In the Northern Territory (NT) and Queensland, Australia, estuarine crocodiles (Crocodylus porosus) are farmed mainly for their skin. There are several types of skin blemishes that reduce the value of hides and the search for a specific causal agent continues. Concomitantly, the acknowledged role of the microbiota in maintaining animal health has lead to a change in thinking about this problem. There is now interest in taking a microbial ecology approach to shed light on crocodile skin homeostasis. In the wild, there is no evidence that crocodile skins have the same blemishes that are present in the skin of farmed crocodiles, so wild crocodile skins were an important component of this study.
We investigated the bacterial microbiota of wild and farmed crocodile skins. As for the latter, samples were collected from crocodile farms in the NT and Queensland. Skins were swabbed, DNA extracted and the bacterial community composition were assessed using high-throughput 16S rRNA genes sequencing. Bacterial communities from the skin of wild crocodiles were significantly different from those of farmed animals, when compared using permutational multivariate analysis of variance of the Bray-Curtis distance matrices. The differential presence and abundance of bacterial taxa between skin types were compared using canonical analysis of principal coordinates and a negative binomial model. Wild crocodile skins had more non-pathogenic marine bacteria (mainly Synthrophobacteriales Alteromonadales Rhodobacteriales, and Oceanospirillales) compared to farmed crocodile skins. In contrast, the latter had a greater abundance of taxa which also contain opportunistic pathogens. These included Burkholderiales, Clostridiales, Bacteroidales, and Actinomycetales. Furthermore, these taxa were more frequent in bacterial communities from blemished skin compared to normal. A key finding was that the bacterial family Dermatophilaceae, found exclusively in farmed animal skins and more abundant in blemished skin compared to normal, comprises the causative microorganisms of the “dermatite granuleuse”, a skin disease that is prevalent in the humid tropics and subtropics and which affects many animal species, including farmed crocodiles.