WALNUT CREEK, CA–To tackle the computational challenges of analyzing the complex world of microbial communities, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has released to the worldwide research community IMG/M, an experimental metagenome data management and analysis system.
IMG/M integrates aggregate genome (also known as metagenome) data from diverse environmental microbial communities with isolate microbial genome data from JGI’s Integrated Microbial Genomes (IMG) system and allows the application of IMG’s comparative analysis tools on metagenome data. New tools also enable the examination of functional annotation profiles across microbial communities and isolated organisms of interest, and the analysis of strain-level heterogeneity within a species population in metagenome data.
Thus far, IMG/M has been used for completing the analysis of biological phosphorus removing (EBPR) sewage sludge communities and for studying the metagenomes of several key microbial communities recently sequenced by DOE JGI, including the hydrogen-producing consortium colonizing the termite hindgut.
“IMG/M has proven to be an extremely useful resource and tool for analyzing our metagenomic data,” said Jared R. Leadbetter, Assistant Professor of Environmental Microbiology at the California Institute of Technology, and collaborator on the termite hindgut microbial community for bioenergy project. “Such datasets are large, complex, and potentially unwieldy. Importantly, IMG/M is more than just an excellent tool to analyze data. The manner in which the results of that analysis are organized and made accessible through a user-friendly interface allows the researcher to rapidly move in a number of different intellectual directions. As a result, the user becomes better educated with and gets a real ‘feel’ for the data in a manner that would not otherwise be possible on such short timescales.”
IMG/M was presented at the recent Keystone Symposium on Microbial Community Genomics in Animals and the Environment, organized by DOE JGI Director Edward M. Rubin and Edward F. DeLong, Professor in the Division of Biological Engineering & Department of Civil and Environmental Engineering at the Massachusetts Institute of Technology.
“IMG/M provides an intuitive interface, and nice complement to IMG for comparing gene content and phylogenetic profiles of microbial genomes, and relating them to the large microbial community datasets now accumulating,” DeLong said. “These are great and sorely needed data-exploration tools.”
IMG/M will be demonstrated at a workshop on April 1, as part of the DOE JGI First Annual User Meeting (http://www.archive.jgi.doe.gov/meetings/usermtg06/index.html).
IMG/M, accessible to the public at http://img.archive.jgi.doe.gov/m, is the result of a collaboration between the DOE JGI and Lawrence Berkeley National Laboratory (LBNL) Biological Data Management and Technology Center (BDMTC).
The DOE Joint Genome Institute, 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. DOE JGI’s Walnut Creek, Calif. Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
The LBNL Biological Data Management and Technology Center (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 (http://img.archive.jgi.doe.gov).