Unravelling the impacts of captivity on saltwater crocodile (Crocodylus porosus) cloacal bacterial communities and physiology.

This study addresses a significant research gap in understanding the impacts of captivity on the bacteriome and physiology of saltwater crocodiles (Crocodylus porosus). Despite their ecological and cultural significance, crocodilians are a taxon that remains underexplored in microbiome research. We investigated cloacal bacteriome samples from both wild and captive populations to identify compositional and functional differences resulting from captivity. Our findings reveal significant alterations in bacterial diversity and community structure in captive crocodiles, with notable shifts at both phylum and family levels; specifically, Bacteroidota and Fusobacteriota dominate in captivity, whereas wild crocodiles exhibit a higher prevalence of Pseudomonadota and Bacillota. The Shannon diversity index indicates a significant reduction in bacterial diversity among captive individuals, likely due to husbandry practices that foster a microbially depauperate environment. Additionally, serum metabolomics analysis shows an enrichment of alcohol sugars in captive crocodiles, alongside a decrease in pantothenic acid. While this is the first study to characterize these traits in saltwater crocodiles, further research is necessary to determine the physiological consequences of these bacterial and metabolic changes on host fitness and adaptability. Longitudinal studies are essential for understanding how bacterial communities evolve over time and in response to environmental factors, which will inform conservation strategies and improve the management of captive populations of crocodilians intended for reintroduction into the wild.