Essentially all animal and plant species have long-term associations with microbial symbionts, often including specific species/strains. In many cases, these associations have been shown to be essential to the normal health and development of the hosts. Among the most common kinds of interactions present in animals are those between extracellular bacteria along the host’s epithelial tissues. The long-term objectives of our research are to define the behavioral, physiological and molecular events that characterize the bacterial colonization of animal epithelium. Our specific aims are to:

1. Determine how specificity is achieved in environmentally transmitted bacteria-host associations. 
2. Identify aspects of bacterial behavior that are essential to tissue tropism. 
3. Characterize the molecular mechanisms that underlie successful tissue colonization. 
4. Define the spatial patterns and temporal dynamics of non-clonal bacterial populations within monospecific associations. 
5. Determine the suite of changes in bacterial gene expression that are induced by the environment of host tissues.

To accomplish these goals we have chosen as a natural study system the symbiotic association of the luminous bacterium Vibrio fischeri within the light-emitting organ of the squid Euprymna scolopes. This system provides a simple and experimentally accessible paradigm for studying specific host-bacterial interactions. Our recent investigations have centered on the events characterizing the initiation, colonization, and persistence of the symbiotic infection in newly hatched juvenile squids using bacterial mutants to manipulate, assay, and observe the results of the complex program of signaling and responses through which the host and bacterium communicate. We believe that this system also serves as a model of infection by pathogenic species of Vibrio and, perhaps, of the evolution of the virulence state in these and other pathogens; that is, bacterial and host determinants that potentiate light-organ symbiosis are revealing convergences with known bacterial virulence factors, and are promoting the discovery of as yet undescribed ones. This work will also aid our understanding of the mechanisms by which the benign colonization of mollusk tissue may serve as a reservoir for human pathogenic Vibrio species.

In recent years, in conjunction with other labs working with Vibrio fischeri and the squid host, we have developed and applied novel technical approaches to facilitate our research aims. Specifically, we have developed molecular genetics in this bacterium, sequenced the genome of almost 100 light organ isolates, and created transposon mutant libraries. In addition, using fluorescently labeled V. fischeri cells and confocal microscopy, we are characterizing the behavior of these bacteria during the initiation and development of symbiosis in living squid. In addition, in collaboration with Institut Pasteur, we are pushing the current boundaries of imaging to identify the interface between the symbiont’s surface and the epithelial cell at the level of cryoEM. Finally, by applying recent molecular genetic advances, we have begun to determine single-cell bacterial transcriptomics on V. fischeri cells in culture, and on symbionts directly isolated from light organs.

1. Small RNA Signaling: How do bacterial sRNAs control the immunology and metabolism of their host?
2. Metabolic Interactions Between the Partners: Do the symbionts transform and return some of the host-derived nutrients they are provided?
3. Symbiont Diversity: What static and dynamic patterns of individual diversity of gene expression exist in natural V. fischeri populations found within E. scolopes light organs? 
4. Competitive Dominance: The earliest site of species specificity in the V. fischeri-E. scolopes partnership is the dominance of V. fischeri in the host-derived mucus.