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- Title
Spatial profiling of microbial communities by sequential FISH with error-robust encoding.
- Authors
Cao, Zhaohui; Zuo, Wenlong; Wang, Lanxiang; Chen, Junyu; Qu, Zepeng; Jin, Fan; Dai, Lei
- 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. Spatial analysis of microbiomes at single cell resolution is challenging. Here the authors report a highly multiplexed method for spatial profiling, sequential error-robust fluorescence in situ hybridisation (SEER-FISH), and show that this allows mapping of microbial communities at micron-scale.
- Subjects
MICROBIAL communities; FISH communities; SPATIAL ecology; COLONIZATION (Ecology); FLUORESCENCE in situ hybridization; MICROBIAL ecology; BACTERIAL communities
- Publication
Nature Communications, 2023, Vol 14, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-023-37188-3