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An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species

Author

Listed:
  • Sigal Leviatan

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Saar Shoer

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Daphna Rothschild

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Maria Gorodetski

    (DayTwo LTD)

  • Eran Segal

    (Weizmann Institute of Science
    Weizmann Institute of Science)

Abstract

The gut is the richest ecosystem of microbes in the human body and has great influence on our health. Despite many efforts, the set of microbes inhabiting this environment is not fully known, limiting our ability to identify microbial content and to research it. In this work, we combine new microbial metagenomic assembled genomes from 51,052 samples, with previously published genomes to produce a curated set of 241,118 genomes. Based on this set, we procure a new and improved human gut microbiome reference set of 3594 high quality species genomes, which successfully matches 83.65% validation samples’ reads. This improved reference set contains 310 novel species, including one that exists in 19% of validation samples. Overall, this study provides a gut microbial genome reference set that can serve as a valuable resource for further research.

Suggested Citation

  • 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.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31502-1
    DOI: 10.1038/s41467-022-31502-1
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    References listed on IDEAS

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    1. 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.
    2. Daphna Rothschild & Sigal Leviatan & Ariel Hanemann & Yossi Cohen & Omer Weissbrod & Eran Segal, 2022. "An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents," PLOS ONE, Public Library of Science, vol. 17(3), pages 1-20, March.
    3. Erica C. Pehrsson & Pablo Tsukayama & Sanket Patel & Melissa Mejía-Bautista & Giordano Sosa-Soto & Karla M. Navarrete & Maritza Calderon & Lilia Cabrera & William Hoyos-Arango & M. Teresita Bertoli & , 2016. "Interconnected microbiomes and resistomes in low-income human habitats," Nature, Nature, vol. 533(7602), pages 212-216, May.
    4. Hilary P. Browne & Samuel C. Forster & Blessing O. Anonye & Nitin Kumar & B. Anne Neville & Mark D. Stares & David Goulding & Trevor D. Lawley, 2016. "Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation," Nature, Nature, vol. 533(7604), pages 543-546, May.
    5. Emmanuelle Le Chatelier & Trine Nielsen & Junjie Qin & Edi Prifti & Falk Hildebrand & Gwen Falony & Mathieu Almeida & Manimozhiyan Arumugam & Jean-Michel Batto & Sean Kennedy & Pierre Leonard & Junhua, 2013. "Richness of human gut microbiome correlates with metabolic markers," Nature, Nature, vol. 500(7464), pages 541-546, August.
    6. Francesco Asnicar & Andrew Maltez Thomas & Francesco Beghini & Claudia Mengoni & Serena Manara & Paolo Manghi & Qiyun Zhu & Mattia Bolzan & Fabio Cumbo & Uyen May & Jon G. Sanders & Moreno Zolfo & Evg, 2020. "Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    7. Alexandre Almeida & Alex L. Mitchell & Miguel Boland & Samuel C. Forster & Gregory B. Gloor & Aleksandra Tarkowska & Trevor D. Lawley & Robert D. Finn, 2019. "A new genomic blueprint of the human gut microbiota," Nature, Nature, vol. 568(7753), pages 499-504, April.
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    Cited by:

    1. Ayya Keshet & Eran Segal, 2024. "Identification of gut microbiome features associated with host metabolic health in a large population-based cohort," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

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