IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v550y2017i7674d10.1038_nature23889.html
   My bibliography  Save this article

Strains, functions and dynamics in the expanded Human Microbiome Project

Author

Listed:
  • Jason Lloyd-Price

    (Harvard T. H. Chan School of Public Health
    The Broad Institute)

  • Anup Mahurkar

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Gholamali Rahnavard

    (Harvard T. H. Chan School of Public Health
    The Broad Institute)

  • Jonathan Crabtree

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Joshua Orvis

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • A. Brantley Hall

    (The Broad Institute)

  • Arthur Brady

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Heather H. Creasy

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Carrie McCracken

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Michelle G. Giglio

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Daniel McDonald

    (University of California San Diego)

  • Eric A. Franzosa

    (Harvard T. H. Chan School of Public Health
    The Broad Institute)

  • Rob Knight

    (University of California San Diego
    University of California San Diego)

  • Owen White

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Curtis Huttenhower

    (Harvard T. H. Chan School of Public Health
    The Broad Institute)

Abstract

The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.

Suggested Citation

  • Jason Lloyd-Price & Anup Mahurkar & Gholamali Rahnavard & Jonathan Crabtree & Joshua Orvis & A. Brantley Hall & Arthur Brady & Heather H. Creasy & Carrie McCracken & Michelle G. Giglio & Daniel McDona, 2017. "Strains, functions and dynamics in the expanded Human Microbiome Project," Nature, Nature, vol. 550(7674), pages 61-66, October.
    • Handle: RePEc:nat:nature:v:550:y:2017:i:7674:d:10.1038_nature23889
    DOI: 10.1038/nature23889
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature23889
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/nature23889?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Sang Chul Park & Il-Ho Park & Joong Seob Lee & Sung Min Park & Sung Hun Kang & Seok-Min Hong & Soo-Hwan Byun & Yong Gi Jung & Seok Jin Hong, 2021. "Microbiome of Unilateral Chronic Rhinosinusitis: A Controlled Paired Analysis," IJERPH, MDPI, vol. 18(18), pages 1-16, September.
    2. Louis J. Cohen & Sun M. Han & Pearson Lau & Daniela Guisado & Yupu Liang & Toshiki G. Nakashige & Thamina Ali & David Chiang & Adeeb Rahman & Sean F. Brady, 2022. "Unraveling function and diversity of bacterial lectins in the human microbiome," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Jing Ma, 2021. "Joint Microbial and Metabolomic Network Estimation with the Censored Gaussian Graphical Model," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 13(2), pages 351-372, July.
    4. Doris Vandeputte & Lindsey Commer & Raul Y. Tito & Gunter Kathagen & João Sabino & Séverine Vermeire & Karoline Faust & Jeroen Raes, 2021. "Temporal variability in quantitative human gut microbiome profiles and implications for clinical research," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    5. Benjamin H. Good & Layton B. Rosenfeld, 2023. "Eco-evolutionary feedbacks in the human gut microbiome," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    6. Soo Hwan Byun & Sunki Lee & Sung Hun Kang & Hyo Geun Choi & Seok Jin Hong, 2020. "Cross-Sectional Analysis of the Association between Periodontitis and Cardiovascular Disease Using the Korean Genome and Epidemiology Study Data," IJERPH, MDPI, vol. 17(14), pages 1-12, July.
    7. Patrick A. Jonge & Koen Wortelboer & Torsten P. M. Scheithauer & Bert-Jan H. Born & Aeilko H. Zwinderman & Franklin L. Nobrega & Bas E. Dutilh & Max Nieuwdorp & Hilde Herrema, 2022. "Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    8. Ying Liao & Yan-Xia Wu & Minzhong Tang & Yi-Wei Chen & Jin-Ru Xie & Yan Du & Tong-Min Wang & Yong-Qiao He & Wen-Qiong Xue & Xiao-Hui Zheng & Qiao-Yun Liu & Mei-Qi Zheng & Yi-Jing Jia & Xia-Ting Tong &, 2024. "Microbes translocation from oral cavity to nasopharyngeal carcinoma in patients," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    9. Kerstin Thriene & Karin B. Michels, 2023. "Human Gut Microbiota Plasticity throughout the Life Course," IJERPH, MDPI, vol. 20(2), pages 1-14, January.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:550:y:2017:i:7674:d:10.1038_nature23889. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.