Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome

Congying Chen (), Yunyan Zhou, Hao Fu, Xinwei Xiong, Shaoming Fang, Hui Jiang, Jinyuan Wu, Hui Yang, Jun Gao and Lusheng Huang ()
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Congying Chen: Jiangxi Agricultural University
Yunyan Zhou: Jiangxi Agricultural University
Hao Fu: Jiangxi Agricultural University
Xinwei Xiong: Jiangxi Agricultural University
Shaoming Fang: Jiangxi Agricultural University
Hui Jiang: Jiangxi Agricultural University
Jinyuan Wu: Jiangxi Agricultural University
Hui Yang: Jiangxi Agricultural University
Jun Gao: Jiangxi Agricultural University
Lusheng Huang: Jiangxi Agricultural University

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.

Date: 2021
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DOI: 10.1038/s41467-021-21295-0

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