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Microbial Dark Matter Project

Motivation

Reconstructing bacterial and archaeal genomes has completely transformed our understanding of microbial metabolism as well as evolutionary processes, and significantly sped up discoveries made in bioprospecting. We are rapidly approaching the 3,000 mark for draft/ finished bacterial and archaeal genomes world-wide and with next generation sequencing technologies dramatically increasing sequence throughput while decreasing cost, we expect this number to considerably increase over the next several years. The vast majority of bacterial and archaeal genomes sequenced to date are of rather limited phylogenetic diversity as they were chosen as based on their physiology and/ or medical importance. These findings gave rise to the initiation of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Project, which aims to populate the tree of life with phylogenetically diverse reference genomes. While the bulk of the microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes of these largely mysterious species.

The Microbial Dark Matter Project aims to use single cell genomics to massively expand the Genomic Encyclopedia of Bacteria and Archaea by targeting 100 single cell representatives of uncultured candidate phyla (phyla proposed on the basis of environmental sequences that have no, or very few cultured representatives). A pilot study of 60 single cell genomes is currently underway. The value of generating these reference genomes stems from improving the reconstruction of the evolutionary history of Bacteria and Archaea to dramatically increasing the discovery rate of novel protein families and biological functions and shedding light on the numerous underrepresented phyla that likely play important roles in the environment. Moreover, these data will improve our ability to interpret sequence data from diverse environments, which will be of tremendous value for microbial ecology and evolutionary studies to come.

PIs: Tanya Woyke, JGI; Jonathan Eisen, University of California, Davis; Phil Hugenholtz, Center of Ecogenomics, Austalia