Can I use Single strand 16S rDNA sequencing to identify lactic acid bacteria up to species level with similarity percentage?
Sequencing of whole 16S rRNA gene should be enough for rough identification. However, similarity of this gene among genus Lactobacillus can be too high for precise identification of species. In that case sequensing of other genes (recN, spo0A, groL, etc) is recommended together with biochemical tests.
Hi Mohammad,
Depending on the complexity of the bacteria (i.e. pure culture vs mixed culture) you can absolutely use 16S rDNA sequences. Depending on the complexity, you could use either Sanger sequencing (for pure isolates) or pyrosequencing/Illumina MiSeq for complex cultures.
As pointed out above, if your particular genus of interest is not well resolved based on 16S rRNA genes, you might want to utilize other molecular markers. When analyzing mixed microbial communities, a similarity cutoff of 97% is commonly used for species-level resolution, however for highly similar species/sequences a 99% similarity cutoff may be more appropriate. You will get the taxonomic assignment of all the 16S rRNA gene sequences in your samples based on a reference database (like greengenes).
If you need more information, you can visit the Earth Microbiome Project website at:
http://www.earthmicrobiome.org/
It may have some useful information and clarifications regarding the technique.
Kind regards,
Riegardt Johnson
I hope my this article may help you out.
https://www.researchgate.net/publication/281176309_Identification_of_Lactobacillus_pentosus_and_Weissella_confusa_isolated_from_Uttapam_batter_fermented_with_Piper_betle_leaves
Article Identification of Lactobacillus pentosus and Weissella confu...
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