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Variation in koala microbiomes within and between individuals: effect of body region and captivity status

Alfano, N, Courtiol, A, Vielgrader, H, Timms, P, Roca, AL & Greenwood, AD 2015, Nature: Scientific Reports, vol. 5, no. 10189.

Sequencing microbes’ 16S ribosomal RNA (rRNA) directly from the sample without culture is an accurate way to assess the relationship between the microbe and the host. The bacterial community, or the microbiome, in the eyes and digestive system of the koala were evaluated here. Captive koala microbiomes mostly resembled those of other animals and wild koalas. Unexpectedly, the microbiome of the koala eye contained many bacteria belonging to the Phyllobacteriaceae family.

  Samples or swabs of the eye, oral cavity, rectum and stool were taken from two captive koalas. The samples’ 16S rRNA gene was sequenced to identify bacterial phyla and genera. The most commonly detected bacteria phyla were Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fusobacteria. The eye microbiome of the koala is similar to that of humans, with the exception of the Phyllobacteriaceae family present in up to 55% of koala sequences. The oral microbiome was very similar to other animals, with Proteobacteria (90%), Bacteroidetes (56%) and Firmicutes (31.64%) being the most detected phyla. The rectal microbiome differed between the two koalas, but once again was similar to other animals. The faecal microbiome of the two koalas was represented by mostly Bacteroidetes and Firmicutes, although their relative quantities varied. The phyla representation was similar to other mammals; however, 66-73% of bacteria detected in rectum samples were not detected in stool samples, while bacteria detected in the stool were commonly detected in rectum. No bacteria were found exclusively in stool samples; thus, faeces contained a portion of the total microbiome found in the gut. The microbiome of captive and wild koalas did not differ.

  In this study, the samples of the two koalas were more similar to other animal’s microbiomes than to each other. This is a common finding even in humans. The difference in koalas’ microbiomes may be due to competition in colonisation between phyla due to many phyla serving a similar purpose; however, the effect of an underlying pathology cannot be excluded. Samples from rectum and stool differed in their microbiome, and this could be explained by the microbiome’s exposure to different levels of food particles, acidity and water as they pass through the digestive system. It is likely that the microbiome of captive and wild koalas did not differ because of the similarity of the captive koalas’ diet to that of a wild koala.

  This is the first study to sequence the microbiome of the eye in the koala and, therefore, represents the baseline for the bacterial communities in koala eye. Future research should focus on using samples from the gut rather than faeces for a complete microbiome sample. Given the similarity of the captive koala microbiome to that of a wild koala, the authors suggest that using captive koalas rather than wild koalas for microbiome research may be acceptable.


Summarised by Alexandra Selivanova


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