thresholds. Strains LaCa7[T] and LaCa117[T] represented closely related but distinguishable genomic lineages, with an ANI value of 95.9% and a dDDH value of 66.4%. Strain LaCa117[T] was closely related to strain SB, to which the effectively but not validly published name 'Corynebacterium kefirresidentii' had previously been applied. Phenotypic and chemotaxonomic characteristics supported the genomic groupings and placement of the strains within the genus Corynebacterium. These findings reveal previously unrecognized diversity among cultivable nasal corynebacteria and demonstrate that routine MALDI-TOF MS identification may be unreliable when suitable reference spectra are absent. Based on the integrated taxonomic evidence, the names Corynebacterium nasorum sp. nov. (type strain LaCa7[T]=DSM 119349[T]=LMG 33882[T]), Corynebacterium kefirresidentii sp. nov. (type strain LaCa117[T]=DSM 119343[T]=LMG 33886[T]), Corynebacterium tuingiense sp. nov. (type strain LaCa142[T]=DSM 119342[T]=LMG 33884[T]), Corynebacterium limaceinasi sp. nov. (type strain LaCa191[T]=DSM 119341[T]=LMG 33883[T]) and Corynebacterium tardum sp. nov. (type strain LaCa116[T]=DSM 119344[T]=LMG 33885[T]) are proposed.},
}

*Corynebacterium/classification/genetics/isolation & purification/chemistry
Humans
Bacterial Typing Techniques
*Phylogeny
DNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Sequence Analysis, DNA
Fatty Acids/chemistry
Genome, Bacterial
Healthy Volunteers
Base Composition
Adult
*Nose/microbiology

@article {pmid42933036,
year = {2026},
author = {Shang, C and Zhu, Z and Liu, Y and Sun, S and Dong, K and Xu, C},
title = {Cascade-targeting elimination of tumor-resident intracellular bacteria with biomimetic nanomedicine for enhancing breast cancer immunotherapy.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {270},
number = {},
pages = {116257},
doi = {10.1016/j.colsurfb.2026.116257},
pmid = {42933036},
issn = {1873-4367},
abstract = {Fusobacterium nucleatum as a typical tumor-resident intracellular bacteria can colonize in breast cancer for promoting immunosuppression and inducing tumor metastasis. Herein, we developed a biomimetic nanomedicine (HM-GZNC) for cascade-targeting elimination of tumor-resident intracellular bacteria and enhancing breast cancer immunotherapy. HM‑GZNC was composed of a ZIF‑8‑derived nanozyme loaded with glycyrrhetinic acid (GA) and coated with a hybrid cell membrane. The hybrid cell membrane from Fusobacterium nucleatum-activated RAW264.7 macrophages and 4T1 breast cancer cells endowed HM‑GZNC with a cascade-targeting capability. Upon NIR irradiation, HM‑GZNC exhibited the enhanced peroxidase-like activity, controlled drug release, and excellent photothermal effects for synergistic killing intratumoral bacteria and breast cancer cells. In vivo experiments showed that HM‑GZNC could precisely localize within tumors for effectively eliminating Fusobacterium nucleatum and inducing immunogenic cell death (ICD). Moreover, HM‑GZNC could promote dendritic cell maturation and antigen presentation, improve the infiltration of CD8[+] and CD4[+] T cells along with the secretion of pro‑inflammatory cytokines for enhancing antitumor immune responses and inhibiting metastasis. The biomimetic nanomedicine provided a novel strategy for developing tumor-associated microbiome-targeted therapies against breast cancer.},
}

@article {pmid42933211,
year = {2026},
author = {Shah, OU and Shuchen, F and Jia, W and Hongfei, S and Luyao, C and Wenjie, Z and Wenping, X},
title = {Integrated multi-omics analysis reveals coordinated root and rhizosphere responses underlying AMF-mediated drought tolerance in kiwifruit.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128791},
doi = {10.1016/j.micres.2026.128791},
pmid = {42933211},
issn = {1618-0623},
abstract = {Drought stress substantially restricts kiwifruit (Actinidia spp.) growth and productivity, yet the mechanisms through which arbuscular mycorrhizal fungi (AMF) promote drought tolerance remain insufficiently understood. To address this gap, root physiological and molecular analyses were integrated with multi-omics profiling of the rhizosphere microbiome to investigate AMF-mediated drought responses under well-watered and drought-stress conditions. Under drought stress, AMF inoculation improved plant growth, root development, cellular ultrastructure, and physiological performance. More importantly, root omics analysis revealed coordinated regulation of drought-responsive pathways involving glutathione metabolism, amino acid biosynthesis, phytohormone regulation, and energy metabolism. Beyond these plant responses, AMF inoculation altered bacterial and fungal community composition, enriched potentially beneficial taxa, and increased rhizosphere network connectivity under drought stress. Within the restructured microbiome, we identified an AMF-specific drought-responsive amplicon sequence variant (ASV) module composed primarily of bacterial taxa and associated with cross-kingdom microbial interactions. Integrated microbial-metabolite network analysis further identified a metabolite feature annotated as 1-piperideine as a candidate associated with selective microbial recruitment in AMF-colonized rhizospheres. Together, these findings suggest that AMF-associated drought tolerance in kiwifruit involves complementary changes in plant physiology, root molecular responses, and rhizosphere microbiome assembly. A mechanistic basis is thereby provided for developing AMF-based strategies to improve kiwifruit production under increasing water limitation.},
}

@article {pmid42933357,
year = {2026},
author = {Laila, U and Zeng, Y and Tan, C and Nazir, A and Abbas, T and Bareen, FE and Kammann, C and Farwa, U and Liang, Y},
title = {Zn-modified biochar coupled with biological nitrification inhibitors mitigates nitrous oxide emissions from alkaline soil through modulation of ammonia-oxidizing microorganisms.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131238},
doi = {10.1016/j.jenvman.2026.131238},
pmid = {42933357},
issn = {1095-8630},
abstract = {Biochar (BC) has generally been employed to mitigate the nitrous oxide (N2O) emissions from agricultural soils, but its response is soil-dependent. Thereby, in soil with proficient nitrification tendency, Zn-modified BC coupled with biological nitrification inhibitors (BNIs) could be more effective in mitigating N2O emissions. The effects of coupled application of Zn-modified biochar and BNIs on N2O emission and its underlying microbial mechanism remain largely unknown. In our study, a 24-day incubation experiment was established representing nine treatments; with three biochars amendments using three settings of BNIs, referred to as: 1) control (without amendment/inhibitor, 2) control with methyl 3-(4-hydroxyphenyl) acrylate -MHPA, 3) control with methyl 3-(4-hydroxyphenyl) Propionate-MHPP, 4) pristine BC without inhibitor, 5) pristine BC with MHPA, 6) pristine BC with MHPP, 7) Zn-modified BC without inhibitor, 8) Zn-modified BC with MHPA, 9) Zn-modified BC with MHPP, all at agronomically recommended dosage. N dynamics were evaluated following the addition of urea. The inclusion of Zn-modified BC in combination with MHPA and MHPP substantially reduced N2O emissions by 94.52% and 96.85% relative to control. Quantification of N-cycling genes indicated that the treatment without BC amendment stimulated the growth of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the entire incubation period. The input of Zn-BC with MHPA and MHPP substantially inhibited the population of AOA and AOB. LEfSe cladogram elucidated the distinct shift in bacterial assemblage across the treatments. Overall, our results demonstrated that Zn-modified BC + MHPP played a key role in the dynamics of ammonia-oxidizing functional microbiome and N turnover, potentially considerably mitigating N2O emissions.},
}

@article {pmid42933395,
year = {2026},
author = {Pedersen, TK and Jain, T and Segerstolpe, Å and Lin, C and Shih, AR and Yuan, L and Ashenberg, O and Kaper, ME and Twardus, SW and Ricciardi, R and Lau, H and Moon, JJ and Brix, S and Xavier, RJ and Graham, DB},
title = {A microbiome-reactive TMIGD2[hi] Th17 subset is spatially enriched at the intestinal epithelium and expanded in inflammatory bowel disease.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2026.09.026},
pmid = {42933395},
issn = {1097-4180},
abstract = {Subsets of intestinal CD4[+] T cells directly recognize commensal bacteria and coordinate tolerance versus protective immunity. Our limited understanding of CD4[+] T cell specificities and corresponding functional phenotypes has created a barrier to deciphering the mechanisms of mucosal homeostasis and inflammation mediated by the adaptive immune system. To address this, we leveraged an immunodominant Bacteroidetes epitope in SusC to perform single-cell profiling of the SusC-specific and total CD4[+] T cell landscapes in intestinal tissues of patients with inflammatory bowel disease (IBD). By analyzing phenotypes and T cell receptor specificities in parallel, we uncovered phenotypic diversification of T helper 17 (Th17) cells in IBD and identified an epithelial-localized, SusC-reactive Th17 subset that is BACH2[lo], GZMA[hi], and expresses the costimulatory receptor TMIGD2. Together, our results highlight the utility of tracking commensal-specific T cell responses to define specialized subsets of Th17 cells associated with loss of tolerance to the microbiome.},
}

