COS 44-5 - Tracking kiwi development through a microbial lens: Temporal trends of the captive Brown Kiwi (Apteryx mantelli) gut microbiome

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 developing Brown Kiwi (Apteryx mantelli), a flightless bird endemic to New Zealand. Temporal dynamics of gut microbial communities in non-model hosts remain difficult to investigate, however, captive-rearing facilities enable this possibility. Kiwi undergo what we call “life stages” that begin in a sterile hatch room, next a brooder box, and lastly to an exposed outdoor pen. We collected fresh fecal samples daily from 44 individuals over 20 consecutive days at the National Kiwi Hatchery in Rotorua, New Zealand, allowing us to track gut bacteria from hatch to sub-adulthood. Additionally, we sampled soil from their environments (e.g. brooder boxes and outdoor pens). Using metabarcoding approaches, we characterized bacterial communities in 832 samples.

Results/Conclusions

After removing contaminants and normalizing the data, we identified a total of 7547 bacterial OTUs. We found that Shannon diversity increased through life stages (ANOVA, p=0.05). Soil found in the outdoor pens had higher Shannon diversity than soil in the brooder boxes (ANOVA, p=0.001). Kiwi feces and soil differed in bacterial composition, however, kiwi microbiomes became more similar to soil through time (PERMANOVA, p=0.01, r²=0.02). To further support this, PCoA showed clustering by soil versus feces, however, there was considerable overlap between groups. Beta-diversity (using Bray-Curtis) increased through time for over 88% of kiwi individuals. 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.