The role of the mammalian gastrointestinal (GI) microbiome in influencing host health, immune system development and function, and more recently behaviour, is well recognised. Much work has been undertaken to determine which factors influence the microbial community composition of the gut microbiome, resulting in the finding that environmental factors such as diet and geography shape the distribution of the dominant bacterial species, Bacteroidetes, Firmicutes and Proteobacteria in the mammalian gut. Research has also found that the functional potential of the gut microbiome can be predicted from the microbial community composition, and that diet is a stronger determinant of gut microbiome function than host phylogeny in mammals. The overarching goal of this project was to characterise the microbial community composition of the koala (Phascolarctos cinereus) gut microbiome in a variety of contexts. In particular, the similarities and differences between microbial communities associated with simple two eucalypt diets at Cape Otway, Victoria (Chapter 2), the microbial communities associated with mixed eucalypt diets at Mountain Lagoon, NSW (Chapter 4), and the stability of the microbial community of Mountain Lagoon koalas over time (Chapter 5). Community composition was linked to functional potential of the gut microbiome from koalas eating simple eucalypt diets at Cape Otway (Chapter 3) by shotgun sequencing of the faecal microbiome, all critical aspects of the nutritional ecology and health of the koala. Differences in diet choice may influence microbial composition, richness and diversity in the dietary specialists' gut microbiome. Using the 16S rRNA gene, I investigated whether koalas eating either of two simple eucalypt diets, consisting of either the highly preferred and relatively nutritious Eucalyptus viminalis (subgenus Symphyomyrtus), or the less preferred and less nutritious Eucalyptus obliqua (subgenus Eucalyptus), had different gut microbial community profiles. I found that although all koala gut microbiomes were dominated by Bacteroidetes and Firmicutes, there were significant diet associated differences in relative abundance of the dominant bacterial genera Parabacteroides, Bacteroides and bacterial taxa in the family Ruminococcaceae. The differences in relative abundance extended to bacterial taxa present at low abundances including, bacterial taxa in the phyla Cyanobacteria, Synergistetes and Proteobacteria, suggesting that there may be differences in functional potential of the gut microbiomes from koalas eating different diets (Chapter 2). Differences in functional potential between the two dominant groups of bacteria Parabacteroides and Ruminococcaceae were assessed with the "Genome Browser" from the Microbial Genome and Metagenome Data Analysis pipeline of the Department of Energy Joint Genome Institute site, and the Carbohydrate-Active Enzymes database. The results of which indicated that the gut microbiomes dominated by Parabacteroides (E. viminalis) would target the more easily degraded carbohydrates e.g. oligosaccharides and starch, where the gut microbiomes dominated by Ruminococcaceae (E. obliqua) would more readily modify and degrade the recalcitrant cell-wall fibre e.g. hemicellulose and cellulose. There were significant differences in gut microbial richness and diversity between the two diets, leading me to consider whether the gut microbial community of the E. viminalis koalas had less diversity because they were more specialised and therefore, more efficient at nutrient extraction (Chapter 2). I used a gene-centric approach to analyse metagenomic data to predict the functional potential of the gut microbiomes influenced by the two diets at Cape Otway. I found that although many of the potentially functional pathways were shared between the metagenomes from the koala microbiomes, indicating a potential core of functional genes shared across the koala gut microbiomes, the phylogenetic and functional profiles separated based on diet (Chapter 3). I considered whether the variation in microbial communities could influence energy extracted from the diet by the koala, and discovered that the microbiomes of koalas eating E. obliqua had the potential to produce the highenergy short chain fatty acid (SCFA) butyrate, where the microbiomes of the koalas eating E. viminalis had the potential to produce the SCFA succinate (Chapter 3). This finding may indicate that koalas eating the lower quality eucalypt diet of E. obliqua may benefit from an increased abundance of butyrate-producing bacterial taxa including Butyrivibrio, Eubacterium and Roseburia, thereby increasing the energy yield of their diet. The results of my previous investigations lead me to consider whether variation in the microbial communities of the koala gut microbiome would be similar across geographically-separated populations, with differences in dietary diversity. I found that reduced dietary diversity influences the community composition of the koala gut microbiome, resulting in a corresponding reduction in microbial richness and diversity (Chapter 4). Leading me to pose the question, can a highly-specialised gut microbiome adapt to a change in diet? My results indicate that it would be difficult, due to the significant differences in microbial richness and diversity detected between the Cape Otway and Mtn Lagoon populations. An important finding during this investigation was, that although the gut microbiomes of the Mountain Lagoon koalas were dominated by the phyla Bacteroidetes and Firmicutes, the next dominant phylum was Synergistetes rather than Cyanobacteria, which was the third dominant phylum of the Cape Otway koala gut microbiomes (Chapters 2 & 4). This may indicate that the Mountain Lagoon koalas encounter a potentially more toxic plant secondary metabolite in their complex diets, compared with the Cape Otway koalas with their simple two eucalypt diets. Bacterial taxa from the phylum Synergistetes has been identified as playing important roles in detoxification of toxic plant secondary metabolites, and toxic amino acids in the ruminant system. This finding indicated that the koala gut microbiome harbours and maintains sitespecific microbiota, which aid the koala in processing its difficult diet. During this investigation, I characterised taxonomic koala core microbiomes present across 50, 95 and 100% of the geographically-separated koala samples (Chapter 4). A taxonomic core microbiome is likely to include shared critical functional genes that enable them to degrade, detoxify and extract essential macro-and micronutrients from its difficult and challenging diet. The findings of my work lead me to investigate the forces which shape the composition of the gut microbiome overtime within and between co-occurring individuals. Therefore, I undertook a short seven-month longitudinal study of the Mountain Lagoon koala population (Chapter 5). I found that there were greater inter-individual differences in microbial relative abundance than there was intraindividual, and that the community composition of the gut microbiomes from individual koalas were relatively stable over the seven-month collection period.
| Date of Award | 2017 |
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| Original language | English |
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