ArticleApplied and environmental microbiology2014
Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification.
Article in Applied and environmental microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 50 citations in OpenAlex.
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- OligoN-Design: A Simple and Versatile Tool to Design Specific Probes and Primers From Large Heterogeneous Datasets.Molecular ecology resources · 2026Article
- Cross hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH enables microbiome imaging with strain level taxonomic resolution.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary assembly of a unique purple-green photosymbiosis revealed by expanded ciliate diversity.The ISME journal · 2026Article
- Decoding type 5 diabetes using spatial omics: microarchitectural and molecular mechanisms of malnutrition-associated diabetes.Frontiers in endocrinology · 2026Review
- Bioinformatics Approaches in Noncoding RNAs Research.Experientia supplementum (2012) · 2026Review
- CLASI-FISH Imaging of Fusobacterium in Oral Microbial Communities.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- TrueProbes: Quantitative Single-Molecule RNA-FISH Probe Design Improves RNA Detection.bioRxiv : the preprint server for biology · 2025Article
- A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment.Nature communications · 2025Article
- A unique symbiosome in an anaerobic single-celled eukaryote.Nature communications · 2024Article
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- A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment.bioRxiv : the preprint server for biology · 2024Article
- Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants.The ISME journal · 2023Article
- Distribution, abundance, and ecogenomics of themSystems · 2023Article
- Spatial profiling of microbial communities by sequential FISH with error-robust encoding.Nature communications · 2023Article
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- High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coralScience advances · 2022Article
- Advances and Challenges in FluorescenceFrontiers in microbiology · 2022Article
- Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their natural environment and is often used to complement next-generation sequencing approaches as an integral part of the full-cycle rRNA approach. A major challenge in FISH is the design of oligonucleotide probes with high sensitivity and specificity to their target group. The rapidly expanding number of rRNA sequences has increased awareness of the number of potential nontargets for every FISH probe, making the design of new FISH probes challenging using traditional methods. In this study, we conducted a systematic analysis of published probes that revealed that many have insufficient coverage or specificity for their intended target group. Therefore, we developed an improved thermodynamic model of FISH that can be applied at any taxonomic level, used the model to systematically design probes for all recognized genera of bacteria and archaea, and identified potential cross-hybridizations for the selected probes. This analysis resulted in high-specificity probes for 35.6% of the genera when a single probe was used in the absence of competitor probes and for 60.9% when up to two competitor probes were used. Requiring the hybridization of two independent probes for positive identification further increased specificity. In this case, we could design highly specific probe sets for up to 68.5% of the genera without the use of competitor probes and 87.7% when up to two competitor probes were used. The probes designed in this study, as well as tools for designing new probes, are available online (http://DECIPHER.cee.wisc.edu).
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