Recently, I've stumbled upon a fact, which hasn't bothered me for many years. The fact is that all universal 16S primers are written as "[FR][0-9]+" (in regex notation), that is they have a position with respect to a reference. I've read through many papers, wherein these primers were introduced, and most of the time the authors say nothing but "E. coli 16S". Anyway, in one case I've found that it is in fact the reference K12 E. coli. But the problem is that it has 7 distinct rRNA operons: rrnA, rrnB, rrnC, rrnD, rrnE, rrnF, rrnG. Do you have a reference showing a particular operon used for the 16S position notation?

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Figure 2. Hypervariable regions within the 16S rRNA gene in Pseudomonas . The plotted line reflects fluctuations in variability amongst aligned 16S rRNA gene sequences of 79 Pseudomonas type strains... (Bodilis et al., 2012)

  • $\begingroup$ Are you sure they differ in sequence at the primer? The sequences of the structural parts of the genes are apparently almost identical. Have you checked GenBank? $\endgroup$ – David Mar 27 '17 at 16:34
  • $\begingroup$ @David I haven't checked that myself, but here is a relevant reference ... or the same strain may have multiple copies of the 16S rRNA gene that differ by 5% for some regions (such as Escherichia coli K12 [12])... (Nguyen et al., 2016) $\endgroup$ – Eli Korvigo Apr 21 '17 at 10:38
  • $\begingroup$ I suspect the primers will be for conserved regions, but don't know. $\endgroup$ – David Apr 21 '17 at 12:05
  • $\begingroup$ @David the primers used in 16S studies usually target one of the hypervariable regions. $\endgroup$ – Eli Korvigo Apr 21 '17 at 12:08
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    $\begingroup$ No David, you were correct in the first place. The primers are placed in extremely conservative regions that flank hypervariable regions. (you were both right) $\endgroup$ – Karl Kjer Nov 17 '17 at 12:18

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