ArticleBMC genomics2020
A comprehensive survey of integron-associated genes present in metagenomes.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 45 citations in OpenAlex.
- High-throughput recovery of integron cassettes for gene discovery screens.Nature microbiology · 2026Article
- Adaptative and ancient co-evolution of integrons withMicrobial genomics · 2025Article
- Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems.Microbiome · 2025Article
- Integrons are anti-phage defence libraries in Vibrio parahaemolyticus.Nature microbiology · 2025Article
- Investigation of integron classes 1, 2, and 3 among multi-drug resistant Staphylococcus aureus isolates in Iran: a multi-center study.BMC infectious diseases · 2024Article
- Global genomic epidemiology ofMicrobial genomics · 2024Article
- The role of New World vultures as carriers of environmental antimicrobial resistance.BMC microbiology · 2024Article
- Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.Nature communications · 2024Article
- Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons.PLoS genetics · 2024Article
- The defensome of complex bacterial communities.Nature communications · 2024Article
- Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems.Science advances · 2024Article
- Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites.Nature microbiology · 2024Article
- Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes.Frontiers in microbiology · 2023Article
- Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world.PloS one · 2023Article
- Discovery of integrons in Archaea: Platforms for cross-domain gene transfer.Science advances · 2022Article
- Novel Mobile Integrons and Strain-Specific Integrase Genes withinMicroorganisms · 2022Article
- IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.Microorganisms · 2022Article
- Unbridled Integrons: A Matter of Host Factors.Cells · 2022Review
- Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities.Microbial genomics · 2022Article
- Biochar and Manure Applications Differentially Altered the Class 1 Integrons, Antimicrobial Resistance, and Gene Cassettes Diversity in Paddy Soils.Frontiers in microbiology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIntegrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging.
resultsHere, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants.
conclusionsOur results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.
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