Australian marsupials are a unique natural resource of great cultural, environmental, and economic significance. However, very little is currently known about the gut microorganisms that have co-evolved with these ‘low methane producer’ animals to support their nutrition and health. By using a combination of molecular and culture-based techniques we aim to characterise the microbial communities to understand how they influence low methane emissions in several native Australian herbivores.
High throughput shotgun sequencing from the faecal material of several herbivorous marsupials including kangaroos, wombats, koalas, gliders, and bettongs was used to characterise gut microbial communities. PCA analysis of 16S rRNA genes from the metagenomic data indicates that these communities are differentiated mainly by the host animal species (r2=0.9, p=0.001) or the diet type (r2=0.8, p=0.001). Consistent with this result, the microbiomes of the same animal species broadly cluster together, irrespective of the geographic location of the host. Furthermore, these animal microbiomes partitioned into distinctive glider, kangaroo/wombat, and koala groups likely based on diet. In total, over 100 high-quality metagenome-assembled genomes (MAGs) were recovered, representing 41-87% of the microbial community. Several MAGs of methane-producing archaea, representing 0.5% of the community, were generated and associated with common methanogen gut lineages. Some of these methanogens have been cultured from marsupial faecal material, including a novel Methanosphaera species from the koala gut divergent to other isolates from this lineage.
By characterising the metabolic capabilities of the marsupial microbial community through metagenomic analyses and the archaea through cultivation studies, we hope to understand the reason for the low methane levels seen in marsupials compared to production herbivores such as ruminants.