I have isolated DNA from a fermented food sample so I also have to design a primer and run PCR. What is the average size of LAB?
It depends fro which purposes you are doing the pcr and for which analysis..eg:sequencing of 16S rDNA for identification of the isolates..with universal primers you will have sequences of 750 bp.
“What is the average size of LAB?” What do you mean with this question? If you mean the average size of the whole genome, it largely depends on the species you are considering (several lactobacilli are from 2 to 3 Mb). If you mean the dimension of a PCR product, there isn't an average size: it depends by the region of the gemone that you want to amplify. If you want to amplify 16 rDNA with universal primers for taxonomic identification (for instance with 27f 5’-AGAGTTTGATCMTGGCTCAG-3’ and 1525r 5’-AAGGAGGTGWTCCARCC) you will obtain an about 1500 bp amplicon. You will get this size from any possible bacterium (1.5 kb is the size of 16s rDNA of all bacteria).
Forward- 16SF, 5 -AGAGTTTGATCCTGGCTCAG-3 ;
Reverse- 16SR, 5 -CTACGGCTACCTTGTTACGA-3
i have used this paper primer Scarpellini, M., Mora, D., Colombo, S., & Franzetti, L. (2002). Development of Genus / Species-Specific PCR Analysis for Identification of Carnobacterium Strains. Pharmacia, 45, 24-29.
as it widely referred ad used them and i had got one band from 8 isolates ..so what is the Mb should should i expect?
With the primers you indicated (16SF and 16SR) you obtain an amplicon of about 1500 bp (i.e. 1.5 kb) from any possible bacterium. Based on the reference you mentioned, you are probably working with carnobacteria. So, considering, for instance, strain Carnobacterium sp. 17-4, you can get exactly a 1527 bp amplicon from this strain.
Dr.Simone i kinda checked about Primers used in a lot of papers referred they had either used this paper .
1.Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–176. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
which i was not able to access
2.The second hit was the paper that i had mentioned before that was widely referred for identification of Lactic acid bacteria
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