ArticleBMC microbiology2012
Coverage evaluation of universal bacterial primers using the metagenomic datasets.
Article in BMC microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers, 1 of them a synthesis that pooled it.
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Who cites it
94 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analyses of studies of the human microbiota.Genome research · 2013Pooled it
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- SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis.ISME communications · 2023Article
- 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
- Isolation, identification, and significance of salivaryFrontiers in cellular and infection microbiology · 2023Article
- The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth?Molecular ecology resources · 2023Review
- Uncovering Hidden Members and Functions of the Soil Microbiome UsingJournal of proteome research · 2022Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe coverage of universal primers for the bacterial 16S rRNA gene plays a crucial role in the correct understanding of microbial community structure. However, existing studies on primer coverage are limited by the lack of appropriate databases and are restricted to the domain level. Additionally, most studies do not account for the positional effect of single primer-template mismatches. In this study, we used 7 metagenomic datasets as well as the Ribosomal Database Project (RDP) to assess the coverage of 8 widely used bacterial primers.
resultsThe coverage rates for bacterial primers were found to be overestimated by previous studies that only investigated the RDP because of PCR amplification bias in the sequence composition of the dataset. In the RDP, the non-coverage rates for all primers except 27F were ≪6%, while in the metagenomic datasets, most were ≫10%. If one considers that a single mismatch near the 3' end of the primer might greatly reduce PCR efficiency, then some phylum non-coverage rates would change by more than 20%. Primer binding-site sequence variants that could not pair with their corresponding primers are discussed.
conclusionsOur study revealed the potential bias introduced by the use of universal bacterial primers in the assessment of microbial communities. With the development of high-throughput, next-generation sequencing techniques, it will become feasible to sequence more of the hypervariable regions of the bacterial 16S rRNA gene. This, in turn, will lead to the more frequent use of the primers discussed here.
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