The genomic landscape of reference genomes of cultivated human gut bacteria.
Nat Commun, 2023/03/25;14(1):1663.
Lin X[1, 2], Hu T[1], Chen J[1, 3, 4], Liang H[1], Zhou J[3], Wu Z[1, 5], Ye C[1], Jin X[1], Xu X[1], Zhang W[1], Jing X[6], Yang T[6], Wang J[1, 7], Yang H[1, 7], Kristiansen K[8, 9, 10, 11], Xiao L[12, 13, 14], Zou Y[15, 16, 17, 18]
Affiliations
PMID: 36966151DOI: 10.1038/s41467-023-37396-x
Impact factor: 17.694
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.
MeSH terms
Humans; Genome, Bacterial; Genomics; Metagenome; Gastrointestinal Microbiome; Bacteria; Metagenomics; Bacteriophages
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