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The genomic landscape of reference genomes of cultivated human gut bacteria

Author

Listed:
  • Xiaoqian Lin

    (BGI-Shenzhen
    South China University of Technology)

  • Tongyuan Hu

    (BGI-Shenzhen)

  • Jianwei Chen

    (BGI-Shenzhen
    BGI-Shenzhen
    University of Copenhagen)

  • Hewei Liang

    (BGI-Shenzhen)

  • Jianwei Zhou

    (BGI-Shenzhen)

  • Zhinan Wu

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • 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
    James D. Watson Institute of Genome Sciences)

  • Huanming Yang

    (BGI-Shenzhen
    James D. Watson Institute of Genome Sciences)

  • Karsten Kristiansen

    (BGI-Shenzhen
    BGI-Shenzhen
    University of Copenhagen
    Aalborg University)

  • Liang Xiao

    (BGI-Shenzhen
    BGI-Shenzhen
    BGI-Shenzhen)

  • Yuanqiang Zou

    (BGI-Shenzhen
    BGI-Shenzhen
    University of Copenhagen
    BGI-Shenzhen)

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.

Suggested Citation

  • 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 Kristian, 2023. "The genomic landscape of reference genomes of cultivated human gut bacteria," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37396-x
    DOI: 10.1038/s41467-023-37396-x
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