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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
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    Cited by:

    1. Minghui Cheng & Yingjie Xu & Xiao Cui & Xin Wei & Yundi Chang & Jun Xu & Cheng Lei & Lei Xue & Yifan Zheng & Zhang Wang & Lingtong Huang & Min Zheng & Hong Luo & Yuxin Leng & Chao Jiang, 2024. "Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. 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.
    3. 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.
    4. Yuanlin Wang & Yaqian Han & Chenhui Yang & Tiancheng Bai & Chenggang Zhang & Zhaotong Wang & Ye Sun & Ying Hu & Flemming Besenbacher & Chunying Chen & Miao Yu, 2024. "Long-term relapse-free survival enabled by integrating targeted antibacteria in antitumor treatment," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    11. Yolanda Y. Huang & Morgan N. Price & Allison Hung & Omree Gal-Oz & Surya Tripathi & Christopher W. Smith & Davian Ho & Héloïse Carion & Adam M. Deutschbauer & Adam P. Arkin, 2024. "Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    12. Kerstin Thriene & Karin B. Michels, 2023. "Human Gut Microbiota Plasticity throughout the Life Course," IJERPH, MDPI, vol. 20(2), pages 1-14, January.

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