# SILVA taxonomy - strange genus names

**URL:** https://forum.qiime2.org/t/silva-taxonomy-strange-genus-names/13813
**Category:** General Discussion
**Tags:** taxonomy
**Created:** [February 28, 2020, 2:23pm UTC](https://forum.qiime2.org/t/silva-taxonomy-strange-genus-names/13813 "2020-02-28T14:23:06Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![GreenDragon](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/g/ce73a5/32.png) [@GreenDragon](https://forum.qiime2.org/u/GreenDragon)
#### Post date: [February 28, 2020, 2:23pm UTC](https://forum.qiime2.org/t/silva-taxonomy-strange-genus-names/13813/1 "2020-02-28T14:23:06Z")

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Hi everyone,  
Is there any sense in SILVA taxonomy genus names like  
"uncultured bacterium", "gut metagenome", or they make no sense and for statistical analysis of gut microbiome composition (and further publication) it is better merge all the 3 taxa below:

D\_3\_\_Clostridiales;D\_4\_\_Clostridiales vadinBB60 group;D\_5\_\_uncultured bacterium  
D\_3\_\_Clostridiales;D\_4\_\_Clostridiales vadinBB60 group;\_\_  
D\_3\_\_Clostridiales;D\_4\_\_Clostridiales vadinBB60 group;D\_5\_\_gut metagenome

to one taxon:  
D\_3\_\_Clostridiales;D\_4\_\_Clostridiales vadinBB60 group;D\_5\_\_unclassified

or  
D\_3\_\_Clostridiales;D\_4\_\_Clostridiales;D\_5\_\_unclassified

I am not a microbiologist, sorry for this basic question. I work with SILVA132 database in QIIME2.

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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 28, 2020, 5:49pm UTC](https://forum.qiime2.org/t/silva-taxonomy-strange-genus-names/13813/2 "2020-02-28T17:49:21Z")

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Welcome to the forum, @GreenDragon!

> [@GreenDragon](#):
>
> Is there any sense in SILVA taxonomy genus names like  
> “uncultured bacterium”, “gut metagenome”

Unfortunately, these annotations are so vague that it is really unclear what they could represent and if they are theoretically same or separate entities. Given that you are receiving these classifications for distinct ASVs is a pretty good indication that they do represent distinct taxa, but you could look at those ASVs to decide for yourself whether it is worth collapsing. If I were in your shoes, I would keep separate.

Though for your purposes maybe it makes sense to collapse for display purposes (e.g., to reduce the number of unique taxa displayed on a heatmap or barplot) — in which case go for it but note this:

> [@GreenDragon](#):
>
> D\_3\_\_Clostridiales;D\_4\_\_Clostridiales vadinBB60 group;\_\_

Note: This is actually unclassified at the D\_5 level (meaning that the classifier could not determine a confident D\_5 classification, as there are many equal matches or no good matches)... the others are classified but to ambiguous taxa, so if you relabel you may want to relabel the unclassified and classified separately, e.g., as:  
D\_3\_\_Clostridiales;D\_4\_\_Clostridiales vadinBB60 group;D\_5\_\_unclassified  
and  
D\_3\_\_Clostridiales;D\_4\_\_Clostridiales vadinBB60 group;D\_5\_\_unknown

Good luck!

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### Author: ![GreenDragon](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/g/ce73a5/32.png) [@GreenDragon](https://forum.qiime2.org/u/GreenDragon)
#### Post date: [February 28, 2020, 6:27pm UTC](https://forum.qiime2.org/t/silva-taxonomy-strange-genus-names/13813/3 "2020-02-28T18:27:09Z")

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> [@GreenDragon](#):
>
> publication

@Nicholas_Bokulich, many thanks!