State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
Nat Commun. 2021 Feb 17;12(1):1106. doi: 10.1038/s41467-021-21295-0.
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.
肠道微生物在猪的健康和生产中起着重要作用。然而，大多数猪肠道微生物的测序基因组和功能信息仍然有限。在这里，我们通过深度宏基因组测序对猪肠道微生物组进行了景观调查，涵盖了广泛的样本来源，从而扩展了基因目录，命名为猪综合基因目录（PIGC），其中包含了 787 个肠道宏基因组中 90%蛋白质同一性聚类的 17237052 个完整基因，其中 28%是未知蛋白。通过分箱分析，获得了 6339 个宏基因组组装基因组（MAG），这些基因组聚类为 2673 个种水平基因组分箱（SGB），其中 86%（2309）SGB 基于当前数据库是未知的。利用现有的基因目录和 MAGs，我们鉴定了野猪和商业杜洛克猪肠道微生物组之间的几个菌株水平差异。PIGC 和 MAGs 为猪肠道微生物组相关研究提供了扩展的资源。
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