Biogeography of the ecosystems of the healthy human body

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

Research output: Contribution to journalArticle

89 Citations (Scopus)

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 data sets 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 data set of subjects and body sites that are deeply sampled by sequencing.

Original languageEnglish
JournalGenome Biology
DOIs
StateAccepted/In press - Jan 14 2013

Fingerprint

Microbiota
Human Body
biogeography
Ecosystem
ecosystems
ecosystem
habitat
Biodiversity
habitats
biodiversity
Metagenomics
standardization
human body
microbiome
rRNA Genes
skin
skin (animal)
Cluster Analysis
mouth
Healthy Volunteers

ASJC Scopus subject areas

  • Genetics
  • Medicine(all)

Cite this

Zhou, Y., Gao, H., Mihindukulasuriya, K. A., Rosa, P. S. L. A., Wylie, K. M., Vishnivetskaya, T., ... Weinstock, G. M. (Accepted/In press). Biogeography of the ecosystems of the healthy human body. Genome Biology. https://doi.org/10.1186/gb-2013-14-1-r1

Biogeography of the ecosystems of the healthy human body. / Zhou, Yanjiao; Gao, Hongyu; Mihindukulasuriya, Kathie A.; Rosa, Patricio S L A; Wylie, Kristine M.; Vishnivetskaya, Tatiana; Podar, Mircea; Warner, Barb; Tarr, Phillip I.; Nelson, David E.; Fortenberry, J.; Holland, Martin J.; Burr, Sarah E.; Shannon, William D.; Sodergren, Erica; Weinstock, George M.

In: Genome Biology, 14.01.2013.

Research output: Contribution to journalArticle

Zhou, Y, Gao, H, Mihindukulasuriya, KA, Rosa, PSLA, Wylie, KM, Vishnivetskaya, T, Podar, M, Warner, B, Tarr, PI, Nelson, DE, Fortenberry, J, Holland, MJ, Burr, SE, Shannon, WD, Sodergren, E & Weinstock, GM 2013, 'Biogeography of the ecosystems of the healthy human body', Genome Biology. https://doi.org/10.1186/gb-2013-14-1-r1
Zhou Y, Gao H, Mihindukulasuriya KA, Rosa PSLA, Wylie KM, Vishnivetskaya T et al. Biogeography of the ecosystems of the healthy human body. Genome Biology. 2013 Jan 14. https://doi.org/10.1186/gb-2013-14-1-r1
Zhou, Yanjiao ; Gao, Hongyu ; Mihindukulasuriya, Kathie A. ; Rosa, Patricio S L A ; Wylie, Kristine M. ; Vishnivetskaya, Tatiana ; Podar, Mircea ; Warner, Barb ; Tarr, Phillip I. ; Nelson, David E. ; Fortenberry, J. ; Holland, Martin J. ; Burr, Sarah E. ; Shannon, William D. ; Sodergren, Erica ; Weinstock, George M. / Biogeography of the ecosystems of the healthy human body. In: Genome Biology. 2013.
@article{7d0e90f1865d422cb6cbc74a6eb44578,
title = "Biogeography of the ecosystems of the healthy human body",
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 data sets 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 data set of subjects and body sites that are deeply sampled by sequencing.",
author = "Yanjiao Zhou and Hongyu Gao and Mihindukulasuriya, {Kathie A.} and Rosa, {Patricio S L A} and Wylie, {Kristine M.} and Tatiana Vishnivetskaya and Mircea Podar and Barb Warner and Tarr, {Phillip I.} and Nelson, {David E.} and J. Fortenberry and Holland, {Martin J.} and Burr, {Sarah E.} and Shannon, {William D.} and Erica Sodergren and Weinstock, {George M.}",
year = "2013",
month = "1",
day = "14",
doi = "10.1186/gb-2013-14-1-r1",
language = "English",
journal = "Genome Biology",
issn = "1474-7596",
publisher = "BioMed Central",

}

TY - JOUR

T1 - Biogeography of the ecosystems of the healthy human body

AU - Zhou, Yanjiao

AU - Gao, Hongyu

AU - Mihindukulasuriya, Kathie A.

AU - Rosa, Patricio S L A

AU - Wylie, Kristine M.

AU - Vishnivetskaya, Tatiana

AU - Podar, Mircea

AU - Warner, Barb

AU - Tarr, Phillip I.

AU - Nelson, David E.

AU - Fortenberry, J.

AU - Holland, Martin J.

AU - Burr, Sarah E.

AU - Shannon, William D.

AU - Sodergren, Erica

AU - Weinstock, George M.

PY - 2013/1/14

Y1 - 2013/1/14

N2 - 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 data sets 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 data set of subjects and body sites that are deeply sampled by sequencing.

AB - 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 data sets 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 data set of subjects and body sites that are deeply sampled by sequencing.

UR - http://www.scopus.com/inward/record.url?scp=84872154220&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84872154220&partnerID=8YFLogxK

U2 - 10.1186/gb-2013-14-1-r1

DO - 10.1186/gb-2013-14-1-r1

M3 - Article

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

ER -