How microbiomes can help inform conservation: landscape characterisation of gut microbiota helps shed light on additional population structure in a specialist folivore

Abstract

Background The koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing widespread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and progressive conservation strategies such as faecal inoculations may be required to bring this species back from the brink of extinction, insight into the variation of host-associated gut microbiota and the factors that shape this variation are fundamental for their success. Despite this, very little is known about the landscape variability and factors affecting koala gut microbial community dynamics. We used large scale field surveys to evaluate the variation and diversity of koala gut microbiotas and compared these diversity patterns to those detected using a population genetics approach. Scat samples were collected from five locations across South East Queensland with microbiota analysed using 16S rRNA gene amplicon sequencing. Results Across the landscape koala gut microbial profiles showed large variability, with location having a large effect on bacterial community composition and bacterial diversity. Certain bacteria were found to be significantly differentially abundant amongst locations; koalas from Noosa showed a depletion in two bacterial orders (Gastranaerophilales and Bacteroidales) which have been shown to provide beneficial properties to their host. Koala gut microbial patterns were also not found to mirror population genetic patterns, a molecular tool often used to design conservation initiatives. Conclusions Our data shows that koala gut microbiotas are extremely variable across the landscape, displaying complex micro- and macro- spatial variation. By detecting locations which lack certain bacteria we identified koala populations that may be under threat from future microbial imbalance or dysbiosis. Additionally, the mismatching of gut microbiota and host population genetic patterns exposed important population structure that has previously gone undetected across South East Queensland. Overall, this baseline data highlights the importance of integrating microbiota research into conservation biology in order to guide successful conservation programs such as species translocation and the implementation of faecal inoculations.

Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time

“…The phylum level composition of the koalas in this study were similar to those of previous koala faecal microbiota studies, being dominated by Bacteroidota and Firmicutes ( Fig. S4 ) ( Brice et al, 2019 ; Littleford-Colquhoun et al, 2022 ). Mountain Lagoon koalas were less distinguishable between each other at the family level, except for the individual Phasco, who had much lower levels of Paludibacteraceae ( Fig.…”

Patterns of Microbiome Composition Vary Across Spatial Scales in a Specialist Insect

“…Integrating landscape ecology, biogeography, and metacommunity theory into host-associated microbiome studies has been complicated. What microbes an animal encounters in its life are influenced in part by the host diet and the environment in which the host interacts ( Littleford-Colquhoun et al, 2022 ). Both the diet and environment are impacted by selective and neutral forces.…”

Safety and efficacy of a feed additive consisting of a tincture derived from the leaves of Eucalyptus globulus Labill. (eucalyptus tincture) for all animal species (FEFANA asbl)

“…The toxicity of eucalyptus leaves is due to a complex mixture of volatile and non-volatile compounds, among which 1,8-cineole and formylated phloroglucinols (Eschler et al, 2000) are the most toxic. The resistance of Koalas against the toxicity of eucalyptus leaves depends on a unique intestinal microflora and the ability to avoid the intake of eucalyptus leaves with high concentrations of toxic formylated phloroglucinol compounds (Moore & Foley, 2005;Littleford-Colquhoun et al, 2022). The safety assessment is based on the highest proposed use levels in feed, which are 50 mg eucalyptus tincture/kg complete feed for all animal species, except for horses, for which the proposed use level is 200 mg/kg complete feed.…”