Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition

作者：Lingyan Ma, Wentao Lyu, Tao Zeng, Wen Wang, Qu Chen, Jiangchao Zhao, Guolong Zhang, Lizhi Lu, Hua Yang, Yingping Xiao · 发表于：iMeta · 年份：2024 · DOI：10.1002/imt2.198 · 被引用次数：80 · 研究领域：Gut microbiota and health、Probiotics and Fermented Foods、Genomics and Phylogenetic Studies

The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome-assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region-specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic-resistance genes. Taken togethe...