Yu Hai-Long, Hou Xin-Wen, Zhao Ji-Xin, Liu Guo-Hua, Meng Jin-Xin, Wei Yong-Jie, Cai Yanan, Liu Jian, Shang Kai-Meng, Ni Hong-Bo, Liu Rui, Ma He, Nan Fu-Long, Zhang Xiao-Xuan, Chen Bei-Ni, Yang Xing
Department of Medical Microbiology and Immunology, School of Basic Medicine, Dali University, Dali, Yunnan Province, China.
College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, China.
Front Vet Sci. 2025 Aug 14;12:1646825. doi: 10.3389/fvets.2025.1646825. eCollection 2025.
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 by the whole gut microbiome, as well as their abundances across different gut regions, remains largely unknown.
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.
Whole-genome clustering analysis identified 2,675 species-level genome bins (SGBs), predominantly from the phyla and . A gene catalog comprising 9.69 million genes revealed that 195,517 genes are involved in the biosynthesis of vitamins B and K, 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) biosynthesis highlighted the predominance of the anaerobic pathway. Additionally, changes in microbial abundance were observed, such as increased abundance of the genera and during bacterial infections, and during parasitic infections.
This study provides detailed metagenomic insights into the capacity of chicken gut microbiome for vitamins B and K 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.
鸡的肠道微生物群在营养吸收和整体健康中起着关键作用，有助于必需维生素的生物合成。然而，整个肠道微生物群对维生素B和K的生物合成及其在不同肠道区域的丰度仍知之甚少。
我们采用了宏基因组测序和基于培养的技术，共收集了25825个基因组（25764个宏基因组组装基因组和61个分离基因组）。经过质量评估和平均核苷酸同一性（ANI）分析后，保留了13734个基因组用于下游分析。
全基因组聚类分析确定了2675个物种水平的基因组箱（SGB），主要来自门和。一个包含969万个基因的基因目录显示，有195517个基因参与维生素B和K的生物合成，呈现出显著的区域差异。与小肠相比，大肠表现出更高的物种丰富度和均匀度。从13734个基因组中，我们发现了3063个能够合成至少一种维生素的高质量基因组。基因组分析表明，只有8.2%的基因组能够产生五种或更多种维生素，而几乎一半的基因组仅限于合成一种。钴胺素（B）生物合成的比较基因组学突出了厌氧途径的优势。此外，还观察到微生物丰度的变化，例如在细菌感染期间属和属的丰度增加，以及在寄生虫感染期间属的丰度增加。
本研究提供了关于鸡肠道微生物群合成维生素B和K能力的详细宏基因组见解，揭示了显著的区域和分类差异。这些结果表明微生物在维生素生物合成中协同作用，通过有针对性地干预微生物对优化家禽健康和营养具有潜在意义。
