Has anybody in this group quantified the bacteria (Firmicutes, Bacteroides) in the ileum and feces of mice using the plasmids having 16s rRNA for respective groups cloned inside. I am getting the results in Ct values and quantity of each unknown sample from the different concentrations of plasmid standard run for each group after running qPCR. I want to show the data as absolute number of bacteria in each sample using the log scale. Can anybody suggest how to do that?
I am trying to understand what you are doing here...
Why are you cloning it into a plasmid when you can quantify directly from the community DNA.
As plasmids are mobile elements and varying in numbers within the cell, I don't see the sence in using them for qantification. I would go with Jay and suggest another (direct) approach like pyro sequ or QPCR on species/groups/phyla etc.
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