BDMTC, JGI Announce IMG/M Upgrade

The DOE Joint Genome Institute (JGI), collaborating with CRD’s Biological Data Management and Technology Center (BDMTC), announced last month an upgrade of the metagenome data management and analysis system, IMG/M, on the anniversary of its launch.

Developed by BDMTC’s data management and software engineers and scientists of JGI’s Genome Biology and Microbial Ecology Programs, IMG/M is a valuable asset for a growing community of biologists. Metagenomics refers to the genomic study of batches of microbes in their natural environments instead of those cultivated individually in lab cultures. IMG/M provides tools for analyzing the capability of microbial communities based on their metagenome sequence—in the context of reference isolate genomes—using a variety of public functional and pathway resources.

Since the release of its initial experimental version in 2006, IMG/M has been used by JGI scientists and their collaborators for analyzing several environmental microbial communities, and has been demonstrated at professional meetings and conferences. The new version of IMG/M will be presented at JGI’s second annual user meeting on March 28 in Walnut Creek, California.

The enhanced version of IMG/M now offers aggregate genome (metagenome) data generated from microbial community samples that have been the subject of recently published studies. These include samples from biological phosphorus removing sludge (Nature Biotechnology Volume 24, Number 10, October 2006), human distal gut (Science 312: 1355-1359, 2 June 2006), a gutless marine worm (Nature 443, 950-955, 26 October 2006) and obese and lean mouse gut (Nature 444, 1027-131, 21 December 2006).

These research projects give scientists valuable clues to how these microbes could help clean up the environment and produce alternative transportation fuels. For example, the phosphorus-removing sludge study, the genome sequence of bacteria Accumulibacter phosphatis is enabling researchers to figure out how the bugs could accumulate massive amounts of phosphorus inside their cells. Being able to cultivate the microbes, which currently are impossible to grow in laboratory culture, can play a key role in reducing phosphorous during wastewater treatment and protecting rivers and lakes from excessive algae blooms.

In addition, IMG/M includes three of the simulated metagenome data sets employed for benchmarking several assembly, gene prediction and binning methods.

“This is the first production version of IMG/M” said Victor Markowitz, head of BDMTC. IMG/M’s reference isolate genomes were included from version 2.0 of JGI's Integrated Microbial Genomes (IMG) system, a total of 2,301 isolate genomes consisting of 595 bacterial, 32 archaeal, 13 eukaryotic, and 1,661 virus genomes. The Computational Biology and Bioinformatics group at Pacific Northwest National Laboratory(PNNL) carried out the large-scale gene similarity computations on the Molecular Sciences Computing Facility supercomputer.

“The support provided by our colleagues at PNNL has been critical in building IMG/M — computations that otherwise would have taken several weeks, were completed in about a day,” said Markowitz.

BDMTC has expertise in the development of biological data management systems and bioinformatics tools. BDMTC is collaborating with DOE JGI on the development and maintenance of IMG and IMG/M.

JGI, supported by the DOE Office of Science, unites the expertise of five national laboratories — Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest — along with the Stanford Human Genome Center to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and clean-up.