Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment

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.

Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh

“…Approximately 200 mg of the pellet from the homogenized skin smears and gut contents was put into a 1·5‐ml Eppendorf tube for DNA extraction (Dahlhausen et al . ). The total DNA from the fish samples was extracted using a DNeasy Blood and Tissue Kit (Qiagen, Crawley, UK) following the manufacturer's instructions.…”

Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices

“…For example, Chlamydia infections are highly prevalent in captive koalas (Phascolarctos cinereus), which are treated with antibiotics. Dahlhausen et al [46] report that individuals that underwent antibiotic therapy and subsequently died harboured gut microbial communities reduced in diversity and abundance of tannin-detoxifying bacteria essential to koala nutrition and survival. Finally, captive environments may reduce populations of beneficial host-associated microbes directly, with downstream effects on host health.…”

Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum

“…In previous work, we identified L. koalarum as the most predictive taxon of koala survival during antibiotic treatment and we suggested that this bacterium is important for koala health ( Dahlhausen et al, 2018 ). Here, we isolated a L. koalarum strain from the feces of a healthy koala and sequenced and characterized its genome.…”

“…Tannins bind proteins followed by the formation of a precipitate, which cannot be digested by koalas or utilized by microbes ( Adamczyk et al, 2017 ). In our previous work, L. koalarum was identified as the most predictive taxon of koala survival during antibiotic treatment ( Dahlhausen et al, 2018 ). Briefly, a co-occurrence network analysis identified four bacterial taxa, including one of the genus Lonepinella , that could be found in feces of koalas that survived their antibiotic treatment after Chlamydia infection.…”