The US Department of Energy’s Joint Genome Institute is planning to sequence 100 culturable microbes as a pilot project that could pave the way for a large-scale international project to sequence thousands of cultured microbes, In Sequence has learned.
The aim of the project, for which new sequencing technologies will play an important role, is to increase the diversity of sequenced genomes for bacteria and archaea, according to Jonathan Eisen, a researcher at the University of California, Davis, who is coordinating the pilot.
“We decided to do this pilot both to generate some very useful data as well as to test methods and approaches,” he said in an e-mail message to In Sequence this week.
The species to be sequenced must pass two criteria, according to Daniel Drell, a program officer with the DOE’s Office of Biological and Environmental Research: They must be able grow in culture so they can be disseminated to other research groups, and must have some phenotypic information known about them for scientists to link with genomic data.
JGI is tapping several collections of cultured microbes to contribute samples to the project. The German Collection of Microorganisms and Cell Cultures, DSMZ, in Braunschweig, Germany, has already agreed to provide DNA for free, according to Eisen, and JGI is in talks with other collections as well.
“This is really important for us because growing 100 diverse isolates is likely to be difficult and possibly expensive,” he said.
Drell said next-generation sequencing technologies will play a “very powerful and important” role in the project because they have already proven their usefulness in microbial sequencing.
“Most likely, 454 will be used with Sanger to generate the shotgun data,” said Eisen, although this has not been finalized yet. The goal is to create finished genomes for all 100 species, he said, although the researchers might not pursue this goal for the most difficult ones.
The pilot project will be supported with discretionary funding from the JGI, according to Eisen, though he did not know the amount.
DOE is interested in the project for a number of reasons, Drell said: It could deliver new genes of interest for the agency’s mission, which includes biological energy sources and waste cleanup.
Also, the sequenced genomes might help interpret data from metagenomic projects by providing a reference, and they could help assign functions to genes in species already sequenced that have not yet been annotated.
This is not the first project to sequence large numbers of microbial genomes. For example, last year, scientists from Washington University, the Institute for Genome Research, and Stanford University launched the Human Gut Microbiome Initiative, which aims to generate “deep draft” genome sequences of 100 cultured bacterial reference species found in the human gut.
The group plans to finish 15 of them using a combination of 454 sequencing and Sanger sequencing. The project, funded by the National Human Genome Research Institute, will probably be completed next year (see In Sequence 4/10/2007).
Macro Microbial Effort
Both projects are testing the waters for a possible large-scale microbial sequencing project proposed by the American Academy of Microbiology and others.
“We decided to do this pilot both to generate some very useful data as well as to test methods and approaches.”
Last month, the AAM published a report entitled “Reconciling Microbial Systematics & Genomics” that resulted from a meeting last fall during which participants made a number of recommendations. One suggested “that the international microbial systematics community should coordinate an initiative to construct draft genome sequences of each of the roughly 6,500 type strains catalogued by the International Committee on the Systematics of Prokaryotes (ICSP),” according to the report.
Such a large-scale project “would significantly advance the integration of genomic information into our understanding of microbial diversity and would enable researchers to map phenotypes to genomes,” the report states.
Drell said that the outcome of the pilots will likely determine how and when such an international project could get off the ground. “My expectation is that the results of the 100-microbe pilot are going to largely be, ‘100 isn’t enough, we need to go to 1,000 or a couple of thousand.’ At that point, it makes no sense for this to be a one-nation project,” he said. Also, other US agencies, such as the National Science Foundation or the US Department of Agriculture, could get involved at that stage.
Eisen agreed, saying that although other projects funded through the DOE’s Community Sequencing Program or the NSF’s Tree of Life program, for example, have already increased the diversity of sequenced microbes, “these projects have still barely touched the diversity of bacteria and archaea,” he said. “Thus it has become clear that a much larger scale project is needed.”