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Investigation of the koala (Phascolarctos cinereus) hindgut microbiome via 16S pyrosequencing

Barker, CJ, Gillet, A, Polkinghorne, A & Timms, P 2013, Veterinary Microbiology, vol. 167, pp. 554-564.

Little is known about the diversity and composition of microorganisms involved in the koala’s digestive process. Consequently, this study performed rRNA gene pyrosequencing of caecum, colon and faecal samples from two wild koalas. Findings reveal a diverse and highly complex ecosystem, with considerable variation of microorganisms at the genus level between individuals.

  Caecum, colon and faecal samples were acquired from two koalas; a male of good body condition (K1) and a highly emaciated female (K2). Samples were processed for DNA extraction, with PCR amplification of regions from the 16S rRNA gene subsequently taking place. Pyrosequencing reads were filtered for quality and classified into operational taxonomic units (OTUs). In K1, 11 phyla were identified across the samples, of which Bacteroidetes and Firmicutes were most abundant. The ratio of Firmicutes:Bacteroidetes (FB) varied across the samples, with a ratio close to 1 in the caecum and a higher ratio in the colon and faecal pellet (6:1 and 3:1 respectively). The following OTUs were identified as being dominant across the hindgut: Ruminococcus (23.4%), Alistipes (12.7%) and Cloacibacillus (10.9%). Alistipes (23.4%), Clostridales (35.1%) and Ruminococcus (35.1%) were dominant in the caecum, colon and faecal pellet respectively. The vast majority of OTUs (99%) were shared among the different sites, suggesting that phylogenetic diversity is comparable throughout the hindgut. In comparing K1 and K2, analyses suggest that each of the microbiomes differed considerably in their phylogeny. Furthermore, the K2 microbiome was distinct across the different gastrointestinal sites and relative abundances of Alistipes, Cloacibacillus and Ruminococcus were less than in K1. Enterobacter and Escherichia-Shigella, known gastrointestinal pathogens, were present at low abundance levels in K2.

  In both koalas, the hindgut ecosystem was dominated by two phyla, Bacteroidetes and Firmicutes; a finding that is consistent with research on other vertebrate microbiomes. As the FB ratio was shown to be most even in the caecum, this suggests that the process of bacterial fermentation carried out at this site may require a higher proportion of Bacteroidetes compared to the colon. Furthermore, concerning the caecum, the identification of Ruminococcus (18.6%) is unsurprising considering its role in the degeneration of plant cell walls, a key aspect in improving digestibility. Highest abundances of Ruminococcus exist in the faecal pellet, as they can capitalise on undigested dietary residue. Importantly, K2 showed significant reductions in Ruminococcus, the implication being decreased cellulose fermentation and in turn, reduced energy and nutrient availability. Alistipes was also prevalent in K1 and is a genus associated with the metabolism of d-pinitol, a cyclitol compound used in producing acetyl-CoA (an energy source). Cyclitols also play a key role in the adaption of eucalypts to aridity and thus, as foliage is likely to contain high levels of inositol, high abundance of Alistipes in the koala hindgut is a clear implication.

  This study examined the koala microbiome, identifying the predominant bacterial communities across the hindgut to reveal considerable intra-individual variation. Comparative analysis of a healthy and diseased koala provided insight into role of the gastrointestinal microbiome in preventing disease and maintaining overall health.

 

Summarised by Julian Radford-Smith

 

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