16S rRNA Gene in Microbial Molecular Identification

Currently, the identification of microbial species is mainly based on genomic information. PCR-based methods are not only faster than traditional culture-based methods but also help identify bacteria that are difficult to grow under laboratory conditions. The sequencing of 16S rDNA is considered to be the "gold standard", because it is present in every prokaryote and allows reconstruction of a global phylogeny. Creative Biolabs focuses on live biotherapeutic product (LBP) development. Our scientists are highly qualified with extensive experience and exceptional skills in the fields of microbial identification.

About the 16S rRNA Gene

The 16S rRNA gene encodes a ribosomal RNA molecule of 30S ribosomal subunit present in all prokaryotic cells, including bacteria and archaea. The 16S rRNA gene is approximately 1500 bases in length and possesses both relatively conserved regions and nine variable regions (V1 through V9), the variable regions range from approximately 50 to 100 bp in length. The variable regions can be specific for a particular group or species, and the commonly used level of similarity to delineate species is 97%.

The schema of ribosome complex and 16S rRNA gene.Fig.1 The schema of ribosome complex and 16S rRNA gene. (Fukuda, 2016)

Bacterial Identification Using 16S rRNA Sequencing

PCR-based bacterial DNA identification by amplification and sequencing of 16S rRNA genes has become a standard molecular approach, both in the laboratory and in clinical settings. The 16S rRNA gene is highly specific to each bacterial species and this makes it an ideal target for identification. Standard methods include PCR amplification of the 16S rRNA gene, followed by sequencing and comparison with known databases for identification.

  • Identification of rare bacteria and bacteria with unusual phenotypic profiles.
  • Identification of slow-growing bacteria.
  • Routine identification.

Flow diagram showing the steps involved in bacterial identification using a 16S rRNA sequencing approach.Fig.2 Flow diagram showing the steps involved in bacterial identification using a 16S rRNA sequencing approach.

Advantages of 16S rRNA

Phylogenetic and taxonomic studies of bacteria using 16S rRNA sequences are currently the most commonly used housekeeping genetic markers for the following reasons:

  • It is universally distributed; It seems to be a good monitor for species differences because it's only weakly horizontally transferred;
  • A large number of sequences have already been determined, at present greater than 1.4 million aligned 16S rRNA sequences are contained within the Ribosomal Database Project II (RDP II) database;
  • The topology of the gene is known;
  • The arrangement of the gene itself allows a variety of different approaches;
  • Ribosomal genes differentiate much more slowly than their flanking sequences.

Researchers have to select a method suitable for their study objective and the analyzed sample, understanding both the advantages and limitations of technologies. In clinical laboratories, 16S rRNA gene sequencing has become increasingly common for identifying biologically identified bacteria or providing reference identification for unusual strains. With our complete suite of microbial genomics solutions for LBP development, Creative Biolabs can be your one-stop-shop. If you are interested in our 16S rRNA sequencing for microbial identification, please contact us for more.

Reference

  1. Fukuda, K.; et al. Molecular approaches to studying microbial communities: targeting the 16S ribosomal RNA gene. Journal of UOEH. 2016, 38(3): 223-232.

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