16S rRNA and the Strategy Used in Bacterial Identification

The topic I made here is not as new and is well known among Microbiologists, although specifically including the conserved sequence present in 16S rRNA as the major part of this topic. 16S rRNA the component of smaller subunit of prokaryotic ribosome, used highly in phylogenies after the major introduction made by Dr. Carl Woese and George E. Fox. Ribosome, a major protein complex which helps in the protein synthesis (translation) consists of two units, larger (50S) and the smaller subunit (30S), together making complete 70S [S stands for the Svedberg Unit, a non-SI unit for sedimentation rate]. In this smaller subunit, there is the presence of 16S rRNA which has the signature sequence for the bacterial identification.

Multiple sequences are present in 16S rRNA of a single bacterium. Signature sequences are specific conserved sequences that are always found in all groups of organisms. The sequences which we name it as unique are present in specifically 16S rRNA region, of 5-10bases long. This helps in the major identification of prokaryotic organisms, archea and eukarya. The average length of the 16S rRNA gene is 1522bp. Previously culturing and the biochemical tests used to be used in the bacterial property identification has been set back after the use of the recent diagnostic techniques. Nucleic acid detection method has overcome the limitations in conventional microbiological methods. [1] Recently NGS-based 16S rRNA sequencing has been cost effective technique for the bacterial identification.

Strategies used using 16S rRNA for Bacterial Identification:

  1. Ribosomes containing 16S rRNA are present in all cells.
  2. RNA genes are highly conserved.
  3. Nucleic Acid detection method is the first and efficient technique.

Universal Primers used for 16S rRNA sequencing[2]:

Primer Name 5’ to 3’ Sequence
8F AGA GTT TGA TCC TGG CTC AG
U1492R GGT TAC CTT GTT ACG ACT T
928F TAA AAC TYA AAK GAA TTG ACG GG
336R ACT GCT GCS YCC CGT AGG AGT CT
1100F YAA CGA GCG CAA CCC
1100R GGG TTG CGC TCG TTG
337F GAC TCC TAC GGG AGG CWG CAG
907R CCG TCA ATT CCT TTR AGT TT
785F GGA TTA GAT ACC CTG GTA
805R GAC TAC CAG GGT ATC TAA TC
533F GTG CCA GCM GCC GCG GTA A
518R GTA TTA CCG CGG CTG CTG G
27F AGA GTT TGA TCM TGG CTC AG
1492R CGG TTA CCT TGT TAC GAC TT

 

[2]Based on the availability of large number of 16S rRNA sequences, along with NCBI’s databases there are multiple other databases which are widely used. They are:

  1. EzTaxon-e contains complete hierarchical taxonomic structure (from phylum rank to species rank) for the domain of bacteria and archaea.

http://eztaxon-e.ezbiocloud.net/

  1. Ribosomal Database Project. http://rdp.cme.msu.edu/
  2. SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
  3. The greengenes web application provides access to the 2011 version of the greengenes 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.

References

  1. 16S Ribosomal RNA Sequencing. Microbiology Virtual Lab, Amrita University Data. http://amrita.vlab.co.in/?sub=3&brch=76&sim=1421&cnt=1
  2. 16S Ribosomal RNA – Wikipedia. http://en.wikipedia.org/wiki/16S_ribosomal_RNA
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About Saumyadip

Science Communicator and Biologist. Keep interests in host-pathogen interaction research. Specifically bacterial infection mechanism, host infection evasion and immune susceptibility of host. Working as Senior Research Fellow at Thrombosis Research Institute, Bangalore.
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