16s metagenomics kit from Ion Torrent


(Magne) #1

Hi,

I analyzed data from human fecal samples generated with the 16s metagenomics kit using Ion Torrent sequencing. The equivalent of OTU table has been generated using the Software Ion Reporter (Thermo Scientific), which I did not done. The analyze diversity revealed lower diversity compared to my preceding analyze that realized with data generated with MiSeq 16s sequencing. I find about 120 bacterial species per human fecal samples instead of 800 Otus…

Any explanations ?
Somebody have a similar experiments ?

Thank you for your contribution.

Best

Fab


(Nicholas Bokulich) #2

Hi @fab,

Comparing OTUs vs. species is like comparing apples and oranges. They are not the same thing, and more than one OTU will correspond to each species so this is expected.

Which OTU table are you generating with QIIME 2? It is not clear what your analysis steps are for each OTU table.


(Magne) #3

Hi Nicholas,
Thank you for your answer.

I agree that bacterial species and OTU are not the same, but I did not think to find a so big difference.

I do not know what parameters were used to generate the table of species obtained with 16s metagenomics kit. I just realized the statistic analyze of data for another lab. In my lab, we use MiSeq 16s sequencing. In the study that we have realized last years, I generated the OTU table using qiime1 , not qiime2.

it was just to know whether other person find similar data…

best

fab