Age and anatomical site shape the gastrointestinal bacterial communities of captive American crocodiles (Crocodylus acutus).

Bacterial communities in the gastrointestinal tract (GIT) play a critical role in the health and physiology of vertebrates, responding to multiple intrinsic and extrinsic factors that modulate their structure and function. However, little is known about how these factors are associated with the dynamics and composition of these bacterial communities, especially in crocodilians. In this study, the structure of oral and cloacal bacterial communities in the GIT of Crocodylus acutus was examined through 16 S rRNA gene sequencing. The influence of factors such as age, sex, season, and anatomical location was evaluated. A total of 54 oral and cloacal samples from 27 adult and juvenile specimens from a captive population in Sinaloa, Mexico, were analyzed. Forty-two bacterial phyla were identified, with Pseudomonadota, Bacillota, and Bacteroidota being the most abundant. Significant differences in bacterial composition and diversity were detected between age groups and body regions, with greater diversity in adult specimens. Functional analysis predicted a predominance of metabolic pathways associated with amino acid and carbohydrate metabolism. This study establishes that age and anatomical site are key determinants in the structure of bacterial communities in C. acutus in captivity, providing the first comprehensive characterization for the species. These results establish a fundamental baseline for future comparative research with wild populations, as well as for the development of management and conservation strategies.