The Gut Microbiota of the Critically Endangered Kākāpō (Strigops habroptilus)

Abstract

The composition of the kākāpō gut microbiota has been the subject of research for the past decade, leading to identification of multiple unusual features for an obligate herbivore. Among animals studied to date, it appears that the gut microbiota of the giant panda is the most similar to that of the kākāpō, although this cursory observation has never been explored in detail. The first aim of this research was to investigate the extent to which these similarities exist at a bacterial community level, using a uniform bioinformatics pipeline to analyse previously published 16S rRNA gene sequence data. This analysis revealed that the gut microbiotas of both animals exhibit low taxonomic diversity and share three particularly abundant bacterial genera. This research also incorporated a comparison of multiple bioinformatic pipelines on the predicted community profile, which showed that each produces differences in the presence and relative abundances of taxa. The second part of this thesis focuses solely on the Escherichia/Shigella bacterium, which has consistently been identified as a dominant component of the kākāpō gut microbiota, and often also in giant panda studies. Firstly, sequences assigned to this genus were compared for the degree of consensus at the level of single nucleotides. This revealed a high degree of sequence similarity both with each other, and with a small number of 16S rRNA gene sequences randomly-selected from two closely-related Escherichia/Shigella species. Secondly, DNA extracts from kākāpō faecal samples were subjected to two absolute quantification assays, to determine the proportion of Escherichia/Shigella within them, free of the biases introduced by 16S rRNA gene sequencing analysis. These data were used to investigate whether particular variables surrounding the host kākāpō influenced the abundance of this bacterium, with the analysis suggesting moderate to no influence. However, potential methodological issues may render these results unreliable. The research conducted in this thesis provides, for the first time, a detailed comparison of the kākāpō and giant panda gut microbiotas, as well as quantification of the Escherichia/Shigella bacterium from kākāpō faecal samples, that can be expanded on in future research.