Dynamics and associations of microbial community types across the human body
Open accessAbstract
A primary goal of the Human Microbiome Project (HMP) was to provide a reference collection of 16S ribosomal RNA gene sequences collected from sites across the human body that would allow microbiologists to better associate changes in the microbiome with changes in health. The HMP Consortium has reported the structure and function of the human microbiome in 300 healthy adults at 18 body sites from a single time point. Using additional data collected over the course of 12-18 months, we used Dirichlet multinomial mixture models to partition the data into community types for each body site and made three important observations. First, there were strong associations between whether individuals had been breastfed as an infant, their gender, and their level of education with their community types at several body sites. Second, although the specific taxonomic compositions of the oral and gut microbiomes were different, the community types observed at these sites were predictive of each other. Finally, over the course of the sampling period, the community types from sites within the oral cavity were the least stable, whereas those in the vagina and gut were the most stable. Our results demonstrate that even with the considerable intra- and interpersonal variation in the human microbiome, this variation can be partitioned into community types that are predictive of each other and are probably the result of life-history characteristics. Understanding the diversity of community types and the mechanisms that result in an individual having a particular type or changing types, will allow us to use their community types to assess disease risk and to personalize therapies.
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The Jensen-Shannon distance between layers of a multiplex system has been used to identify community-based associations in the human microbiome, in agreement with biological expectation.
“In another application the Jensen -Shannon distance between layers of a multiplex system has been used to identify community-based associations in the human microbiome 32 , where the microbial network corresponding to each body site is represented by a layer in a multiplex network, in perfect agreement with biological expectation 92 .”
From Complex networks from classical to quantum (2019) · cites this paper as [92]
The paper reports associations between community types at different body sites, including within the oral cavity and vagina (section labeled Abstract; page unavailable). It does not report using Jensen–Shannon distance between layers of a multiplex network to identify those associations. Its Extended Data Figure 1 instead uses Jensen–Shannon divergence between stool samples for an ordination. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe remaining gut microbiota composition is diverse and dynamic, and acute and chronic dietary exposures significantly affect the overall microbial community.
“However, the composition of the remaining gut microbiota is remarkably diverse and dynamic, with both acute and chronic dietary exposures significantly affecting the overall microbial community (8,11).”
From The contributory role of gut microbiota in cardiovascular disease (2014) · cites this paper as [11]
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- Authors
- Ding, T., & Schloss, P. D.
- Affiliations
- University of Michigan (US)
- Corresponding author
- Schloss, Patrick D.
- Venue
- Nature
- Published
- 2014-04-16
- Volume
- 509
- Issue
- 7500
- Pages
- 357-360
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4139711
- OpenAlex
- W2111358533
- Cited by
- 885
- References
- 32
- Citations by year
- 2026: 24 · 2025: 63 · 2024: 59 · 2023: 72 · 2022: 92 · 2021: 84 · 2020: 91 · 2019: 74 · 2018: 68 · 2017: 72 · 2016: 69 · 2015: 94 · 2014: 22 · 2012: 1
- FWCI
- 35.10
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (R01HG005975)
- National Institute of General Medical Sciences (R01GM099514)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK034933)
- 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, 16S rRNA gene sequences, Human Microbiome Project, breastfeeding, gender differences, educational attainment, oral microbiota, gut microbiota, vaginal microbiota, microbial community stability, interindividual variability
- MeSH terms
- Breast Feeding, Disease Susceptibility, Educational Status, Feces, Female, Health, Humans, Life Style, Male, Mouth, Organ Specificity, RNA, Ribosomal, 16S, Sex Characteristics, Time Factors, Vagina, Human Body, Gastrointestinal Tract, Metagenome, Precision Medicine, Microbiota
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