Infectious disease is a major disruptor of the pork industry. It can reduce production rates, trigger trade restrictions, and lead to large-scale mortality of the pigs themselves. Despite these serious impacts, the common diagnostic tools don’t capture the full range of potential pathogens, and the high rate of multiple pathogen co-infection further complicates diagnosis. Despite this, few studies have systematically characterized pig pathogens. To close this gap, researchers sequenced the microbial gene expression from pig clinical samples. This allowed researchers to characterize the diversity, abundance, genomes, and epidemiological history of a range of potential pathogens. They identified 34 RNA virus species, 9 DNA virus species, 7 bacterial species, and 3 fungal species as potential pathogens. Most were known pig pathogens, except for two of the fungi, which were novel members of the genus Pneumocystis. Most of the clinical cases had more than two pathogen species, with some pathogens showing tightly correlated patterns of co-occurrence or abundance. The clinical signs and necropsy results also supported a multiple-pathogen model. These results suggest that it is best to consider a panel of co-infecting pathogens to determine the cause of disease in pigs rather than focus on individual infectious agents.