We isolated bacteria from various samples. It is identified by biochemical tests as Lactobacillus spp. Now we are going to sequencing it for species level identification. I'm a little confused about the selection of the correct primer for PCR. If anyone would know of one, I'd appreciate it!
Marimuthu,
I suggest that you better start with 16S rRNA sequencing see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC120105/ and http://www.ajol.info/index.php/ajb/article/viewFile/71377/60327 or http://onlinelibrary.wiley.com/doi/10.1016/j.femsle.2004.08.049/pdf), and after proving that you bacteria belong to Lactobacillus - MLST as described by http://mic.sgmjournals.org/content/157/3/727.full.pdf
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2075077/
You shold create a library by cloning digested fragment of the bacterial genome in cloning vectors. than you can sequence by using universal primers.
Marimuthu,
I suggest that you better start with 16S rRNA sequencing see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC120105/ and http://www.ajol.info/index.php/ajb/article/viewFile/71377/60327 or http://onlinelibrary.wiley.com/doi/10.1016/j.femsle.2004.08.049/pdf), and after proving that you bacteria belong to Lactobacillus - MLST as described by http://mic.sgmjournals.org/content/157/3/727.full.pdf
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2075077/
You can follow Alex.... 16s rRNA can give you clear species level identification...
you can use universal 16S rRNA primer ( 27F;AGAGTTTGATCMTGGCTCAG, 1492R;GGTTACCTTGTTACGACTT)
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