JCVI is playing a leading role in the emerging research area to identify and characterize the human microbiome--the microbial populations that natively inhabit the human body--and to determine its role in health and disease. These communities may provide clues to human development, evolution, immunity, nutritional needs, and overall health. JCVI's pioneering research in metagenomic analysis of marine microbes (Global Ocean Sampling Expedition) has paved the way for similar analyses of microbes that inhabit the human body.
The Human Microbiome Project (HMP) was initiated by NIH to probe the richness of the microbial communities living in and on the human body in an effort to help us understand their role in human health and disease. A major objective of the HMP is to try to define a core set of microbial species that are associated with the human body known as the "core microbiome". Changes to this core microbiome may eventually be correlated with changes in human health. The NIH is supporting a coordinated effort to characterize the human microbiome with work conducted at four sequencing centers: the J.Craig Venter Institute, Baylor College of Medicine, the Broad Institute, and Washington University School of Medicine. Over the next five years the centers will generate a microbial genome reference set of at least 1000 genomes. In addition, the centers will characterize the microbial communities from multiple body sites in a large pool of consented individuals. This extensive sampling at individual body sites will help to determine whether there is a core microbiome at each site and help scientists to probe the relationship between health status and changes in the human microbiome.
JCVI was involved in the initial HMP sequencing efforts in 2008 to generate data needed for scaling up HMP efforts and to "jumpstart" the HMP. This phase provided key data needed for the design of a cost effective large scale production. JCVI has produced annotated genome sequences for over 332 microbial strains representing a broad distribution of phylotypes from different niches of the human body and produced small-subunit 16S rRNA sequences from metagenomic specimens. In May of 2009 JCVI received a 4-year award from NIAID for the development of a microbial genome reference set of 200 genomes. Metagenomic sequencing will also be done to characterize the microbial communities (bacterial, viral,and phage) from 15-18 body sites including the oral cavity, skin, vagina, the GI tract, and the nasopharyngeal tract. Samples from an initial pool of 250 individuals will be collected at the clinical centers of two of the participating centers. The extensive sampling is expected to dramatically increase our knowledge of both the microbial diversity and core microbiome at each body site.
Other projects supported by the HMP involve investigations of the relationships between disease and changes in the human microbiome. These initiatives includes a series of demonstration projects to look at the microbiomes of various diseases and JCVI is involved in two such projects in addition to a project to develop new tools for computational analysis of the human microbiome data. The ethical, legal and social implications raised by human microbiome research will also be investigated. A complete list of projects funded by the NIH is available at http://nihroadmap.nih.gov/hmp/fundedresearch.asp.