Hello Anjali Patil

16S ribosomal RNA would be a better technique for molecular characterization of bacteria. Sequence analysis of the 16S ribosomal RNA (rRNA) gene has been widely used to identify bacterial species and perform taxonomic studies. Bacterial 16S ribosomal RNA genes contain nine hypervariable regions (V1 – V9) that demonstrate considerable sequence diversity among different bacteria. Species-specific sequences within a given hypervariable region constitute useful targets for diagnostic assays and other scientific investigations.

It is important that you identify the regions within the target gene that supply the most taxonomic information in the smallest stretch of nucleotides. Also, the benefit of small amplicon size would include increase assay sensitivity.

You could use PCR with universal or specific primers to initially amplify the 16S rRNA genes of bacteria before being sequenced to help in the identification of unknown or novel bacterial species.

You may want to refer to the paper attached below for more information. It may be helpful.

Article A detailed analysis of 16S ribosomal RNA gene segments for t...

In addition to genomic characterization you would also want to look into the phenotypic characterization by characterizing on the basis of colony morphology, Gram’s reaction, sporulation test, motility tests, enzymatic reactions, and biochemical tests. Additionally, antibiotic sensitivity test and detection of enterotoxin either by ELISA or PCR could also be made a part of the study.

You may want to refer to the paper attached below for more information on the phenotypic characterization.

https://www.frontiersin.org/articles/10.3389/fmicb.2020.599606/full

Best.

I think it is important to be clear that when you are studying the sequence of the 16s RNA when you actually sequence the 16s DNA gene. So there is no need to actually look at the RNA itself, you only need to look at the DNA for the 16s gene.

To simplify what is said above by Michael J. Benedik

• There is no difference, it is not 16S rRNA, but it is 16S rRNA gene which is DNA sequence. There is no such thing like 16S rDNA.

If you ask this question, it is very clear that you lack basic understanding of the topic, thus I would suggest to pause and learn basics before doing anything experimentally or designing any study.

Abhijeet Singh Sir thanks for your suggestion.

But I had this doubt only after reviewing so many research papers. Some scientists used the 16Sr DNA technique as well for the molecular characterization of thermophilic bacteria. In fact I had thought the same before that no such thing exist like 16S rDNA, But it is.

Sorry for that typing error but my doubt was genuine and your opinion would be beneficial for me . So it would be a great help if you,ll give your valuable suggestions.

Thank you.

Michael J. Benedik

Thank you sir.

All those terms are different ways of saying the same thing, characterizing The 16S rRNA gene. So you are looking at the DNA of the gene in order to infer the RNA sequence.