Biogeography of the ecosystems of the healthy human body

Yanjiao Zhou, Hongyu Gao, Kathie A. Mihindukulasuriya, Patricio S.La Rosa, Kristine M. Wylie, Tatiana Vishnivetskaya, Mircea Podar, Barb Warner, Phillip I. Tarr, David E. Nelson, J. Dennis Fortenberry, Martin J. Holland, Sarah E. Burr, William D. Shannon, Erica Sodergren, George M. Weinstock

Research output: Contribution to journalArticlepeer-review

233 Scopus citations

Abstract

Background: Characterizing the biogeography of the microbiome of healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from a limited set of subjects. Here, we analyzed one of the largest microbiome datasets to date and generated a biogeographical map that annotates the biodiversity, spatial relationships, and temporal stability of 22 habitats from 279 healthy humans. Results: We identified 929 genera from more than 24 million 16S rRNA gene sequences of 22 habitats, and we provide a baseline of inter-subject variation for healthy adults. The oral habitat has the most stable microbiota with the highest alpha diversity, while the skin and vaginal microbiota are less stable and show lower alpha diversity. The level of biodiversity in one habitat is independent of the biodiversity of other habitats in the same individual. The abundances of a given genus at a body site in which it dominates do not correlate with the abundances at body sites where it is not dominant. Additionally, we observed the human microbiota exhibit both cosmopolitan and endemic features. Finally, comparing datasets of different projects revealed a project-based clustering pattern, emphasizing the significance of standardization of metagenomic studies. Conclusions: The data presented here extend the definition of the human microbiome by providing a more complete and accurate picture of human microbiome biogeography, addressing questions best answered by a large dataset of subjects and body sites that are deeply sampled by sequencing.

Original languageEnglish
Article numberR1
JournalGenome Biology
Volume14
Issue number1
DOIs
StatePublished - Jan 14 2013

Funding

The authors are grateful to the NIH Common Fund Human Microbiome Project Consortium for generating and making available many of the datasets used in this study. The research leading to these results received funding from the National Institutes of Health, grant U54HG004968 to George Weinstock, The Genome Institute at Washington University. Tatiana Vishnivetskaya and Mircea Podar were supported by NIH-NHGRI grant 1R01HG004857 and by the Oak Ridge National Laboratory (managed by UT-Battelle, LLC, for the U.S. Department of Energy). Martin J. Holland was supported by the Wellcome Trust Grant 079246/Z/06/Z. Phillip I. Tarr was supported by NIH grants UH3 AI083265 and 5P30 DK052574 (Biobank) for the Digestive Diseases Research Core Center. J. Dennis Fortenberry was supported by NIH grant UH3 AI094641. The authors are grateful to the NIH Common Fund Human Microbiome Project Consortium for generating and making available many of the datasets used in this study. The research leading to these results received funding from the National Institutes of Health, grant U54HG004968 to George Weinstock, The Genome Institute at Washington University. Tatiana Vishnivetskaya and Mircea Podar were supported by NIH-NHGRI grant 1R01HG004857 and by the Oak Ridge National Laboratory (managed by UTBattelle, LLC, for the U.S. Department of Energy). Martin J. Holland was supported by the Wellcome Trust Grant 079246/Z/06/Z. Phillip I. Tarr was supported by NIH grants UH3 AI083265 and 5P30 DK052574 (Biobank) for the Digestive Diseases Research Core Center. J. Dennis Fortenberry was supported by NIH grant UH3 AI094641.

Keywords

  • Biodiversity
  • Biogeography
  • Human microbiome
  • Temporal stability

Fingerprint

Dive into the research topics of 'Biogeography of the ecosystems of the healthy human body'. Together they form a unique fingerprint.

Cite this