Diversity and function of gut microbiota in wild and zoo populations of a critically endangered bird

We characterise the gut microbiome of wild and zoo managed regent honeyeaters, providing the first characterisation of both taxonomic and functional diversity of wild versus zoo bred populations of this threatened species. Using high throughput Illumina sequencing of faecal samples from 17 wild and 38 zoo managed regent honeyeaters, we found an overwhelming presence of Firmicutes in both populations, but significantly lower microbial diversity in wild than zoo birds. Despite these differences, functional inferences of the microbial communities present revealed a similar trend in taxa function in both groups. These results suggest that the diverse gut microbial communities of the two populations contribute to the same metabolic processes. For regent honeyeater, this observation suggests that dietary management of the species ex situ may be adequate. More generally, our results demonstrate that taxonomic versus functional inferences of microbiomes in conservation breeding programs may suggest different conclusions, indicating the necessity to examine both in order to generate reliable biological inferences and management recommendations.