Stephanie Bond

Background The lower respiratory tract microbiota of the horse is different in states of health and disease, but the bacterial and fungal composition of the healthy respiratory tract of the horse has not been studied in detail. Hypothesis The respiratory tract environment contains distinct niche microbiotas, which decrease in species richness at more distal sampling locations. Objective Characterize the bacterial and fungal microbiotas along the upper and lower respiratory tract of the horse. Animals Healthy Argentinian Thoroughbred horses (n = 11) from the same client‐owned herd. Methods Prospective cross‐sectional study. Eleven upper and lower respiratory tract anatomical locations (bilateral nasal, bilateral deep nasal, nasopharynx, floor of mouth, oropharynx, arytenoids, proximal and distal trachea, guttural pouch) were sampled using a combination of swabs, protected specimen brushes, and saline washes. Total DNA was extracted from each sample and negative control, and the 16S rRNA gene (V4) and ITS2 region were sequenced. Community composition, alpha‐diversity, and beta‐diversity were compared among sampling locations. Results Fungal species richness and diversity were highest in the nostrils. More spatial heterogeneity was found in bacterial composition than in fungal communities. The pharyngeal microbiota was most similar to the distal tracheal bacterial and fungal microbiota in healthy horses and therefore may serve as the primary source of bacteria and fungi to the lower respiratory tract. Conclusions and Clinical Importance The pharynx is an important location that should be targeted in respiratory microbiota research in horses. Future studies that investigate whether biomarkers of respiratory disease can be reliably detected in nasopharyngeal swab samples are warranted.