Taormina, M.J., Jemielita, M., Stephens, W.Z., Burns, A.R., Troll, J.V., Parthasarathy, R., and Guillemin, K. (2012) Investigating bacterial-animal symbioses with light sheet microscopy. The Biological bulletin. 223(1):7-20.
Microbial colonization of the digestive tract is a crucial event in vertebrate development, required for maturation of host
immunity and establishment of normal digestive physiology. Advances in genomic, proteomic, and metabolomic technologies are
providing a more detailed picture of the constituents of the intestinal habitat, but these approaches lack the spatial and
temporal resolution needed to characterize the assembly and dynamics of microbial communities in this complex environment.
We report the use of light sheet microscopy to provide high-resolution imaging of bacterial colonization of the intestine
of Danio rerio, the zebrafish. The method allows us to characterize bacterial population dynamics across the entire organ and the behaviors
of individual bacterial and host cells throughout the colonization process. The large four-dimensional data sets generated
by these imaging approaches require new strategies for image analysis. When integrated with other “omics” data sets, information
about the spatial and temporal dynamics of microbial cells within the vertebrate intestine will provide new mechanistic insights
into how microbial communities assemble and function within hosts.