A framework for human microbiome research

Abstract

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

Figure 1. Rates of gene and OTU discovery from HMP taxonomic and metagenomic data

Accumulation curves for a, OTU counts from 16S data (all body sites) b, clustered gene index counts from metagenomic data (all applicable body sites) and c, the ratio of average unique genes contributed versus unique OTUs encountered with increasing sample counts (Supplementary Information). Ratios given for each curve in c represent the average number of unique genes contributed per unique OTU at the final sample count. Curves for stool, buccal mucosa and anterior nares suggest that the proportion of gene-to-taxa discovery has stabilized. In contrast, the curve for supragingival plaque suggests relatively fewer new genes are being contributed per additional OTU. Error bars represent 95% confidence intervals.