@article {pmid42933401,
year = {2026},
author = {van Uden, AM and Zweers, H and Vasquez, AA and Wansink, DG and 't Hoen, PAC and Gusinac, A and de Baaij-Daalmeyer, A and Gerrits, K and Melchers, WJG and van Engelen, B and Ederveen, THA and Braakman, HMH},
title = {Exploring the gut microbiome in children and young adults with myotonic dystrophy type 1.},
journal = {Journal of neuromuscular diseases},
volume = {},
number = {},
pages = {22143602261496624},
doi = {10.1177/22143602261496624},
pmid = {42933401},
issn = {2214-3602},
abstract = {Myotonic Dystrophy type 1 (DM1) is a complex multisystem disorder, and affected children commonly present with gastrointestinal and neurodevelopmental challenges. Despite the high prevalence of these symptoms, their underlying mechanisms remain poorly understood. The gut microbiome is known to be involved in gastrointestinal and neurodevelopmental disorders, and emerging research suggests that it could also play a contributory role in various neuromuscular diseases. However, the gut microbiota of children with DM1 remains unexplored. This pilot study compared gut microbiota profiles of 10 children and one young adult with DM1, to that of their unaffected siblings (n=11). Three-day food records and faecal samples were collected, and bacterial taxa were analysed through 16S rRNA marker-gene sequencing. A within-family paired-sample design accounted for potential confounders, such as diet and lifestyle. Results revealed that overall microbial diversity and community structure were similar between groups. Moreover, participants with DM1 showed a significant lower relative abundance of the bacterial genus Faecalibacterium (mean 4.9% ± 2.1%) compared to their unaffected siblings (mean 9.1% ± 4.4%)(p=0.005). This finding should be considered exploratory, as its univariate analysis was uncorrected for multiple testing. Faecalibacterium is a key gut bacterium, and reduced abundance has been reported in several DM1-associated gastrointestinal and neurodevelopmental disorders. Although causality cannot be inferred from this exploratory study the observed reduction may be relevant to gastrointestinal and neurodevelopmental challenges frequently seen in DM1. If larger further studies confirm its role, targeting Faecalibacterium relative abundance could become a potential therapeutic strategy for alleviating gastrointestinal and neurodevelopmental symptoms in DM1.},
}

@article {pmid42933406,
year = {2026},
author = {Lee, JH and Kim, SH and Kim, EK and Lee, KA and Bhin, J and Hwang, D and Lee, DG and Bahn, YS and Lee, WJ},
title = {The antimicrobial peptide pileup promotes enterocyte shedding to maintain gut homeostasis in aging Drosophila.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.09.077},
pmid = {42933406},
issn = {1879-0445},
abstract = {Cellular turnover is a fundamental biological process that counteracts aging by activating stem cells to replace aging cells. This process is especially critical for maintaining the intestinal epithelium, one of the most rapidly renewing tissues in the body. However, the replacement of aging enterocytes cannot be explained solely by the generation of new cells from intestinal stem cells (ISCs); it also requires the complementary process of physically removing aging enterocytes through shedding. Compared with the well-characterized regulation of ISCs, the mechanisms governing enterocyte shedding remain poorly understood. Here, we identify pileup, a novel age-associated antimicrobial peptide (AMP) in Drosophila, as both a genetic marker and a key regulator of enterocyte shedding. Reactive oxygen species (ROS) generated through age-related mitochondrial dysfunction, a process facilitated by Autophagy-related gene 1 (ATG1) kinase, activate hypoxia-inducible factor 1α, which induces pileup expression specifically in aging enterocytes. Pileup then compromises the membrane of these cells and triggers c-Jun N-terminal kinase (JNK) activation, which we propose promotes their shedding. Notably, pileup has three homologs, and loss of all four genes leads to tumorous cell accumulation, gut barrier dysfunction, microbiome dysbiosis, and premature death. Our findings reveal a previously unrecognized role for AMPs in the turnover of aging host cells, extending their classical function beyond microbial defense. This work provides new mechanistic insights into enterocyte shedding and underscores its essential role in preserving gut homeostasis during aging.},
}

@article {pmid42933603,
year = {2026},
author = {Ahamed, F and Palepu, S and Pal, D and Bandyopadhyay, A and Sengupta, M and Hossain, CM and Das, S and Somashekara, J and Goswami, K},
title = {Impact of supplementation of a package of iron folic acid (IFA) with probiotics on haemoglobin levels in the elderly with mild to moderate anaemia: A double-blind, randomised controlled trial (PRobiotics in Anaemia Trial for Healthy Ageing Management - PRATHAM).},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {105208},
doi = {10.1016/j.clnesp.2026.105208},
pmid = {42933603},
issn = {2405-4577},
abstract = {INTRODUCTION: The growing geriatric population has increased the burden of age-related conditions such as anaemia, highlighting the need for effective strategies to promote healthy ageing. This study evaluated the effect of supplementation of iron and folic acid (IFA) with probiotics on haematological, inflammatory, and gut microbiome parameters among elderly individuals with mild-to-moderate anaemia.

METHODOLOGY: This community-based, placebo-controlled, double-blind, randomised controlled trial was conducted among individuals aged ≥60 years from the "AIIMS SBIMB Study on Healthy Ageing (ASTHA)" cohort. A total of 200 participants were randomised in a 1:1 ratio. The intervention group received daily IFA tablets containing 60 mg of elemental iron and 500 μg of folic acid, along with probiotic capsules containing Streptococcus faecalis, Bifidobacterium, and Lactobacillus (30 billion CFUs/capsule) for 12 weeks. The control group received IFA tablets with placebo capsules containing one milligram of oral rehydration solution (ORS). Haemoglobin, ferritin, hepcidin, CRP, acute infections, and gut microbiome diversity were assessed at baseline and 12 weeks. An intention-to-treat (ITT) analysis was performed as the primary analysis, with a per-protocol analysis conducted as a sensitivity analysis.

RESULTS: A total of 184 study participants completed follow-up; missing endline biochemical data for the remaining participants were imputed using the last observation carried forward approach. The mean change in haemoglobin in the intervention and control groups was 1.0 ± 1.1 g/dL and 1.2 ± 1.1 g/dL, respectively (p=0.439). Hepcidin increased in both groups, with no significant between-group difference (p=0.550). Ferritin increased significantly more in the control group than in the intervention group (20.6 ± 34.2 ng/mL vs 10.0 ± 20.4 ng/mL; p=0.033). Baseline alpha-diversity was higher in the intervention group, while most endline diversity measures were comparable between groups.

CONCLUSION: IFA with probiotics did not provide additional benefit in haemoglobin or ferritin responses compared with IFA alone over 12 weeks, and there were no significant between-group differences in hepcidin or most gut microbiota alpha-diversity measures at endline.

CTRI/2023/09/057830.},
}

@article {pmid42933652,
year = {2026},
author = {Liu, L and Wu, R and Gao, Z and Fang, F and Chang, C and Hou, Z and Wang, H and Zhang, D and Wang, Z},
title = {Hydroxyproline Enhances Branched-Chain Amino Acid Effects on Lifespan and Healthspan in Caenorhabditis elegans.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101898},
doi = {10.1016/j.tjnut.2026.101898},
pmid = {42933652},
issn = {1541-6100},
abstract = {Food-derived protein hydrolysates frequently contain both collagen-associated hydroxyproline (Hyp) and branched-chain amino acids (BCAAs), but the biological consequences of their combination remain unclear. This study tested whether Hyp changes the effects of leucine (Leu), isoleucine (Ile), and valine (Val) on lifespan and healthspan-related phenotypes in Caenorhabditis elegans and whether these treatment effects are accompanied by coordinated microbial and metabolic remodeling. Amino acid concentrations that did not strongly disrupt bacterial food clearance were selected for lifespan, stress-resistance, motility, muscle-integrity, biochemical, microbiome, metabolomic, and transcriptomic analyses. Hyp+BCAA combinations improved lifespan- and healthspan-related phenotypes in a BCAA- and dose-dependent manner. The strongest combined treatments enhanced resistance to thermal and oxidative stress, preserved age-associated motility and muscle structure, reduced oxidative and lipofuscin-associated markers, and increased ATP-related readouts. Multi-omics profiling showed that these direct treatment effects were accompanied by distinct C. elegans-associated microbiota signatures, altered NAD precursor-related metabolites including nicotinic acid ribonucleoside (NaR), and a Leu+Hyp transcriptional response enriched for energy metabolism, proteostasis, and extracellular-matrix remodeling. Integrated microbiome-metabolome analysis identified a positive association between Rhodococcus abundance and NaR levels. These findings demonstrate that, under the tested culture conditions, Hyp+BCAA exposure improves longevity-related phenotypes and identifies microbial composition, NAD precursor metabolism, and host energy homeostasis as candidate, testable mediators.},
}

@article {pmid42933673,
year = {2026},
author = {Turner, D and Kenigsberg, S and Plotkin, L and Aharoni-Frutkoff, Y and Sokolik, M and Focht, G and Gasasa, S and Turpin, W and Waslyk, AM and Ledder, O and Griffiths, AM and Martincevic, I and Huynh, HQ and Godny, L and Avni-Biron, I and Torres, J and Panaccione, R and Jacobson, K and Otley, A and Sharar-Fischler, T and Li, Q and Azulay, A and Sigall-Boneh, R and Lee, SH and Croitoru, K},
title = {TASTY AND HEALTHY DIET REDUCES FECAL CALPROTECTIN IN HIGH-RISK FIRST-DEGREE RELATIVES OF PATIENTS WITH CROHN'S DISEASE: PIONIR RANDOMIZED CROSSOVER TRIAL.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.10.376},
pmid = {42933673},
issn = {1528-0012},
abstract = {BACKGROUND: With the rising prevalence of inflammatory bowel disease (IBD), preventing new-onset disease becomes a priority. The PIONIR (Preventing IBD ONset in Individuals at Risk) randomized controlled trial explored whether the Tasty&Healthy (T&H) diet reduces inflammatory markers in high-risk first-degree relatives (FDRs) of patients with Crohn's disease (CD).

METHODS: FDRs with persistently elevated fecal calprotectin (FC, >70μg/g) and, at most, nonspecific mucosal abnormalities (edema or ≤10 aphthous ulcers) on video-capsule endoscopy or ileocolonoscopy were randomized to T&H or habitual diet (HD) for 8 weeks, followed by crossover for additional 8 weeks. Treatment effect on the primary outcome, FC response, was analyzed using generalized estimating equations for the two-period, two-sequence crossover design, following the intention-to-treat principle.

