On a world-wide basis, co-infections involving porcine reproductive and respiratory syndrome virus
(PRRSV) and porcine circovirus type 2 (PCV2) are common and contribute to a range of polymicrobial
disease syndromes in swine. Both viruses compromise host defenses, resulting in increased susceptibility
to infections by primary and secondary pathogens that can affect growth performance as well as
increased morbidity and mortality. An experimental population of 95 pigs was co-infected with PRRSV
and PCV2. At 70 days post-infection (dpi), 20 representative pigs were selected as having the best or
worst clinical outcome based on average daily gain (ADG) and the presence of clinical disease. Worst
clinical outcome pigs had prolonged and greater levels of viremia as measured by qPCR. Serum, lung and
fecal samples collected at 70 dpi were analyzed using a comprehensive DNA microarray technology, the
Lawrence Livermore Microbial Detection Array, to detect over 8000 microbes. Bacterial species, such as
Bacillus cereus, were detected at a higher rate in the serum of worst performing pigs. At the level of the
fecal microbiome, the overall microbial diversity was lower in the worst clinical outcome group. The
results reinforce the importance of pathogen load in determining clinical outcome and suggest an
important role of microbial diversity as a contributing factor in disease.