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How justifiable is 16S rDNA sequences for taxonomic identification of bacteria?

Image credit: https://www.peoplespharmacy.com/articles/does-your-microbiota-change-when-you-take-nexium

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Nitish
Nitish Nov 26, 2020
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Microbial, especially bacterial taxonomy, is dominated by the comparative analysis of a small stretch of their genomes called 16S rDNA. Since Carl Woese separated Archea as the 'third form of life', ribosomal RNAs have been the major decider of bacterial grouping systematics. In almost every major field related to microbial taxonomy and genomics, it is advisable to compare their ribosomal sequences rather than the whole genome. No doubt it is easy and rapid as compared to the whole genome comparison, but still, it has certain limitations that need to be highlighted.

In the case of bacteria, 16S rDNA is a ~1500 base pair nucleotide stretch in the non-coding region of their genome, and have nine variable regions within it. Moreover, these variable regions are also prone to nucleotide substitution, deletion depending upon their position, and susceptibility to natural forces. Though the ribosomal RNAs are essential for translation purposes and supposed to be conserved in all the microbes. Additionally, they are less prone to mutations as compared to other parts of the genome. But that does not mean they are also efficient in classifying the microbes. However, it is ok to restrict the 16S rDNA sequence analysis for genus-level classification, but there are so many reports where the authors have used this stretch to classify the microbes up to the strain also. Which is in my opinion, not a rational approach.
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Only 16S analysis is not reliable if the similarity is more than 97%

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Shubhankar Kulkarni
Shubhankar Kulkarni Nov 27, 2020
Some bacterial species that have been studied in great detail are similar to others in their genetic makeup to about 98 or 99%. For example, there are separate species from the genii pseudomonas, rhizobacteria, or corynebacterium with a similarity of more than 98% but are still two distinct species.

The International Code of Nomenclature of Prokaryotes (ICNP) is constantly updated and it dictates the necessary assays to be conducted in order to record a novel species. Additional methods used to correctly identify (distinguish between) bacterial species are:
  1. Sequencing the housekeeping genes: Sometimes, 16S sequences may match perfectly but the housekeeping gene sequences do not. They are then used to identify species.
  2. Whole-genome sequencing: With sequencing techniques readily available and the reduced cost of sequencing, the entire genomes are sequenced, so that the researchers can play around looking at different genes specific only to that genus for further detailed identification.
  3. Chemotaxonomy: The polar lipid content and the fatty acid content are some of the criteria used to identify a species.
  4. Biochemical analysis: To detect the presence of certain enzymes, such as catalases, oxidases, ureases, gelatinases, etc., that are produced by the bacteria.
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