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Old 01-29-2015, 09:44 AM   #6
n2hasan
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Location: Denver, CO

Join Date: Sep 2009
Posts: 6
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Hello Jennifer,

Is there something specifically that you are interested in? I have made some progress, although not as much as I had hoped, so I might not be able to answer you question(s). I have a conference call with ThermoFisher about the 16S Metagenomics kit later today. As the kit and IonReporter are currently configured, you must analyze the data in a different workflow (Qiime) to really make interesting/relevant comparisons between samples.

The kit is pretty flexible. There are two reaction pools that amplify different sets of the V regions of the 16s, so you can amplify a subset or all depending on if that is necessary for your question(s) of interest. The lab side of the kit ends up being laborious in comparison to going with an adapted 16s V4 analysis on the PGM. I'd much rather set up several sets of PCR, pool then do a single cleanup as opposed to a 2 PCRs, pooling then going through ligating barcodes and all the purification steps done in the Ion library construction. Also, the recommendation of read numbers per sample is really dependent upon your sample complexity and question in mind. Our clinical samples aren't that diverse depending on what taxonomic level of resolution you desire (family, genus vs. species), so we find that you can analyze more samples and use fewer reads than are recommended by ThermoFisher.

Best Regards,

Nabeeh
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