Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kakapo chick faeces and associated nest litter

Background The critically endangered kakapo is a flightless, nocturnal parrot endemic to Aotearoa New Zealand. Recent efforts to describe the gastrointestinal microbial community of this threatened herbivore revealed a low-diversity microbiota that is often dominated by Escherichia-Shigella bacteria. Given the importance of associated microbial communities to animal health, and increasing appreciation of their potential relevance to threatened species conservation, we sought to better understand the development of this unusual gut microbiota profile. To this end, we conducted a longitudinal analysis of faecal material collected from kakapo chicks during the 2019 breeding season, in addition to associated nest litter material. Results Using an experimental approach rarely seen in studies of threatened species microbiota, we evaluated the impact of a regular conservation practice on the developing kakapo microbiota, namely the removal of faecal material from nests. Artificially removing chick faeces from nests had negligible impact on bacterial community diversity for either chicks or nests (p > 0.05). However, the gut microbiota did change significantly over time as chick age increased (p < 0.01), with an increasing relative abundance of Escherichia-Shigella coli over the study period and similar observations for the associated nest litter microbiota (p < 0.01). Supplementary feeding substantially altered gut bacterial diversity of kakapo chicks (p < 0.01), characterised by a significant increase in Lactobacillus bacteria. Conclusions Overall, chick age and hand rearing conditions had the most marked impact on faecal bacterial communities. Similarly, the surrounding nest litter microbiota changed significantly over time since a kakapo chick was first placed in the nest, though we found no evidence that removal of faecal material influenced the bacterial communities of either litter or faecal samples. Taken together, these observations will inform ongoing conservation and management of this most enigmatic of bird species.

Automated summary

This study analyzed the fecal samples of kakapo chicks and the nest litter to understand the development of their gut microbiota. The results showed that the age and hand rearing conditions of the chicks had a significant impact on the bacterial communities in their excrement. The microbiota of the nest litter also changed over time since the chick was placed in the nest.