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Related Experiment Video

Updated: Aug 6, 2025

Author Spotlight: Integrated OPTIR-FISH for Single-Cell Metabolic and Identity Analysis in Complex Environments

Author Spotlight: Integrated OPTIR-FISH for Single-Cell Metabolic and Identity Analysis in Complex Environments

Published on: February 23, 2024

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

Zhaohui Cao^1,2, Wenlong Zuo¹, Lanxiang Wang¹

¹CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.

Nature Communications

|March 18, 2023

Summary

This summary is machine-generated.

We developed SEER-FISH, a new imaging method for high-resolution microbiome mapping. This technique accurately identifies and maps microbial communities in situ, revealing their spatial organization on plant roots.

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Published on: July 9, 2021

Area of Science:

Microbiology
Ecology
Biotechnology

Background:

Spatial analysis of microbiomes at single-cell resolution is challenging.
Current methods lack high multiplexity and accuracy for complex microbial communities.

Purpose of the Study:

To present SEER-FISH, a novel imaging method for high-resolution spatial microbiome profiling.
To demonstrate SEER-FISH's capability for accurate taxonomic identification and biogeographical mapping of microbial communities.

Main Methods:

Sequential Error-Robust Fluorescence In Situ Hybridization (SEER-FISH) for multiplexed RNA profiling.
Error-correction strategies for enhanced accuracy in taxonomic identification.
Application to plant rhizosphere microbial communities for in situ analysis.

Main Results:

SEER-FISH significantly increases multiplexity and accuracy in microbiome profiling.
Accurate taxonomic identification and abundance quantification of diverse bacterial taxa.
Micron-scale mapping reveals microbial cell clustering and spatial re-organization on plant roots in response to metabolites.

Conclusions:

SEER-FISH is a powerful tool for spatial microbiome analysis at single-cell resolution.
The method enables detailed insights into microbial biogeography and community dynamics in situ.
SEER-FISH advances the study of microbial ecology in complex environments.