Genome-scale metabolic models (GEMs) are valuable in describing an organism's entire metabolism using genomic information and have made huge impact on systems biology and metabolic engineering. Here we review current state of microbial GEMs and their use in various applications. There has recently been much interest in reconstructing GEMs for microbial communities, reflecting the increasing importance of microbiome. Analyses of recent work suggest that the GEMs for the best studied microorganisms, new or less studied microorganisms, and also microbial communities need to be thoroughly validated with experimental data beyond simple gene essentiality and nutrient utilization capabilities. In this paper, computational modeling resources and frameworks developed recently for reconstructing GEMs of microorganisms and microbial communities together with their applications are reviewed.