Major genome release paves way for future biotech products

A major release of reference genomes is expected to pave the way for future health, biotechnology and agricultural products.

Almost a decade’s worth of work led by the US Department of Energy Joint Genome Institute (DOE JGI) has resulted in the release of 1003 phylogenetically diverse bacterial and archaeal reference genomes.

“These findings will jumpstart biotechnology applications and be extremely useful for interpreting environmental data,” said University of Queensland School of Chemistry and Molecular Biosciences researcher Professor Philip Hugenholtz. Professor Hugenholtz is a co-author of the paper published in Nature Biotechnology.

Professor Hugenholtz was a staff scientist at DOE JGI from 2004 to 2010. As lead taxonomy curator, he selected genomes to be sequenced, participated in analysis and was a co-author of the original paper. In late 2010 he returned to UQ to establish and direct the Australian Centre for Ecogenomics, which provides an Australian focal point for sequence-based analysis of microbial communities.

The US DOE is interested in learning more about this biodiversity because microbes play important roles in regulating Earth’s biogeochemical cycles — processes that govern nutrient circulation in terrestrial and marine environments, for example.

“The importance of sequencing reference organisms from culture collections for exploration of microbial dark matter cannot be overstated,” said Hugenholtz.

“Without reference organisms, it’s akin to navigating a country without signposts.

“We now understand bacteria are involved in almost every aspect of daily life, yet we have a poor understanding of how these organisms relate to each other and the full extent of their genetic capabilities.”

DOE JGI’s Prokaryotic Super Program head and paper senior author Dr Nikos Kyrpides said bacteria and archaea were the most biodiverse of free-living organisms on Earth.

“They have already conquered every environment on the planet, so they have found ways to survive under the harshest of conditions with different enzymes and with different biochemistry,” he said.

Uncovering the functions of genes, enzymes and metabolic pathways through genome sequencing and analysis has wide applications in biological, biomedical, agricultural and environmental sciences.

The effort is part of the DOE JGI’s Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative to sequence thousands of bacterial and archaeal genomes and fill in branches of the tree of life, with the first 56 GEBA genomes published in 2009. The microorganisms in the new study were isolated from environments ranging from sea water and soil, to plants, and to cow rumen and termite guts, then sequenced at DOE JGI. The genomes were publicly released immediately after sequencing to maximise their use by the larger scientific community. The project included researchers at UQ, Leibniz Institute DSMZ in Germany, University of Georgia, Michigan State University and Newcastle University in UK.

Nature Biotechnology artwork by Zosia Rostomian from Berkeley Lab Creative Services.