Bacteria live almost exclusively in communities with other microorganisms, and often in association with multicellular hosts. These communities are capable of maintaining complex structural and functional stability over time, and exhibit fascinating properties of resiliency in response to environmental changes. This is a result of interactions between microbes and the environment and amongst members of the community. A multitude of chemical interactions occur in microbial communities where primary and secondary metabolites contribute to a wealth of interactions between organisms. The chemicals include a variety of nutrients, toxic or neutral metabolic byproducts, antibiotics, and cell-cell signaling molecules. These chemical and physical signals mitigate microbial relationship that can be competitive, cooperative or neutral, and thus are responsible for determining community structure. In turn, the surrounding community changes the microenvironment of individual cells that respond to chemical and environmental cues in a combinatorial manner. Pathogens must contend with this complex ecology during infection. For pathogens, these other microbes are the normal microbiota of the human host (the human microbiome). The human microbiome is poorly defined and composed of thousands of organisms of which relatively few have been characterized. We are working to define the normal microbiota and to understand the role of small molecule signaling in the ecology of the normal microbiota of the human host.
One of our primary areas of research investigates the role of normal flora-pathogen interactions in health and disease in the area of respiratory infections with a focus in cystic fibrosis. A polymicrobial perspective on these infections has lead to identification of overlooked pathogens in airway disease as well as synergistic interactions between avirulent organisms and pathogens. This is a fundamentally different view of airway infections and has lead to direct benefits to patients through altered treatment strategies.