Pouch microbiome changes during lactation in the short-beaked echidna (Tachyglossus aculeatus)

Abstract

Monotreme and marsupial early development is characterised by a short gestation, the birth of the young at an early stage of development, and a long lactation in the pouch or pseudo-pouch. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich world. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiome during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Swab samples were obtained from wild and captive echidna pseudo-pouches outside of breeding season, during courtship and breeding, and during lactation. 16S rRNA gene metabarcoding revealed that the pseudo-pouch microbiome undergoes dramatic changes during lactation, with a reduction in bacterial taxa that may be pathogenic. These changes were not observed in samples taken outside of breeding season or during courtship and mating. This showed that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. This study pioneers pouch microbiome research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programs in the future.