GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities
Pam Engelberts, Jun Ye, Donovan Parks, Eilish McMaster +5
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70% confidenceA new genome-based FISH approach, GenomeFISH, is presented, which can differentiate strains within complex microbial communities with high sensitivity and specificity.
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Abstract
Abstract 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 optimisation 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 the gold standard in the visualisation of complex microbial systems.
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- Journal
- Research Square
- Year
- 2024