Characterizing core microbiota and regulatory functions of the pig gut microbiome

生物 基因组 肠道菌群 微生物群 普雷沃菌属 微生物学 基因 遗传学 细菌 生物化学
作者
Jun Hu,Jianwei Chen,Libao Ma,Qiliang Hou,Yong Zhang,Xiangfeng Kong,Xingguo Huang,Zhonglin Tang,Hong Wei,Xiangru Wang,Xianghua Yan
出处
期刊:The ISME Journal [Springer Nature]
卷期号:18 (1) 被引量:9
标识
DOI:10.1093/ismejo/wrad037
摘要

Abstract Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host–microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as “steroid hormone biosynthesis,” “primary bile acid biosynthesis,” “phenylalanine, tyrosine and tryptophan biosynthesis,” and “phenylalanine metabolism”) in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.
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