I want to know the Relative abundance of Antimicrobial Resistance Genes by qPCR (I Will compare the abundance of ARGs and the abundance of bacteria in my sample). I Will use ARGs primers and 16s rRNA. I do not want to know the expression of the genes. Which method should I use, relative quantification (by livak method) or absolute quantification?
Thank you for the answer
If you are intersted in quantifying how many copies of the gene are present in the bacterial genome, it would be better to perfrom absolute quantification. you would need a generate a standard curve for this. Also, if you are using 16s rRNA as control, you would need to know the copy numbe of 16S rRNA in the bacterial strain you are using. I would suggest that you use Single-Copy Genes as control, so that the control gene copy number directly correspond to the number of bacterial genomes in your sample.
Alternatively if you only want to compare the gene copy number in different strains just perfrom qPCR without standard curve and present results as ratio of resistence gene to single-copy gene (can also be rRNA gene).
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