The gut microbiome of the critically endangered kakapo

Abstract

The kakapo is one of New Zealand's iconic endemic birds, possessing an array of characteristics that are unique among avians. The kakapo is also critically endangered, and only survives through an intensive management e ort by the Department of Conservation. In order to aid in conservation practices and decision making, detailed research has been conducted previously into the ecology, physiology, genetics and breeding behaviour of the kakapo. By contrast, the interactions between kakapo and the microorganisms associated with them have remained unexplored. In order to address this lack of knowledge regarding the kakapo microbiota, cultivation-based and state-of-the-art molecular techniques were employed with the overall aim of identifying the common microbes that inhabit the kakapo gastrointestinal tract and understanding the patterns that in uence them. Analysis of bacterial 16S rRNA genes revealed that the kakapo gut harbours a bacterial community of low taxonomic diversity, dominated by members of just two bacterial phyla (Proteobacteria and Firmicutes). Unexpectedly, the age of the bird played little role in shaping the kakapo microbiota, with both phylogenetic and functional data indicating no di erence between age groups. By contrast, other studied factors did impact upon the microbiota, such as sampling location within the gut as well as antibiotic treatment and captivity. These analyses showed that although the kakapo microbiota is in uenced by antibiotic treatment the e ect is short lived, with the kakapo microbiota returning to a `normal' state within weeks of release back into the wild. Genomic and metagenomic analyses rea rmed the nding of low taxonomic diversity at broad phylogenetic levels, but showed that at ne-scale resolution (bacterial species and strains) the kakapo microbiota is much more diverse than inferred from traditional (16S rRNA-based) marker gene analysis. The functional potential of gut microbes was also examined, and was similar to that of other herbivore gut systems, despite the low taxonomic diversity. This thesis represents the rst concerted e ort to study the kakapo microbiota and provides a foundation of knowledge for guiding future study and management practices.