# The same three genus belongs to different family
**URL:** https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755
**Category:** General Discussion
**Created:** [February 25, 2020, 3:05am UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755 "2020-02-25T03:05:02Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@Zhanzhan](https://forum.qiime2.org/u/Zhanzhan)
#### Post date: [February 25, 2020, 3:05am UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/1 "2020-02-25T03:05:02Z")
Hello, everyone!
As shown in the picture, there are three same genus(g\_\_Clostridium), but why did they belong to different families? I use q2-classify-sklearn to perform taxonomy annotation. Is it normal? Can I combine this thress genus(g\_\_Clostridium) in downstream analysis such as differential abundance analysis?
 
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 25, 2020, 5:31am UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/2 "2020-02-25T05:31:22Z")
Hi @Zhanzhan, great question.
> [@Zhanzhan](#):
>
> there are three same genus(g\_\_Clostridium), but why did they belong to different families?
This is because Clostridium is polyphyletic, the taxonomy is a mess, many genera historically assigned to Clostridium (e.g., using traditional techniques) do not place in that genus based on molecular phylogenies.
> [@Zhanzhan](#):
>
> I use q2-classify-sklearn to perform taxonomy annotation.
Nothing to do with the classifier, everything to do with the reference taxonomy that you are using — the classifier can only operate as accurately as the training data you feed it.
> [@Zhanzhan](#):
>
> Can I combine this thress genus(g\_\_Clostridium) in downstream analysis such as differential abundance analysis?
I would discourage it — these are distinct clades, even if the names are misleadingly similar. If you want to disambiguate these, you could label both the family and genus that they are assigned.
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### Author:  [@Zhanzhan](https://forum.qiime2.org/u/Zhanzhan)
#### Post date: [February 25, 2020, 8:11am UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/3 "2020-02-25T08:11:11Z")
@Nicholas_Bokulich OK, I got it！Thanks！
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### Author:  [@Jaroslaw\_Grzadziel](https://forum.qiime2.org/u/Jaroslaw_Grzadziel)
#### Post date: [February 26, 2020, 8:41am UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/4 "2020-02-26T08:41:46Z")
What was the reference database ?
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### Author:  [@Zhanzhan](https://forum.qiime2.org/u/Zhanzhan)
#### Post date: [February 26, 2020, 1:37pm UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/5 "2020-02-26T13:37:44Z")
@Jaroslaw_Grzadziel Hello! I used Greengenes database.
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### Author:  [@Jaroslaw\_Grzadziel](https://forum.qiime2.org/u/Jaroslaw_Grzadziel)
#### Post date: [February 26, 2020, 1:51pm UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/6 "2020-02-26T13:51:18Z")
Hi, thank you for a reply 😉
I would recommend to use one of most up-to-date reference database, like RDP, Silva or GTDB.
Greengenes is outdated and should be forgotten 🙂
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [February 26, 2020, 6:48pm UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/7 "2020-02-26T18:48:36Z")
The database doesn't solve the core issue, though, which is genus Clostridia is a polyphyletic clade. The GTDP update helps, but you're fighting against set taxonomic names that existed before we got good at molecular phylogeny.
So, perhaps a second option is to embrace your ASVs and work with the molecular barcodes.
Best,
Justine
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### Author:  [@Zhanzhan](https://forum.qiime2.org/u/Zhanzhan)
#### Post date: [February 28, 2020, 7:26am UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/9 "2020-02-28T07:26:35Z")
@Jaroslaw_Grzadziel Thank you for your advice. But if RDP can be used in qiime2? Silva demands high ram and my device can not work if I use silva.
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### Author:  [@Zhanzhan](https://forum.qiime2.org/u/Zhanzhan)
#### Post date: [February 28, 2020, 7:28am UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/10 "2020-02-28T07:28:07Z")
@jwdebelius I know it. Thank you very much!
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 28, 2020, 5:54pm UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/11 "2020-02-28T17:54:09Z")
> [@Zhanzhan](#):
>
> Silva demands high ram and my device can not work if I use silva.
There are ways around this, see this post and the following post in the same topic:
> [@Memory and Classification for 18S](https://forum.qiime2.org/t/memory-and-classification-for-18s/13810/4):
>
> Hi @fhermanto96, Have you tried try one of the newer SILVA 138 classifiers here: [https://forum.qiime2.org/t/silva-138-classifiers/13131](https://forum.qiime2.org/t/silva-138-classifiers/13131) They should have a smaller memory footprint... especially the versions of the classifiers which were made without the species label (only goes down to genus). -Mike
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [March 30, 2020, 11:59pm UTC](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755/12 "2020-03-30T23:59:28Z")
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