RESULTS: Twenty-nine FDRs were randomized (n=14 T&H-first, n=15 HD-first). At week 8, median FC was lower with T&H (64μg/g [IQR 44-127]) vs. HD (112μg/g [74-227]; P=.022). FC decreased by ≥50% in 71% on T&H versus 27% on HD (RR=2.68 [95%CI 1.09-6.60]; P=.016). Across both crossover periods, estimated marginal mean FC declined from 185μg/g [95%CI 144-237] by 61% to 72μg/g [95%CI 57-91] with T&H, versus 38% to 114μg/g [95%CI 93-140] with HD (ratio 0.63 [95%CI 0.51-0.80], translating to 37% overall decrease with T&H; P<0.001). Six microbial species differed between diets after FDR correction. By week 8, 79% rated T&H acceptable and 83% had good or complete adherence.

CONCLUSION: These findings demonstrate the modifiability of low-grade intestinal inflammation in healthy high-risk FDRs with persistent FC elevation but without diagnostic endoscopic evidence of CD, supporting long-term dietary prevention trials (ClinicalTrials.gov #NCT05211518).},
}

@article {pmid42933708,
year = {2026},
author = {Khan, S and Chen, M and Chen, Z and Liang, Z and Abbas, M and Ahmad, S and Hassan, MU and Xie, S and Chen, D},
title = {PFAS and microbiota dysbiosis: An emerging link to respiratory toxicity.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110732},
doi = {10.1016/j.cbpc.2026.110732},
pmid = {42933708},
issn = {1532-0456},
abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants of increasing concern because of their widespread use, environmental mobility, bioaccumulation, and multisystem toxicity, including immunotoxicity, hepatotoxicity, neurotoxicity, reproductive toxicity, and endocrine disruption. Regulatory restrictions on legacy PFAS have accelerated the use of short-chain, ether-containing, and other replacement compounds, including GenX/HFPO derivatives, 6:2 Cl-PFESA, OBS, and ultrashort-chain PFAS; however, their respiratory and toxicological profiles remain incompletely characterized. Although ingestion through food and drinking water is the major exposure route for the general population, inhalation through indoor dust, aerosols, occupational emissions, and firefighting-related sources may be relevant in high-exposure settings, while the actual dose reaching human lung tissue remains poorly defined. Emerging evidence indicates that PFAS-induced toxicity may also involve disruption of host-microbiota interactions. The lung microbiome, despite its low biomass, contributes to mucosal immunity, epithelial homeostasis, and respiratory defense, while the gut-lung axis enables intestinal microbial signals to influence pulmonary inflammation. PFAS-associated gut dysbiosis can alter short-chain fatty acids, bile-acid metabolism, tryptophan-derived metabolites, and microbial products such as lipopolysaccharide, thereby providing plausible mechanistic links between intestinal disturbance and pulmonary immune responses. However, direct evidence that PFAS causally remodel the lung microbiota or that microbiota-derived signals mediate PFAS-induced lung injury remains limited. This review integrates current evidence from epidemiological, in vitro, and in vivo studies to evaluate PFAS-associated respiratory toxicity, with particular emphasis on emerging PFAS, exposure relevance, pulmonary inflammation and injury, and microbiota-mediated mechanisms along the gut-lung axis. By distinguishing established pulmonary effects from emerging microbiota-related hypotheses, this review identifies critical knowledge gaps and highlights priorities for future exposure assessment, mechanistic research, and risk evaluation.},
}

@article {pmid42933735,
year = {2026},
author = {Zhang, L and Wang, K and Chai, D and Mo, T and Jiang, W and Ma, W and Yu, B and Shi, Q and Ding, P and Deng, W and Wang, W and Zhao, K and Chen, C},
title = {Intestinal Candida albicans promotes HCC progression and anti-PD-1 resistance via IL-17A and Trem2[+] macrophages.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2026.10.018},
pmid = {42933735},
issn = {1600-0641},
abstract = {BACKGROUND & AIMS: Whether intestinal fungal dysbiosis contributes to hepatocellular carcinoma (HCC) progression and resistance to immune checkpoint inhibitors (ICIs) remains unclear. We investigated how gut Candida albicans influences HCC progression, immune remodeling, and response to ICI therapy.

METHODS: Fecal and tumor samples from patients with HCC, liver cirrhosis, and healthy controls were analyzed using ITS2 sequencing, immune profiling, and correlation analyses. Mechanistic studies focused on four complementary autochthonous murine HCC models and cell-based assays, integrating single-cell and bulk RNA sequencing, genetic and pharmacologic perturbations, Kaede photoconversion, fungal antigen recall assays, antifungal treatment, and anti-PD-1 therapy.

RESULTS: Fecal C. albicans abundance was higher in HCC patients and was associated with advanced disease, shorter overall survival, and reduced durable clinical benefit. Across HCC models, C. albicans gavage increased tumor burden and induced a Th17/IL-17A-skewed microenvironment characterized by Trem2[+] macrophage accumulation and impaired CD8[+] T cell infiltration and function. Antifungal treatment attenuated tumor progression, whereas IL-17A blockade or deficiency largely abrogated C. albicans-associated tumor promotion. Mechanistically, IL-17A induced tumor-derived MCP-1 through ACT1-TRAF6-TAK1 signaling to recruit macrophages and upregulated PAI-1, which activated TGF-β/Smad3 signaling to promote an immunosuppressive Trem2[+] macrophage state. These macrophages limited CD8[+] T cell recruitment and effector function through coordinated CXCL10 repression and GAL-1 induction, while potentially reinforcing Th17 responses through IL-1β and IL-6. Kaede photoconversion demonstrated enhanced mesenteric lymph node-to-liver Th17 trafficking, while fungal antigen recall assays revealed preferential Th17 responsiveness to C. albicans. C. albicans also impaired anti-PD-1 efficacy in vivo, whereas antifungal treatment partially restored therapeutic responsiveness.

CONCLUSIONS: Intestinal C. albicans promotes HCC progression and anti-PD-1 resistance through an IL-17A-Trem2[+] macrophage circuit, supporting its potential as a biomarker and therapeutic target.

IMPACT AND IMPLICATIONS: Intestinal fungal dysbiosis is increasingly recognized as a component of the gut-liver axis, but its functional contribution to HCC has remained poorly defined. Our study identifies intestinal Candida albicans as a promoter of HCC progression in experimental models and delineates an IL-17A-MCP-1/PAI-1-Trem2[+] macrophage circuit that links fungal exposure to impaired CD8[+] T-cell immunity and reduced response to PD-1 blockade. These findings are relevant to researchers and clinicians seeking microbiome-associated determinants of HCC progression and immunotherapy resistance. Fecal C. albicans abundance and components of this immune circuit may warrant evaluation as biomarkers for patient stratification and as potential targets for combination therapy. However, the clinical associations reported here are based on modest observational cohorts, and antifungal treatment was tested as a proof-of-concept intervention in mice. Larger prospective studies and more selective therapeutic approaches will therefore be required before these findings can inform clinical management.},
}

@article {pmid42933792,
year = {2026},
author = {Sun, Y and Stradner, MH and Fessler, J and Reisch, MK},
title = {Predictors of treatment response in rheumatoid arthritis: a narrative review.},
journal = {RMD open},
volume = {12},
number = {4},
pages = {},
pmid = {42933792},
issn = {2056-5933},
abstract = {Rheumatoid arthritis (RA) is a common autoimmune disease having diverse responses to disease-modifying antirheumatic drugs. Although treat-to-target strategies have improved disease management, therapeutic selection remains largely empirical and a substantial proportion of patients fail to achieve adequate clinical response to their therapies. Therefore, reliable biomarkers capable of predicting treatment response before therapy initiation are urgently needed to guide personalised treatment decisions. Current evidence suggests that multiple categories of biomarkers may contribute to the prediction of treatment responses across different therapeutic agents in RA, including clinical characteristics, serological markers, cytokine profiles, genetic and transcriptomic signatures, immune-cell phenotypes, synovial pathotypes and microbiome features. This review summarises current biomarker strategies for predicting therapeutic response in RA and discusses their potential utility in improving precision medicine. However, most individual biomarkers show limited predictive power, partly due to the complex and dynamic nature of RA pathogenesis. Combining biomarkers from multiple biological dimensions, together with the continued exploration of novel predictive markers, may improve the robustness and accuracy of treatment response prediction in RA.},
}

@article {pmid42933939,
year = {2026},
author = {O'Donnell, JEM and Zeef, DH and Gopan, A and Muise, AM},
title = {Genetics of Inflammatory Bowel Disease-What is Unsought Goes Undetected.},
journal = {Gastroenterology clinics of North America},
volume = {55},
number = {4},
pages = {653-672},
doi = {10.1016/j.gtc.2026.05.016},
pmid = {42933939},
issn = {1558-1942},
mesh = {Humans ; *Inflammatory Bowel Diseases/genetics ; Genetic Testing ; Genetic Predisposition to Disease ; Precision Medicine ; },
abstract = {Inflammatory bowel disease (IBD) affects nearly 1% of North Americans and arises from complex interactions between genetics, environment, and the gut microbiome. This article examines IBD's genetic architecture-spanning monogenic, oligogenic, and polygenic disease-and highlights that genetic evaluation should not be limited by age. A negative genetic screen does not exclude a genetic basis for disease, as emerging mechanisms like mosaicism and regulatory variants may go undetected. The authors advocate for immunogenetic pathway-based classification to enable precision therapeutics, improve treatment outcomes, and reduce adverse effects, emphasizing that what is unsought in genetic testing will inevitably go undetected.},
}

Humans
*Inflammatory Bowel Diseases/genetics
Genetic Testing
Genetic Predisposition to Disease
Precision Medicine

