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Moving pictures of the human microbiome
Open accessAbstract
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).](/paper-figures/601978f4a5f14dce850c1ad072f786d6/moving-pictures-of-the-human-microbiome-figure-1.jpg)
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“the fine structure of the healthy microbiota seems to be unique to individuals; intra-individual differences across time are typically much smaller than differences between individuals (Caporaso et al., 2011;Costello et al., 2009).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Caporaso et al., 2011
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Metadata
- 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
- Venue
- Genome Biology
- Published
- 2011-05-30
- Volume
- 12
- Issue
- 5
- Pages
- R50-R50
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- 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
- 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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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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