The culture-independent study of microbial communities has been driven by metagenomic sequencing. While this can reveal overall bacterial community composition, all spatial information is generally lost during DNA extraction. However, the spatial organisation of microbial communities is key to their function. Consequently, a better mechanistic understanding of microbe-microbe and microbe-host interactions critically depends on the availability of spatial technologies. In our group we are developing a multiplexed FISH-based assay to detect different bacteria simultaneously in situ. We are currently primarily applying this technology to understand the spatial architecture of bacterial communities in tumour tissues and how this shapes their interactions with tumour and immune cell populations.