# Multiple regions of 16S rRNA
**URL:** https://forum.qiime2.org/t/multiple-regions-of-16s-rrna/16670
**Category:** User Support
**Created:** [September 22, 2020, 11:58pm UTC](https://forum.qiime2.org/t/multiple-regions-of-16s-rrna/16670 "2020-09-22T23:58:58Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@mshahin](https://forum.qiime2.org/u/mshahin)
#### Post date: [September 22, 2020, 11:58pm UTC](https://forum.qiime2.org/t/multiple-regions-of-16s-rrna/16670/1 "2020-09-22T23:58:58Z")
Hello,
I am facing a problem with 16s rRNA (7 hypervariable regions) sequence data analysis. I analyzed the data (fastq files) with Qiime2 using ASV approaches but finally didn't identified species levels. Mostly it says uncutured bacteria. I used updated Silva database to compare. Whereas, using the same data I received species level identification from the ion reporter (Thermofisher Scientific). They said they used Green gene database. And their approach was OTU, not ASV. Why the same data did show different results?
Akthough this is well known that green gene database is not updated regularly and OTU approach is a back dated method, my question is why I was unable to identify at species level using Silva database and ASV approach?
Please help me with your expert advice and discussion. Thanks!
Shahin
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [September 23, 2020, 9:05am UTC](https://forum.qiime2.org/t/multiple-regions-of-16s-rrna/16670/2 "2020-09-23T09:05:08Z")
Hi @mshahin,
I think there are a couple things going on. My suspecion is that Thermo-Fisher has adapted the Greengenes database and done some custom classification to improve resolution. (Against the license, but 🤷♀️? Where as Silva has fewer classified sequences because it's a more general database. To be honest, I'd want to know more about how Thermo-Fisher developed their database, but I suspect that's proprietary. You may want to look at the previous thread about the Thermo-Fisher sequencing, if you haven't checked it out yet:
[https://forum.qiime2.org/t/possible-analysis-pipeline-for-ion-torrent-16s-metagenomics-kit-data-in-qiime2/13476/84](https://forum.qiime2.org/t/possible-analysis-pipeline-for-ion-torrent-16s-metagenomics-kit-data-in-qiime2/13476/84)
And some further discussion/comparison of databases
> [@Why is NCBI not used for training classifiers?](https://forum.qiime2.org/t/why-is-ncbi-not-used-for-training-classifiers/14743):
>
> So maybe I am misunderstanding but from what I have seen people always using either GreenGenes or SILVA. Is there a reason why people don't use NCBI for classifiers? Also do people normally update their classifiers with every new release of SILVA? Just trying to get a better idea on the logic behind classifier things!
> [@reference databases: SILVA vs. Greengenes vs. GTDB](https://forum.qiime2.org/t/reference-databases-silva-vs-greengenes-vs-gtdb/14778):
>
> Sorry just another question that has stemmed from this! I know in the past that SILVA was viewed as being a better option than others (such as GreenGenes) but what about ones such as GTDB? I imagine the database choice is going to largely influence the classified taxonomy output so want to make sure that I make educated choices!
> [@What is the difference between Greengenes and SILVA?](https://forum.qiime2.org/t/what-is-the-difference-between-greengenes-and-silva/1560):
>
> Dear Sir, Thank you for your support. It took me to 12 hours to set my classifier(Greengenes99%OTS) the recent one. I used the commands that you have sent to me. Every thing is fine now. Finally I got ref.seqs.qza file. I have a final question what is the difference between Greengenes99% and Silva123 and 128 databases. Will they give information upto species level? Some say you should choose Silva and some say you should choose Greengenes? Could you elaborate? I would be thankful. With best re…
Best,
Justine
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [September 23, 2020, 10:15am UTC](https://forum.qiime2.org/t/multiple-regions-of-16s-rrna/16670/4 "2020-09-23T10:15:35Z")
Hi @mshahin,
The brilliant @Nicholas_Bokulich has also suggested checking your classifier regions! What classifier have you used? Is it V4 specific? Full 16s? Some other classifier?
Best,
Justine
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### Author:  [@mshahin](https://forum.qiime2.org/u/mshahin)
#### Post date: [September 23, 2020, 10:51pm UTC](https://forum.qiime2.org/t/multiple-regions-of-16s-rrna/16670/7 "2020-09-23T22:51:54Z")
> [@What is the difference between Greengenes and SILVA?](https://forum.qiime2.org/t/what-is-the-difference-between-greengenes-and-silva/1560/1):
>
> recent o
Thanks @jwdebelius
I used full 16S classifier.
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [September 24, 2020, 7:26am UTC](https://forum.qiime2.org/t/multiple-regions-of-16s-rrna/16670/8 "2020-09-24T07:26:21Z")
Hi @mshahin,
My suspicion would then be that they used a specially curated version of greengenes.
My question for you is whether you trust their curation.
Best,
Justine
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [October 25, 2020, 1:26pm UTC](https://forum.qiime2.org/t/multiple-regions-of-16s-rrna/16670/9 "2020-10-25T13:26:23Z")
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