Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities, however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Here we describe Mackinac, a Python package that combines ModelSEEDs ability to automatically reconstruct metabolic models with COBRApys advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms.