Nasopharyngeal bacterial and fungal microbiota in normal horses and horses with nasopharyngeal cicatrix syndrome

Background The nasopharyngeal bacterial and fungal microbiota of normal horses and those with nasopharyngeal cicatrix syndrome (NCS) are unknown. Hypotheses/Objectives To describe the microbiota from nasopharyngeal washes of healthy horses and of horses acutely affected with NCS. Animals Twenty‐six horses acutely affected with NCS horses and 14 unaffected horses. Methods Prospective, observational cohort study. Horses were recruited by investigators through personal communications in central Texas. Bacterial (16s RNA) and fungal (internal transcribed spacer) microbiota from nasopharyngeal washes were evaluated. Polymerase chain reaction for detection of Pythium insidiosum was performed. Results Results indicated that 6 fungal genera (Alternaria, Bipolaris, Microascus, Spegazzinia, Paraconiothyrium, Claviceps) and 1 bacterial genera (Staphylococcus) were significantly different between affected and unaffected horses. The fungal genus Bipolaris had increased abundance in NCS affected horses and on NCS affected farms. Pythium insidiosum was absent in the nasopharyngeal wash of all horses, irrespective of health status. Conclusion and Clinical Importance Significant differences were identified in the fungal microbiota in horses affected with NCS and farms affected with NCS compared to those unaffected. Therefore, Bipolaris warrants further investigation.