All animals live in close interaction with a wide variety of microbes called the microbiome. The importance of this microbiome in health and disease of animals and humans is becoming increasingly clear in the recent years. However, understanding the complex interactions between host and microbes is difficult- the large variety of different microbial species and their detailed effect on host tissues is mostly unclear despite considerable research efforts. In order to begin to understand such interactions between host and microbes, the study of simpler model systems is essential. Natural associations between a single species of bacteria with an animal host are therefore the ideal systems with which to gain an understanding of detailed interkingdom interactions. 

Two-species (binary, host-bacterium) interactions do exist naturally in most animals, including mammals. One binary symbiosis is between the Hawaiian bobtail squid (Euprymna scolopes) and the marine bacterium Vibrio fischeri. This bacterial species is known for its ability to produce bioluminescence- they can emit light. The squid has a specialized light-emitting organ (i.e., photophore) into which it specifically takes up V. fischeri (only this species and no other). The bioluminescence of the bacteria inside the light organ allows the squid to camouflage their shadow from predators against the moonlight from above.  

The overall aim of this project is to understand, on the molecular level, how V. fischeri cells interact with their squid host. We will use cryo-electron tomography (cryo-ET) as our main research tool. Cryo-ET, similar to a medical CAT-scan, involves tilting the specimen within the microscope and collecting a series of 2D projection images at regular intervals. These images are then computationally back-projected to generate a three-dimensional volume of the specimen that can be viewed and analyzed in any orientation. Cryo-ET allows us to study basic concepts of life by directly imaging structures at the molecular level. 

In this project, we will use cryo-ET in order to decipher how and when microbes utilize certain molecular machines during their life cycle, from colonization, during active symbiosis and upon reentering into the environment. Our approach will allow us to study the presence and architecture of several bacterial molecular machines such as chemotaxis systems, flagella, pili and a diverse array of secretion systems, and dissect their specific roles in situ in a near native state, in three dimensions and at macromolecular resolution.

The current state of the art is, quite simply, that no one has visualized the interactions of a host and a specific microbial symbiont at sufficient magnification and resolution to reveal the operation of sub-micron sized bacterial nanomachinery (e.g., type 6 secretion system injectors). Our goal is to provide the first imaging of such interactions, providing a technical and scientific guide to those researchers who wish to image similar structures in more complex microbial consortia such as those in the gut.

• host-microbe interactions