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bioRxiv · 10.1101/2021.05.27.445923

Spatial profiling of microbial communities by sequential FISH with error-robust encoding

Cao, Z.·Zuo, W.·Wang, L.·Chen, J.·Qu, Z.·Jin, F.·Dai, L.
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Abstract

Spatial analysis of microbiomes at single cell resolution with high multiplexity and accuracy has remained challenging. Here we present spatial profiling of a microbiome using sequential error-robust fluorescence in situ hybridization (SEER-FISH), a highly multiplexed and accurate imaging method that allows mapping of microbial communities at micron-scale. We show that multiplexity of RNA profiling in microbiomes can be increased significantly by sequential rounds of probe hybridization and dissociation. Combined with error-correction strategies, we demonstrate that SEER-FISH enables accurate taxonomic identification in complex microbial communities. Using microbial communities composed of diverse bacterial taxa isolated from plant rhizospheres, we show that SEER-FISH can quantify the abundance of each taxon and map microbial biogeography on roots. SEER-FISH should enable accurate spatial profiling of the ecology and function of complex microbial communities.

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Cao, Z., Zuo, W., Wang, L., Chen, J., Qu, Z., Jin, F., Dai, L.. 2021-05-27. Spatial profiling of microbial communities by sequential FISH with error-robust encoding. https://doi.org/10.1101/2021.05.27.445923

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