A professor asked me to design primers for the detection of Pseudomonas spp.. The idea is to detect Pseudomonas reads in cancer samples. According to an article, many bacteria could be potentially involved in cancer besides H. pylori. I am not sure if designing primers will assure the detection of the bacteria since we would with reads. If the objective is to detect Pseudomonas spp. in cancer samples, the bacteria reads from one sample will probably differ from another sample. I am not an expert in primer design so what is your opinion on this topic?
Let's say it is possible to design primers for detection of Pseudomonas spp. in different cancer samples, what would be the in silico approach to accomplish the primer design? I initially thought about analyzing the whole genome sequences of Pseudomonas spp. but the analysis is extremely extensive (for both the average computers and humans). The second strategy I came up with is to analyze specific gene sequences like 16S rRNA. This strategy would analyze several 16S rRNA sequences from the genus to find conserved regions and design primers. Unfortunately, after a quick analysis using MUSCLE for sequence alignment and UGENE for alignment visualization, there are no truly identical sequences between the 288 Pseudomonas sequences I analyzed. Even in "conserved regions", one sequence is different than the others or the conserved region does not fit the ideal primer characteristics (e.g. Tm, length, GC content, less than 4 consecutive G residues, etc). Are universal primers truly universal? What's your ideas on designing universal primers for the identification of bacteria at the genus level?