How do single nucleotide variations in the 16S rRNA gene affect the accuracy and sensitivity of microbial identification using 16S rRNA sequencing?
The question is incomplete if you do not provide how would you generate the sequence data. If is is short amplicon seq or full length. And at what taxonomic level you want to go.
Agree with comment above. You also take into consideration other factors such as the choice of database, sequencing chemistry and OTU clustering parameters (similarity % etc). So the short answer is "it depends".
For the nature of microorganisms itself and how the incorporate DNA from other microorganisms it is very difficult to exactly identify strains from the same species, even at genus level we can find 100% or near 100% of identity in 16S sequences from different genus. And the opposite, since some microorganisms have more than one 16S molecules, those from the same species are more different between them than with the 16S of another species or even genus.
Try this new 16S database with all sequences on it identified at species level and without redundancy, so the size is up to 10 times less than the common ones (SILVA, GTDB, RDP, Greengenes).
https://mimt.bu.biopolis.pt
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