Species level identification in oral microbiome samples?

[JenBarb]

Hello,
I am new to the area of microbiome sequencing so any thoughts/ideas/suggestions here would be greatly appreciated however my main question is the following: Is it possible to get species level detail for oral microbiome samples when sequencing the V4 region only? If yes, what are the best bioinformatic tools to use?

We will be using the Illumina sequencing platform for our samples. Are there any thoughts regarding using Illumina Genome Analyzer vs Ion Torrent for sequencing?

Thank you so much for any thoughts regarding these topics.
-Jennifer

[ZWB]

I think in most cases you will have a hard time getting to the species level using just the V4 region. With Illumina's 600 cycle kit for the MiSeq it's now possible to sequence V1-V3 or other longer regions that will lead to greater species level identification. We typically use UPARSE and/or QIIME to analyze our 16S metagenomic data and have so far been fairly satisfied with the results. I should note that only the MiSeq has the 600 cycle kit, so you won't be able to use a GA to sequence the longer regions.

Zach

[JenBarb]

ZWB, Thank you for your reply. We do not have the option for MiSeq. I am on the data processing end of our project but we are trying to determine the best cost/benefit ratio for the lab work. Apparently we have the option to use either Genome Analyzer or Ion Torrent. Do you know if we would be able to get species detail by sequencing the V3-V4 together? or if there are primers developed for that?
I have been reading up on QIIME but have not heard about UPARSE. I will have to check that out as well.