The pulmonary microbiota in lung disease: The relationship between microbial community structure, age, disease stage, prognosis and severity of lung disease has been increasingly elucidated with the application of next-generation sequencing of the pulmonary microbiome. My laboratory studies the relationship between microbial community structure and disease pathogenesis in a variety of acute and chronic lung diseases to better understand microbial influences on disease pathogenesis and treatment response.

Microbial genomic diagnostics in infectious and non-infectious diseases: The human microbiome is the physiological equivalent of many other human organs or organ systems. Its role in host metabolism, immune responses, pathogen colonization resistance and treatment responsiveness are increasingly well described. We hope to develop and apply microbial genomic assays of microbiome structure and function to clinical medicine as a diagnostic test equivalent to other common tests of organ function.

Therapeutic manipulation of the microbiome: Many infectious and non-infectious diseases involve pathological perturbations of the microbiome - 'dysbiosis'. Treatments that restore a healthy microbiome have the potential to improve disease outcomes. We hope to apply the therapeutic manipulation of the human microbiome to a number of infectious and non-infectious conditions in pre-clinical and clinical models.