Human Microbiome Project, Reference Genomes, Rationale, Selection, Acquisition, Sequencing, and Annotation

Introduction

The National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)-funded Human Microbiome Project (HMP) sampled 300 subjects at 15 or 18 body sites, dependent on sex, then sequenced DNAs from these samples by 16S rDNA and whole-genome shotgun methods, with the goal to identify and characterize the microbial communities resident at different body sites in these healthy human subjects. Demonstration projects, which were microbiome studies with emphases on disease or specific aspects of human health, were also a part of the HMP. A third and critical component of the HMP was the reference genome sequencing initiative (NIH HMP Working Group et al. 2009; Proctor 2011). The goal of this initiative was to obtain genome sequences of commensal organisms that inhabit the human body. Prior to this, most of the limited number (ca. 200) bacterial genome sequences of human origin in the National Center for Biotechnology Information (NCBI) database represented...