Title |
Biogeography of the ecosystems of the healthy human body
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Published in |
Genome Biology, January 2013
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DOI | 10.1186/gb-2013-14-1-r1 |
Pubmed ID | |
Authors |
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 |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United Kingdom | 3 | 27% |
France | 1 | 9% |
Spain | 1 | 9% |
Unknown | 6 | 55% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 6 | 55% |
Scientists | 4 | 36% |
Science communicators (journalists, bloggers, editors) | 1 | 9% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 6 | 2% |
Switzerland | 1 | <1% |
Korea, Republic of | 1 | <1% |
Germany | 1 | <1% |
Sweden | 1 | <1% |
Italy | 1 | <1% |
United Kingdom | 1 | <1% |
Israel | 1 | <1% |
Unknown | 318 | 96% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 67 | 20% |
Student > Ph. D. Student | 57 | 17% |
Student > Master | 45 | 14% |
Student > Bachelor | 27 | 8% |
Student > Doctoral Student | 19 | 6% |
Other | 57 | 17% |
Unknown | 59 | 18% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 114 | 34% |
Medicine and Dentistry | 45 | 14% |
Biochemistry, Genetics and Molecular Biology | 42 | 13% |
Immunology and Microbiology | 20 | 6% |
Computer Science | 6 | 2% |
Other | 40 | 12% |
Unknown | 64 | 19% |