Moving pictures of the human microbiome

James G Caporaso, Christian L. Lauber, Elizabeth K. Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I. Gordon, Rob Knight

Research output: Contribution to journalArticle

467 Citations (Scopus)

Abstract

Background: Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.Results: We find that despite stable differences between body sites and individuals, there is pronounced variability in an individual's microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members.Conclusions: DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.

Original languageEnglish (US)
Article numberR50
JournalGenome Biology
Volume12
Issue number5
DOIs
StatePublished - May 30 2011
Externally publishedYes

Fingerprint

Microbiota
time series analysis
temporal variation
microbial ecology
obesity
malnutrition
limiting factor
DNA
habitat
Crohn disease
inflammatory bowel disease
Ecology
DNA Sequence Analysis
Inflammatory Bowel Diseases
Malnutrition
Crohn Disease
Ecosystem
microbiome
detection limit
sequence analysis

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., ... Knight, R. (2011). Moving pictures of the human microbiome. Genome Biology, 12(5), [R50]. https://doi.org/10.1186/gb-2011-12-5-r50

Moving pictures of the human microbiome. / Caporaso, James G; Lauber, Christian L.; Costello, Elizabeth K.; Berg-Lyons, Donna; Gonzalez, Antonio; Stombaugh, Jesse; Knights, Dan; Gajer, Pawel; Ravel, Jacques; Fierer, Noah; Gordon, Jeffrey I.; Knight, Rob.

In: Genome Biology, Vol. 12, No. 5, R50, 30.05.2011.

Research output: Contribution to journalArticle

Caporaso, JG, Lauber, CL, Costello, EK, Berg-Lyons, D, Gonzalez, A, Stombaugh, J, Knights, D, Gajer, P, Ravel, J, Fierer, N, Gordon, JI & Knight, R 2011, 'Moving pictures of the human microbiome', Genome Biology, vol. 12, no. 5, R50. https://doi.org/10.1186/gb-2011-12-5-r50
Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J et al. Moving pictures of the human microbiome. Genome Biology. 2011 May 30;12(5). R50. https://doi.org/10.1186/gb-2011-12-5-r50
Caporaso, James G ; Lauber, Christian L. ; Costello, Elizabeth K. ; Berg-Lyons, Donna ; Gonzalez, Antonio ; Stombaugh, Jesse ; Knights, Dan ; Gajer, Pawel ; Ravel, Jacques ; Fierer, Noah ; Gordon, Jeffrey I. ; Knight, Rob. / Moving pictures of the human microbiome. In: Genome Biology. 2011 ; Vol. 12, No. 5.
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