Captivity reduces diversity and shifts composition of the Brown Kiwi microbiome

Priscilla A. San Juan,Isabel Castro,Manpreet K. Dhami

doi:10.1186/s42523-021-00109-0

Priscilla A. San Juan, Isabel Castro + Show 1 more

Open Access

https://doi.org/10.1186/s42523-021-00109-0

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Abstract

BackgroundCaptive rearing is often critical for animals that are vulnerable to extinction in the wild. However, few studies have investigated the extent to which captivity impacts hosts and their gut microbiota, despite mounting evidence indicating that host health is affected by gut microbes. We assessed the influence of captivity on the gut microbiome of the Brown Kiwi (Apteryx mantelli), a flightless bird endemic to New Zealand. We collected wild (n = 68) and captive (n = 38) kiwi feces at seven sites on the north island of New Zealand.ResultsUsing bacterial 16 S rRNA and fungal ITS gene profiling, we found that captivity was a significant predictor of the kiwi gut bacterial and fungal communities. Captive samples had lower microbial diversity and different composition when compared to wild samples. History of coccidiosis, a gut parasite primarily affecting captive kiwi, showed a marginally significant effect.ConclusionsOur findings demonstrate captivity’s potential to shape the Brown Kiwi gut microbiome, that warrant further investigation to elucidate the effects of these differences on health.

Highlights

Captive rearing is often critical for animals that are vulnerable to extinction in the wild
Fresh fecal samples were collected from seven sites on the north island of New Zealand (Fig. 1a, Supplementary Table 1) during January – April 2019.Bacterial 16 S Ribosomal ribonucleic acid (rRNA) (V4 region) [15] and fungal ITS genes [16] were amplified using Deoxyribonucleic nucleic acid (DNA) extracted from captive (n = 38) and wild kiwi fecal samples (n = 68)
Bacterial communities clustered by captivity across spatially independent sites with little overlap between the 95 % confidence interval ellipses (Fig. 1b, PERMANOVA, r2 = 0.07, p = 0.001)

Summary

Introduction

Captive rearing is often critical for animals that are vulnerable to extinction in the wild. Few studies have investigated the extent to which captivity impacts hosts and their gut microbiota, despite mounting evidence indicating that host health is affected by gut microbes. We assessed the influence of captivity on the gut microbiome of the Brown Kiwi (Apteryx mantelli), a flightless bird endemic to New Zealand. We collected wild (n = 68) and captive (n = 38) kiwi feces at seven sites on the north island of New Zealand. Few studies have investigated the impact of captivity, a severe lifestyle shift, on avian gut microbiota. Fewer studies have compared wild and captive gut bacteria and fungi across spatially distinct sites that vary by climate and vegetation [8], which are expected to differ in microbial species pools, a potential source for gut microbes. In the case of the Brown Kiwi (Apteryx mantelli), predation from introduced

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