The Koala ( Phascolarctos cinereus ) faecal microbiome differs with diet in a wild population

• Published in: PeerJ (San Francisco, CA) CA), 2019-04, Vol.7, p.e6534, Article e6534
• Main Authors: Brice, Kylie L, Trivedi, Pankaj, Jeffries, Thomas C, Blyton, Michaela D J, Mitchell, Christopher, Singh, Brajesh K, Moore, Ben D
• Format: Article
• Language: English
• Subjects: Analysis; Antibiotics; Biodiversity; Chemical defense; Community composition; Community structure; Conservation Biology; Cyanobacteria; Diet; Dietary specialist; Diversity indices; Ecology; Eucalyptus; Eucalyptus viminalis; Foliage; Folivore; Food; Formylated phloroglucinol compounds (FPCs); Genera; Genes; Genomes; Genomics; Herbivores; Herbivory; Intestinal microflora; Leaves; Marsupial; Marsupials; Metabolism; Metabolites; Microbiology; Microbiome; Microbiomes; Microbiota; Microbiota (Symbiotic organisms); Microorganisms; Molecular Biology; Nitrogen; Nutrient deficiency; Nutrients; Parabacteroides; Phascolarctos cinereus; Plant metabolites; Plant secondary metabolites (PSMs); Population; RNA; rRNA 16S; Ruminococcaceae; Secondary metabolites; Soil sciences; Species; Zoology
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.6534

The diet of the koala ( ) is comprised almost exclusively of foliage from the genus (family Myrtaceae). produces a wide variety of potentially toxic plant secondary metabolites which have evolved as chemical defences against herbivory. The koala is classified as an obligate dietary specialist, and although dietary specialisation is rare in mammalian herbivores, it has been found elsewhere to promote a highly-conserved but low-diversity gut microbiome. The gut microbes of dietary specialists have been found sometimes to enhance tolerance of dietary PSMs, facilitating competition-free access to food. Although the koala and its gut microbes have evolved together to utilise a low nutrient, potentially toxic diet, their gut microbiome has not previously been assessed in conjunction with diet quality. Thus, linking the two may provide new insights in to the ability of the koala to extract nutrients and detoxify their potentially toxic diet. The 16S rRNA gene was used to characterise the composition and diversity of faecal bacterial communities from a wild koala population (  = 32) comprising individuals that predominately eat either one of two different food species, one the strongly preferred and relatively nutritious species , the other comprising the less preferred and less digestible species Alpha diversity indices indicated consistently and significantly lower diversity and richness in koalas eating . Assessment of beta diversity using both weighted and unweighted UniFrac matrices indicated that diet was a strong driver of both microbial community structure, and of microbial presence/absence across the combined koala population and when assessed independently. Further, principal coordinates analysis based on both the weighted and unweighted UniFrac matrices for the combined and separated populations, also revealed a separation linked to diet. During our analysis of the OTU tables we also detected a strong association between microbial community composition and host diet. We found that the phyla Bacteroidetes and Firmicutes were co-dominant in all faecal microbiomes, with Cyanobacteria also co-dominant in some individuals; however, the diet produced communities dominated by the genera and/or , whereas the associated diets were dominated by unidentified genera from the family Ruminococcaceae. We show that diet differences, even those caused by differential consumption of the foliage of two species from the same plant genus, can profoundly affect the gut micro