ArticleApplied and environmental microbiology2008
Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH.
Article in Applied and environmental microbiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
41 citing papers in PubMed, 159 citations in OpenAlex.
- From observable fermentation data to hidden cell states: A modeling study of a mixotrophic Clostridium coculture under perfusion mode.PLoS computational biology · 2026Article
- Survival of a potential bacterial biocontrol agent in the soil and its impact on microbial communities.Pest management science · 2026Article
- Surface sediment microbial communities remain viable, culturable, and metabolically active during sequential heating.Frontiers in microbiology · 2026Article
- Metagenomic analysis of heavy water-adapted bacterial communities.Microbial genomics · 2025Article
- GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities.The ISME journal · 2025Article
- Article
- Micromonas, a small pigmented flagellate, predominates the nanoflagellate and photosynthetic picoeukaryote communities in the northern South China Sea.Environmental microbiology reports · 2024Article
- Research progress in isolation and identification of rumen probiotics.Frontiers in cellular and infection microbiology · 2024Review
- Imaging biofilms using fluorescenceFrontiers in cellular and infection microbiology · 2023Review
- FISHing for ciliates: Catalyzed reporter deposition fluorescenceFrontiers in microbiology · 2022Article
- Infective endocarditis: Role of molecular techniques in early diagnosis.Saudi journal of biological sciences · 2021Review
- Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts.The ISME journal · 2021Article
- Preparation and Characterization of a New Monoclonal Antibody Specific AgainstFrontiers in veterinary science · 2021Article
- An Introduction to Fluorescence in situ Hybridization in Microorganisms.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- A pipeline for targeted metagenomics of environmental bacteria.Microbiome · 2020Article
- NOTIFy (non-toxic lyophilized field)-FISH for the identification of biological agents by Fluorescence in situ Hybridization.PloS one · 2020Article
- Detection of Ampicillin-ResistantNanomaterials (Basel, Switzerland) · 2019Article
- Optimizing locked nucleic acid/2'-O-methyl-RNA fluorescence in situ hybridization (LNA/2'OMe-FISH) procedure for bacterial detection.PloS one · 2019Article
- Laser-induced breakdown spectroscopy (LIBS): a novel technology for identifying microbes causing infectious diseases.Biophysical reviews · 2018Review
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 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a method that is widely used to detect and quantify microorganisms in environmental samples and medical specimens by fluorescence microscopy. Difficulties with FISH arise if the rRNA content of the probe target organisms is low, causing dim fluorescence signals that are not detectable against the background fluorescence. This limitation is ameliorated by technical modifications such as catalyzed reporter deposition (CARD)-FISH, but the minimal numbers of rRNA copies needed to obtain a visible signal of a microbial cell after FISH or CARD-FISH have not been determined previously. In this study, a novel competitive FISH approach was developed and used to determine, based on a thermodynamic model of probe competition, the numbers of 16S rRNA copies per cell required to detect bacteria by FISH and CARD-FISH with oligonucleotide probes in mixed pure cultures and in activated sludge. The detection limits of conventional FISH with Cy3-labeled probe EUB338-I were found to be 370 +/- 45 16S rRNA molecules per cell for Escherichia coli hybridized on glass microscope slides and 1,400 +/- 170 16S rRNA copies per E. coli cell in activated sludge. For CARD-FISH the values ranged from 8.9 +/- 1.5 to 14 +/- 2 and from 36 +/- 6 to 54 +/- 7 16S rRNA molecules per cell, respectively, indicating that the sensitivity of CARD-FISH was 26- to 41-fold higher than that of conventional FISH. These results suggest that optimized FISH protocols using oligonucleotide probes could be suitable for more recent applications of FISH (for example, to detect mRNA in situ in microbial cells).
Indexed as
Identifiers
What OpenQuestion holds
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.