{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T02:25:21Z","timestamp":1793931921014,"version":"4.8.0"},"reference-count":68,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T00:00:00Z","timestamp":1755129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Vet. Sci."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>The chicken gut microbiome plays a pivotal role in nutrient absorption and overall health, contributing to the biosynthesis of essential vitamins. However, the biosynthesis of vitamins B and K<jats:sub>2<\/jats:sub> by the whole gut microbiome, as well as their abundances across different gut regions, remains largely unknown.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We employed both metagenomic sequencing and culture-based techniques, collecting a total of 25,825 genomes (25,764 metagenome-assembled genomes and 61 isolated genomes). After quality assessment and average nucleotide identity (ANI), 13,734 genomes were retained for downstream analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Whole-genome clustering analysis identified 2,675 species-level genome bins (SGBs), predominantly from the phyla <jats:italic>Bacillota, Bacteroidota, Pseudomonadota,<\/jats:italic> and <jats:italic>Actinomycetota<\/jats:italic>. A gene catalog comprising 9.69 million genes revealed that 195,517 genes are involved in the biosynthesis of vitamins B and K<jats:sub>2<\/jats:sub>, exhibiting significant regional variation. The large intestine exhibited greater species richness and evenness compared to the small intestine. From the 13,734 genomes, we discovered 3,063 high-quality ones capable of synthesizing at least one vitamin. Genomic analysis revealed that a mere 8.2% of genomes were capable of producing five or more vitamins, while almost half were limited to synthesizing just one. Comparative genomics of cobalamin (B<jats:sub>12<\/jats:sub>) biosynthesis highlighted the predominance of the anaerobic pathway. Additionally, changes in microbial abundance were observed, such as increased abundance of the genera <jats:italic>Phocaeicola<\/jats:italic> and <jats:italic>Faecalibacterium<\/jats:italic> during bacterial infections, and <jats:italic>Limisoma<\/jats:italic> during parasitic infections.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>This study provides detailed metagenomic insights into the capacity of chicken gut microbiome for vitamins B and K<jats:sub>2<\/jats:sub> biosynthesis, revealing significant regional and taxonomic variations. These results suggest a collaborative microbial effort in vitamin biosynthesis, with potential implications for optimizing poultry health and nutrition through targeted microbial interventions.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fvets.2025.1646825","type":"journal-article","created":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T15:55:32Z","timestamp":1755186932000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut 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