ArticleNature communications2023
Spatial profiling of microbial communities by sequential FISH with error-robust encoding.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it, 60 citations in OpenAlex.
- Root colonization by beneficial rhizobacteria.FEMS microbiology reviews · 2024Pooled it
- Social lives of bacteria as revealed through CLASI-FISH.Essays in biochemistry · 2026Review
- Rapid and robust diagnosis of bloodstream infections by single-cell analysis.Science advances · 2026Article
- Micro-scale spatial metagenomics opens a new era in microbiome ecology.Trends in microbiology · 2026Review
- From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.Plants (Basel, Switzerland) · 2026Review
- Spatial mapping of microbial communities by an integrated automation platform of sequential FISH.Cell reports methods · 2026Article
- Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.Nature microbiology · 2026Article
- Review
- Holo-2bRAD: A Hologenomic Method for High-Resolution Analysis of Coral Microbiomes During Bleaching.Microorganisms · 2026Article
- Cross hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH enables microbiome imaging with strain level taxonomic resolution.bioRxiv : the preprint server for biology · 2026Article
- Review
- Slicing overcomes the bacterial cell wall barrier to fluorescenceMicrobiology spectrum · 2026Article
- Spatial structure: shaping the ecology and evolution of microbial communities.FEMS microbiology reviews · 2026Review
- Small-scale biogeography of biofilms and its implications for sequencing-based studies.ISME communications · 2026Article
- Visualizing C. difficile During Murine Infection.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A spatial-microbial-metabolic-immune framework for high-risk oral potentially malignant disorders: an evidence-ranked review for malignant transformation risk stratification.Frontiers in cellular and infection microbiology · 2026Review
- Interrogation of imaging-based interspecies dynamics in the oral microbiome.Journal of oral microbiology · 2026Review
- MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data.Microbiome · 2025Article
- Understanding the development of bacterial colony: Physiology, new technology, and modeling.Quantitative biology (Beijing, China) · 2025Review
- Tetrahedral DNA dendritic nanostructure-enhanced FISH for high-speed, sensitive spatial transcriptomics.Nature communications · 2025Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.