In this paper, HMP researchers report comparing data from the sequenced reference genomes to human metagenomic data in the public domain to identify proteins, determine gene functionality and link metagenomic data to individual microbial species. From an analysis of 547,968 predicted proteins, the HMP researchers report 29,987 unique proteins, which suggests a far greater diversity in the human microbiome than previously suspected.
"The Science paper is a milestone in the human microbiome research with the release to the public of 178 finished or high quality draft genomes from organisms isolated from various sites in the human body," says Kyrpides. "It signals the beginning of a much larger effort that aims to provide a more comprehensive genetic catalog of the microbes living in the human body. The impact of understanding what is the normal microbial flora, what is its core genetic content, and how perturbations of the normal microbial flora of the human body can shift from protecting our bodies into causing diseases will eventually be enormous."
Kyrpides, Markowitz and their colleagues at the DACC are playing a critical role in fulfilling an NIH call for development of common sequencing and annotation standards that have not existed before. Lack of common language and a clearing house for genome data have been among the most daunting problems in genomics research.
Says Markowitz, "The greatest challenge ahead will be handling hundred of metagenomic datasets generated as part of the HMP, which will represent several orders of magnitude more data than the datasets presented in the current paper. We need to develop novel analysis and visualization methods to handle this massive increase in data."
Adds Kyrpides, "New sequencing technologies and our ability to generate orders of magnitude more data compared to only a year or two ago are changing the field entirely, and are mandating a social shift a
|Contact: Lynn Yarris|
DOE/Lawrence Berkeley National Laboratory