Beyond the Genome, and into the Microbial Metagenome

Baylor College of Medicine's Sarah Highlander talked microbes at this year's Beyond the Genome conference in Washington, DC, this week. Specifically, Highlander discussed the work she and others have done with NIH's Human Microbiome Project, and how that work could translate into a better understanding of human metagenomics. The rationale for large-scale microbial reference genome sequencing is that there is a need for a catalog of sequenced human isolates, which could, in turn, provide a foundation for the interpretation of whole-genome sequencing metagenomics, and other 'omics data. In addition, Highlander said, such a catalog would be useful in helping to update phylogenies and the tree of life. The HMP project started in September 2007, and since then 740 genomes have been submitted to NCBI. Of those, 24 are considered "gold-standard finished," Highlander said. In addition, there are another 689 that are either high-quality or improved high-quality drafts. There are another 250 sequences in progress, and since the project looks to hit 1,000 genomes soon, the goal has been expanded to 3,000 sequences. The problem, Highlander said, is that no one knows where they're going to get 2,000 more microbes to sequence, so the HMP is looking for input from the research community. Researchers are also working on viral reference genomes and small eukaryotes. HMP had hoped to award grants for research on other eukaryotes as well, like protists and helminthes, but Highlander said funding cuts will make that unlikely.