In many endangered species, reproductive failure is a major barrier to recovery. The critically endangered kākāpō (Strigops habroptilus) exemplifies this challenge: 61% of their eggs fail to hatch, and of these 73% show no sign of development. Undeveloped eggs have previously been attributed to male infertility, but recent studies of non-threatened bird species suggest fertilisation failure is rare in the wild. The underlying causes of fertilisation failure and embryo death differ, so distinguishing between them is essential for effective conservation management. Here we show that the majority (72%, n=124) of undeveloped kākāpō eggs are fertilised, and combine this with conservation programme data on natural copulations, artificial inseminations, and paternity of developed eggs, to generate the most precise estimate to date of fertility in a wild population. We also demonstrate, for the first time in a wild bird, that artificial insemination results in greater numbers of sperm reaching the egg.

Gut microbiota play an essential role in host health with important implications for conservation management of threatened wildlife. While factors such as diet, medication and habitat are known to shape the microbiota, our understanding of the entirety of factors, including the complex role of host genomic background, remains incomplete. Our research on the interaction between the host genome and gut microbiota of the critically endangered kākāpō (Strigops habroptilus), a flightless parrot endemic to Aotearoa New Zealand, represents, to our knowledge, one of the most comprehensive studies of the gastrointestinal bacterial diversity and its relationship with host genomic diversity for virtually an entire threatened species. We conducted a 16S rRNA gene‐based analysis of faecal samples representing the gut microbiota for 84% of kākāpō. This survey was leveraged with exceptional metadata to tease apart the impact of host genomic diversity and factors including sex, age, diet, antibiotics, disease, habitat and sampling date on the kākāpō gut microbiota. We find evidence of a highly polygenic genomic architecture of the gut microbiota and identify putative associations between bacterial diversity and functional pathways related to intestinal homeostasis, inflammation, immunity and metabolism. This improved understanding of the kākāpō gut microbiota—and its relationship with host genomics—can directly benefit kākāpō conservation by providing new insights into the role of the gut microbiome in kākāpō health and disease mitigation. Overall, we anticipate that an integration of microbiome studies in conservation research and management will improve our understanding and realisation of the One Health concept.