Abstract
Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that eat a specialized diet of almost exclusively eucalyptus leaves. Microbes in koala intestines are known to break down otherwise toxic compounds, such as tannins, in eucalyptus leaves. Infections by Chlamydia, obligate intracellular bacterial pathogens, are highly prevalent in koala populations. If animals with Chlamydia infections are received by wildlife hospitals, a range of antibiotics can be used to treat them. However, previous studies suggested that koalas can suffer adverse side effects during antibiotic treatment. This study aimed to use 16S rRNA gene sequences derived from koala feces to characterize the intestinal microbiome of koalas throughout antibiotic treatment and identify specific taxa associated with koala health after treatment. Although differences in the alpha diversity were observed in the intestinal flora between treated and untreated koalas and between koalas treated with different antibiotics, these differences were not statistically significant. The alpha diversity of microbial communities from koalas that lived through antibiotic treatment versus those who did not was significantly greater, however. Beta diversity analysis largely confirmed the latter observation, revealing that the overall communities were different between koalas on antibiotics that died versus those that survived or never received antibiotics. Using both machine learning and OTU (operational taxonomic unit) co-occurrence network analyses, we found that OTUs that are very closely related to Lonepinella koalarum, a known tannin degrader found by culture-based methods to be present in koala intestines, was correlated with a koala’s health status. This is the first study to characterize the time course of effects of antibiotics on koala intestinal microbiomes. Our results suggest it may be useful to pursue alternative treatments for Chlamydia infections without the use of antibiotics or the development of Chlamydia-specific antimicrobial compounds that do not broadly affect microbial communities.
Highlights
AND SIGNIFICANCEThe koala, Phascolarctos cinereus, is an arboreal marsupial native to Australia with multiple unique aspects to its biology
Using the Random Forest model, we examined the microbiome of all of the individuals in the antibiotic treatment group and determined the set of Operational taxonomic units (OTUs) that create the highest distinction among the individuals that survived and the individuals that died
We found no significant difference in koala hospital location (t = 0.544, df = 77.0, p = 0.587), koala sex (t = 1.81, df = 86.2, p = 0.073), antibiotic treatment regime (t = 1.84, df = 52.9, p = 0.071), or whether the koala was administered antibiotics (t = 1.1413, df = 52.692, p-value = 0.2589)
Summary
AND SIGNIFICANCEThe koala, Phascolarctos cinereus, is an arboreal marsupial native to Australia with multiple unique aspects to its biology. Joeys (baby koalas) live in their mother’s pouch, relying on milk for nutrition for the first two months of life prior to switching to the consumption of pap for up to another six months. Pap consumption is an essential physiological activity for joeys as they transition to the adult koala diet consisting almost exclusively of eucalyptus leaves (Osawa et al, 1995; Cork, Hume & Dawson, 1983). It is assumed that koalas rely on tannindegrading bacteria that colonize the koala intestines once a joey begins consuming pap from its mother (Osawa et al, 1995; Goel et al, 2005). Tannin-degrading bacteria are common amongst all animals with a high tannin diet, including koalas, and are thought to allow these animals to survive off of tannin-rich diets (Kohl, Stengel & Dearing, 2015; Gasse, 2014)
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