Elusive aetiology of exudative cloacitis in the critically endangered kākāpō

ABSTRACT The kākāpō ( Strigops habroptilus ) is a critically endangered, flightless parrot endemic to Aotearoa New Zealand. While an intensive recovery programme has led to considerable successes in kākāpō conservation, management of this iconic species has been complicated since 2002 by the emergence of the inflammatory syndrome exudative cloacitis. Cloacitis is a significant threat to kākāpō health yet its origin remains unknown. With recent increases in prevalence coupled with the first detection of cases originating on islands beyond where it was initially detected, understanding the risk factors that lead to this condition remains a high priority for kākāpō conservation. Here we undertake a pathogen discovery approach incorporating metagenomic (DNA) and metatranscriptomic (RNA) sequencing of faecal and cloacal swab samples from affected and healthy kākāpō. We report, for the first time, differentially higher transcript abundances from five bacterial taxa in cloacitis versus healthy birds, as well as abundant Clostridium sensu stricto 1 bacteria in severe cloacitis cases. Furthermore, affected birds exhibited significantly higher expression of hok / gef genes that encode for toxin proteins in bacteria including Escherichia coli , the dominant member of the kākāpō microbiome. While not directly identifying specific risk factors, our results contribute to ongoing efforts to elucidate the underlying causes of exudative cloacitis in kākāpō.