Selection and sequencing of strains as references for human microbiome studies

Abstract

Metagenomics is a rapidly changing field of microbial biology that provides insights into the diversity and functional capacity of the microbial communities. In order to improve the phylogenetic and physiological interpretation of metagenomic data, it is essential to produce sequence data for individual reference strains. The NIH-supported Human Microbiome Project (HMP) plans to sequence the genomes of 900 reference strains representing isolates from all major body sites. This Chapter describes the approaches used by the strain selection groups of the HMP and International Human Microbiome Consortium (IHMC) to achieve this goal as well as some current and future challenges and opportunities facing those interested in metagenomics of the human body. Although advances in DNA sequencing technology have helped make the selection and sequencing of reference strains less dependent on cultivation and large quantities of DNA, using the data in pursuit of strain isolation and purification should not be neglected. The international collaborations that have developed via the leadership of North American and European research groups have also created an excellent opportunity to undertake a pangenomic analysis of human microbiomes, which may substantially increase the value of comparative analysis of metagenomic datasets, leading to a better understanding of host-microbiome relationships in health and disease.