The Virtual Institute for Microbial Stress and Survival (VIMSS, http://vimss.lbl.gov/) funded by the Dept. of Energy's Genomics:GTL Program, is dedicated to using integrated environmental, functional genomic, and comparative sequence and phylogeny data to understand mechanisms by which microbes and microbial communities survive in uncertain environments while carrying out processes of interest for bioremediation and energy generation. To support this work, VIMSS has developed a Web portal, along with computational analysis and an underlying database, for comparative functional genomics of bacteria and archaea. MicrobesOnline (http://www.microbesonline.org) has been enabling comparative genome analysis since 2003. The portal currently includes 702 complete microbial genomes (662 bacterial, 40 archaeal, 1770 viruses, 268 plasmids) and offers a suite of analysis and tools including: comprehensive gene family and domain annotations, information on three dimensional structure representatives and similarities, an interactive gene expression heatmap browser along with functionality for gene expression profile searches, a multi-species genome browser, operon and regulon predictions, a combined gene and species phylogeny browser, a gene ontology browser, a metabolic pathway browser, a workbench for sequence analysis (including sequence motif detection, motif searches, sequence alignment and phylogeny reconstruction), and capabilities for community annotation of genomes. VIMSS integrates functional genomic data and provides novel web-based viewing and analysis tools for gene expression microarray, proteomic, metabolomic, and phenotype microarray data. Currently, these data are mostly project generated for wild-type and mutants of Desulfovibrio vulgaris and Shewanella oneidensis exposed to stress conditions found at DOE field sites. However, the organism scope is being expanded, and recently the E. coli gene expression data compendium from the Many Microbes Microarray Database (M3D) has been imported into MicrobesOnline. Additionally VIMSS has developed capabilities to analyze microarray experiments performed on multiple species simultaneously. Selecting an organism or gene of interest in MicrobesOnline leads to information about and data viewers for VIMSS experiments conducted on that organism and involving that gene or gene product. It is possible to view microarray data from multiple stress conditions as an interactive heatmap and to analyze correlations between gene expression results from different experiments. Among the major new features is the ability to search the microarray data compendium for genes with gene expression profiles similar to a query expression profile (either based on a gene or set of genes). Such new compendium-wide functionalities allow to observe patterns in gene expression changes across multiple conditions and genes, and to search for similarities to these patterns. The information integration and analysis performed by VIMSS serves not only to generate insights into the stress responses and their regulation in these microorganisms, but also to document VIMSS experiments, allow contextual access to experimental data, and facilitate the planning of future experiments. VIMSS also is incorporating into MicrobesOnline publicly available functional genomics data from published research, so as to centralize and synergize data on and analysis of microbial physiology and ecology in a unified comparative functional genomic framework.