Microbiomes from scats of wild and captive short-beaked echidna

The short-beaked echidna (Tachyglossus aculeatus) is an iconic Australian species and the most widespread native mammal. Echidnas are cryptic animals, therefore much is still unknown about many aspects of their biology. Furthermore, wild echidna populations are under threat and echidnas held in captivity have had severe gastric health problems. Here, we collected echidna scats from across Australia and from two zoos feeding echidnas four different diets and performed 16S metabarcoding on the scats to investigate the bacterial communities. We characterised and compared the microbiomes of wild and captive echidnas and compared the bacterial communities from echidnas fed the four different diets in captivity. This was the largest geographical microbiome study for any single non-human species, the first microbiome study for echidnas and for any monotreme (egg-laying mammal).