ArticleBMC bioinformatics2018
Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Unexplored biosynthetic gene clusters in bacteria isolated from Brazilian stingless bee honey with activity against multidrug-resistant pathogens.Current research in microbial sciences · 2026Article
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- Inositol phosphates as an overlooked phosphorous source in marine ecosystems.The ISME journal · 2025Article
- Effect of the 16S rRNA Gene Hypervariable Region on the Microbiome Taxonomic Profile and Diversity in the Endangered FishMicroorganisms · 2024Article
- Antimicrobial resistance profiles of and associated risk factors forJAC-antimicrobial resistance · 2024Article
- DeGenPrime provides robust primer design and optimization unlocking the biosphere.Bioinformatics advances · 2024Article
- Primer selection impacts the evaluation of microecological patterns in environmental microbiomes.iMeta · 2023Article
- Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioHScientific reports · 2023Article
- State of the Art for Diagnosis of Bacterial Vaginosis.Journal of clinical microbiology · 2023Review
- The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability.Microbial ecology · 2023Review
- In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.Microbiome · 2023Article
- Methods for detection and identification of beer-spoilage microbes.Frontiers in microbiology · 2023Review
- Impact of waterpipe smoking on the salivary microbiome.Frontiers in oral health · 2023Article
- Evaluation of PCR primers to identify Porphyromonas endodontalis in apical periodontitis clinical samples.Archives of microbiology · 2022Article
- Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays.PNAS nexus · 2022Article
- Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics.Frontiers in microbiology · 2022Review
- Modeling Microbial Community Networks: Methods and Tools.Current genomics · 2021Review
- Review
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10 authors.
Funding
Abstract
backgroundTargeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. The accuracy of this approach strongly depends on the choice of primer pairs and, in particular, on the balance between efficiency, specificity and sensitivity in the amplification of the different bacterial 16S sequences contained in a sample. There is thus the need for computational methods to design optimal bacterial 16S primers able to take into account the knowledge provided by the new sequencing technologies.
resultsWe propose here a computational method for optimizing the choice of primer sets, based on multi-objective optimization, which simultaneously: 1) maximizes efficiency and specificity of target amplification; 2) maximizes the number of different bacterial 16S sequences matched by at least one primer; 3) minimizes the differences in the number of primers matching each bacterial 16S sequence. Our algorithm can be applied to any desired amplicon length without affecting computational performance. The source code of the developed algorithm is released as the mopo16S software tool (Multi-Objective Primer Optimization for 16S experiments) under the GNU General Public License and is available at http://sysbiobig.dei.unipd.it/?q=Software#mopo16S .
conclusionsResults show that our strategy is able to find better primer pairs than the ones available in the literature according to all three optimization criteria. We also experimentally validated three of the primer pairs identified by our method on multiple bacterial species, belonging to different genera and phyla. Results confirm the predicted efficiency and the ability to maximize the number of different bacterial 16S sequences matched by primers.
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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.