Microbial communities, ranging from the root microbiome of crops to the gut microbiota of animals, do not distribute themselves randomly. Understanding how complex microbial communities are spatially organized is critical for deciphering species interactions and microbiome function.
In a study published in Cell Reports Methods , Prof. DAI Lei's team from the Shenzhen Institutes of Advanced Technology (SIAT) of the Chinese Academy of Sciences developed a sequential error-robust FISH spatial mapping platform (SEER-Map) which enables fully automated, high-multiplexity spatial profiling of complex microbial communities at single-cell resolution.
SEER-Map integrates custom fluidics with a programmable fluorescence microscope. It can realize autonomous execution of 40 sequential FISH rounds, totaling approximately 15 hours without manual intervention. Throughout the process, high signal stability in hybridization is maintained across all imaging channels, with residual fluorescence remaining below 5% after each dissociation step. An error-robust barcoding scheme ensures highly reliable species identification.
Researchers applied SEER-Map to a synthetic bacterial community colonizing Arabidopsis thaliana roots, and mapped 28 out of 30 inoculated strains, revealing structured microbial clustering and complex species co-occurrence patterns. By comparing wild-type and coumarin-deficient mutants, they detected genotype-specific colonization shifts. For instance, they observed a greatly enhanced abundance of Lysobacter sp. near the root tip exclusively in the mutant.
SEER-Map eliminates manual variability and ensures rigorous reproducibility by automating the entire workflow from pretreatment to data processing. It provides researchers with a powerful lens to explore the community structure and functional dynamics of diverse microbial ecosystems.
Cell Reports Methods