The koala (Phascolarctos cinereus) is an obligate dietary specialist, due to its ability to overcome a difficult diet that is nutritionally challenging and toxic to many animals. Their diet is composed almost exclusively of Eucalyptus, which has evolved a wide range of plant secondary metabolites, many of which function as effective defenses against herbivory.
Relatively little is known about the composition and diversity of the gut microbiome of koalas, despite their importance in extracting nutrients from a challenging diet. Thus, knowledge of microbes driving the gut microbiota of koalas ingesting specific diets would assist in development of targeted inoculations, given prior to translocation or, release after rehabilitation.
This study investigated the microbiome of 33 wild koalas from Cape Otway, Victoria, Australia, using DNA extracted from faecal samples collected from two time-points. We utilised the Illumina MiSeq platform together with the QIIME pipeline and PRIMER v6 to identify significant differences in the gut microbiota within one population of animals known to separate into two diet types. Analysis of cuticular n-alkane markers confirmed that 20 koalas were feeding on the preferred species Eucalyptus viminalis, and 13 on the less-preferred Eucalyptus obliqua. E. viminalis woodland at Cape Otway has experienced die-off caused by overbrowsing by koalas. Thus, some koalas have been forced into eucalypt species they would not normally consume.
Bacteroidetes and Firmicutes dominated all faecal microbiomes at the phylum level, however, there were significant differences at genus level which produced distinct separation between the two groups that were highly correlated to diet, suggesting different microbial communities may enable koalas to extract valuable nutrients from their challenging diets.
These results will direct further investigations into important microbial genes and gene functions which impact on digestive processes including nutrient extraction and detoxification, and health of koala populations consuming varied eucalypt diets throughout Australia.