Comparison between V3V4 and full-length sequencing of 16S rRNA genes

Erroneous DNA G+C content data determined by HPLC and thermal melting experiments are no longer required for species descriptions
03/24/2016
16S rRNA and 16S rRNA Gene
05/15/2017

Comparison between V3V4 and full-length sequencing of 16S rRNA genes

Microbiome taxonomic profiling (MTP) is a method to elucidate taxonomic composition of the complex microbial community. The currently available and widely used NGS platforms are Illumina MiSeq (pair-end 250 bp) targeting V3V4 region and Pacific Biosciences (PacBio) targeting full-length. Here, we give statistics on lengths of amplicons.

Various PCR primers that are frequently used to parts of 16S rRNA gene are given here.

The amplification of primers used by ChunLab are:

  • MiSeq primers targeting V3V4 region of Bacteria
341F CCTACGGGNGGCWGCAG
805R GACTACHVGGGTATCTAATCC
  • PacBio primers targeting full-length 16S rRNA of Bacteria
27F AGRGTTYGATYMTGGCTCAG
1492R RGYTACCTTGTTACGACTT

Statistics of amplicon lengths

The lengths were calculated from reference sequences included in EzBioCloud 16S databases (Yoon et al. 2017). The values are without primers.

 

Last Updated Mar. 20, 2017 (JC)

Jon

Jon is a scientist & entrepreneur dedicated to developing bioinformatics related to bacterial systematics, genomics, and microbiome. He is a professor at Seoul National Univ. and founder of ChunLab, Inc. He is best known as a creator of EzBioCloud (formerly EzTaxon) database, and recipient of Bergey Award.
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