ArticleSystematic and applied microbiology2012
CLASI-FISH: principles of combinatorial labeling and spectral imaging.
Article in Systematic and applied microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 105 citations in OpenAlex.
- Imaging nucleic acids in biofilms.Essays in biochemistry · 2026Review
- Micro-scale spatial metagenomics opens a new era in microbiome ecology.Trends in microbiology · 2026Review
- Spatial structure: shaping the ecology and evolution of microbial communities.FEMS microbiology reviews · 2026Review
- CLASI-FISH Imaging of Fusobacterium in Oral Microbial Communities.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Examining Oral Microbial Communities at the Gingival Interface During Health and Inflammatory Diseases.Advances in experimental medicine and biology · 2026Review
- You are what your fungus eats: diet shapes the microbial garden of a fungus-growing ant.NPJ biofilms and microbiomes · 2025Article
- MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data.Microbiome · 2025Article
- Microbial signals in primary and metastatic brain tumors.Nature medicine · 2025Article
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies.Molecular oral microbiology · 2025Article
- Microbiome in cancer metastasis: biological insights and emerging spatial omics methods.Frontiers in cellular and infection microbiology · 2025Review
- Bacterial interactions on nutrient-rich surfaces in the gut lumen.Infection and immunity · 2024Review
- The wound microbiota: microbial mechanisms of impaired wound healing and infection.Nature reviews. Microbiology · 2024Review
- Ecology ofBiofilm · 2024Review
- Microbial Symphony: Navigating the Intricacies of the Human Oral Microbiome and Its Impact on Health.Microorganisms · 2024Review
- The gut microbiota and its biogeography.Nature reviews. Microbiology · 2024Review
- Omics for deciphering oral microecology.International journal of oral science · 2024Review
- Combinatorial fluorescent labeling of live anaerobic bacteria via the incorporation of azide-modified sugars into newly synthesized macromolecules.Nature protocols · 2023Review
- Single-cell transcriptomics refuels the exploration of spiralian biology.Briefings in functional genomics · 2023Review
- Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling.Nature protocols · 2023Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Although the number of phylotypes present in a microbial community may number in the hundreds or more, until recently, fluorescence in situ hybridization has been used to label, at most, only a handful of different phylotypes in a single sample. We recently developed a technique, CLASI-FISH for combinatorial labeling and spectral imaging - fluorescence in situ hybridization, to greatly expand the number of distinguishable taxa in a single FISH experiment. The CLASI technique involves labeling microbes of interest with combinations of probes coupled with spectral imaging to allow the use of fluorophores with highly overlapping excitation and emission spectra. Here, we present the basic principles and theory of CLASI-FISH along with some guidelines for performing CLASI-FISH experiments. We further include a protocol for creating fluorescence spectral reference standards, a vital component of successful CLASI-FISH.
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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.