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

Abstract

Metagenomic analysis of 16S ribosomal RNA has been used to profile microbial communities at high resolution, and to examine their association with host diet or diseases. We examined the oral and gut microbiome composition of two captive koalas to determine whether bacterial communities are unusual in this species, given that their diet consists almost exclusively of Eucalyptus leaves. Despite a highly specialized diet, koala oral and gut microbiomes were similar in composition to the microbiomes from the same body regions of other mammals. Rectal swabs contained all of the diversity present in faecal samples, along with additional taxa, suggesting that faecal bacterial communities may merely subsample the gut bacterial diversity. Furthermore, the faecal microbiomes of the captive koalas were similar to those reported for wild koalas, suggesting that captivity may not compromise koala microbial health. Since koalas frequently suffer from ocular diseases caused by Chlamydia infection, we also examined the eye microbiome composition of two captive koalas, establishing the healthy baseline for this body part. The eye microbial community was very diverse, similar to other mammalian ocular microbiomes but with an unusually high representation of bacteria from the family Phyllobacteriaceae.

Figure 1. Relative abundance of bacterial phyla.

Pie chart representation of the relative abundances of the most common phyla found in the eye, mouth, rectum and faeces of the two koalas. The relative abundance values of each phylum for each sample are reported in Suppl. Tab. 1.

Figure 2. Principal Coordinate Analysis (PCoA) and UPGMA tree of Unifrac distances of the eye, mouth, rectal and faecal samples of two captive koalas.

Panel A represents a 2 dimensional unweighted PCoA plot by sample type. Panel B represents the UPGMA clustering on unweighted Unifrac distances. Nodal supports were assessed by jackknife using 1,000 replicates. The two plots highlight that the samples tended to cluster by body region but not by koala specimen.

Figure 3. Heatmap analysis of the most abundant bacterial genera detected across all samples.

The heatmap depicts the relative percentage of 16S rRNA gene sequences assigned to each bacterial genus (y axis) across the 8 samples analysed (x axis). The heatmap colors represent the relative percentage of the microbial genus assignments within each sample. Square colors shifted towards bright blue indicate higher abundance. The relative abundance values of each genus for each sample are reported in Suppl. Tab. 4.

Figure 4. Heatmap analysis of the main bacterial phyla detected across mammalian species.

The heatmap depicts the relative percentage of 16S rRNA gene sequences assigned to each bacterial phylum (y axis) across different mammalian species (x axis). The heatmap colors represent the relative percentage of the microbial phylum assignments within each species. Square colors shifted towards bright green indicate higher abundance. When a study reports average abundance values for more species, it is indicated how many species where used in the study. When more than one study per species is available, each study is indicated with a different letter. Blank squares correspond to NA, i.e. not available data, for those phyla for which the abundance values were not reported in the corresponding publication. The relative abundance values of each phylum for each species are reported in Suppl. Tab. 5.

Figure 5. A Venn diagram showing the overlap between the rectal swab and the faeces of koala SN265 in the most abundant genera detected.

While 15 genera were shared between rectal swab and faeces, and 41 genera were detected only in the rectal swab, there were no genera unique to the faeces.