The genomic landscape of reference genomes of cultivated human gut bacteria

Xiaoqian Lin, Tongyuan Hu, Jianwei Chen, Hewei Liang, Jianwei Zhou, Zhinan Wu, Chen Ye, Xin Jin, Xun Xu, Wenwei Zhang, Xiaohuan Jing, Tao Yang, Jian Wang, Huanming Yang, Karsten Kristiansen (), Liang Xiao () and Yuanqiang Zou ()
Additional contact information
Xiaoqian Lin: BGI-Shenzhen
Tongyuan Hu: BGI-Shenzhen
Jianwei Chen: BGI-Shenzhen
Hewei Liang: BGI-Shenzhen
Jianwei Zhou: BGI-Shenzhen
Zhinan Wu: BGI-Shenzhen
Chen Ye: BGI-Shenzhen
Xin Jin: BGI-Shenzhen
Xun Xu: BGI-Shenzhen
Wenwei Zhang: BGI-Shenzhen
Xiaohuan Jing: BGI-Shenzhen
Tao Yang: BGI-Shenzhen
Jian Wang: BGI-Shenzhen
Huanming Yang: BGI-Shenzhen
Karsten Kristiansen: BGI-Shenzhen
Liang Xiao: BGI-Shenzhen
Yuanqiang Zou: BGI-Shenzhen

Nature Communications, 2023, vol. 14, issue 1, 1-11

Abstract: Abstract Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage–bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.

Date: 2023
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DOI: 10.1038/s41467-023-37396-x

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