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What is 16S rRNA?

16S ribosomal RNA (or 16S rRNA) is the component of the 30S small subunit of a prokaryotic ribosome, roughly 1500 base pairs. Figure 1A shows how 16S rRNA is involved in a prokaryotic ribosome. The bacterial 16S rRNA gene contains nine hypervariable regions (V1-V9) ranging from 30-100 base pairs, flanked by conserved regions (Figure 1C). You can find 16S rRNA sequences in databases such as Ribosomal database project (RDP), Greengenes database, Silva, and Human microbiome project (HMP).

(A) (B)
3 The 2D and 3D structure of the 16S rRNA gene. Individual regions are shown in the same color
 The regions and primers of 16S rRNA.

Figure 1. 16S rRNA gene. (A) The involvement of 16S rRNA gene in a prokaryotic ribosome. (B) The 2D and 3D structure of the 16S rRNA gene. Individual regions are shown in the same color (Yang et al. 2016). (C) The regions and primers of 16S rRNA.

16S rRNA as molecular marker

16S rRNA gene is characterized by ubiquity and evolutionary properties, which allow it to become an important molecular marker in microbial ecology. Carl Woese and George E. Fox pioneered the use of 16S rRNA in phylogenetics. And according to Yang et al. (Figure 2), red regions (V2 and V8) have a poor phylogenetic resolution at the phylum level. Green regions (V4, V5, and V6) are associated with the shortest geodesic distance, which implies that they may be the optimal choice for phylogeny-related analyses, including phylogenetic analysis of novel bacteria phyla.

Illustration of different variable regions (Yang et al. 2016).

Figure 2. Illustration of different variable regions (Yang et al. 2016).

16S rRNA sequencing

Since 16S rRNA gene is conserved in bacteria, and contain hypervariable regions that can provide species-specific signature sequences, 16S rRNA sequencing is widely used in identification of bacteria and phylogenetic studies. 16S rRNA sequencing is featured by fast speed, cost-efficiency, and high-precision. It has been widely applied in basic research, as well as medical, forensic, agricultural, and industrial microbiology.

The workflow of 16S rRNA sequencing for human microbiome analysis

Figure 3. The workflow of 16S rRNA sequencing for human microbiome analysis.

16S rRNA sequencing generally uses the next/third generation sequencing technology to read the PCR products which are amplified with suitable universal primers of one or several regions of 16S rRNA. The common sequencing platforms for 16S rRNA sequencing include Illumina MiSeq, Roche 454, Illumina MiSeq/HiSeq, and Pacific Bioscience. The former three platforms only cover 100 to 600 base pairs per single read, while the Pacific Bioscience can produce full-length 16S rRNA.

Table 1. The common 16S rRNA sequencing regions by various platforms.

Platform Common Sequencing regions
Illumina MiSeq V3-V4, about 428 bp
Roche 454 V1-V3, about 510 bp;
V3-V5, about 428 bp;
V6-V9, about 548 bp
Illumina HiSeq V4, about 252 bp
Pacific Bioscience V1-V9 (full-length), about 1500 bp

Advantages and applications of 16S rRNA sequencing

  • Identification and taxonomic classification of bacterial species
  • Discovery of novel pathogens
  • Phylogenetic classification
  • Metagenomic survey of bacterial populations
  • Clinical microbiology


  1. Case R J, Boucher Y, Dahllöf I, et al. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Applied and environmental microbiology, 2007, 73(1): 278-288.
  2. Yang B, Wang Y, Qian P Y. Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. BMC bioinformatics, 2016, 17(1): 135.
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