@article {pmid42934177,
year = {2026},
author = {Kanehisa, M and Furumichi, M and Sato, Y and Matsuura, Y and Ishiguro-Watanabe, M},
title = {KEGG for characterizing genomes and pathways in the biosphere.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag1042},
pmid = {42934177},
issn = {1362-4962},
support = {JPMJND2203//NBDC Database Integration Coordination Program/ ; //Japan Science and Technology Agency/ ; //NBDC Program of the Japan Science and Technology Agency/ ; },
abstract = {The KEGG database (https://www.kegg.jp) has been developed as a model of the biological systems. By organizing knowledge of cellular and organism-level functions in the form of molecular wiring diagrams, the model enables generating new knowledge and finding practical applications. The KO (KEGG Orthology) dataset plays the basic role of organizing knowledge. KO is an ortholog with functional relevance, generalizing experimental evidence in specific organisms to other organisms. KEGG molecular networks, including pathway maps and modules, are generic networks with KOs as network nodes, and thus KEGG mapping from genomes to pathways can be applied to any organism. As the number of KOs increases and the KO annotation rate improves, KEGG mapping is further expanded. A set of KOs in the genome and a set of modules in the metabolic pathways are now used to characterize various data objects in the biosphere, including organisms, organism groups, microbiomes, viruses, and their combinations, such as endosymbiont-host, microbiome-host, and virus-host relationships. Furthermore, a simple measure of similarity either by KO compositions or module compositions is introduced to compare organism groups. The resulting similarity dendrograms possibly reflect similarity of cellular functions or, more specifically, metabolic functions, which can be compared with phylogenetic trees.},
}

@article {pmid42934212,
year = {2026},
author = {Short, I and Martínez-Pérez, C and Miravet-Verde, S and Sunagawa, S and Stocker, R and Alcolombri, U},
title = {Alteromonas macleodii breaches the diatom frustule triggering protoplast emergence and programmed necrosis-like death in Thalassiosira rotula.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42934212},
issn = {2041-1723},
support = {542395//Simons Foundation/ ; 542395//Simons Foundation/ ; LT0050/2023-L//Human Frontier Science Program (HFSP)/ ; LT0050/2023-L//Human Frontier Science Program (HFSP)/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Diatoms/microbiology/physiology/cytology ; *Alteromonas/physiology/genetics ; Necrosis ; },
abstract = {Diatom-bacteria interactions drive biogeochemical fluxes at the base of the marine food-web. Although bacteria are increasingly recognised as important drivers of algal mortality, the diversity of algicidal strategies remains understudied. Here we show that Alteromonas macleodii, a recurrent member of Thalassiosira rotula's microbiome, breaches the diatom's silica frustule, inducing >95% of cells to emerge from their shells within 72 h, exposing protoplasts to lysis and exploitation. Whilst protoplast formation was induced by diverse bacteria, A. macleodii uniquely caused population-wide collapse, used here to characterise this diatom stress response. Dual transcriptomics indicated the presence of a programmed necrosis-like cell death pathway in diatoms underpinning T. rotula's terminal morphological change, alongside upregulation of bacterial motility, chemotaxis and opportunistic metabolism. These findings reveal a potent algicidal strategy, recasting A. macleodii as an antagonist that exploits diatom mortality for its own benefit, removes the ballast provided by their frustules and thus reshapes oceanic carbon cycling.},
}

*Diatoms/microbiology/physiology/cytology
*Alteromonas/physiology/genetics
Necrosis

@article {pmid42934317,
year = {2026},
author = {},
title = {Laying the foundations for clinical microbiome research.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {23},
number = {11},
pages = {805},
pmid = {42934317},
issn = {1759-5053},
}

@article {pmid42934449,
year = {2026},
author = {Kolawole, O and van Diepeningen, AD and Martens, JG and Arrizabalaga-Larrañaga, A and Black, L and van Overbeek, L},
title = {Wheat Ear Microbiome State as a Transferable Indicator of Within-Season Mycotoxin Risk.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42934449},
issn = {1432-184X},
mesh = {*Triticum/microbiology/chemistry ; Seasons ; *Microbiota ; *Mycotoxins/analysis ; Bacteria/isolation & purification/genetics/classification ; *Fungi/genetics/isolation & purification/classification/metabolism ; Trichothecenes/analysis ; Weather ; RNA, Ribosomal, 16S/genetics ; Food Contamination/analysis ; },
abstract = {Weather based models are central to mycotoxin risk assessment, but field level discrimination can be limited when environmental training data are sparse and models must transfer to locations not used during training. We tested whether wheat ear microbiome state provides a transferable biological indicator for within season classification of trichothecene contamination under strict spatial holdout, with relevance for food and feed safety. Across three winter wheat trial locations within a single production year, ears were sampled at BBCH 77 to 83, corresponding to mid to late grain filling, and paired bacterial 16 S rRNA gene and fungal ITS profiles were analysed alongside LC-MS/MS measurements of DON and T-2 + HT-2. Under leave one location out evaluation, microbiome informed models achieved substantially higher discrimination of higher versus lower contamination than station level weather summaries under identical spatial holdout. Weather features added little in the single season dataset, but simulation analyses indicated that environmental predictors become more learnable with temporal replication, supporting a future two stage framework in which early season weather context is refined by within season microbiome state. Portability screening and drop one ablation prioritised microbial indicators with sign consistent associations across locations and non-redundant predictive value. Together, these findings provide proof of concept that wheat ear microbiome state can support spatially transferable within season mycotoxin risk classification and targeted surveillance when environmental training data are limited.},
}

*Triticum/microbiology/chemistry
Seasons
*Microbiota
*Mycotoxins/analysis
Bacteria/isolation & purification/genetics/classification
*Fungi/genetics/isolation & purification/classification/metabolism
Trichothecenes/analysis
Weather
RNA, Ribosomal, 16S/genetics
Food Contamination/analysis

@article {pmid42934450,
year = {2026},
author = {Gu, Z and Shen, Y and Li, Y and Mi, L and Shu, C and Zhang, J and Geng, L},
title = {Early phyllosphere remodeling in maize after herbivory uncovers candidate insecticidal bacteria from feeding-altered taxa.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42934450},
issn = {1573-0972},
support = {2022ZD040150204//Major Project of Agricultural Biological Breeding/ ; 2024YFE0214100//National Key Research and Development Program of China/ ; },
mesh = {*Zea mays/microbiology ; Animals ; *Plant Leaves/microbiology ; *Herbivory ; Spodoptera/physiology/microbiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology/physiology ; Microbiota ; Phylogeny ; Pest Control, Biological ; Insecticides ; DNA, Bacterial/genetics ; },
abstract = {The "cry for help" hypothesis suggests that herbivore-stressed plants reshape their microbiome for defense, yet the speed and systemic characteristics of the phyllosphere bacterial response to chewing herbivores remain poorly understood. To address this, we examined how larval feeding by fall armyworm (Spodoptera frugiperda) affects the phyllosphere bacterial community within undamaged maize (Zea mays) leaves. We combined 16S amplicon sequencing, culturomics, and machine learning to characterize microbial community dynamics and culture-dependent recover candidate biocontrol strains from herbivory-altered taxa. Localized larval feeding on a single leaf induced rapid changes in the phyllosphere bacterial community of distal undamaged leaves within 12 h. Herbivory modified bacterial cooccurrence network topology. A significantly enriched OTU7 was isolated and identified as Enterobacter strain P12A2, which exhibited high toxicity against S. frugiperda. This study indicates that herbivory-induced systemic changes in the phyllosphere bacterial community of undamaged leaves may serve as a source for identifying novel biological resources. These findings provide a promising basis for developing microbiome-based strategies for sustainable pest management.},
}

*Zea mays/microbiology
Animals
*Plant Leaves/microbiology
*Herbivory
Spodoptera/physiology/microbiology
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Larva/microbiology/physiology
Microbiota
Phylogeny
Pest Control, Biological
Insecticides
DNA, Bacterial/genetics

@article {pmid42934476,
year = {2026},
author = {Smith, C and Garza, K and Azari, H and Vellers, H and Abdelrahman, M and Dhanasekara, CS and Salmon, AB and Liang, H and Fernandez, E and Musi, N and Massett, MP and Albracht-Schulte, K},
title = {Aerobic exercise training alters gastrointestinal microbiota and enhances exercise capacity in UM-HET3 mice.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {42934476},
issn = {2509-2723},
support = {P30 AG013319/AG/NIA NIH HHS/United States ; },
abstract = {Aerobic exercise attenuates age-related physiological decline, potentially through favorable modulation of gut microbiota diversity. The purpose of this study was to characterize aerobic exercise training (ET)-induced alterations in the gut microbiome of aging, genetically heterogeneous UM-HET3 mice and examine associations between microbial shifts and changes in body composition (body weight, lean mass, and fat mass) and exercise capacity (total work, distance, and duration). Male UM-HET3 mice were assigned to sedentary (SED; n = 16) or ET (n = 17) groups. ET mice trained 5 days per week for 4 weeks at 65% of maximal work output. Body composition and exercise capacity were assessed before and after the intervention. Post-intervention fecal samples were analyzed by 16S rRNA gene sequencing (SED, n = 13; ET, n = 13). ASVs were taxonomically classified using QIIME2 with the SILVA 138.1 reference database. Alpha and beta diversity analyses were conducted in R, and Spearman's correlations assessed relationships between phylum-level abundances and physiological outcomes. ET mice exhibited greater alpha diversity, with a higher median richness (219.5), although differences were not statistically significant. Principal coordinate analysis of beta diversity demonstrated significant separation between groups (P = 0.01), indicating distinct microbial community composition. At the phylum level, ET was associated with modest shifts in gut microbial composition, characterized by higher relative abundances of Firmicutes and Verrucomicrobiota and lower abundances of Bacteroidota and Desulfobacterota compared to SED mice. Collectively, these findings indicate that aerobic exercise training induces distinct shifts in gut microbiota composition in middle-aged UM-HET3 mice despite underlying genetic heterogeneity.},
}

@article {pmid42934723,
year = {2026},
author = {Rungrojn, A and Chaisiri, K and Thaipadungpanit, J and Batty, EM and Taweethavonsawat, P and Thempachana, O and Kongkaew, W and Morand, S and Blacksell, SD},
title = {Environmental and host-associated determinants of microbiome variation in the brown dog tick Rhipicephalus linnaei in Thailand.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42934723},
issn = {1756-3305},
support = {JCPET02//Royal Society of Tropical Medicine and Hygiene/ ; MOTIP-ECIA 2024/001//MOTIP/ ; 315982/Z/24/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Thailand/epidemiology ; *Microbiota ; Dogs ; RNA, Ribosomal, 16S/genetics ; Female ; *Rhipicephalus/microbiology ; Male ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Bacteria/classification/genetics/isolation & purification ; *Dog Diseases/parasitology/microbiology/epidemiology ; Phylogeny ; Coxiella/isolation & purification/genetics ; },
abstract = {BACKGROUND: The brown dog tick, Rhipicephalus linnaei, is an important vector of veterinary and zoonotic pathogens worldwide. The composition of the tick-associated microbiome may influence tick physiology, adaptation, and vector competence; however, factors shaping the microbiome of R. linnaei in Southeast Asia remain poorly understood.

