Abstract
The upper and lower airways of healthy humans are reported to harbor stable and consistent bacterial populations, and the composition of these communities is altered in individuals affected with several respiratory diseases. Data regarding the presence of airway microbiota in other animals are scant and a better understanding of the composition and metabolic function of such bacterial populations is essential for the development of novel therapeutic and diagnostic modalities for use in both veterinary and human medicine. Based on targeted next-generation sequencing of feces and samples collected at multiple levels of the airways from 16 healthy female dogs, we demonstrate that canine airways harbor a topographically continuous microbiota with increasing relative abundance of proteobacterial species from the upper to lower airways. The lung-associated microbiota, as assessed via bronchoalveolar lavage fluid (BALF), was the most consistent between dogs and was dominated by three distinct taxa, two of which were resolved to the species level and one to the level of family. The gene content of the nasal, oropharyngeal, and lung-associated microbiota, predicted using the Phylogenetic Investigations into Communities by Reconstruction of Unobserved States (PICRUSt) software, provided information regarding the glyoxylate and citrate cycle metabolic pathways utilized by these bacterial populations to colonize such nutrient-poor, low-throughput environments. These data generated in healthy subjects provide context for future analysis of diseased canine airways. Moreover, as dogs have similar respiratory anatomy, physiology, and immune systems as humans, are exposed to many of the same environmental stimuli, and spontaneously develop similar respiratory diseases, these data support the use of dogs as a model species for prospective studies of the airway microbiota, with findings translatable to the human condition.
Highlights
The influence on host health of the complex and dynamic community of microbes present in the gastrointestinal tract, i.e., the gut microbiota, has become a rapidly expanding area of biomedical research
While the upper airways are routinely exposed to high bacterial loads derived from the oral and nasal cavities, the lungs, including bronchi, bronchioles, and alveoli, have historically been considered sterile in healthy individuals [18,19,20], a belief based on the lack of growth using traditional microbiological techniques and absence of histological evidence of microbes
Repeated discrepancies in environmental and gastrointestinal samples between microbial densities observed via light microscopy and results of attempted cultivation, i.e., the great plate count anomaly, demonstrated that the majority of bacteria are refractory to in vitro cultivation [21]
Summary
The influence on host health of the complex and dynamic community of microbes present in the gastrointestinal tract, i.e., the gut microbiota, has become a rapidly expanding area of biomedical research. The respiratory tract was not included in the HMP, partially owing to the long-held belief that the airways, and the lower airways, were largely devoid of colonizing microbial populations and any bacteria detected there were either transient or the result of defective clearance mechanisms. This belief was based on the lack of discernible colonization via histological examination and negative results using traditional culture-based microbiological methods. Whether such changes in microbial composition represent examples of dysbiosis of the airway microbiota contributing to the disease pathogenesis, or are reactions to altered host physiology is not clear
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