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Cited by 150Gut microbiota and healthMicrobial Community Ecology and PhysiologyOral microbiology and periodontitis research

The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.

Exploration of bacterial community classes in major human habitats

Open access
Zhou, Yanjiao, Mihindukulasuriya, Kathie A, Gao, Hongyu, La Rosa, Patricio S, Wylie, Kristine M, Martin, John C, Kota, Karthik, Shannon, William D, Mitreva, Makedonka, Sodergren, Erica, Weinstock, George M·2014·Genome Biology
DOI 10.1186/gb-2014-15-5-r66PMC PMC4073010
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Abstract

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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Crossref · 10.1186/gb-2014-15-5-r66

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Figures

Figure 1 Examples of community classes of human body habitats as illustrated by PCoA. PCoA was used to visualize the community classes in different habitats. Samples are color-coded according to their community classes within the habitat. Only the major community classes from retroauricular crease are colored. The community classes show better separation in retroauricular crease and vaginal sites with higher silhouette values, and a less clear separation in stool and anterior nares with lower silhouette values.
Figure 1 Examples of community classes of human body habitats as illustrated by PCoA. PCoA was used to visualize the community classes in different habitats. Samples are color-coded according to their community classes within the habitat. Only the major community classes from retroauricular crease are colored. The community classes show better separation in retroauricular crease and vaginal sites with higher silhouette values, and a less clear separation in stool and anterior nares with lower silhouette values.CC BY · PubMed Central
Figure 2 Examples of indicator taxa between community classes. Indicator taxa driving the differentiation of community classes were identified using the indval function in the labdsv package in R. Boxplots are labeled according to the dominant taxa in the community class. (A-D) The colors represent different community classes. The relative abundances of dominant taxa (y-axis) in each community class are plotted for the type I habitat left retroauricular crease (A), and the type II habitat anterior nares (B), stool (C), and subgingival plaque (D). In (D), the name of the community classes are designated as a generic term, cluster 1 or cluster 2, because of the very low silhouette value (<0.2).
Figure 2 Examples of indicator taxa between community classes. Indicator taxa driving the differentiation of community classes were identified using the indval function in the labdsv package in R. Boxplots are labeled according to the dominant taxa in the community class. (A-D) The colors represent different community classes. The relative abundances of dominant taxa (y-axis) in each community class are plotted for the type I habitat left retroauricular crease (A), and the type II habitat anterior nares (B), stool (C), and subgingival plaque (D). In (D), the name of the community classes are designated as a generic term, cluster 1 or cluster 2, because of the very low silhouette value (<0.2).CC BY · PubMed Central
Figure 3 Community class comparisons across all habitats. Cluster similarity was analyzed using the ARI. A large overlap of carriers was detected between community classes in left and right retroauricular creases as well as within three vaginal sites. The color saturation and size of the circles represent the degree of cluster similarity. The circles along the diagonal from top left to bottom right, with an ARI equal to 1, indicate self-comparison.
Figure 3 Community class comparisons across all habitats. Cluster similarity was analyzed using the ARI. A large overlap of carriers was detected between community classes in left and right retroauricular creases as well as within three vaginal sites. The color saturation and size of the circles represent the degree of cluster similarity. The circles along the diagonal from top left to bottom right, with an ARI equal to 1, indicate self-comparison.CC BY · PubMed Central
Figure 4 Examples of demographic factor correlations with community classes. (A) Gender differences in retroauricular crease samples, with females more prevalent in the Staphylococcus community class. (B) Gender differences in community classes of antecubital fossa. The Propionibacterium community class has significantly more males than females while the non-Propionibacterium community classes have significantly more females than males. (C) The Staphylococcus community class in anterior nares is dominated by females, and the female proportion is significantly higher than in the other three community classes. (D) The ages of subjects in the Propionibacterium community class and the other community classes of retroauricular crease are significantly different. Asterisks indicate statistically significant differences.
Figure 4 Examples of demographic factor correlations with community classes. (A) Gender differences in retroauricular crease samples, with females more prevalent in the Staphylococcus community class. (B) Gender differences in community classes of antecubital fossa. The Propionibacterium community class has significantly more males than females while the non-Propionibacterium community classes have significantly more females than males. (C) The Staphylococcus community class in anterior nares is dominated by females, and the female proportion is significantly higher than in the other three community classes. (D) The ages of subjects in the Propionibacterium community class and the other community classes of retroauricular crease are significantly different. Asterisks indicate statistically significant differences.CC BY · PubMed Central
Figure 5 Dynamics of community classes over time. (A-C) Subjects from different community classes switch to other community classes or maintain their original community class in different habitats: (A) retroauricular crease, (B) anterior nares, and (C) stool. The colored circles represent different community classes. The names of community classes are followed by the number of subjects belonging to the community classes at the first visit. Subjects transferring to other community classes at the second visit are indicated by arrows along with the number of subjects that switched. The number inside each community class indicates the number of subjects maintaining the same community class at the second visit.
Figure 5 Dynamics of community classes over time. (A-C) Subjects from different community classes switch to other community classes or maintain their original community class in different habitats: (A) retroauricular crease, (B) anterior nares, and (C) stool. The colored circles represent different community classes. The names of community classes are followed by the number of subjects belonging to the community classes at the first visit. Subjects transferring to other community classes at the second visit are indicated by arrows along with the number of subjects that switched. The number inside each community class indicates the number of subjects maintaining the same community class at the second visit.CC BY · PubMed Central

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Research works printed but not linked: 4

  1. NCBI SRA: HMP 16s rRNA gene. [http://www.ncbi.nlm.nih.gov/sra/?term=SRP002395]
  2. NCBI BioProject: HMP shotgun data. [http://www.ncbi.nlm.nih.gov/bioproject/48479]
  3. Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K: cluster: Cluster Analysis Basics and Extensions. 2013, R package version 1.14.4.
  4. HMP Metadata. [http://www.ncbi.nlm.nih.gov/gap/?term=phs000228.v3.p1]

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Metadata

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
Publisher
Springer Science and Business Media LLC
Published
2014-05-07
Volume
15
Issue
5
Pages
R66-R66
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/gb-2014-15-5-r66
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
Licence
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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