A number of molecular techniques have been recommended for accurate species identification and strain typing of LAB species. We are aware of the draw backs of 16SrRNA typing. I have used several other techniques too but if someone has vast experience in this field would they help me identifying the most suitable and of course economical. Kindly suggest solutions?
Dear Dr. Naheed Mojgani,
For strain typing it is suggested 16S rRNA gene sequence analysis. The multiplex PCR assay can also be tried where in case the 16 S rRNA gene analysis is sufficient to differentiate among species. For strain differentiation RAPD is suggested.
For probiotic traits typing, you should follow the WHO/FAO guidelines. The essential probiotic traits include pH and bile tolerance under gut physiological conditions. The strains should have other characteristics such as antagonistic to harmful pathogens of food borne microbes. Strains should have capacity to colonize in the gut. Besides, the strains with beta-galactosidase production ability and cholesterol assimilating ability is always preferable.
Regards,
A K Dubey
You might check out Multilocus Sequence typing. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837765/ for a Lactobacillus-specific example. Good luck!
Hi Naheed: below is a link to one of our papers on molecular and probiotic profiling of LAB strains.
https://tspace.library.utoronto.ca/bitstream/1807/70634/1/cjm-2015-0481.pdf
Best regards