METHODS: A total of 131 R. linnaei ticks were collected from dogs across five provinces in Thailand, representing different geographical and ecological settings. Full-length bacterial 16S rRNA sequencing was performed using Oxford Nanopore Technology to characterise bacterial community composition. Microbiome diversity and structure were evaluated by geographical region, sampling area (urban versus rural), blood-feeding status, tick sex, and developmental stage using alpha diversity metrics, Bray-Curtis dissimilarities, principal coordinates analysis, PERMANOVA, and ANCOM-BC2 differential abundance analysis.

RESULTS: The microbiome of R. linnaei was dominated by Candidatus Coxiella mudrowiae, which was detected in all ticks. Significant differences in bacterial community composition were observed between geographical regions, sampling areas, and blood-feeding status. Urban ticks showed lower bacterial diversity than rural ticks, and engorged ticks showed altered microbial diversity compared with feeding ticks. Sex- and developmental stage-associated differences were less pronounced. Differential abundance analysis identified several bacterial taxa associated with ecological and host-related factors. Putative tick-associated bacterial taxa, including Anaplasma and Ehrlichia species, were identified at low frequency.

CONCLUSIONS: This study demonstrates that geography, habitat type, and blood-feeding status are associated with variation in the microbiome of R. linnaei in Thailand. The findings provide new insights into the ecological factors shaping tick-associated bacterial communities in Southeast Asia and highlight the utility of full-length 16S rRNA Nanopore sequencing for vector microbiome investigations.},
}

Animals
Thailand/epidemiology
*Microbiota
Dogs
RNA, Ribosomal, 16S/genetics
Female
*Rhipicephalus/microbiology
Male
*Tick Infestations/veterinary/parasitology/epidemiology
*Bacteria/classification/genetics/isolation & purification
*Dog Diseases/parasitology/microbiology/epidemiology
Phylogeny
Coxiella/isolation & purification/genetics

@article {pmid42934726,
year = {2026},
author = {Auguste, M and Bosi, E and Saad, J and Oliveri, C and Doni, L and Marchese, A and Travers, MA and Toulza, E and Boulo, V and Courtay, G and Petton, B and Koechlin, H and Montagnani, C and Di Cesare, A and Corno, G and Andree, KB and Gairin, I and Furones, D and Broquard, C and Wegner, KM and Destoumieux-Garzón, D and Vezzulli, L},
title = {The resistome of European coastal environments revealed by high-resolution targeted metagenomics in oysters.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934726},
issn = {2049-2618},
mesh = {Animals ; *Metagenomics/methods ; Europe ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Ostreidae/microbiology ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Antimicrobial resistance is a major global health threat, and the environment is increasingly recognised as a key reservoir of antibiotic resistance genes (ARGs). In marine ecosystems, filter-feeding organisms such as oysters are sentinel species that reflect the microbiological diversity of their environment. Here, we investigated the ARG content of the Pacific oyster Magallana gigas across four European coastal sites, contrasting anthropogenically impacted aquaculture sites (Bay of Brest, Ebro Delta, Thau lagoon) with natural oyster reefs (Sylt island). ARGs sequencing was enriched using a targeted probe-and-capture metagenomic approach employing 37,826 RNA baits covering over 2000 ARG sequences. Moreover, a novel bioinformatic pipeline ARGifier was specifically designed for sensitive, high-resolution detection and classification of ARGs in metagenomic samples dominated by host DNA.

RESULTS: This strategy was able to overcome limitations of cultivation-based methods and whole metagenomic sequencing, enabling the detection of more than 33,000 ARG sequences in the oyster resistome spanning over 450 genes distributed over 23 resistance classes. Reads assigned to ARGs represented 0.23% of all raw reads and 25.02% of host-depleted reads. Accordingly, comparison of targeted metagenomics and pool-seq analysis of cultured isolates (culturomics) in specific pathogen-free oysters revealed that metagenomics captured dominant, community-wide resistance determinants, whereas culturomics recovered a broader diversity of ARGs due to their presence in genomes of cultivable strains. The oyster resistome across the four farming sites was dominated by multidrug efflux systems associated with intrinsic and housekeeping-related mechanisms, suggesting an environmentally shaped resistance profile. Clinically relevant ARGs, including extended-spectrum Beta-Lactamase, carbapenem, colistin, and vancomycin resistance genes, were detected in low abundance at all sites, with higher enrichment in anthropogenically impacted areas. In addition, several ARGs were associated with plasmids, indicating mobilization potential. Taxonomic analysis revealed that a limited subset of bacteria, particularly Betaproteobacteria and Actinomycetes, carried a disproportionately high number of ARGs despite their low relative abundance in the oyster microbiome.

CONCLUSIONS: Overall, this study delivers a comprehensive inventory of ecologically and clinically relevant ARGs in European coastal environments, positioning farmed and wild oysters as sentinel organisms for monitoring antimicrobial resistance in coastal waters. Our findings highlight the circulation of ARGs within coastal marine ecosystems, which may act as reservoirs and potential sources of mobilisable antimicrobial resistance. Video Abstract.},
}

Animals
*Metagenomics/methods
Europe
*Bacteria/genetics/classification/drug effects/isolation & purification
*Ostreidae/microbiology
Metagenome
Anti-Bacterial Agents/pharmacology
Microbiota
Sequence Analysis, DNA

@article {pmid42934733,
year = {2026},
author = {Nichols, HL and Brettell, LE and Saldaña, MA and Hegde, S and Heinz, E and Vaccaro, K and Hughes, GL and Coon, KL},
title = {Vertical transmission of mosquito microbiota and its effects on offspring development.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934733},
issn = {2049-2618},
mesh = {Animals ; *Aedes/microbiology/growth & development ; Female ; Larva/microbiology/growth & development ; *Bacteria/classification/isolation & purification/genetics ; *Gastrointestinal Microbiome ; Infectious Disease Transmission, Vertical ; *Mosquito Vectors/microbiology ; },
abstract = {BACKGROUND: The mosquito's gut microbiota plays a crucial role in determining its capacity to transmit harmful viruses and parasites. Accordingly, manipulating mosquito gut microbiota is a promising avenue for reducing the transmission of mosquito-borne human pathogens. A successful microbial control campaign will require a thorough understanding of how bacteria are transmitted within mosquito populations. In two parallel but complementary studies using the yellow fever mosquito Aedes aegypti as a focal host species, we surveyed the vertical transmission of bacteria from individual mothers to cohorts of offspring maintained in a closed system.

RESULTS: Laboratory- and field-derived mothers deposited bacteria that support offspring development, and the relative abundances of commonly transmitted taxa correlated with offspring fitness. Maternally transmitted bacteria were detected in both larval and adult offspring, and the relative abundances of specific taxa differed between life stages. Microbiota composition in adult offspring closely resembled that of mothers, despite dramatic shifts in the relative abundance of specific community members during the larval stage. Variability in microbiota composition among offspring was also greater than variability across the population of egg-laying mothers. Eggs that underwent a period of desiccation before hatching produced larval communities dominated by endospore-forming bacteria that were rare in maternal samples.

CONCLUSIONS: Overall, our results demonstrate vertical transmission of mosquito-associated microbiota across generations, including bacterial taxa that could potentially be leveraged for mosquito and mosquito-borne disease control Video Abstract.},
}

Animals
*Aedes/microbiology/growth & development
Female
Larva/microbiology/growth & development
*Bacteria/classification/isolation & purification/genetics
*Gastrointestinal Microbiome
Infectious Disease Transmission, Vertical
*Mosquito Vectors/microbiology

@article {pmid42934758,
year = {2026},
author = {Skonieczna, B and Nazarko, N and Godlewska, E and Wasiluk, N and Czech, EK and Wilczewska, AZ and Regulska, E and Car, H and Niemirowicz-Laskowska, K},
title = {Nanoparticles and their significant risks: a comprehensive review of toxicological and regulatory perspectives.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {},
pmid = {42934758},
issn = {1477-3155},
support = {NCN/2019/35/B/ST5/03391//Narodowe Centrum Nauki/ ; PRTR-C17.I1//Advanced Materials programme/ ; B.SUB.25.215//Uniwersytet Medyczny w Bialymstoku/ ; B.SUB.25.257//Uniwersytet Medyczny w Bialymstoku/ ; },
mesh = {Humans ; *Nanoparticles/toxicity/chemistry ; Animals ; Gastrointestinal Microbiome/drug effects ; Oxidative Stress/drug effects ; Tissue Distribution ; Drug Carriers/toxicity/chemistry ; Liver/drug effects ; },
abstract = {BACKGROUND: Nanoparticles are increasingly important as drug carriers due to their ability to enhance solubility, stability, and selective delivery of therapeutic agents, enabling accumulation at disease sites, interaction with cell-surface receptors, and penetration of biological barriers such as the blood-brain barrier. Despite these numerous advantages, their potential toxicity remains a key obstacle to safe clinical use. Emerging evidence suggests that nanoparticles may alter the composition of the gut microbiome, potentially affecting metabolism, immune homeostasis, neurobehavioral pathways, and reproductive function by influencing hormonal regulation and fertility.

