On the one-year anniversary of the launch of the experimental metagenome data management and analysis system, IMG/M, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has released the latest upgrade. Targeting DOE JGI's expanding user base, IMG/M provides tools for analyzing the functional 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. 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). In addition, IMG/M includes three of the simulated metagenome data sets employed for benchmarking several assembly, gene prediction, and binning methods (its Web site). 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. IMG/M will be demonstrated at a workshop on March 28, as part of the DOE JGI Second Annual User Meeting (its Web site). IMG/M, accessible to the public at http://img.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. Additional information about DOE JGI can be found at: its Web site.