Background There are limited data on potential dysbiosis of the airway microbiota in horses with asthma. Hypothesis/Objectives We hypothesized that the respiratory microbiota of horses with moderate asthma is altered. Our objectives were (a) to quantify tracheal bacterial populations using culture and qPCR, (2) to compare aerobic culture and qPCR, and (c) to correlate bacterial populations with bronchoalveolar lavage fluid (BALF) cytology. Animals Eighteen horses with moderate asthma from a hospital population and 10 controls. Methods Prospective case‐control study. Aerobic culture was performed on tracheal aspirates, and streptococci, Pasteurella multocida, Chlamydophila spp., Mycoplasma spp., as well as 16S (bacterial) and 18S (fungal) rRNA subunits were quantified by qPCR. Results Potential pathogens such as Streptococcus spp., Actinobacillus spp., and Pasteurellaceae were isolated from 8, 5, and 6 horses with asthma and 3, 0, and 2 controls, respectively. There was a positive correlation between Streptococcus spp. DNA and 16S rRNA gene (r ≥ 0.7, P ≤ 0.02 in both groups), but the overall bacterial load (16S) was lower in asthma (1.5 ± 1.3 versus 2.5 ± 0.8 × 104 copy/μL, P < 0.05). There was no association between microbial populations and clinical signs, tracheal mucus or BALF inflammation. Conclusions and Clinical Importance This study does not support that bacterial overgrowth is a common feature of chronic moderate asthma in horses. Lower bacterial load could suggest dysbiosis of the lower airways, either as a consequence of chronic inflammation or previous treatments, or as a perpetuating factor of inflammation.

OBJECTIVE To quantify dectin-1 expression in bronchoalveolar lavage fluid (BALF), create polyclonal antibodies against equine dectin-1 and localize it in tissues, and quantify fungal exposure in pastured and stabled asthmatic and nonasthmatic horses. SAMPLES BALF samples from 6 controls and 6 horses with severe asthma. Stored lung and nasal wash samples. PROCEDURES Dectin-1 expression was quantified by quantitative PCR (qPCR). Purified peptide from equine dectin-1 was used to generate polyclonal antibodies and was confirmed with immunological testing. Fungal exposure was quantified in BALF samples by counting fungal-like intracellular particles in phagocytic cells, by qPCR quantification of the “universal” 18S rRNA fungal gene, and by quantifying 36 specific fungi in equine and dust samples using qPCR assays. RESULTS Equine dectin-1 was localized in tissues and cells, and functional isoforms were upregulated significantly in BALF after stabling. Pastured horses from both groups had low levels of fungi in BALF, and there was a significant increase in some specific fungi, most notably for Eurotium amstelodami, Wallemia sebi, and Aspergillus niger after stabling. However, stabled asthmatic horses had fewer phagocytized particles, less 18S rRNA signal, and fewer specific fungi compared to nonasthmatic horses. CLINICAL RELEVANCE Stabling increases exposure to fungi, but asthmatic horses had fewer fungi reaching their lower airways, presumably resulting from congestion and narrowing of the airways. Exposure to fungi could contribute to airway inflammation by increasing dectin-1 functional isoforms, and exposure to indoor molds should be avoided.