Blog of Jonathan Eisen, Professor at UC Davis, Open Science advocate, Guardian of Microbial Diversity, Fighter of #Badomics Words and Microbiomania , and YAMMMs . Plus lots more things. See Lab Page and Twitter @phylogenomics for more info.
I have seen these papers cited when correcting for rRNA gene copy number:Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) rrndb: theRibosomal RNA Operon Copy Number Database. Nucl. Acids Res., 29,181-184.Lee ZM-P, Bussema C, Schmidt TM (2009) rrnDB: documenting the numberof rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res, 37,D489-D493.However, I wonder if anyone has ever thought about how ploidy would affect 16S rDNA qPCR? For example:http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016392If some species typically have 20 genome copies per cell and others have 1 genome copy per cell, this would make conversion of gene copy numbers to cells pretty much impossible unless you measure the ploidy for every species in your system. And if you don't do the conversion, then what do gene copy numbers mean?
Thanks .. and agree that ploidy could be a big big big problem.