ArticleJournal of applied microbiology2017
16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria.
Article in Journal of applied microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 2 of them syntheses that pooled it.
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Who cites it
34 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Changes in the fecal microbiota of breast cancer patients based on 16S rRNA gene sequencing: a systematic review and meta-analysis.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2024Pooled it
- Microbiota and seminal quality: A systematic review.JBRA assisted reproduction · 2023Pooled it
- The diagnostic potential of combined quantitative polymerase chain reaction and next-generation sequencing using the same primers for periprosthetic joint infection.Microbiology spectrum · 2026Article
- Biodiversity and Natural Product Potential of Indonesian Actinomycetes.Journal of microbiology and biotechnology · 2026Review
- Temporal microbiome dynamics and fish health-associated dysbiosis in freshwater aquarium systems: a case study from River Wonders Singapore.Frontiers in microbiology · 2026Article
- Detection of Gram-positive and Gram-negative bacteria in brain abscesses by 16S rRNA in situ hybridization.Journal of neuropathology and experimental neurology · 2025Article
- The utility of 16S rRNA gene sequencing on intraoperative specimens from intracranial infections: an 8-year study in a regional UK neurosurgical unit.British journal of neurosurgery · 2024Article
- Preliminary profile of the gut microbiota from amerindians in the Brazilian amazon experiencing a process of transition to urbanization.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- On-Site Inactivation for Disinfection of Antibiotic-Resistant Bacteria in Hospital Effluent by UV and UV-LED.Antibiotics (Basel, Switzerland) · 2024Article
- Potato Resistant Starch Type 1 Promotes Obesity Linked with Modified Gut Microbiota in High-Fat Diet-Fed Mice.Molecules (Basel, Switzerland) · 2024Article
- Establishment of a mandible defect model in rabbits infected with multiple bacteria and bioinformatics analysis.Frontiers in bioengineering and biotechnology · 2024Article
- Evaluation of 16S rRNA genes sequences and genome-based analysis for identification of non-pathogenicFrontiers in microbiology · 2024Article
- Research progress on the application of 16S rRNA gene sequencing and machine learning in forensic microbiome individual identification.Frontiers in microbiology · 2024Review
- Microbiologically influenced corrosion of AISI 202 and 316L stainless steels under manganese-oxidizing biofilms.3 Biotech · 2024Article
- The Metabolomics Changes in Luria-Bertani Broth Medium under Different Sterilization Methods and Their Effects onMetabolites · 2023Article
- The first taxonomic and functional characterization of human CAVD-associated microbiota.Microbial cell (Graz, Austria) · 2023Article
- Virulence factors and mechanisms of paediatric pneumonia caused by Enterococcus faecalis.Gut pathogens · 2023Article
- Comparative study of multiple approaches for identifying cultivable microalgae population diversity from freshwater samples.PloS one · 2023Article
- Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes.Genes · 2022Article
- Automated 16S Sequencing Using an R-Based Analysis Module for Bacterial Identification.Microbiology spectrum · 2022Article
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Authors and funding
9 authors.
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Abstract
aimsTest the choice of 16S rRNA gene amplicon and data analysis method on the accuracy of identification of clinically important bacteria utilizing a benchtop sequencer. METHODS AND
resultsNine 16S rRNA amplicons were tested on an Ion Torrent PGM to identify 41 strains of clinical importance. The V1-V2 region identified 40 of 41 isolates to the species level. Three data analysis methods were tested, finding that the Ribosomal Database Project's SequenceMatch outperformed BLAST and the Ion Reporter Metagenomics analysis pipeline. Lastly, 16S rRNA gene sequencing mixtures of four species through a six log range of dilution showed species were identifiable even when present as 0·1% of the mixture.
conclusionsSequencing the V1-V2 16S rRNA gene region, made possible by the increased read length Ion Torrent PGM sequencer's 400 base pair chemistry, may be a better choice over other commonly used regions for identifying clinically important bacteria. In addition, the SequenceMatch algorithm, freely available from the Ribosomal Database Project, is a good choice for matching filtered reads to organisms. Lastly, 16S rRNA gene sequencing's sensitivity to the presence of a bacterial species at 0·1% of a mixture suggests it has sufficient sensitivity for samples in which important bacteria may be rare. SIGNIFICANCE AND IMPACT OF THE STUDY: We have validated 16S rRNA gene sequencing on a benchtop sequencer including simple mixtures of organisms; however, our results highlight deficits for clinical application in place of current identification methods.
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