ArticleApplied and environmental microbiology2012
Wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil DNA library.
Article in Applied and environmental microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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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.
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Who cites it
29 citing papers in PubMed, 61 citations in OpenAlex.
- Bacterial Proteomics and Antibiotic Resistance Identification: Is Single-Cell Analysis a Worthwhile Pursuit?Pathogens (Basel, Switzerland) · 2025Review
- Helping proteins come in from the cold: 5 burning questions about cold-active enzymes.BBA advances · 2024Review
- ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics.Nucleic acids research · 2023Article
- Aggregation-Based Bacterial Separation with Gram-Positive Selectivity by Using a Benzoxaborole-Modified Dendrimer.Molecules (Basel, Switzerland) · 2023Article
- Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics.Antibiotics (Basel, Switzerland) · 2021Article
- Antibiotic resistance: Global health crisis and metagenomics.Biotechnology reports (Amsterdam, Netherlands) · 2021Article
- Functional Metagenomic Screening for Antimicrobial Resistance in the Oral Microbiome.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Rapid determination of carbapenem resistance by low-cost colorimetric methods: Propidium Iodide and alamar blue staining.Journal of microbiology (Seoul, Korea) · 2020Article
- Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance.Applied and environmental microbiology · 2020Article
- Microbial Diversity and Antimicrobial Resistance Profile in Microbiota From Soils of Conventional and Organic Farming Systems.Frontiers in microbiology · 2019Article
- Discovery of Novel Antibiotic Resistance Determinants in Forest and Grassland Soil Metagenomes.Frontiers in microbiology · 2019Article
- Diverse Distribution of Resistomes in the Human and Environmental Microbiomes.Current genomics · 2018Review
- Recent Advances in Function-based Metagenomic Screening.Genomics, proteomics & bioinformatics · 2018Review
- The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always.Microbiome · 2018Article
- Genetic Diversity and Functional Analysis of Sigma Factors inEvolutionary bioinformatics online · 2018Article
- BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation.Nucleic acids research · 2017Article
- Next-generation approaches to understand and combat the antibiotic resistome.Nature reviews. Microbiology · 2017Review
- Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments.Microbial ecology · 2017Review
- Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay.Applied and environmental microbiology · 2016Article
- Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil.Journal of microbiology (Seoul, Korea) · 2015Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Most genes for antibiotic resistance present in soil microbes remain unexplored because most environmental microbes cannot be cultured. Only recently has the identification of these genes become feasible through the use of culture-independent methods. We screened a soil metagenomic DNA library in an Escherichia coli host for genes that can confer resistance to kanamycin, gentamicin, rifampin, trimethoprim, chloramphenicol, or tetracycline. The screen revealed 41 genes that encode novel protein variants of eight protein families, including aminoglycoside acetyltransferases, rifampin ADP-ribosyltransferases, dihydrofolate reductases, and transporters. Several proteins of the same protein family deviate considerably from each other yet confer comparable resistance. For example, five dihydrofolate reductases sharing at most 44% amino acid sequence identity in pairwise comparisons were equivalent in conferring trimethoprim resistance. We identified variants of aminoglycoside acetyltransferases and transporters that differ in the specificity of the drugs for which they confer resistance. We also found wide variation in protein structure. Two forms of rifampin ADP-ribosyltransferases, one twice the size of the other, were similarly effective at conferring rifampin resistance, although the short form was expressed at a much lower level. Functional metagenomic screening provides insight into the large variability in antibiotic resistance protein sequences, revealing divergent variants that preserve protein function.
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Registered trials
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