Analyses of the stability and core taxonomic memberships of the human microbiome.

Kelvin Li,Barbara A Methé,Monika Bihan,Bryan A White

doi:10.1371/journal.pone.0063139

Abstract

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.

Highlights

The ability to identify and define the nature and extent of common or core microbial community membership versus those less prevalent within human body habitats across multiple individuals is a subject of significant interest and importance [1,2,3]
We present results extending previous investigations of human microbiome core membership as revealed across body habitats and regions, from 16S profiles generated by the Human Microbiome Project (HMP)
The Core Genera Core taxonomic members of the microbiome for each body habitat were defined by the following pairs of abundance versus ubiquity cutoffs: a.) 10% | 75% b.) 1% | 80% c.) 0.1% | 85% d.) 0.01% | 90% These logarithmically decreasing abundances were selected to illustrate the rate at which the enrollment of the core membership would grow as lower abundant organisms were considered

Summary

Introduction

The ability to identify and define the nature and extent of common or core microbial community membership versus those less prevalent within human body habitats across multiple individuals is a subject of significant interest and importance [1,2,3] The presence of these shared taxa as defined by their ubiquity and abundance is critical for improving our understanding of microbial diversity and stability arrangements across space and time and establishing the frameworks for further understanding the roles that interconnected evolutionary, ecological and stochastic processes may play in shaping these patterns [4,5]. This is critical for driving future research in directly testing the influences of evolution, ecology and stochastic processes on biogeographic patterns and facilitating the ability to use taxonomic profiles as possible diagnostic markers of health and disease states

Methods

Results

Conclusion