ReviewNature protocols2023
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling.
Review in Nature protocols, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed, 59 citations in OpenAlex.
- An engineered bacterial symbiont maps micron-scale sugar gradients in the honeybee gut.PLoS biology · 2026Article
- Micro-scale spatial metagenomics opens a new era in microbiome ecology.Trends in microbiology · 2026Review
- Towards Cellular Resolution of Tryptic Peptides in Tissue Sections by MALDI MS Imaging: A Focus on Enzyme Application and Reproducibility.Analytical chemistry · 2026Article
- Multimodal spatial omics: From data acquisition to computational integration.Patterns (New York, N.Y.) · 2026Review
- Mass spectrometry-based metabolomics approaches to interrogate host-microbiome interactions in mammalian systems.Natural product reports · 2026Review
- Potential of Clinical Care-Collected Gut Biopsies for Advancing Personalised Medicine in Inflammatory Bowel Disease.United European gastroenterology journal · 2026Review
- Bis(4-(1,3-benzoxazol-2-yl)) phenyl analogues as novel matrices for Fourier transform ion cyclotron resonance mass spectrometric imaging of lipids in dual ion mode in vulvar squamous cell carcinomas.Analytical and bioanalytical chemistry · 2026Article
- Layer-by-layer decoding of contemporary and historic painting composition using MALDI mass spectrometry imaging and machine learning.Science advances · 2026Article
- Applications and technical challenges of MALDI mass spectrometry imaging in microbial ecosystems and metabolic network research.Archives of microbiology · 2026Review
- Chemical Signaling and Metabolomic Crosstalk in Endophytic Fungi-Medicinal Plant Symbioses for Natural Product Discovery and Sustainable Bioproduction.Metabolites · 2026Review
- MALDI-FISH for Colocalization of Brominated Metabolites andJournal of natural products · 2026Article
- Mathematical Framework for Quantifying Delocalization in MALDI-MSI via a Composite Scoring Approach.ACS measurement science au · 2026Article
- Mass spectrometry imaging tutorial: From cancer biomarker discovery to clinical applications.Analytica chimica acta · 2026Review
- Article
- Spatial structure: shaping the ecology and evolution of microbial communities.FEMS microbiology reviews · 2026Review
- Dissecting the role ofFrontiers in microbiology · 2026Article
- Interrogation of imaging-based interspecies dynamics in the oral microbiome.Journal of oral microbiology · 2026Review
- Biodiversity-Driven Natural Products and Bioactive Metabolites.Plants (Basel, Switzerland) · 2025Review
- Reference-guided computational framework identifies microenvironment metabolic subtypes and targets using pan-cancer single-cell datasets.Genome medicine · 2025Article
- Spatial biology using single-cell mass spectrometry imaging and integrated microscopy.Nature communications · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
Label-free molecular imaging techniques such as matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enable the direct and simultaneous mapping of hundreds of different metabolites in thin sections of biological tissues. However, in host-microbe interactions it remains challenging to localize microbes and to assign metabolites to the host versus members of the microbiome. We therefore developed a correlative imaging approach combining MALDI-MSI with fluorescence in situ hybridization (FISH) on the same section to identify and localize microbial cells. Here, we detail metaFISH as a robust and easy method for assigning the spatial distribution of metabolites to microbiome members based on imaging of nucleic acid probes, down to single-cell resolution. We describe the steps required for tissue preparation, on-tissue hybridization, fluorescence microscopy, data integration into a correlative image dataset, matrix application and MSI data acquisition. Using metaFISH, we map hundreds of metabolites and several microbial species to the micrometer scale on a single tissue section. For example, intra- and extracellular bacteria, host cells and their associated metabolites can be localized in animal tissues, revealing their complex metabolic interactions. We explain how we identify low-abundance bacterial infection sites as regions of interest for high-resolution MSI analysis, guiding the user to a trade-off between metabolite signal intensities and fluorescence signals. MetaFISH is suitable for a broad range of users from environmental microbiologists to clinical scientists. The protocol requires ~2 work days.
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.