Gut microbiota of the threatened takahē: biogeographic patterns and conservation implications

Annie G West; Anne DeLaunay; Phil Marsh; Elena K Perry; Megan Jolly; Brett D Gartrell; An Pas; Andrew Digby; Michael W Taylor

doi:10.1186/s42523-021-00158-5

Gut microbiota of the threatened takahē: biogeographic patterns and conservation implications

Anim Microbiome. 2022 Jan 25;4(1):11. doi: 10.1186/s42523-021-00158-5.

Authors

Annie G West¹, Anne DeLaunay¹, Phil Marsh², Elena K Perry^{1

3}, Megan Jolly⁴, Brett D Gartrell⁴, An Pas⁵, Andrew Digby², Michael W Taylor⁶

Affiliations

¹ School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
² Takahē Recovery Programme, Department of Conservation, Lakefront Drive, Te Anau, New Zealand.
³ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
⁴ School of Veterinary Science, Massey University, Palmerston North, New Zealand.
⁵ New Zealand Centre for Conservation Medicine, Auckland Zoo, Auckland, New Zealand.
⁶ School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand. mw.taylor@auckland.ac.nz.

Abstract

Background: The Aotearoa New Zealand takahē (Porphyrio hochstetteri), once thought to be extinct, is a nationally threatened flightless rail under intensive conservation management. While there has been previous research into disease-related microbes in takahē, little is known about the microbes present in the gastrointestinal tract. Given the importance of gut-associated microbes to herbivore nutrition and immunity, knowledge of these communities is likely to be of considerable conservation value. Here we examined the gut microbiotas of 57 takahē at eight separate locations across Aotearoa New Zealand.

Results: Faecal samples, taken as a proxy for the hindgut bacterial community, were subjected to 16S rRNA gene amplicon sequencing using Illumina MiSeq. Phylogenetic analysis of > 2200 amplicon sequence variants (ASVs) revealed nine main bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Campilobacterota, Firmicutes, Fusobacteriota, Planctomycetota, Proteobacteria, and Verrucomicrobiota) that accounted for the majority of sequence reads. Location was a significant effect (p value < 0.001, 9999 permutations) that accounted for 32% of the observed microbiota variation. One ASV, classified as Lactobacillus aviarius, was present in all samples at an average relative abundance of 17% (SD = 23.20). There was strong evidence (p = 0.002) for a difference in the abundance of the genus Lactobacillus between locations. A common commensal bacterium previously described in takahē, Campylobacter spp., was also detected in most faecal samples.

Conclusions: Location plays a pivotal role in the observed variation among takahē gut bacterial communities and is potentially due to factors such as supplemental feeding and medical treatment experienced by birds housed in captivity at one of the eight sampled sites. These data present a first glimpse of the previously unexplored takahē gut microbiota and provide a baseline for future microbiological studies and conservation efforts.

Keywords: Avian; Bird; Conservation; Endangered; Microbiome; Microbiota.