Host-Microbe Interactions in the Nasal Cavity of Dogs with Chronic Idiopathic Rhinitis

Chronic rhinitis (CR) is a frustrating clinical syndrome in dogs and our understanding of the disease pathogenesis in is limited. Increasingly, host-microbe interactions are considered key drivers of clinical disease in sites of persistent mucosal inflammation such as the nasal and oral cavities. Therefore, we applied next generation sequencing tools to interrogate abnormalities present in the nose of dogs with CR and compared immune and microbiome profiles to those of healthy dogs. Host nasal cell transcriptomes were evaluated by RNA sequencing, while microbial communities were assessed by 16S rRNA sequencing. Correlation analysis was then used to identify significant interactions between nasal cell transcriptomes and the nasal microbiome and how these interactions were altered in animals with CR. Notably, we observed significant downregulation of multiple genes associated with ciliary function in dogs with CR, suggesting a previously undetected role for ciliary dysfunction in this syndrome. We also found significant upregulation of immune genes related to the TNF-a and interferon pathways. The nasal microbiome was also significantly altered in CR dogs, with overrepresentation of several potential pathobionts. Interactome analysis revealed significant correlations between bacteria in the genus Porphyromonas and the upregulated host inflammatory responses in dogs with CR, as well as defective ciliary function which was correlated with Streptococcus abundance. These findings provide new insights into host-microbe interactions in a canine model of CR and indicate the presence of potentially causal relationships between nasal pathobionts and the development of nasal inflammation and ciliary dysfunction. Nasal swabs were collected under general anesthesia by gently swabbing the distal third of the nasal cavity using 6-inch PurFlock Ultra, sterile flocked collection devices (Puritan Medical Products, Guilford, ME). Swabs (2 swabs obtained per each nostril) were placed in 15 ml conical tubes (Corning Inc. Corning, NY) containing RNA later (ThermoFisher Scientific, Waltham, MA) and stored at 4C prior to RNA and DNA extraction. To extract RNA from nasal cells, swabs were vortexed for 1 min at high speed to dislodge cells, PBS was then added to RNA later at a ratio of 1:5. Cells were pelleted, then processed for RNA extraction using Qiagen RNeasy micro kit (Qiagen, Hilden, Germany) following manufactures instructions or DNA extraction as described below.