Robert P Dickson, John R Erb-Downward, Nicole R Falkowski, Ellen M Hunter, Shanna L Ashley, Gary B Huffnagle

The "gut-lung axis" is commonly invoked to explain the microbiome's influence on lung inflammation. Yet the lungs harbor their own microbiome which is altered in respiratory disease. The relative influence of gut and lung bacteria on lung inflammation is unknown. To determine if baseline lung immune tone reflects local (lung-lung) or remote (gut-lung) microbe-host interactions. We compared lung, tongue, and cecal bacteria in forty healthy, genetically-identical 10-week old mice using 16S rRNA gene quantification and sequencing. We measured inflammatory cytokines using a multiplex assay of homogenized lung tissue. We compared lung bacteria in healthy mice treated with varied durations of systemic antibiotics. Lung bacterial communities are highly variable among mice, cluster strongly by cage, by shipment, and by vendor, and are altered by antibiotics in a microbiologically predictable manner. Baseline lung concentrations of two key inflammatory cytokines (IL-1α, IL-4) are correlated with the diversity and community composition of lung bacterial communities. Lung concentrations of these inflammatory cytokines correlated more strongly with variation in lung bacterial communities than with that of the gut or mouth. In the lungs of healthy mice, baseline innate immune tone more strongly reflects local (lung-lung) microbe-host interactions than remote (gut-lung) microbe-host interactions. Our results independently confirm the existence and immunologic significance of the murine lung microbiome, even in health. Variation in lung microbiota is likely an important, underappreciated source of experimental and clinical variability. The lung microbiome is an unexplored therapeutic target for the prevention and treatment of inflammatory lung disease.