Which one from them should be used for identification of Lactic acid bacteria
16S rRNA sequencing normally refers to the sequencing of the 16S rRNA gene so you would be sequencing the DNA not the RNA anyways. This approach is very commonly used in metagenomic studies and should be helpful in identifying the types of bacteria you have in your sample including of the lactobacillus genus (lactic acid bacteria). You should look for specific primers that might have been previously optimized to identify the types of bacteria you are investigating. On the other hand, if you actually do want to sequence the rRNA, then the steps will be more complicated and I am not sure how much more it would reveal other than the fact that the 16S genes are actually being expressed (look up the difference between sequencing DNA and RNA).
Muhammad,
please read https://www.researchgate.net/post/What_is_the_difference_between_rDNA_and_rRNA
Its nothing but PCR amplifying and sequencing of ribosomal RNA gene sequence by using 16S rRNA specific primers which binds and amplify its respective genomic DNA.
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