Insights from Metagenomics on Microbial Biosynthesis of Vitamins B and K2 in Chicken Gut

Hai-Long Yu^1,2,3Xin-Wen Hou⁴Ji-Xin Zhao⁴Guo-Hua Liu⁵Jinxin Meng^4,6Yong-Jie Wei⁴Yanan Cai³Jian Liu⁴Kai-Meng Shang⁴Hong-Bo Ni⁴Rui Liu⁴He Ma⁴Fulong Nan⁴Xiao-Xuan Zhang⁴Bei-Ni Chen²Xing Yang^1*

• ¹Dali University, Dali, China
• ²Changchun Sci-Tech University, Changchun, China
• ³Jilin Agricultural University, Changchun, China
• ⁴Qingdao Agricultural University, Qingdao, China
• ⁵Hunan Agricultural University, Changsha, China
• ⁶Zhejiang University, Hangzhou, China

This study aims to understand microbe-mediated biosynthesis of vitamins B and K2 in the chicken gut. 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 obtained. Whole-genome clustering analysis identified 2,675 species-level genome bins (SGBs), predominantly from the phyla Bacillota, Bacteroidota, Pseudomonadota, and Actinomycetota. A gene catalog comprising 9.69 million genes revealed that 195,517 genes are involved in the biosynthesis of vitamins B and K2, exhibiting significant regional variation. The large intestine exhibited greater species richness and evenness compared to the small intestine. After analyzing 13,734 non-redundant 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 (B12) biosynthesis highlighted the predominance of the anaerobic pathway. Additionally, changes in microbial abundance were observed, such as increased abundance of the genera Phocaeicola and Faecalibacterium during bacterial infections, and Limisoma during parasitic infections. We primarily presented a comprehensive gene catalog and identified 3,063 microbial genomes involved in the biosynthesis of vitamins B and K2 in chickens. Our findings provide detailed metagenomic insights into the capacity of chicken gut microbiome for vitamins B and K2 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.