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Biogeography of the ecosystems of the healthy human body

Yanjiao Zhou1, Hongyu Gao1, Kathie A Mihindukulasuriya1, Patricio S La Rosa2, Kristine M Wylie1, Tatiana Vishnivetskaya34, Mircea Podar4, Barb Warner5, Phillip I Tarr6, David E Nelson7, J Dennis Fortenberry8, Martin J Holland9, Sarah E Burr109, William D Shannon2, Erica Sodergren1 and George M Weinstock1*

Author Affiliations

1 The Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108 USA

2 Department of Medicine, Division of General Medical Sciences, Washington University School of Medicine, St. Louis, MO, 63110 USA

3 University of Tennessee, Knoxville, TN, 37916 USA

4 Oak Ridge National Laboratory, Oak Ridge, TN, 37831 USA

5 Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO, 63110 USA

6 Department of Pediatrics, Division of Pediatric Gastroenterology, Washington University School of Medicine, St. Louis, MO, 63110 USA

7 Department of Biology, Indiana University, Bloomington, IN, 47405 USA

8 Section of Adolescent Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202 USA

9 London School of Hygiene and Tropical Medicine, London, WC1E 7HT United Kingdom

10 Medical Research Council Unit, The Gambia, Fajara, 1000 The Gambia

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Genome Biology 2013, 14:R1  doi:10.1186/gb-2013-14-1-r1

Published: 14 January 2013



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.


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.


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.

Biogeography; Human microbiome; Biodiversity; Temporal stability