“We saw there’s an enormous amount of discovery that can be done through the study of microbes for which we don’t know anything about,” said Kyrpides, who quickly proposed funding for a much larger sequencing effort.
This latest batch of more than 1,000 genomes included 845 “singletons” — the only sequenced representative of their species. Analysis of the genomes also revealed a 10 percent increase in novel protein families.
Jonathan Eisen, an evolutionary biologist at the University of California Davis, helped launch the microbial genome encyclopedia project at the DOE. He said that the value of this open genomic reference library is twofold: first, it provides researchers worldwide with a more accurate catalog of the diversity of life; and second, it identifies new proteins and enzymes that can used for a variety of purposes, from developing new cures for chronic diseases to efficiently generating natural gas from biomass.
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Eisen noted that data from the first 56 genomes analyzed in 2009 led to the discovery of new forms of cellulase, the enzyme that breaks down plant material for biofuel production. Researchers also scanned the growing genomic encyclopedia to find novel variants of the Cas9 protein that may improve upon the popular CRISPR gene-editing technology, said Kyrpides.
In its mission to fill the microbial gaps in the tree of life, the DOE team searched high and low for microbes that fell outside of the spotlight. The latest batch of 1,000 bacteria and archaea — primitive single-celled organisms without a nucleus or membrane-bound organelles — were sampled from extreme environments like oil springs, industrial waste sites, and the funkier corners of the human body.
The effort to sequence unknown microbes has already paid off in some appropriately unexpected ways. Eisen points to a 2015 paper that revealed some key differences between the gut microbes of modern Westerners and those living in the digestive tracts of a hunter-gatherer tribe in Peru. One microbe in particular, Treponema, was present in large numbers in the hunter-gatherers but almost non-existent in folks from Oklahoma. The researchers were able to match the mysterious gut microbe’s genome with its closest relative, a Treponoma species found in pigs, because it was already in the DOE encyclopedia.