Analysis of skin mycobiota associated with alopecia in captive cynomolgus macaques (Macaca fascicularis) based on Oxford Nanopore Technologies

<ns3:p> Backgrounds Alopecia in captive non-human primates (NHPs) is a major animal welfare concern in many primate facilities. Some studies suggested that the mycobiome, considered fungal communities in specific areas, could influence the pathogenesis of alopecia. However, the pathogenesis mechanism of alopecia in cynomolgus macaques is poorly known. Objectives This study aims to investigate the association between alopecia and skin mycobiota in cynomolgus macaques. Methods Skin swab samples were collected from five areas where alopecia is common (arm, dorsal, head, leg, and ventral areas) of 47 healthy and 50 alopecic macaques. The samples were extracted for DNA. Oxford Nanopore Technologies (ONT) was applied to explore the skin mycobiota based on full-length Internal Transcribed Spacer (ITS) sequencing. Results Our findings showed that alpha and beta diversities significantly differed between alopecic and healthy macaques among the five areas. <ns3:italic>Wallemia sebi</ns3:italic> was associated with alopecia in the arm. Furthermore, <ns3:italic>Candida albicans</ns3:italic> , <ns3:italic>Rhodotorula mucilaginosa</ns3:italic> , <ns3:italic>Exophiala dermatitidis</ns3:italic> , and <ns3:italic>Candida parapsilosis</ns3:italic> were prevalent in the dorsal and head areas. Moreover, <ns3:italic>Aspergillus penicillioides</ns3:italic> was dominant in the dorsal and ventral areas. <ns3:italic>Pseudozyma sp., Moesziomyces antarcticus</ns3:italic> , and <ns3:italic>Cladosporium dominicanum</ns3:italic> were uniquely found in the head area. <ns3:italic>Apiotrichum domesticum</ns3:italic> was highly observed in the leg and ventral areas. Lastly, <ns3:italic>Cladosporium halotolerans</ns3:italic> was uniquely detected in the ventral area. Conclusion These microorganisms may be associated with the development of alopecia in cynomolgus macaques. These findings might be useful for biomedical research and therapeutic management strategies of animal health in primate facilities in the future. </ns3:p>