Skin microbiota of quaker parrots (Myiopsitta monachus) with normal feathering or feather loss via next-generation sequencing technology

Background: Feather damaging behavior (feather picking) is a common malady of captive parrots. Diagnosis is challenging as a primary disadvantage to clinicians faced with diagnosis of parrot skin disease remains the lack of normative data for the healthy parrot epidermal microbiology. The objective of this pilot study was to establish bacterial and fungal cutaneous microbiota baselines for quaker parrots with and without feather loss.Methods: Healthy quaker parrots (Myiopsitta monachus n = 12) with intact feathers were compared to 12 quaker parrots with evidence of feather loss via next-generation DNA sequencing of bacteria and fungus swabbed from skin.Results: Of 351 bacterial and 97 fungal species identified, no statistical differences occurred in bacteria or fungal alpha-diversity or beta-diversity based on age, sex, or feather loss. However, enclosure affected bacterial betadiversity. The most abundant bacterial species for fully feathered quaker parrots were Exiguobacterium indicum, Sphingomonas yabuuchiae, and Corynebacterium spp.,. Fragaria/Populus euphratica, S. yabuuchiae, and E. indicum for quaker parrots with feather loss. Lactobacillales, Acinetobacter, Kocuria sp., and Streptococcus epidermidis were significantly enriched in fully feathered quaker parrots, while Streptococcaceae, Methylobacterium, Clostridiales, Nocardioidaceae, Nesterenkonia, and Actinomycetospora were significantly enriched in quaker parrots with feather loss. Both groups had Cladosporium halotolerans/sphaerospermum as the predominant fungus, while Capnodiales was significantly enriched in quaker parrots with feather loss.Conclusions and clinical relevance: Use of next generation microbial sequencing as a preliminary diagnostic tool of bacterial and fungal communities of captive birds allows veterinarians to confirm cytologic diagnoses and circumvent the limitations of culture testing. Diagnostic implications include the potential transmission of pathogenic bacteria and/or fungi and pathogen resistance between cohoused birds.