Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion
Miriam E.Shiffman1, Rochelle M. Soo1, Paul G. Dennis2, Mark Morrison3, Gene W.Tyson1 and Philip Hugenholtz1
1Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
2School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
3The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
The koala has evolved to become a specialist Eucalyptus herbivore since diverging from its closest relative, the wombat, a generalist herbivore. This niche adaptation involves, in part, changes in the gut microbiota. The goal of this study was to compare koala and wombat fecal microbiomes using metagenomics to identify potential differences attributable to dietary specialization. Several populations discriminated between the koala and wombat fecal communities, most notably S24-7 and Synergistaceae in the koala, and Christensenellaceae and RF39 in the wombat. As expected for herbivores, both communities contained the genes necessary for lignocellulose degradation and urea recycling partitioned and redundantly encoded across multiple populations. Secondary metabolism was over represented in the koala fecal samples, consistent with the need to process Eucalyptus secondary metabolites. The Synergistaceae population encodes multiple pathways potentially relevant to Eucalyptus compound metabolism, and is predicted to be a key player in detoxification of the koala’s diet. Notably, characterized microbial isolates from the koala gut appear to be minor constituents of this habitat, and the metagenomes provide the opportunity for genome-directed isolation of more representative populations. Metagenomic analysis of other obligate and facultative Eucalyptus folivores will reveal whether putatively detoxifying bacteria identified in the koala are shared across these marsupials.