Can kiwi trust their gut? Captive rearing alters the Brown Kiwi (Apteryx mantelli) microbiome

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Priscilla A. San Juan, Department of Biology, Stanford University, Stanford, CA, Isabel Castro, Wildlife and Ecology Group, Massey University, Palmerston North, New Zealand and Manpreet K. Dhami, Manaaki Whenua Landcare Research, Lincoln, New Zealand

Background/Question/Methods
Captive rearing is often critical for animals that are vulnerable to extinction in the wild. However, few studies have investigated the extent at 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.
Results/Conclusions
Using bacterial 16S 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 bacterial (ANOVA, p < 0.001) and fungal (ANOVA, p = 0.012) diversity and different composition when compared to wild samples (PERMANOVA, r2 = 0.07, p = 0.001). To further support this difference, ordination (NMDS) showed clustering by captivity status. Firmicutes dominated the gut microbiome of wild kiwi, while Proteobacteriadominated in captive kiwi. History of coccidiosis, a gut parasite primarily affecting captive kiwi, showed a marginally significant effect on bacteria (r2 = 0.048, p =0.095) and fungi (r2 = 0.074, p = 0.087). Our findings demonstrate captivity’s potential to shape the Brown Kiwi gut microbiome, but further investigation is needed to elucidate the effects of these differences on welfare.