The genomic landscape of reference genomes of cultivated human gut bacteria

• Published in: Nature communications Vol. 14; no. 1; pp. 1663 - 11
• Main Authors: Lin, Xiaoqian, Hu, Tongyuan, Chen, Jianwei, Liang, Hewei, Zhou, Jianwei, Wu, Zhinan, Ye, Chen, Jin, Xin, Xu, Xun, Zhang, Wenwei, Jing, Xiaohuan, Yang, Tao, Wang, Jian, Yang, Huanming, Kristiansen, Karsten, Xiao, Liang, Zou, Yuanqiang
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.03.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/326/325/2482; 631/326/41/2530; Bacteria; Bacteriophages - genetics; Digestive system; Feces; Gastrointestinal Microbiome - genetics; Gastrointestinal tract; Gene clusters; Genome, Bacterial - genetics; Genomes; Genomics; Humanities and Social Sciences; Humans; Intestinal microflora; Metabolites; Metagenome - genetics; Metagenomics; Microbiota; multidisciplinary; Phages; Science; Science (multidisciplinary); Species; Species classification
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-37396-x

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. Here, the authors present an expanded version of the Cultivated Genome Reference (CGR), termed CGR2, a catalog that includes 3324 high-quality draft genomes based on gut bacterial isolates from Chinese individuals, and classifies 527 species from 8 phyla, including 179 previously unidentified species, and provides information of secondary metabolite biosynthetic gene clusters and gut phage-bacteria interactions.