AIM OF THE REVIEW: This review provides a detailed analysis of the toxicological aspects of nanoparticles, including cytotoxicity, oxidative stress, potential genotoxicity, and effects on immune responses such as inflammation and immunosuppression. In vivo biodistribution, organ accumulation, and effects on liver enzymes are also discussed, emphasizing the role of the liver in drug metabolism and the potential risk of impaired detoxification. Additionally, the review examines the effects of nanoparticles on the gut microbiome and reproductive system. It emphasizes their capacity to disrupt the microbial balance, the intestinal barrier integrity, and reproductive hormone homeostasis. We discuss regulatory issues for nanotechnology-based medicinal products, emphasizing the importance of standardized testing protocols and long-term safety assessments. Finally, future perspectives and developmental directions for nanoparticles have been highlighted.

CONCLUSION: This review highlights the need for a comprehensive understanding of nanoparticle toxicity mechanisms, which is crucial for their safe design and further development in nano-based therapy.},
}

Humans
*Nanoparticles/toxicity/chemistry
Animals
Gastrointestinal Microbiome/drug effects
Oxidative Stress/drug effects
Tissue Distribution
Drug Carriers/toxicity/chemistry
Liver/drug effects

@article {pmid42934845,
year = {2026},
author = {Li, Y and Wang, W and Liu, W},
title = {CNTN4: A Possible Candidate Gene for Microbiota-Gut-Brain Axis in Autism Spectrum Disorders and Attention-Deficit/Hyperactivity Disorder.},
journal = {Autism : the international journal of research and practice},
volume = {},
number = {},
pages = {13623613261493643},
doi = {10.1177/13623613261493643},
pmid = {42934845},
issn = {1461-7005},
abstract = {The gut microbiota plays a significant role in autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD), though findings vary substantially across studies. Using gut microbiome data from a genome-wide association study of 5,959 participants and summary statistics from 46,351 ASD and 55,374 ADHD cases, we conducted bidirectional Mendelian randomization (MR) analyses with inverse variance weighting as the primary method. Reverse MR analysis assessed potential reverse causality. We annotated single nucleotide polymorphisms (SNPs) with SNP-nexus to identify associated genes, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to characterize their functional roles. Seventeen gut microbial taxa showed causal associations with ASD risk, while 27 were linked to ADHD. Reverse MR analysis revealed associations between aSD and species Desulfovibrio piger as well as species Bacillus U, but no reverse causality was detected for ADHD. Biological annotation identified five novel conserved genes in host-microbiome interactions shared by ASD and ADHD, with CNTN4 emerging as a common candidate gene. These findings support a potential causal relationship between gut microbiota and ASD/ADHD risk while uncovering novel conserved genes implicated in host-microbiome interactions for both disorders.Lay AbstractDistinct gut microbiota profiles were observed in individuals with ADHD and ASD. Seventeen microbial species showed significant associations with ASD, while 27 were linked to ADHD. CNTN4 emerged as a potential candidate gene shared across both neurodevelopmental conditions and host-microbiome interactions.},
}

@article {pmid42934883,
year = {2026},
author = {Zhang, J and Li, P and Wu, H and Zhang, Z and Wang, Z and Liu, Y and Xu, M and Chen, F and Yang, Y},
title = {Oral Irrigation and Microbiome Remodeling after Oral Cancer Reconstruction.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345261489246},
doi = {10.1177/00220345261489246},
pmid = {42934883},
issn = {1544-0591},
abstract = {Patients with oral cancer undergoing free flap reconstruction face significant surgical trauma, making the prevention of postoperative wound infection and the maintenance of oral microecological balance critical. This study systematically evaluated oral microbiome changes before and after surgery and assessed the effectiveness of postoperative oral irrigation using 2 different regimens. In an exploratory randomized controlled trial, 60 patients were assigned to receive oral irrigation with either bipolar water or a combination of hydrogen peroxide and sodium bicarbonate solution. Saliva and irrigation samples were collected at 7 time points, preoperatively and before and 5 minutes after oral irrigation on postoperative days 1, 4, and 7, and analyzed using specialized sequencing techniques to determine microbial abundance and diversity. Clinical outcomes, including wound infection rates and patient comfort, were also recorded. The results indicated that surgical treatment reduced the diversity of the oral microbiota and altered its composition. Before surgery, the oral cavity was dominated by potentially pathogenic taxa, which shifted toward oral resident microorganisms postoperatively. Continued oral irrigation promoted a transition from an unstable, anaerobic-enriched state toward a relatively stable community structure dominated by facultative anaerobes. While no differences were observed between the 2 groups regarding wound infection rates or microbial composition, the bipolar water group reported higher patient comfort and required shorter irrigation times. Furthermore, the bipolar water group maintained more stable microbial diversity, whereas the hydrogen peroxide group exhibited more pronounced fluctuations and higher fungal detection rates. In conclusion, surgery induces early microbial imbalance, but staged oral irrigation facilitates the stabilization of the oral microecosystem. Bipolar water is an effective alternative for perioperative care, helping to maintain microbial stability while improving the patient experience.},
}

@article {pmid42935490,
year = {2026},
author = {Tomita, K and Nakano, T and Morozumi, S and Okahashi, N and Arita, M},
title = {Microbiome-dependent phytosterol sulfates production and tissue distribution in mice.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117883},
pmid = {42935490},
issn = {2589-0042},
abstract = {Microbial biotransformation of dietary lipids, such as cholesterol, influences host homeostasis. Despite extensive studies on animal sterols in host-microbiota interactions, the role of phytosterols in homeostasis remains unclear. In this study, we characterized phytosterol sulfates as microbiota-derived metabolites using untargeted lipidomic data mining. The levels of sitosterol sulfate (SIS), campesterol sulfate, and stigmasterol sulfate, the three major phytosterol sulfates, along with coprostanol sulfate, were reduced in the feces of germ-free mice compared with those of specific pathogen-free mice. We characterized a series of Bacteroidota species and their sterol sulfotransferases that produced phytosterol sulfates more efficiently than mammalian enzymes. Furthermore, SIS significantly accumulated in host tissues in a microbiota- and age-dependent manner, whereas unconjugated phytosterols were mostly undetectable. Our work provides insights into host-microbiome interactions via gut bacterial phytosterol metabolism.},
}

@article {pmid42935576,
year = {2026},
author = {Lee, SH and Na, SI and Park, SC and Cho, BR and Lee, BK and Cho, YJ and Cho, H and Youk, HJ and Ryu, DR},
title = {Effect of a potassium-competitive acid blocker on the gut microbiota in patients undergoing percutaneous coronary intervention: a randomized pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1942212},
pmid = {42935576},
issn = {2235-2988},
mesh = {Humans ; Pilot Projects ; Female ; *Percutaneous Coronary Intervention/adverse effects ; Male ; *Gastrointestinal Microbiome/drug effects ; *Proton Pump Inhibitors/administration & dosage/adverse effects/therapeutic use ; Prospective Studies ; Aged ; Middle Aged ; *Pantoprazole/administration & dosage/adverse effects/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Dysbiosis/chemically induced ; Gastrointestinal Hemorrhage/prevention & control ; },
abstract = {BACKGROUND AND AIM: Proton pump inhibitors (PPIs) are routinely used in patients undergoing percutaneous coronary intervention (PCI) to prevent gastrointestinal bleeding associated with dual-antiplatelet therapy (DAPT). However, long-term PPI use has been linked to gut microbiota dysbiosis. Tegoprazan, a potassium-competitive acid blocker (P-CAB), may exert distinct effects on the gut microbiome. This study compared the longitudinal effects of tegoprazan and pantoprazole on gut microbiota composition in patients with angina undergoing PCI.

METHODS: This prospective, randomized, controlled pilot study randomized 38 patients 1:1:1 to tegoprazan 50 mg once daily, pantoprazole 40 mg once daily, or no acid-suppressive therapy for 24 weeks. Five participants did not provide baseline fecal samples, and nine discontinued participation before week 24. Thus, 24 participants with paired baseline and week-24 fecal samples were included in the final analysis. Fecal samples were analyzed using 16S rRNA gene sequencing.

RESULTS: No drug-related adverse events or gastrointestinal bleeding occurred in any group. Observed amplicon sequence variant (ASV) richness was significantly higher at week 24 than at baseline in the overall cohort (p = 0.003) and P-CAB group (p = 0.016), whereas the Shannon index showed no significant changes. Paired PERMANOVA with permutations restricted by patient ID revealed significant differences in Bray-Curtis beta diversity between baseline and week 24 in the P-CAB group (R² = 0.070, p = 0.031) and PPI group (R² = 0.059, p = 0.008), but not in the no acid-suppressive therapy group (R² = 0.021, p = 0.691). In the formal cross-arm analysis, the treatment group-by-visit interaction was not significant for Bray-Curtis beta diversity (R² = 0.021, pseudo-F = 0.505, p = 0.270). Although nominal within-arm taxonomic changes were observed, no treatment group-by-visit interaction survived Benjamini-Hochberg correction in ANCOM-BC2.

