The vast majority of commercial brewing is conducted under strict fermentation procedures using well-defined strains of Saccharomyces. There is a growing trend, however, to use more traditional techniques that encourage or even purposely introduce non-brewing yeasts and/or bacteria. This realm of mixed culture fermentation has reached the point that several breweries focus on it exclusively and many more have established “house cultures” that are used repeatedly over time. The origins of these mixed cultures are incredibly diverse and the exact species of organisms in each one is largely unknown. Previous efforts have utilized 16S and ITS sequencing to identify the makeup of specific cultures but these have focused on either one brewery or just one culture over time. Here we utilize shallow shotgun metagenomics to characterize 37 different samples from 18 different breweries across the United States. These data show similarities both within and between breweries, techniques, and age, and give a broad census for mixed culture fermentation in the craft brewing industry.