Protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization

The tick gut harbors a relatively diverse microbial community that includes commensal, beneficial, and pathogenic bacterial species. Here, we present a protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization. We describe steps for tick dissection, tissue fixation, hybridization, washing, and mounting. We then detail procedures for microscopy imaging of the whole-mounted samples. Although the procedure is designed for gut tissue samples, it can be readily modified for use with other tissue types. For complete details on the use and execution of this protocol, please refer to Hodžić et al.1.