Natal soil consumption shifts gut microbiome in captive Ōkārito kiwi (Apteryx rowi)

TL;DR

Adding natal soil to the diet of captive Ōkārito kiwi altered their gut microbiome, increasing bacterial diversity and specific taxa like Firmicutes and Malasseziales.

Contribution

First study to use natal soil as a probiotic for wild birds and describe the gut microbiome of the critically endangered Ōkārito kiwi.

Findings

Natal soil increased Firmicutes and Malasseziales in the gut microbiome of Ōkārito kiwi.

Fungal communities in the gut changed rapidly after soil amendment.

No significant health or growth differences were observed between treatment and control groups.

Abstract

Captive-rearing programmes for endangered birds, such as those in place for kiwi conservation in Aotearoa-New Zealand, can unintentionally deprive the birds access to a microbially-diverse and ‘natural’ developmental environment i.e., their natal rohe (territory). These programmes introduce external variables such as increased exposure to diseases, unnatural and incomplete diets, antimicrobial usage, and artificial cohabited environments, which have the potential to impact rearing success outcomes. In this research, we investigated whether the introduction of natal soils, as a direct probiotic and a source of wild microorganisms, to the captive-reared ground-foraging Ōkārito kiwi (Apteryx rowi) chick diet would impact their gut microbiome. Using 16S rRNA gene and ITS sequencing to identify the key taxonomic groups present, we assess the community composition differences with the introduction of natal soils into the diet of captive-reared Ōkārito kiwi.

Results showed a distinct gut microbial community associated with Ōkārito kiwi in captivity. Bacterial diversity in Ōkārito kiwi gut increased with age, with the relative abundances of dominant taxonomic groups changing over time. Bacterial phyla Firmicutes, Proteobacteria and Actinobacteria, and the fungal orders Malasseziales and Trichosporon dominated the gut community. Exposure to natal Ōkārito soils influenced the composition of the gut microbiome in Ōkārito kiwi, especially on the temporal trends of key bacterial taxa. Kiwi with natal-soil-amended diets harboured an increased proportion of Firmicutes and Malasseziales compared to the ‘Control’ group. The fungal community in the Ōkārito kiwi gut was more transitory, changing rapidly following soil amendment. No significant changes to growth rates or overall health were found between ‘Control’ and ‘Treatment’ groups.

The findings of this study represent the first description of the gut microbiome of the critically endangered Ōkārito kiwi, Apteryx rowi, and the first documented use of natal soil as a probiotic amendment for wild birds. Results show that mediation of the gut microbial communities of captive-reared ground-foraging birds can be achieved through the introduction of natal soils in their diet.

The online version contains supplementary material available at 10.1186/s42523-025-00445-5.

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