Cited by 1,138Gut microbiota and healthMicrobial Community Ecology and PhysiologyOral microbiology and periodontitis research

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Moving pictures of the human microbiome

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Caporaso, J Gregory, 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·2011·Genome Biology

DOI 10.1186/gb-2011-12-5-r50PMC PMC3271711

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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.

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Figure 1 Principal coordinates analysis of unweighted UniFrac distances between samples. (a) Costello et al. [6] samples. (b) M3, F4 time series samples. (c) M3, F4 time series, PC1 versus time (days). Panels (a,b) and (c) show two independent principal coordinates analyses. To compare the Costello et al. 454 data (a) with the time series Illumina data (b), these data were generated in a single principal coordinates analysis of UniFrac distances at 500 sequences per sample. Panel (c) does not contain the 454 data, so makes use of the increased sampling depth possible on Illumina (evenly sampled to 5,000 sequences per sample for UniFrac calculations).CC BY · PubMed Central

Figure 2 Temporal core microbiome. Fraction of species-level operational taxonomic units (OTUs) composing the core microbiota by number of samples in which an OTU must be present to be considered part of the core.CC BY · PubMed Central

Figure 3 Community membership. Community membership summary for all OTUs in (a) M3 gut, (b) F4 gut, (c) M3 tongue, (d) F4 tongue, (e) M3 left palm, (f) F4 left palm, (g) M3 right palm, and (h) F4 right palm. Points are OTUs colored by their median relative abundance computed over all samples where they occur, and pie charts summarize the class-level taxa observed as persistent and transient OTUs.CC BY · PubMed Central

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Authors: Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., Gordon, J. I., & Knight, R.
Affiliations: University of Colorado Boulder (US)
Cooperative Institute for Research in Environmental Sciences (US)
Stanford Medicine (US)
University of Maryland, Baltimore (US)
Washington University in St. Louis (US)
Howard Hughes Medical Institute (US)
Corresponding author: Knight, Rob
ORCID: Caporaso, J Gregory
Lauber, Christian L
Costello, Elizabeth K
Stombaugh, Jesse
Knights, Dan
Ravel, Jacques
Fierer, Noah
Gordon, Jeffrey I
Knight, Rob
Venue: Genome Biology
Publisher: Springer Science and Business Media LLC
Published: 2011-05-30
Volume: 12
Issue: 5
Pages: R50-R50
ISSN: 1465-6906 (ISSN-L)
1474-760X
DOI: 10.1186/gb-2011-12-5-r50
PMC: PMC3271711
OpenAlex: W2126218947
Cited by: 1,138
References: 21
Citations by year: 2026: 25 · 2025: 50 · 2024: 69 · 2023: 80 · 2022: 68 · 2021: 88 · 2020: 102 · 2019: 93 · 2018: 83 · 2017: 84 · 2016: 78 · 2015: 79 · 2014: 78 · 2013: 82 · 2012: 61
FWCI: 30.93
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/2.0/ (tdm)
creativecommons.org/licenses/by/2.0/ (vor)
Locations: Genome biology (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
eScholarship (California Digital Library) (submittedVersion)
Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
Funders: Howard Hughes Medical Institute
Bill and Melinda Gates Foundation
Crohn's and Colitis Foundation of America
Amazon Web Services
Crohn's and Colitis Foundation
National Institutes of Health (5u01ai070921-07, DK078669)
National Human Genome Research Institute (R01HG004872, HG004872, HG004872-02S1)
National Institute of Allergy and Infectious Diseases (AI070921, AI083264, UH2AI083264)
National Institute of Diabetes and Digestive and Kidney Diseases (DK078669, P01DK078669)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Keywords: human microbiome, temporal variation, core microbiome, microbial community dynamics, body site differences, interindividual variability, microbiome sequencing
MeSH terms: Bacteria, Computer Simulation, Humans, Obesity, Organ Specificity, RNA, Ribosomal, 16S, Seasons, Time Factors, Inflammatory Bowel Diseases, Genomics, Gastrointestinal Tract, Metagenome, High-Throughput Nucleotide Sequencing

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