Abstract
Ĺkariko rowi (Apteryx rowi) are one of the rarest species of kiwi and a highly endangered bird of national importance to Aotearoa New Zealand. Over the past decade, sporadic cases of dermatosis have been reported in wild rowi. The chronic skin disease leads to lesions, lichenification and feather loss. Previous efforts have been unsuccessful in identifying a causative agent, however, a species of nematode and a virus from the Circoviridae family have previously been identified in kiwi with the disease. Here, we used a total infectome approach, where bacteria, archaea, viruses, parasites and other microorganisms can be identified by metatranscriptomics (i.e. total RNA sequencing). Such as approach has been highly effective to pathogen discovery, especially in understudied hosts. We investigated all microbial associations with the 2023 outbreak of rowi dermatosis. Full-thickness skin biopsies from the site of dermatitis allowed, for the first time, a total infectome investigation at the site of disease. Metatranscriptomic data identified divergent, novel viruses as well as a species of nematode in high relative abundance. More specifically, a highly abundant hepacivirus within the Flaviviridae was detected exclusively in mild cases of dermatitis across all sample types, including in both active and chronic infections. The abundance of transcripts from a parasitic nematode of the Eucoleus genus was also notable, reflected in a significant shift in the non-viral microbial composition within severe cases of dermatitis. While there are limitations for any molecular-based disease investigation, this thesis has discovered novel and highly abundant microorganisms, opening a new line of enquiry for further exploration of dermatosis in rowi.