ArticleProceedings of the National Academy of Sciences of the United States of America2011
Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 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
180 citing papers in PubMed, 340 citations in OpenAlex.
- Social lives of bacteria as revealed through CLASI-FISH.Essays in biochemistry · 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
- Live tissue microbiota and bacterial translocation: mechanisms and translational perspectives in cardiometabolic diseases.Reviews in endocrine & metabolic disorders · 2026Review
- Interplay of Spatial Structure and Interactions in Microbial Communities.Environmental microbiology · 2026Review
- BEEP Learning: Multi-View Image Decomposition for Massively Multiplexed Biological Fluorescence Microscopy.bioRxiv : the preprint server for biology · 2026Article
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- A Bayesian multivariate spatial point pattern model: application to oral microbiome FISH image data.Biostatistics (Oxford, England) · 2026Article
- In situ visualization of Clostridioides difficile phenotypic heterogeneity and single-cell morphology during gut infection.Nature communications · 2026Article
- Slicing overcomes the bacterial cell wall barrier to fluorescenceMicrobiology spectrum · 2026Article
- Oral microbiome alterations and their association with long-term heavy metal exposure and early health effects.Journal of oral microbiology · 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
- A Review of the Impact of Green Tea (Current pharmaceutical design · 2026Review
- CLASI-FISH Imaging of Fusobacterium in Oral Microbial Communities.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Epidemiology of bacterial biofilms on polyps and normal tissues in a screening colonoscopy cohort.Gut microbes · 2025Observational
- Laser-assisted microbial culturomics.Nature communications · 2025Article
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
- Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies.Molecular oral microbiology · 2025Article
- Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer.NPJ biofilms and microbiomes · 2025Article
120 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
- Commented on by
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Microbes in nature frequently function as members of complex multitaxon communities, but the structural organization of these communities at the micrometer level is poorly understood because of limitations in labeling and imaging technology. We report here a combinatorial labeling strategy coupled with spectral image acquisition and analysis that greatly expands the number of fluorescent signatures distinguishable in a single image. As an imaging proof of principle, we first demonstrated visualization of Escherichia coli labeled by fluorescence in situ hybridization (FISH) with 28 different binary combinations of eight fluorophores. As a biological proof of principle, we then applied this Combinatorial Labeling and Spectral Imaging FISH (CLASI-FISH) strategy using genus- and family-specific probes to visualize simultaneously and differentiate 15 different phylotypes in an artificial mixture of laboratory-grown microbes. We then illustrated the utility of our method for the structural analysis of a natural microbial community, namely, human dental plaque, a microbial biofilm. We demonstrate that 15 taxa in the plaque community can be imaged simultaneously and analyzed and that this community was dominated by early colonizers, including species of Streptococcus, Prevotella, Actinomyces, and Veillonella. Proximity analysis was used to determine the frequency of inter- and intrataxon cell-to-cell associations which revealed statistically significant intertaxon pairings. Cells of the genera Prevotella and Actinomyces showed the most interspecies associations, suggesting a central role for these genera in establishing and maintaining biofilm complexity. The results provide an initial systems-level structural analysis of biofilm organization.
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.