EcoHealth survey of Herpetofauna in South Africa

Abstract

In this project, the samples were taken from reptiles’ oral and cloacal cavities. The majority of samples originated from healthy-appearing captive reptiles therefore the bacteria detected in this study form part of the natural bacterial microbiome of various reptile species. Samples were taken from Bitis arietans, Dendroaspis polylepis, Dispholidus typus, Hemachatus haemachatus, Naja annulifera, Naja mossambica, Pseudaspis cana, Python natalensis, Matobosaurus validus, Varanus albigularis, Stigmochelys pardalis, and Crocodylus niloticus. Cloacal samples (n = 80) underwent growth on selective media for screening of Salmonella. The results showed an isolation success of 88.75 % of Salmonella across all samples. The use of Xylose Lysine Deoxycholate agar (isolation success of 81.25 %) had a highly significant (p = 0.017) influence on the isolation success when compared to the use of Brilliant Green agar (isolation success of 61.25 %). Multiple other factors were tested but none had a statistically significant influence of the isolation success of Salmonella. The oral samples (n = 53) underwent analyses of the bacterial 16S rRNA gene, obtained from Next- Generation sequencing, to determine the microbiome of the snakes sampled. A total of 706 unique taxa were detected in the oral cavity. The most abundant bacteria detected were identified as Staphylococcus (77.78 %) followed by Enterobacter (4.56 %), an unidentified genus within Weeksellaceae (3.21 %), Alcaligenes (2.16%), and Bacteroides (1.74 %). Generally, a host species that were part of the Elapidae family had lower levels of bacterial diversity and richness when compared to species from other families. The classification of Elapidae did not have a significant influence on bacterial richness (p = 0.0506) but greatly influenced bacterial diversity (p = 0.0202) and the composition of the microbiome (p = 0.019). Host species had the greatest influence on the bacterial richness (p < 0.0001), diversity (p < 0.0001) and the composition of the microbiome (p = 0.001). Days in captivity had no significant influence on bacterial richness (p = 0.462) but did highly influence bacterial diversity (p = 0.0004) yet both values increased as days in captivity increased.