CONCLUSION: Tegoprazan was well tolerated, with no drug-related adverse events or gastrointestinal bleeding during the 24-week follow-up. Both acid-suppressive treatment groups showed modest longitudinal microbiome changes. The taxon-level findings were exploratory and hypothesis-generating and should not be interpreted as definitive evidence of treatment-specific differential effects. Larger, adequately powered studies are required to confirm these observations.},
}

Humans
Pilot Projects
Female
*Percutaneous Coronary Intervention/adverse effects
Male
*Gastrointestinal Microbiome/drug effects
*Proton Pump Inhibitors/administration & dosage/adverse effects/therapeutic use
Prospective Studies
Aged
Middle Aged
*Pantoprazole/administration & dosage/adverse effects/therapeutic use
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Dysbiosis/chemically induced
Gastrointestinal Hemorrhage/prevention & control

@article {pmid42935596,
year = {2026},
author = {Kool, J and Konstanti, P and van Dijken, H and Chu, MLJN and Nanlohy, NM and Bijvank, E and van Woudenbergh, E and van Beek, J and van Baarle, D and Fuentes, S},
title = {Linking nasopharyngeal and oropharyngeal microbiota to immune responses during influenza-like illness in an aging population.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117929},
pmid = {42935596},
issn = {2589-0042},
abstract = {Older adults are vulnerable to influenza-like illness (ILI). To study how infection shapes the respiratory microbiota, we profiled nasopharyngeal (NP) and oropharyngeal (OP) communities alongside local immune mediators in adults aged 60-88, comparing asymptomatic, ILI, and recovery states. NP communities clustered into three community state types (CSTs): Moraxella-dominated (CST-1), Haemophilus/Streptococcus/Staphylococcus-associated (CST-2), and Corynebacterium/Dolosigranulum-dominated (CST-3). During infection, compositional shifts were restricted to the NP niche, where CST-1 and CST-2 were more frequent. Streptococcus, Haemophilus and Moraxella were positively associated with inflammatory and interferon-related mediators, including IL-6, CXCL9 and CXCL10, while Corynebacterium showed negative associations. Immune activation was strong in the NP but limited in the OP, and stayed above healthy levels at follow-up, suggesting incomplete recovery. NP composition was also associated with symptom burden, viral and bacterial co-detection and smoking status. These site-specific microbiota-immune relationships identify the nasopharynx as the primary site of immune modulation during ILI in older adults.},
}

@article {pmid42935632,
year = {2026},
author = {Bae, YJ and Daily, JW and Park, S},
title = {Gut Microbiota as a Mechanistic Nexus between Type 2 Diabetes and Alzheimer's Disease: Insulin Resistance, Neuroinflammation, and Functional Food Strategies.},
journal = {Preventive nutrition and food science},
volume = {31},
number = {5},
pages = {},
pmid = {42935632},
issn = {2287-1098},
abstract = {Type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD) share substantial pathological overlap, including brain-specific insulin resistance driven by impaired insulin receptor substrate-1/phosphoinositide 3-kinase/protein kinase B signaling, glycogen synthase kinase-3β dysregulation, tau hyperphosphorylation, and amyloid-β accumulation. Brain-insulin resistance is a key mechanistic link between peripheral metabolic dysfunction and neurodegeneration, although the upstream regulatory pathways remain incompletely defined. Gastrointestinal depletion of butyrate-producing microbial taxa and enrichment of pro-inflammatory genera have been independently documented in T2DM and AD. Gut microbiota dysbiosis propagates insulin resistance through at least five pathways: short-chain fatty acid depletion, lipopolysaccharide (LPS)-mediated endotoxemia, bile acid dysregulation, tryptophan-kynurenine imbalance, and vagus nerve disruption. Critically, LPS translocation and kynurenine-driven neurotoxicity propagate AD-relevant neuroinflammation independently of peripheral metabolic dysfunction, implicating a bidirectional gut-brain mechanism. These risks are amplified in Asian populations, who exhibit a lower pancreatic β-cell mass and attenuated insulin secretion that confer disproportionate vulnerability to glucotoxic cycling and its neurological complications. Such a population-specific dimension remains largely absent from reviews. Against this backdrop, traditional Asian fermented foods (chungkookjang, kimchi, and natto) and plant-derived functional ingredients (Eucommia ulmoides, gooseberry, and black garlic) have a preclinical capacity to restore microbial balance, attenuate insulin resistance, and exert neuroprotection. This review integrates these strands into a unified mechanistic and translational framework, positioning gut microbiota modulation through culturally grounded dietary strategies as a tractable approach to reducing the converging burdens of T2DM and AD in Asians.},
}

@article {pmid42935770,
year = {2026},
author = {Wang, S and Chen, D and Yang, D and Gao, L and Zhang, Y},
title = {Modulation of Toll-like receptor signaling by intestinal bacteria in colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1963456},
pmid = {42935770},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/immunology/metabolism/pathology ; *Toll-Like Receptors/metabolism ; *Signal Transduction ; Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Bacteria/metabolism/immunology ; Dysbiosis ; },
abstract = {The gut microbiota contributes to intestinal homeostasis through dynamic interactions with epithelial, immune and stromal cells. Disruption of the balance, often termed dysbiosis, has been associated with colorectal cancer (CRC). At the same time, selected commensal bacteria have shown protective effects. Toll-like receptors (TLRs) provide an important molecular interface through which host cells detect bacterial components and initiate cellular responses. This Mini Review examines current evidence that intestinal bacteria and their products modulate TLR signaling in CRC, with effects that may promote or restrain tumor development. The reported mechanisms involve CRC cells as well as immune and stromal compartments within the tumor microenvironment. The available evidence does not support assigning a fixed biological effect to a bacterial species or TLR. Instead, the reported outcomes appear to vary with the nature of the bacterial stimulus, the responding cell and the disease setting. Resolving this context dependence may clarify how host cells translate bacterial stimuli through TLRs into responses that influence CRC progression and treatment response.},
}

Humans
*Colorectal Neoplasms/microbiology/immunology/metabolism/pathology
*Toll-Like Receptors/metabolism
*Signal Transduction
Tumor Microenvironment/immunology
*Gastrointestinal Microbiome/immunology
Animals
*Bacteria/metabolism/immunology
Dysbiosis

@article {pmid42935883,
year = {2026},
author = {Zhang, L and Jiang, T and Cao, R and Han, L and Ni, L},
title = {The liver-gut-bone axis in hepatic osteodystrophy: mechanisms, clinical evidence and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1935323},
pmid = {42935883},
issn = {2235-2988},
mesh = {Humans ; *Liver/pathology/metabolism ; *Bone and Bones/pathology/metabolism ; *Liver Diseases/complications ; Gastrointestinal Microbiome ; Animals ; Dysbiosis ; *Bone Diseases, Metabolic/etiology/therapy ; },
abstract = {Hepatic osteodystrophy (HOD) is an important but under-recognized complication of chronic liver disease (CLD), characterized by reduced bone mass, impaired bone microarchitecture and increased fragility fracture risk. Its skeletal phenotype and pathogenic mechanisms vary substantially according to CLD aetiology and disease stage. In metabolic dysfunction-associated steatotic liver disease (MASLD), skeletal risk is closely associated with metabolic dysfunction and hepatic fibrosis; alcohol-associated liver disease combines direct ethanol-related osteotoxicity with malnutrition and endocrine abnormalities; viral hepatitis-associated bone disease is influenced by persistent inflammation, disease stage and antiviral exposure; and cholestatic liver diseases are characterized by disrupted bile acid homeostasis, fat-soluble vitamin malabsorption and impaired bone formation. The liver-gut-bone axis provides an integrative framework linking these disease-specific features. Gut dysbiosis, intestinal barrier dysfunction, microbial translocation and altered metabolites, including short-chain fatty acids, bile acids and tryptophan-derived metabolites, may contribute to abnormal bone remodelling through inflammatory, metabolic and nutritional pathways. Cirrhosis further amplifies skeletal injury through sarcopenia, malnutrition and endocrine dysfunction. However, human evidence establishing a complete causal liver-gut-bone pathway remains limited. Current management should therefore focus on treatment of the underlying liver disease, fracture-risk assessment, nutritional and lifestyle interventions and evidence-based anti-osteoporotic therapy, while microbiota- and metabolite-targeted strategies remain investigational. Future prospective studies integrating microbiome and metabolomic profiling with bone turnover, microarchitecture and fracture outcomes are needed to clarify causal mechanisms and improve individualized management of CLD-associated HOD.},
}

Humans
*Liver/pathology/metabolism
*Bone and Bones/pathology/metabolism
*Liver Diseases/complications
Gastrointestinal Microbiome
Animals
Dysbiosis
*Bone Diseases, Metabolic/etiology/therapy

@article {pmid42936070,
year = {2026},
author = {Jiang, P and Yang, X and Zhang, C and Li, Y and Xu, C},
title = {Mendelian randomization of gut microbiota and exploratory testing of preventive effect of commercial Rothia mucilaginosa in constipated mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1941480},
pmid = {42936070},
issn = {1664-302X},
abstract = {Constipation is linked to gut microbiota dysbiosis, but causal microbial contributors and tractable bacterial interventions remain incompletely defined. This study first performed two-sample Mendelian randomization using Dutch Microbiome Project gut-microbiome Genome-Wide Association Study (GWAS) data (N = 7,738) and a European constipation GWAS (N = 411,623) to identify gut taxa linked to constipation. Then, in vitro metabolomics and a loperamide-induced constipation mouse model were used in male C57BL/6 mice to exploratorily test whether the commercial Rothia mucilaginosa strain BNCC363031 prevents loperamide-induced constipation. In an exploratory two-sample MR screen across 207 gut taxa, genetically predicted Rothia was nominally associated with lower constipation risk [odds ratio (OR) = 0.916, p = 0.0041], and the species-level Rothia mucilaginosa showed a concordant nominal protective association (OR = 0.921, p = 0.0232). In mice (n = 8 per group), preventive gavage partially restored loperamide-suppressed defecation: the cross-day mean fecal pellet count in the last 3 h per day was higher in the Rothia mucilaginosa group (RG) than in model controls (MCs) (7.94 vs. 4.41; p = 0.0306) but lower than in normal controls (NCs) (13.16; p = 0.00162), whereas body weight; small-intestinal transit; and immunohistochemical zonula occludens-1 (ZO-1), Claudin-1, and mucin 2 (MUC2) H-scores were unchanged. A fecal 16S V4 signal corresponding to R. mucilaginosa was detected at a very low abundance in only 2/8 RG mice; in vitro metabolomics identified candidates of secreted metabolites, including acetic acid. This study provides a reference for research on Rothia mucilaginosa in the context of constipation.},
}

@article {pmid42936086,
year = {2026},
author = {Gosain, M and Kaur, M and Talukdar, D and Tanwar, S and Jana, P and Karmakar, SP and Verma, J and Bakshi, S and Kamboj, K and Verma, P and Pareek, M and Raghavan, S and Kshetrapal, P and Bhatnagar, S and Bhattacharya, J and Garg, PK and Wadhwa, N and Das, B},
title = {Upper respiratory virome signatures reflect COVID-19 severity and post-recovery shifts.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1925299},
pmid = {42936086},
issn = {1664-302X},
abstract = {INTRODUCTION: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection profoundly affects the upper respiratory tract, yet the dynamics of the resident virome across different stages of Coronavirus Disease 2019 (COVID-19) and recovery remain poorly understood.

