A molecular inventory of the faecal microbiomes of 23 marsupial species

Bowerman, K. L.; Soo, R. M.; Chaumeil, P.-A.; Blyton, M. D.; Sorensen, M.; Gunbilig, D.; Malig, M.; Islam, M.; Zaugg, J.; Wood, D. L.; Liachko, I.; Auch, B.; Morrison, M.; Krause, L.; Lindberg Moller, B.; Neilson, E. H.; Hugenholtz, P.

doi:10.1101/2025.08.31.672981

bioRxiv · 10.1101/2025.08.31.672981

A molecular inventory of the faecal microbiomes of 23 marsupial species

Bowerman, K. L.·Soo, R. M.·Chaumeil, P.-A.·Blyton, M. D.·Sorensen, M.·Gunbilig, D.·Malig, M.·Islam, M.·Zaugg, J.·Wood, D. L.·Liachko, I.·Auch, B.·Morrison, M.·Krause, L.·Lindberg Moller, B.·Neilson, E. H.·Hugenholtz, P.

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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 eucalyptus folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages were 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. Impact statementDespite their ecological and evolutionary importance, marsupials remain underrepresented in microbiome research. Here, we present the most extensive faecal microbiome dataset to date for this group, encompassing metagenomic, metabolomic, and proximity ligation data from 23 marsupial species. As in other animals, we find the microbial community structure reflects the host species, and some marsupials carry expanded sets of certain microbial lineages indicative of within-host evolution. This work substantially expands the genomic landscape of host-associated microbes and viruses in a poorly studied mammalian clade. Data summaryRaw read data, prokaryotic MAGs [≥]50% complete with [≤]10% contamination are available via the European Nucleotide Archive under project PRJEB89408. The full set of viral genomes, clustered protein database and metabolite data (raw and processed) are available via https://doi.org/10.48610/14e37e9. Prokaryotic MAGs are also available via https://figshare.com/s/87443d80817f57aadc16.

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Bowerman, K. L., Soo, R. M., Chaumeil, P.-A., Blyton, M. D., Sorensen, M., Gunbilig, D., Malig, M., Islam, M., Zaugg, J., Wood, D. L., Liachko, I., Auch, B., Morrison, M., Krause, L., Lindberg Moller, B., Neilson, E. H., Hugenholtz, P.. 2025-09-01. A molecular inventory of the faecal microbiomes of 23 marsupial species. https://doi.org/10.1101/2025.08.31.672981

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