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

Zhaohui Cao, Wenlong Zuo, Lanxiang Wang, Junyu Chen, Zepeng Qu, Fan Jin and Lei Dai ()
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Zhaohui Cao: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
Wenlong Zuo: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
Lanxiang Wang: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
Junyu Chen: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
Zepeng Qu: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
Fan Jin: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
Lei Dai: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: 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 apply SEER-FISH to quantify the abundance of each taxon and map microbial biogeography on roots. At micron-scale, we identify clustering of microbial cells from multiple species on the rhizoplane. Under treatment of plant metabolites, we find spatial re-organization of microbial colonization along the root and alterations in spatial association among microbial taxa. Taken together, SEER-FISH provides a useful method for profiling the spatial ecology of complex microbial communities in situ.

Date: 2023
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DOI: 10.1038/s41467-023-37188-3

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