Identification of Bacterial Species by Combined Bioinformatic and Polymerase Chain Reaction

Abstract

The identification will be carried out by comparing a potential PCR product obtained from an unknown species with other PCR products specific to 5 known species, using the same five set of pairs of primers specific of these five species respectively. This implies that each PCR product obtained for each species has to be specific to each species and can be considered as a marker in this exercise. This specificity will be based on the uniqueness of the chosen template that is to be used for each PCR. In addition, since the PCR products will not be sequenced, they will be differentiated by their size, which will be identified by agarose gel electrophoresis. The PCR product can only be used as a marker that defines a species if the amplified sequence is unique to this species. Therefore, the first step in this exercise will be to identify a suitable sequence to amplify for each species. Following the identification of a suitable template, the size of the PCR will have to be defined; since the comparative analysis will be based not only on the presence of a product but also its size, all PCR products should have different sizes identifiable on agarose gel. Since the size of a PCR product is defined by the location of primers along the sequence, the second step in this exercise will be to design suitable primers. Finally, having defined specific template and primers for each species, PCR will be carried out using the DNA of unknown species as a template with all five sets of primers so that a successful PCR product and its size would identify the unknown species as one of the five species.