# A molecular inventory of the faecal microbiomes of 23 marsupial species

## TL;DR

This study explores the faecal microbiomes of 23 marsupial species, revealing new microbial genomes and how diet and captivity influence microbiome composition.

## Contribution

The study provides a novel molecular inventory of marsupial faecal microbiomes, including thousands of newly identified prokaryotic and viral genomes.

## Key findings

- Host phylogeny is the main driver of microbiome composition in marsupials.
- Koalas and southern greater gliders have distinct microbiomes adapted to their eucalypt diet.
- Captive marsupials show higher prevalence of antimicrobial resistance genes compared to wild ones.

## Abstract

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 reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.