METHODS: This study profiled alterations in the virome and microbiome in 143 SARS-CoV-2-positive adults, stratified by disease severity (Non-Severe, Severe, Critical), compared with 96 RT-PCR-negative controls. Nasal and oral swabs underwent targeted viral enrichment and next-generation sequencing, followed by virome profiling.

RESULTS: The respiratory virome of SARS-CoV-2-positive individuals was dominated by SARS-CoV-2, with co-detected viruses such as Human Mastadenovirus C, which increased with disease severity and persisting post-recovery. Alpha diversity was highest in Non-Severe cases and declined in Severe and Critical groups, suggesting increasing disruption of the virome with disease severity. Beta diversity showed clear separation between controls and cases, and across severity levels. LEfSe identified distinct viral signatures differentiating infection status, and logistic regression of key viral taxa accurately classified Critical versus post-recovery samples (AUC = 0.91). Although the study focused on viruses, bacterial taxa including Rothia mucilaginosa and Haemophilus parahaemolyticus were also detected with severity-linked variation, highlighting viral-bacterial interactions. Longitudinal paired analysis revealed consistent post-recovery enrichment of Streptococcus-specific bacteriophages across all severity groups, suggesting restoration of Streptococcus-associated phage dynamics during convalescence.

DISCUSSION: Overall, this study reveals SARS-CoV-2-associated alterations in the respiratory virome and microbiome and highlights specific microbial taxa with potential as biomarkers for disease severity and post-infection recovery.},
}

@article {pmid42936144,
year = {2026},
author = {Zhang, Y and Bian, N and Dong, Z and Ren, B and Li, J},
title = {From correlation to causation: dissecting the detection methodologies of oral bacterial-fungal crosstalk in health and disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1937704},
pmid = {42936144},
issn = {1664-302X},
abstract = {In the oral microecosystem, cross-kingdom interactions between bacteria and fungi are pivotal ecological events that determine the equilibrium between oral health and disease. Historically, technical limitations have confined research to describing correlations in microbial community composition, hindering the elucidation of underlying pathogenic mechanisms. This review aims to systematically outline the evolution of detection technologies for oral bacterial-fungal interactions and critically discuss the paradigm shift from identifying "associative correlations" to deciphering "causal mechanisms." The literature search encompassed studies ranging from traditional culture and molecular identification to high-throughput sequencing for ecological network construction, as well as cutting-edge multi-omics integration and high-resolution imaging technologies. Beyond cataloguing technical advances, we critically evaluate the level of causal inference supported by each methodological class, with particular attention to temporality, confounding, ecological simplification, and the need for perturbational validation in disease-relevant models. Representative studies are used to illustrate how evidence can progress from co-occurrence and spatial proximity to functional dependency and mechanism.},
}

@article {pmid42936186,
year = {2026},
author = {Lahtinen, E and Hugerth, LW and Edfeldt, G and Säfholm, A and Kornfält, S and Strevens, H and Schuppe-Koistinen, I},
title = {Effect of pHyph, A novel antibiotic-free treatment, on bacterial vaginosis symptoms and vaginal microbiome composition.},
journal = {European journal of obstetrics & gynecology and reproductive biology: X},
volume = {32},
number = {},
pages = {100497},
pmid = {42936186},
issn = {2590-1613},
abstract = {BACKGROUND: Bacterial vaginosis (BV) is the most prevalent vaginal infection among reproductive-age women and is associated with increased susceptibility to gynecological complications. Current antibiotic treatments achieve high initial cure rates but show high rates of recurrence, partly due to their inability to remove persistent biofilms. pHyph is a novel, non-antibiotic treatment that lowers vaginal pH, promoting Lactobacillus growth and biofilm disruption.

OBJECTIVE: To evaluate the immediate and long-term effects of pHyph on the vaginal microbiome, BV resolution, and symptom reduction.

STUDY DESIGN: In a randomized, controlled, partially blinded study, 61 women with clinically diagnosed BV were randomized to immediate (IT, n = 35) or delayed (DT, n = 26) treatment. Vaginal swabs were collected before treatment, after 6 days, and during maintenance to Day 70. Microbiome composition was analyzed using a qPCR panel targeting 47 bacterial and 6 fungal species.

RESULTS: Compared to controls, pHyph reduced the abundance of multiple BV-associated species and increased Lactobacillus iners following 6-day treatment (median 8.96 ×10[3] [Q1-Q3: 3.10 ×10[3]-2.72 ×10[4]] vs. median 9.44 × 10² [Q1-Q3: 0.00-4.29 × 10 ³] normalized qPCR counts, p < 0.05). Additionally, pHyph reduced BV-related symptoms, particularly fishy odor (p < 0.05). Treatment promoted a shift to CST III microbiome composition, and maintenance dosing was associated with sustained Lactobacillus abundance up to Day 70.

CONCLUSIONS: pHyph shows potential as an alternative BV treatment by reducing BV-associated pathogens while promoting lactobacilli. Extended dosing may enhance microbiome stability.},
}

@article {pmid42936198,
year = {2026},
author = {Han, Y and Liu, J and Song, C and Fu, L and Gu, Y and Zeng, Y and Zou, Z},
title = {Multi-omics insights into immune dysregulation and candidate biological programs in kawasaki disease: toward precision immunomodulation.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1960681},
pmid = {42936198},
issn = {2296-2360},
abstract = {Kawasaki disease (KD) is an immune-mediated pediatric vasculitis characterized by dynamic interactions among genetic susceptibility, innate and adaptive immune activation, endothelial dysfunction, and vascular remodeling. Although intravenous immunoglobulin (IVIG) therapy substantially reduces coronary complications, 10%-20% of patients show persistent or recurrent fever after initial IVIG treatment, and reliable clinically validated molecular approaches for diagnosis, treatment-response prediction, and coronary-risk stratification remain unavailable. Recent advances in multi-omics technologies, including genomics, epigenomics, transcriptomics, single-cell sequencing, proteomics, metabolomics, and microbiome profiling, have expanded our understanding of KD-associated immune dysregulation. However, the clinical interpretation of these molecular findings remains challenging because of limited cohort sizes, heterogeneous control populations, treatment-related confounding, and insufficient external validation. In this review, we integrate evidence across multiple molecular layers and propose a framework in which current KD multi-omics findings converge into candidate biological programs rather than fixed molecular subtypes. These programs may represent temporally dynamic biological states along a shared inflammatory trajectory, influenced by disease phase, cellular composition, genetic background, and treatment exposure. Synthesized from convergent multi-omics evidence rather than derived from formal molecular classification, these candidate biological programs include myeloid inflammatory activation characterized by S100A8/A9 and IL-1/NF-κB signaling, interferon-associated immune responses, and vascular injury/remodeling responses involving endothelial activation and extracellular matrix regulation. Current evidence supports biologically meaningful molecular programs that may contribute to clinical heterogeneity, but prospective validation is required before molecular signatures can be applied as clinical classifiers or treatment-selection tools. Integrating multi-omics approaches with functional validation, longitudinal sampling, and multicenter studies may facilitate the development of precision immunomodulation strategies for Kawasaki disease.},
}

@article {pmid42936271,
year = {2026},
author = {Ben Said, M and Selmi, R and Belkahia, H},
title = {Vector-borne zoonotic bacteria in Tunisia: from fragmented data to an integrated One Health surveillance framework.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1951493},
pmid = {42936271},
issn = {1664-302X},
abstract = {Vector-borne and vector-associated bacterial zoonoses represent an important component of infectious disease epidemiology in Tunisia. This review synthesizes available evidence on major bacterial groups, including Rickettsia, Bartonella, Anaplasma, Ehrlichia, Borrelia, Coxiella burnetii, and other arthropod-associated bacteria, using a One Health framework integrating human, animal, vector, wildlife, and environmental compartments. The available evidence reveals heterogeneous levels of knowledge across bacterial taxa. Rickettsia represents the most established tick-associated zoonotic system, with Rickettsia conorii as the main confirmed human pathogen, while additional species have been detected mainly in arthropods or animal-associated settings. Bartonella has a significant clinical association with blood culture-negative endocarditis, whereas other bacterial groups show predominantly animal- or vector-associated evidence. Coxiella burnetii remains a major zoonotic concern linked to livestock, camels, reproductive materials, and environmental exposure. For Borrelia, Anaplasma, and Ehrlichia, substantial evidence of circulation exists in vectors and animals, but human clinical relevance remains incompletely characterized. Across bacterial groups, a recurrent limitation is the imbalance between molecular detection in vectors or animal hosts and confirmed evidence of transmission or human disease. Detection of bacterial DNA should therefore be interpreted cautiously and not considered equivalent to infection, reservoir competence, or vectorial transmission. Additional arthropod-associated bacteria identified through microbiome studies require further investigation to clarify their ecological significance. The Tunisian evidence base demonstrates active circulation of diverse vector-associated bacteria but remains fragmented across clinical, veterinary, entomological, and ecological domains. Strengthening integrated One Health surveillance through coordinated human diagnosis, animal sentinel systems, vector monitoring, environmental investigations, and advanced molecular approaches is essential to better assess zoonotic risks in Tunisia and the wider North African-Mediterranean region.},
}