A molecular inventory of the faecal microbiomes of 23 marsupial species

Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where despite their iconic status, direct sequencing-based analyses remain limited. Here we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a catalogue of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two distantly related eucalyptus folivore specialists (koalas and greater gliders), suggesting convergent solutions to this challenging diet. Expansion of several bacterial and viral lineages were observed in these and other marsupial hosts that likely provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals reflecting human intervention. This resource contributes an important chapter in our ongoing understanding of animal microbiomes.