Gut Microbiome of the Critically Endangered New Zealand Parrot, the Kakapo (Strigops habroptilus)

Abstract

The kakapo, a parrot endemic to New Zealand, is currently the focus of intense research and conservation efforts with the aim of boosting its population above the current ‘critically endangered’ status. While virtually nothing is known about the microbiology of the kakapo, given the acknowledged importance of gut-associated microbes in vertebrate nutrition and pathogen defense, it should be of great conservation value to analyze the microbes associated with kakapo. Here we describe the first study of the bacterial communities that reside within the gastrointestinal tract (GIT) of both juvenile and adult kakapo. Samples from along the GIT, taken from the choana (≈throat), crop and faeces, were subjected to 16 S rRNA gene library analysis. Phylogenetic analysis of >1000 16 S rRNA gene clones, derived from six birds, revealed low phylum-level diversity, consisting almost exclusively of Firmicutes (including lactic acid bacteria) and Gammaproteobacteria. The relative proportions of Firmicutes and Gammaproteobacteria were highly consistent among individual juveniles, irrespective of sampling location, but differed markedly among adult birds. Diversity at a finer phylogenetic resolution (i.e. operational taxonomic units (OTUs) of 99% sequence identity) was also low in all samples, with only one or two OTUs dominating each sample. These data represent the first analysis of the bacterial communities associated with the kakapo GIT, providing a baseline for further microbiological study, and facilitating conservation efforts for this unique bird.

Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo

“…DNA extraction was performed on samples by using a previously described bead-beating method (12). PCR was performed by using the following 16S rRNA gene-specific primers targeting bacteria: 533f (5=-GTG for 45 s; and a final elongation step at 72°C for 10 min, with one negativecontrol run for each primer pair.…”

“…Since the 1980s, kakapos have been subjected to an intensive management program focused on preserving the species and eventually restoring the population to self-sustaining levels (3)(4)(5). In an effort to optimize management practices, the New Zealand Department of Conservation has collaborated with researchers from a wide range of biological disciplines, including behavioral ecology, physiology, genetics, nutrition, and, recently, microbiology (6)(7)(8)(9)(10)(11)(12).…”

“…Our previous research into the GI tract-associated bacteria of the kakapo revealed a community dominated by only a few operational taxonomic units (OTUs), mainly from the phyla Proteobacteria and Firmicutes and apparently lacking in archaea (12,25). The kakapo GI tract appears to have a low phylum-level diversity of bacteria compared to other birds (25,26), and this has led to speculation of a population bottleneck for the gut microbiota.…”

“…Previous research into the development of the gut microbiota in other host species has shown that the microbiota of juveniles differs significantly from that of adults in both avians and mammals (32)(33)(34)(35)(36), although it is not clear whether this pattern is reflected in the kakapo (12). In many avian species, the juvenile microbiota is a dynamically changing community (37-39) that gradually develops toward the adult community structure (33,36), but the changes in microbiota as the subject ages vary by host.…”

Effects of immune supplementation and immune challenge on bacterial assemblages in the avian cloaca

“…Swabbing orifices, mucosa, and other surfaces of animals is a widely applicable and nonlethal alternative. Recent avian studies include data from swabs of cloacae (Klomp et al 2008), choanae (Waite et al 2012), and eggshells (Grizard et al 2014). However, some swabbing procedures collect only subsets of the bacteria residing in swabbed areas (Grizard et al 2014).…”