The lung microbiome in equine asthma

There is evidence that lung microbiome differs between asthmatic patients and healthy subjects (1), and that microbial dysbiosis could play a role in asthma by contributing to the perpetuation of inflammation and altering response to therapy. However, the effect of environmental conditions and medication is unknown and difficult to control (1, 2). We hypothesized that A) the environment influences lung, nasal and oral bacterial microbiome and B) the microbiome in the equine asthmatic lung is primarily affected by disease status.

Six asthmatic horses and 6 controls receiving no medication were kept on pasture (“Low antigen exposure”), then exposed to indoor allergens by being housed in a barn and fed good quality hay (“Moderate exposure”) and then poor quality hay (“High exposure”), in a cross-over design. Lung function was recorded and bronchoalveolar lavage, as well as oral and nasal rinses were collected. 16S rRNA gene sequencing was performed with the Illumina MiSeq platform. Sequences were analyzed using mothur (3) and the vegan package in R.

Horses with asthma developed airway obstruction and inflammation with moderate and high antigen exposure, while controls showed only mild inflammation in the high exposure environment. Lung, oral and nasal communities clustered strongly by environmental conditions (PERMANOVA, P=0.004, <0.001, 0.02). Lung communities were composed of a large number of low-abundance sequences and were not dominated by any specific operational taxonomic unit. Their composition however was significantly different between healthy and asthmatic horses at the family level of taxonomic designation (P=0.006), which was not the case for oral and nasal communities. Oral and nasal communities were distinct from the lung communities, and had greater richness and diversity.

This study shows that in these untreated animals housed together, pulmonary, oral and nasal microbiome is influenced by environmental conditions but that only pulmonary microbiome differs between horses with and without asthma. The difference between asthmatic and healthy horses was mainly present when airway inflammation was present in horses with asthma but not in controls, suggesting that the altered lung microbiome observed in asthma is not inherent but coincident with inflammation.