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New insights from uncultivated genomes of the global human gut microbiome

Author

Listed:
  • Stephen Nayfach

    (United States Department of Energy Joint Genome Institute
    Lawrence Berkeley National Laboratory)

  • Zhou Jason Shi

    (Gladstone Institutes
    Chan-Zuckerberg Biohub)

  • Rekha Seshadri

    (United States Department of Energy Joint Genome Institute
    Lawrence Berkeley National Laboratory)

  • Katherine S. Pollard

    (Gladstone Institutes
    Chan-Zuckerberg Biohub
    University of California San Francisco
    University of California San Francisco)

  • Nikos C. Kyrpides

    (United States Department of Energy Joint Genome Institute
    Lawrence Berkeley National Laboratory)

Abstract

The genome sequences of many species of the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3,810 faecal metagenomes, from geographically and phenotypically diverse humans. These genomes provide reference points for 2,058 newly identified species-level operational taxonomic units (OTUs), which represents a 50% increase over the previously known phylogenetic diversity of sequenced gut bacteria. On average, the newly identified OTUs comprise 33% of richness and 28% of species abundance per individual, and are enriched in humans from rural populations. A meta-analysis of clinical gut-microbiome studies pinpointed numerous disease associations for the newly identified OTUs, which have the potential to improve predictive models. Finally, our analysis revealed that uncultured gut species have undergone genome reduction that has resulted in the loss of certain biosynthetic pathways, which may offer clues for improving cultivation strategies in the future.

Suggested Citation

  • Stephen Nayfach & Zhou Jason Shi & Rekha Seshadri & Katherine S. Pollard & Nikos C. Kyrpides, 2019. "New insights from uncultivated genomes of the global human gut microbiome," Nature, Nature, vol. 568(7753), pages 505-510, April.
  • Handle: RePEc:nat:nature:v:568:y:2019:i:7753:d:10.1038_s41586-019-1058-x
    DOI: 10.1038/s41586-019-1058-x
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    Cited by:

    1. Shuqin Zeng & Dhrati Patangia & Alexandre Almeida & Zhemin Zhou & Dezhi Mu & R. Paul Ross & Catherine Stanton & Shaopu Wang, 2022. "A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Mingyue Cheng & Shuai Luo & Peng Zhang & Guangzhou Xiong & Kai Chen & Chuanqi Jiang & Fangdian Yang & Hanhui Huang & Pengshuo Yang & Guanxi Liu & Yuhao Zhang & Sang Ba & Ping Yin & Jie Xiong & Wei Mia, 2024. "A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Adina Howe & Nejc Stopnisek & Shane K. Dooley & Fan Yang & Keara L. Grady & Ashley Shade, 2023. "Seasonal activities of the phyllosphere microbiome of perennial crops," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. J. L. Rolando & M. Kolton & T. Song & Y. Liu & P. Pinamang & R. Conrad & J. T. Morris & K. T. Konstantinidis & J. E. Kostka, 2024. "Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Bin Ma & Caiyu Lu & Yiling Wang & Jingwen Yu & Kankan Zhao & Ran Xue & Hao Ren & Xiaofei Lv & Ronghui Pan & Jiabao Zhang & Yongguan Zhu & Jianming Xu, 2023. "A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    6. Li Zhang & Karen R. Jonscher & Zuyuan Zhang & Yi Xiong & Ryan S. Mueller & Jacob E. Friedman & Chongle Pan, 2022. "Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    7. Joe J. Lim & Christian Diener & James Wilson & Jacob J. Valenzuela & Nitin S. Baliga & Sean M. Gibbons, 2023. "Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Elio L Herzog & Melania Wäfler & Irene Keller & Sebastian Wolf & Martin S Zinkernagel & Denise C Zysset-Burri, 2021. "The importance of age in compositional and functional profiling of the human intestinal microbiome," PLOS ONE, Public Library of Science, vol. 16(10), pages 1-13, October.
    9. Fiona B. Tamburini & Dylan Maghini & Ovokeraye H. Oduaran & Ryan Brewster & Michaella R. Hulley & Venesa Sahibdeen & Shane A. Norris & Stephen Tollman & Kathleen Kahn & Ryan G. Wagner & Alisha N. Wade, 2022. "Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    10. Sigal Leviatan & Saar Shoer & Daphna Rothschild & Maria Gorodetski & Eran Segal, 2022. "An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    11. Chan Yeong Kim & Junyeong Ma & Insuk Lee, 2022. "HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    12. Ziye Wang & Ronghui You & Haitao Han & Wei Liu & Fengzhu Sun & Shanfeng Zhu, 2024. "Effective binning of metagenomic contigs using contrastive multi-view representation learning," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    13. Djawad Radjabzadeh & Jos A. Bosch & André G. Uitterlinden & Aeilko H. Zwinderman & M. Arfan Ikram & Joyce B. J. Meurs & Annemarie I. Luik & Max Nieuwdorp & Anja Lok & Cornelia M. Duijn & Robert Kraaij, 2022. "Gut microbiome-wide association study of depressive symptoms," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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