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

Abstract

Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.

The koala gut microbiome is largely unaffected by host translocation but rather influences host diet

“…In humans, Akkermanisa muciniphila has been shown to feed on host mucin, allowing it to survive when nutrients become limiting such as during host starvation (Derrien et al, 2004). Captive and wild adult koalas have been reported to carry Akkermanisa at an average relative abundance of 1.5%-3.1% and 2.2%, respectively (Eisenhofer et al, 2022;Blyton et al, 2022aBlyton et al, , 2022b. In this study, Akkermansia increased in relative abundance in the control koalas from an average of 2% to 4.9% in June 2016.…”

“…The explanatory variables in the analysis included the proportion of each food tree species at each time point as well as the principal coordinates generated from the unscaled food tree species proportions. Koala ID was included as a covariate in this analysis to account for interindividual differences in fecal microbiome composition (Eisenhofer et al, 2022). Forward and backward selection was used to select significant explanatory variables based on adjusted p-values.…”

“…Koalas maternally inherit their gut microbiomes through the ingestion of a special feces (pap) around the time of pouch emergence and prior to the joeys' transition from a milk-based diet onto a diet of Eucalyptus leaves (Osawa et al, 1993;Blyton et al, 2022aBlyton et al, , 2022b). This appears to lead to varying, but individual koala microbiomes that are temporally stable (Eisenhofer et al, 2022). Eisenhofer et al (2022) found that captive koalas sourced from different populations but fed on a similar diet maintained distinct microbiomes.…”

“…This appears to lead to varying, but individual koala microbiomes that are temporally stable (Eisenhofer et al, 2022). Eisenhofer et al (2022) found that captive koalas sourced from different populations but fed on a similar diet maintained distinct microbiomes. In contrast, wild koalas in a single population, feeding on diverse diets, had more similar microbiomes.…”

“…However, koalas are unusual as they inherit their gut microbiomes maternally by feeding on pap (special maternal feces that has a higher microbial density than normal feces and a higher abundance of rare taxa) around the time of pouch emergence (Osawa et al, 1993;Blyton et al, 2022aBlyton et al, , 2022b. Wild adult koalas have temporally stable fecal microbiomes over the course of several months when they are left in their established home ranges, despite some variation in the food tree species eaten (Eisenhofer et al, 2022;Blyton et al, 2023). Additionally, in 2013 koalas in Cape Otway, Victoria, that fed on E. viminalis starved to death when that species was defoliated due to overbrowsing rather than feeding on the readily available E. obliqua (Whisson et al, 2016).…”