GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities

Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditional FISH has several limitations, including limited phylogenetic resolution, difficulty visualising certain lineages, and the​​ design and optimis​ation of​ new probes is time consuming and does not scale​ to the ​known​ diversity of microbial life. Here, we present GenomeFISH, a high-throughput, genome-based FISH approach that can differentiate strains within complex communities. Fluorescent probes are generated from the genomes of single cells, which are ​obtained ​from environmental or clinical samples through fluorescence activated single-cell sorting (FACS). GenomeFISH can ​distinguish between ​strains with up to 99% average nucleotide identity and was successfully applied to visualise strains in mock communities and human faecal samples. Given the superior sensitivity and specificity of GenomeFISH, we envisage it will become widely used for the visualisation of complex microbial systems.