Exploration of bacterial community classes in major human habitats
Open accessAbstract
Background: Determining bacterial abundance variation is the first step in understanding bacterial similarity between individuals. Categorization of bacterial communities into groups or community classes is the subsequent step in describing microbial distribution based on abundance patterns. Here, we present an analysis of the groupings of bacterial communities in stool, nasal, skin, vaginal and oral habitats in a healthy cohort of 236 subjects from the Human Microbiome Project. Results: We identify distinct community group patterns in the anterior nares, four skin sites, and vagina at the genus level. We also confirm three enterotypes previously identified in stools. We identify two clusters with low silhouette values in most oral sites, in which bacterial communities are more homogeneous. Subjects sharing a community class in one habitat do not necessarily share a community class in another, except in the three vaginal sites and the symmetric habitats of the left and right retroauricular creases. Demographic factors, including gender, age, and ethnicity, significantly influence community composition in several habitats. Community classes in the vagina, retroauricular crease and stool are stable over approximately 200 days. Conclusion: The community composition, association of demographic factors with community classes, and demonstration of community stability deepen our understanding of the variability and dynamics of human microbiomes. This also has significant implications for experimental designs that seek microbial correlations with clinical phenotypes.
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At the phylum level, Lentisphaerae and Acidobacteria were detected after running.
“At the phylum level, Lentisphaerae and Acidobacteria, whose functions in the human gut are unknown, were detected after running.”
From The athletic gut microbiota (2020) · cites this paper as [20]
In amateur runners before and after a half-marathon, alpha diversity showed few differences, but abundances of certain microbiota members differed before and after running.
“According to the alpha diversity analysis, there were few differences in diversity, nevertheless, abundances of certain microbiota members showed differences before and after running.”
From The athletic gut microbiota (2020) · cites this paper as [20]
At the species level there was a marked increase in the families Coriobacteriaceae and Succinivibrionaceae after running.
“At the species level there was a marked increase in the families Coriobacteriaceae and Succinivibrionaceae.”
From The athletic gut microbiota (2020) · cites this paper as [20]
Half-marathon running reduced the abundance of fecal Ezakiella, Romboutsia, and Actinobacillus, but increased the abundance of Coprococcus and Ruminococcus bicirculans.
“At the genus level, half-marathon running reduced the abundance of fecal Ezakiella, Romboutsia, and Actinobacillus, but increased the abundance of Coprococcus and Ruminococcus bicirculans.”
From The athletic gut microbiota (2020) · cites this paper as [20]
The pentose phosphate pathway was the most enriched pathway after a half-marathon run.
“Interestingly, the pentose phosphate pathway, a metabolic pathway parallel to glycolysis and involving the oxidation of glucose, was the most enriched pathway after a half-marathon run.”
From The athletic gut microbiota (2020) · cites this paper as [20]
Prevotella is normally found in only a small percentage of healthy individuals in European and American cohorts.
“Prevotella is normally found in only a small percentage of healthy individuals in European and American cohorts [1, 2, 20, 210].”
From The athletic gut microbiota (2020) · cites this paper as [20]
The anterior nares are enriched for lipophilic skin colonizers, including Staphylococcus, Propionibacterium and Corynebacterium, because sebum is produced by sebaceous glands.
“The anterior nares are closest to the external environment and are lined with a skin-like keratinized squamous epithelium, including serous and sebaceous glands, the latter of which produces sebum, which leads to the enrichment of lipophilic skin colonizers, including Staphylococcus spp., Propionibacterium spp. and Corynebacterium spp.46,47,48.”
From The microbiota of the respiratory tract: gatekeeper to respiratory health (2017) · cites this paper as [48]
Bacteria frequently found in other respiratory niches, including Moraxella, Dolosigranulum and Streptococcus, have also been observed in the anterior nares.
“Bacteria that are frequently found in other respiratory niches, including Moraxella spp., Dolosigranulum spp. and Streptococcus spp., have also been observed in the anterior nares29,43,48,49.”
From The microbiota of the respiratory tract: gatekeeper to respiratory health (2017) · cites this paper as [48]
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- NCBI SRA HMP 16s rRNA gene [ http://www.ncbi.nlm.nih.gov/sra/?term=SRP002395]
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- Authors
- Zhou, Y., Mihindukulasuriya, K. A., Gao, H., La Rosa, P. S., Wylie, K. M., Martin, J. C., Kota, K., Shannon, W. D., Mitreva, M., Sodergren, E., & Weinstock, G. M.
- Affiliations
- Washington University in St. Louis (US)
- Indiana University School of Medicine (US)
- Corresponding author
- Weinstock, George M
- ORCID
- Venue
- Genome Biology
- Published
- 2014-05-07
- Volume
- 15
- Issue
- 5
- Pages
- R66-R66
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4073010
- OpenAlex
- W2150785952
- Cited by
- 149
- References
- 54
- Citations by year
- 2026: 8 · 2025: 10 · 2024: 10 · 2023: 10 · 2022: 15 · 2021: 21 · 2020: 19 · 2019: 16 · 2018: 4 · 2017: 13 · 2016: 8 · 2015: 11 · 2014: 3
- FWCI
- 4.78
- 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)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
- IUScholarWorks (Indiana University) (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U54HG004968)
- Common Fund
- 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, enterotypes, gut microbiota, nasal microbiota, skin microbiome, vaginal microbiota, oral microbiota, microbial community stability, demographic factors, Human Microbiome Project
- MeSH terms
- Bacteria, Demography, Feces, Female, Humans, Mouth, Nose, Skin, Vagina, Microbiota
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