Please advise me on what suitable primers I can use to analyse my 16S rRNA? I will send the sample for ion torrent sequencing hence need a suitable primer (Universal?). I read few paper saying to analyse the V6 region of the genome? But still haven't find the primer sequence yet.
Life Technologies will release a new kit for 16S sequencing on Ion PGM next month. You should talk to them. This kit will cover more than one region.
Best wishes.
We have done a lot of work validating primers on the PGM. In general, I would recommend targeting V1-V2 or V2-V3. We have found these to work the best for the standards we have been using (BEI and our own mock communities). However, it may depend on the type of sample you are working with. Most of our work here was focused on human microbiome associated bugs.
We also have been testing, as part of the early access program, the new Life PGM "Metagenome" kit (as an aside, it is 16S based, so it is not really metagenome, IMO). I would recommend it once it is available. However, one thing to keep in mind. What we have seen in mock communities is that some primers (i.e., variable regions) work much better than others. Hence, pooling reads from multiple primers is not always the best strategy.
One final note, perhaps the best thing Life could do is get read lengths up another 100 or 150bp or so, as they promise with upcoming chemistries. Anyone on the early access for the new isothermal or Hi-Q chemistry? Is that panning out?
Feel free to contact me directly if you would like more information.
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