The gastrointestinal microbiome of fasting wild and farm-raised American alligators

The gastrointestinal (GI) tract microbiomes from fasting (winter season), wild and farm-raised American alligators (A. mississippiensis) were analyzed by 454 pyrosequencing of the V4-V6 region of the 16S rRNA gene. The microbial assemblages in both animals differed along the GI tract, likely reflecting varying digestive system metabolic functions, as well as distinct rearing histories and diets between the animals. Fecal material did not mirror the composite GI microbiome, missing certain phyla (e.g., Actinobacteria) and over-representing others (e.g., Fusobacteria). The overall wild alligator gut microbiome was compositionally unique from what has been identified from mammals and birds, thereby providing new evidence for the evolution of reptilian host-microbe associations and interactions.