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Dynamics and associations of microbial community types across the human body



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 health1. 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 point2,3. Using additional data collected over the course of 12–18 months, we used Dirichlet multinomial mixture models4 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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Figure 1: Analysis of stool samples reveals four community types.
Figure 2: Community-type associations are strongest within a body region, but also exist between stool and the oral cavity.
Figure 3: Dynamics of community types at various body sites indicates that community type stability is correlated with the diversity of the community type.

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We thank J. Crabtree of the HMP Data Analysis and Coordination Center for his assistance in obtaining the sequencing and metadata files. The analysis described in this study was supported by grants from the National Institutes of Health (R01HG005975, R01GM099514 and P30DK034933).

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Authors and Affiliations



T.D. and P.D.S. designed and executed the analysis and prepared the manuscript.

Corresponding author

Correspondence to Patrick D. Schloss.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Comparison of community type assignments for non-metric dimensional scaling (NMDS) ordination of Jensen–Shannon divergence values between stool samples using DMM (a) and PAM-based clustering (b).

The stress computed for this ordination was 0.19 and the R2 between the input distance matrix and the distance matrix calculated between the points in the ordination was 0.90.

Extended Data Figure 2 The frequency of community types for body sites where there was a significant association with the subject’s gender.

ac, Percentage of female and male tongue communities that affiliated with each of the tongue (a; n = 288 unique individuals; median P = 2 × 10−3), right retroauricular crease (b; n = 268 unique individuals; median P = 9 × 10−5) and right antecubital fossa community types (c; n = 136 unique individuals; median P = 3 × 10−5).

Extended Data Figure 3 The frequency of vaginal community types among women with and without a college degree.

ac, Percentage of women with and without a college degree whose vaginal communities affiliated with the vaginal introitus (a; n = 74 unique individuals; median P = 2 × 10−3), mid-vagina (b; n = 64 unique individuals; median P = 8 × 10−4) and posterior fornix (c; n = 61 unique individuals; median P = 4 × 10−4) community types.

Extended Data Table 1 Most common characteristics of the individuals included in the HMP healthy cohort
Extended Data Table 2 Comparison of PAM- and DMM-based approaches to assigning samples to community types
Extended Data Table 3 Average contingency table of stool and saliva community types

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Ding, T., Schloss, P. Dynamics and associations of microbial community types across the human body. Nature 509, 357–360 (2014).

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