Review and re-analysis of domain-specific 16S primers.

By G. C. Baker, Jacques J. Smith, D. Cowan. Journal of Microbiological Methods, 2003

1,890 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/cfc8b8e4434c9580ffef75e141c04fbbfe7f023a

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Citations in the corpus

Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar (2014, methodology): “To amplify the V4-V5 hypervariable regions of 16S rRNA genes for pyrosequencing, universal primers 519F (50-CAGCMGCCGCGGTAATWC-30) and 926R (50-CCGTCAATTCMTTTRAGTT-30)were used in PCR (Baker et al., 2003).”
Testing the functional significance of microbial community composition. (2009, background): “This primer pair amplifies small subunit rRNA genes from all three domains (Archaea, Bacteria, and Eukarya) (Baker et al. 2003, Cullen and MacFarlane 2005, Martiny et al. 2006) yielding a PCR product that is 850–1100 base pairs (bp) in length.”
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies (2012, background): “Using suboptimal primers, or more precisely, primer pairs, can lead to under-representation (14) or selection against single species or even whole groups (15–17).”
Current challenges and best-practice protocols for microbiome analysis (2019, methodology): “The most commonly used target gene for bacterial identification is 16S rRNA (or 16S rDNA), which is the gold standard in microbial typing [15, 16].”
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions (2010, positive): “As compositional studies like these depend on amplicon generation, they are subject to PCR bias of varying degrees (13,14).”
Pyrosequencing analysis of the Oral Microflora of healthy adults (2008, methodology): “Primers were designed to provide the best combination between a high phylogenetic recovery and limited distance to the V6 hypervariable region (Baker et al., 2003; Horz et al., 2005).”
Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis (2016, methodology): “Referring to the previous studies [11, 12], 10 markers located in conserved regions of the 16S rRNA genes were selected to divide the full-length aligned 16S rRNA sequences into nine sub-regions (Additional file 1: Table S1).”
Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies (2009, methodology): “Using the RDP classifier and the BLAST program, Baker et al. (2003) and Huws et al. (2007) have investigated the species specificity and coverage spectrum of the known primers.”
Disentangling the spatial patterns in community composition of prokaryotic and eukaryotic lake plankton (2011, methodology): “For the tRFLP analysis, PCR amplification of 16S ribosomal genes was achieved by using primers FAME8F (FAM-59-AGAGTTTGATCCTGGCTCAG-39) and E939R (59-CTTGTGCGGGCCCCCGTCAATTC-39) (Baker et al. 2003) with reaction conditions optimized for the enzyme DyNAzyme II (Finnzymes).”
A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. (2007, background): “…specificity Each hypervariable region of the 16S rRNA gene is flanked by a conserved sequence (Baker et al., 2003); this has made it possible to design “universal” PCR primers that can amplify 16S rRNA hypervariable regions from a large number of different bacterial species (Baker et al., 2003).”
Linking microbial communities, functional genes and nitrogen-cycling processes in forest floors under four tree species (2016, neutral): “677 678 Primer Target Primer Name Primer Sequence (5’-3’) Reference All Bacteria (16S rRNA) 519F 907R CAG CMG CCG CGG TAA NWC CCG TCA ATT CMT TTR AGTT Baker et al. (2003) Muyzer et al. (1995) All Fungi (ITS) ITS-1F 5.8s TCC GTA GGT GAA CCT GCG G CGC TGC GTT CTT CAT CG Gardes and Bruns (1993) Vilgaly”
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. (2009, background): “However, several other regions are also in use (Baker et al. 2003; Edwards et al. 2006; Sogin et al. 2006; Huse et al. 2007; Roesch et al. 2007; Andersson et al. 2008).”
Examining the global distribution of dominant archaeal populations in soil (2011, methodology): “These primers have been shown to effectively amplify a broad range of archaeal groups when using an optimized cycling protocol (Baker et al., 2003), which we used here.”