The taxonomic status,"metagenome",in Silva database

User Support
#1

Dear QIIME2 users

When I used the SILVA_132_QIIME_release database to classify, I got some taxonomic status named “metagenome”.I didn’t know what should I do about this.

On the one hand, there are no one by the name of “metagenome” in systematics.On the other hand ,it is a real classification come from Silva database.

What should I do? Can I just remove the classification, or rename them to uncultured bacterium or unclassfied bacterium?

Thanks in advance for the help.

#2

Hi @ZhengQu,

Last time I was working with Silva, I went through and reclassified those as “unspecified genus X” (and similiar) using a custom python script. (Missing levels ended up as unclassified.) It’s ugly, but it worked?

Best,
Justine

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#3

Hi! I encountered them as well. Left them without changes for now since they are not significant in my data. But found some errors in Silva 132 database beside it.

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#4

Dear @jwdebelius

Thanks for your reply!
I will try to use your python script to clean silva taxonomy.

Best Regards
Zheng Qu

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#5

Dear ZhengQu,
As others already mentioned, I customized those undefined taxa in my Silva in a way that “metagenome, environmental…” and others came to “unclassified_X” and that’s how I deal with them.
All the best,

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#6

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