Evidence map›Paper›PMID 40621946›Full record

ArticleThe ISME journal2025

GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities.

J Pamela Engelberts, Jun Ye, Donovan H Parks, Eilish S McMaster, Allison S McInnes, Ben J Woodcroft, James G Volmer, Simon J McIlroy, Gene W Tyson

Abstract readEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in The ISME journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

J Pamela EngelbertsCentre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba 4102, QLD, Australia.ORCID 0000-0002-1185-3741
Jun YeAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4067, QLD, Australia.
Donovan H ParksAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4067, QLD, Australia.ORCID 0000-0001-6662-9010
Eilish S McMasterCentre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba 4102, QLD, Australia.ORCID 0000-0002-7415-8690
Allison S McInnesCentre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba 4102, QLD, Australia.
Ben J WoodcroftCentre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba 4102, QLD, Australia.ORCID 0000-0003-0670-7480
James G VolmerCentre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba 4102, QLD, Australia.ORCID 0000-0001-8245-2817
Simon J McIlroyCentre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba 4102, QLD, Australia.
Gene W TysonCentre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba 4102, QLD, Australia.ORCID 0000-0001-8559-9427

Funding

Australian Government Research Discovery Grant DP200102310Australian Research Council Fellowships FL230100159Australian Research Council Fellowships FT190100211Australian Research Council Fellowships FT210100521Heising-Simons Foundation 2022-4087
6 · The paper itself

Abstract

Fluorescence in situ hybridization (FISH) is a powerful tool for visualizing the spatial organization of microbial communities. However, traditional FISH has several limitations, including limited phylogenetic resolution, difficulty visualizing certain lineages, and the design and optimization of new probes is time consuming and does not scale to the known diversity of microbial life. Here, we present GenomeFISH, a high-throughput, genome-based FISH approach that can differentiate strains within complex communities. Fluorescent probes are generated from the genomes of single cells, which are obtained from environmental or clinical samples through fluorescence activated single-cell sorting. GenomeFISH can distinguish between strains with up to 99% average nucleotide identity and was successfully applied to visualize strains in mock communities and human fecal samples. Given the superior sensitivity and specificity of GenomeFISH, we envisage it will become widely used for the visualization of complex microbial systems.

Indexed as

BacteriaGenome, BacterialIn Situ Hybridization, FluorescenceMicrobiotaFecesFluorescent DyesHumansSensitivity and SpecificityFluorescent Dyesfluorescence in situ hybridization (FISH)GenomeFISHhigh-throughputmicrobial ecologysingle amplified genomes (SAGs)single-cell genomicsstrainswhole-genome hybridization

Identifiers

PMID40621946
PMCPMC12344553

What OpenQuestion holds

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Registered trials

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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.