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Microbial Genomics logo Microbial Genomics

Volume 12, Issue 1

A molecular inventory of the faecal microbiomes of 23 marsupial species Open Access

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 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): diprotodont , gut , marsupial , metagenomics , microbiome and phage
Funding
This study was supported by the:
  • Villum Fonden (Award 13167)
    • Principal Award Recipient: ElizabethH. J. Neilson
  • Bill and Melinda Gates Foundation (Award INV-044643)
    • Principal Award Recipient: IvanLiachko
  • Novo Nordisk Fonden (Award 0054890)
    • Principal Award Recipient: ElizabethH. J. Neilson
  • Villum Fonden (Award 023054/00007523)
    • Principal Award Recipient: BirgerLindberg Møller
  • Australian Research Council (Award DP250103673)
    • Principal Award Recipient: PhilipHugenholtz
  • Australian Research Council (Award DP150104202)
    • Principal Award Recipient: PhilipHugenholtz
© 2026 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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A molecular inventory of the faecal microbiomes of 23 marsupial species
M Gen 12, 001601 (2026); https://doi.org/10.1099/mgen.0.001601
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