Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome
Open accessAbstract
Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa ("core"), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat's microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of "minor" oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region.
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Compared with other colonized body sites, the oral microbiome has the largest core set of microbes that are shared among unrelated individuals.
“The NIH Human Microbiome Project assessed the microbial compositions, encompassing both relative abundance and representative microbes, in 9 intraoral sites from 200 participants and found that, compared with other colonized body sites (such as the gut and the skin), the oral microbiome has the largest core set of microbes that are shared among unrelated individuals.130, 159”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [159]
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- Authors
- Li, K., Bihan, M., & Methé, B. A.
- Affiliations
- J. Craig Venter Institute (US)
- Corresponding author
- Methé, Barbara A.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-05-06
- Volume
- 8
- Issue
- 5
- Pages
- e63139
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3646044
- OpenAlex
- W2003025043
- Cited by
- 235
- References
- 37
- Citations by year
- 2026: 6 · 2025: 15 · 2024: 10 · 2023: 14 · 2022: 15 · 2021: 19 · 2020: 39 · 2019: 14 · 2018: 18 · 2017: 16 · 2016: 19 · 2015: 28 · 2014: 17 · 2013: 5
- FWCI
- 10.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Figshare (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institute of Allergy and Infectious Diseases (#AI084844, U54AI084844)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- human microbiome, core microbiome, taxonomic diversity, 16S rRNA gene sequencing, Human Microbiome Project, oral microbiota, skin microbiome, gut microbiota, vaginal microbiota, microbial abundance, interpersonal variability, temporal stability, two-parameter model
- MeSH terms
- Bacteria, Feces, Female, Humans, Mouth, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Skin, Vagina, Sequence Analysis, DNA, Molecular Typing, Microbiota
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