Gut microbial differences in healthy and sick farmed American alligators (Alligator mississippiensis) during a disease outbreak.

American alligators (Alligator mississippiensis) in production systems within the United States experience occasional disease outbreaks and die-offs. However, outbreak management is limited by an incomplete understanding of common causes of mortality in commercially raised crocodilians. In this study, we examined the gut microbiota of healthy (n = 18) and sick alligators (n = 17) during an active outbreak on an alligator farm in Southeast, USA. Sick alligators were all exhibiting generalized signs of disease. The gut microbial composition of alligators with disease differed significantly from that of healthy alligators. One ASV in the genus Peptostreptococcus and one in the genus Wolinella were found at increased relative abundances in alligators with disease while one ASV, Clostridium sensu stricto 13, was found at increased relative abundances in healthy alligators. Notably, the Peptostreptococcus ASV was found in all but two of the 17 alligators with disease and was not detected in any healthy alligator. Chlamydia species were also found at increased abundance in alligators with disease; although, Chlamydia was widely present in healthy alligators too. Additional studies are required to assess the clinical significance of these taxa as primary / secondary pathogens or protective (probiotic) species.