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.
Highlights
Recent developments in culture-independent methods based on large-scale comparative analyses of 16S ribosomal RNA and metagenomics have the potential to profile microbial communities at high resolution even in complex environments like the intestinal microbiota[8]
Principal coordinate analysis of unweighted UniFrac distances, which measure the similarity between bacterial communities based on phylogenetic distances, showed that koala microbial communities clustered by body region
We estimated the robustness of the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree by jackknife and confirmed the clustering of the samples according to body region, with the faecal and the eye samples clustering with maximal jackknife support (100%), while the nodes regarding the rectal and the oral samples being less resolved (Fig. 2B)
Summary
Recent developments in culture-independent methods based on large-scale comparative analyses of 16S ribosomal RNA and metagenomics have the potential to profile microbial communities at high resolution even in complex environments like the intestinal microbiota[8]. A recent study[14] employed high-throughput GS FLX pyrosequencing to describe the composition of the koala microbiome across the hindgut in two wild koalas This demonstrated that the koala hindgut microbiome is a complex and diverse environment and that the bacterial communities vary considerably in different regions of the intestine. This body region was included to obtain a comparison point independent to digestion associated organs and to establish a baseline for the microbiome of healthy koala eyes, since wild and captive koalas frequently suffer from ocular infections caused by the highly prevalent Chlamydia, which is regarded as the primary disease threat to the species[19,20] Such high incidence of chlamydial infection has been correlated with the presence of the recently described koala retrovirus (KoRV)[21]. We assessed whether captivity plays a role in shaping the koala faecal microbiome by comparing results from captive animals with existing data on wild koalas
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