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21 May 2010NIH/National Human Genome Research Institute
Genomic collection of human microbes published
The Human Microbiome Project (HMP) published an analysis of 178 genomes from microbes that live in or on the human body. The researchers discovered novel genes and proteins that serve functions in human health and disease, adding a new level of understanding to what is known about the complexity and diversity of these organisms. The paper is published in the May 21 issue of the journal Science.
The human microbiome consists of all the microorganisms that reside in or on the human body. Outnumbering cells in the human body by 10 to 1, some of the microorganisms cause illnesses, but many are necessary for good health. Currently, researchers can grow only some of the bacteria, fungi and viruses in a laboratory setting. However, new genomic techniques can identify minute amounts of microbial DNA in an individual and determine its identity by comparing the genetic signature to known sequences in the project's data base.
Launched in 2008 as part of the NIH Common Fund's Roadmap for Medical Research, the HMP is a $157 million, five-year effort that will implement a series of increasingly complicated studies that reveal the interactive role of the microbiome in human health.
The 178 microbial genomes in this report launch the HMP reference collection that eventually will total approximately 900 microbial genomes of bacteria, viruses and fungi. These data will then be used by HMP researchers to characterize the microbial communities found in samples taken from healthy human volunteers and, later, those with specific illnesses. Samples are currently being collected for HMP from five areas of the body: the digestive tract, the mouth, the skin, the nose and the vagina.
One of the primary goals of the HMP reference collection is to expand researchers' ability to interpret data from metagenomic studies. Metagenomics is the study of a collection of genetic material (genomes) from a mixed community of organisms. Comparing metagenomic sequence data with genomes in the reference collection can help researchers determine whether they are novel or already existing sequences.
To evaluate whether the reference collection of genomes was meeting the goal above, the researchers compared 16.8 million microbial sequences found in public databases to the genome sequences in the HMP reference collection. They found that 62 genomes in the reference collection showed similarity with 11.3 million microbial sequences in public databases and 6.9 million of these – about 41 percent – correspond with genome sequences in the reference collection.
This analysis demonstrates that genomes sequenced as part of the reference collection add directly to an understanding of the human microbiome. However, researchers cautioned that at least one-third of the metagenomic sequences are still not represented by any genome in the reference collection and that this analysis focused only on the gastrointestinal tract. The authors added that additional genomes likely exist in other body sites and the completion of the reference collection should address many of the remaining organisms not accounted for in this analysis.
The initial stage of the HMP, which includes the current study, focused on bacteria, but future genome sequencing and human microbiome studies also will capture information about more complex microbes and viruses. The effort so far also has allowed researchers to create a framework for data resources and standards. In addition, the project is supporting the development of innovative technologies and computational tools, coordination of data analysis, and an examination of some of the ethical, legal and social implications of human microbiome research.
The Human Microbiome Jumpstart Reference Strains Consortium: A Catalog of Reference Genomes from the Human Microbiome. Science, Vol. 328, pp.994-999, doi: 10.1126/science.1183605.
