Scientists Begin Genomic Encyclopedia of Microbes

January 8, 2010 — Earth is estimated to have about 150 million species of microbes in, on, around and under its surface. The genomes of only about 2,000 have been and are being decoded. A vast unknown realm awaits investigation.

To cast light on this invisible and largely unknown world, the U.S. Department of Energy's Joint Genome Institute has initiated a "genomic encyclopedia" to begin piecing together the tree of life within this vast terrain.

In the Dec. 24 issue of the journal Nature, scientists with the multi-institutional government-led institute, including University of Virginia biologist Martin Wu, published an analysis of the first 56 microbes sequenced thus far in the fledgling genomic encyclopedia. The organisms represent two of the three domains of the microbial tree of life.

The researchers have identified protein and gene families and enhanced their knowledge of the microbe's phylogeny.

"A key prerequisite for studying microbial evolution and diversity is the accurate determination of the evolutionary relationships among the organisms of interest," Wu said. "The explosive growth of bacterial genomic sequences makes it possible to reconstruct the bacterial tree of life on the genome level."

Most studies in microbiology have exploited a narrow subset of the evolutionary diversity of bacteria and archaea selected because they cause diseases or are of other human interest, rather than for fundamental understanding. As a result, only a few branches have been sequenced. The Joint Genome Institute's approach is to sequence little-studied microbial species that will inform understanding of other microbes and complex microbial communities.

"We are only scratching the surface," Wu said. "The vast majority of microbes remain hidden from us because they have not been cultured yet."

"What distinguishes [this project] is that it is less about the individual genomes and more about building a more balanced catalog of the diversity of genomes present on the planet, which in turn should facilitate searches for novel functions and our understanding of the complex processes of the biosphere," said senior author Jonathan Eisen, a science team leader with the Joint Genome Institute and the University of California, Davis.

Over time, information flowing from the project will shed light on the diversity of gene families and improve understanding of how microbes acquire new functions. A key outcome will be new genetic products and enzymes previously unknown to biologists.

Already, several of the characterized microbes from the "volume" of the genome encyclopedia are paying dividends. Researchers have discovered, for example, a novel set of cellulases – enzymes capable of breaking down plant material into sugars that can be rendered into transportation fuel – in a variety of organisms.

The project was launched in May 2007. Investigators intend to extend the research well beyond the pilot phase to sequence hundreds, and perhaps even thousands, of genomes from additional unknown microbes.

Wu joined U.Va. this past fall as an assistant professor of biology. He came from UC-Davis where he was a staff scientist. He studies how microbes evolve, adapt and diversify at the molecular, organismal and community levels, drawing upon the fields of genomics, evolutionary biology, computational biology and ecology. He also plans to integrate his cutting-edge genomic research with undergraduate teaching.

— By Fariss Samarrai