ArticleNature microbiology2024
Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes.
Article in Nature microbiology, 2024. 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.
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- Social lives of bacteria as revealed through CLASI-FISH.Essays in biochemistry · 2026Review
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 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
- Diversity and ecological roles of hidden viral players in groundwater microbiomes.Nature communications · 2026Article
- Slicing overcomes the bacterial cell wall barrier to fluorescenceMicrobiology spectrum · 2026Article
- ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.Microbiome · 2025Article
- The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.Current opinion in microbiology · 2025Review
- Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species.Briefings in bioinformatics · 2025Article
- Bacterial immune systems as causes and consequences of microbiome structure.PLoS biology · 2025Article
- Spatial Transcriptomics to Study Virus-Host Interactions.Annual review of virology · 2025Review
- Polymicrobial Biofilms: Interkingdom Interactions, Resistance and Therapeutic Strategies.Microbial biotechnology · 2025Review
- Bacterial evolution in the oral microbiome: the role of conjugative elements and horizontal gene transfer.Journal of bacteriology · 2025Review
- Effects of Lactation Lactoferrin Deficiency on Intestinal Microbiota in Different Mice Models.Nutrients · 2025Article
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.National science review · 2025Article
- Bacteriophage-driven microbial phenotypic heterogeneity: ecological and biogeochemical importance.NPJ biofilms and microbiomes · 2025Review
- Unveiling plasmid diversity and functionality in pristine groundwater.Environmental microbiome · 2025Article
- Leveraging the microbiome to combat antibiotic resistant gynecological infections.npj antimicrobials and resistance · 2025Review
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Authors and funding
12 authors.
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Abstract
The exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. Here we combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH to enable simultaneous visualization of both MGEs and bacterial taxa. We spatially mapped bacteriophage and antimicrobial resistance (AMR) plasmids and identified their host taxa in human oral biofilms. This revealed distinct clusters of AMR plasmids and prophage, coinciding with densely packed regions of host bacteria. Our data suggest spatial heterogeneity in bacterial taxa results in heterogeneous MGE distribution within the community, with MGE clusters resulting from horizontal gene transfer hotspots or expansion of MGE-carrying strains. Our approach can help advance the study of AMR and phage ecology in biofilms.
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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.