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uloeber 09-03-2019 02:52 AM

Taxonomy tree conflicts in Greengenes V 13.5
Hi all,
I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was updated most recently, SILVA is the biggest database and the unassigned OTUs could then be classified by HITdb.
I was not surprised, that tree conflicts occurred, but what was surprising was that greengenes itself (V 13.5 05/2019) included conflicting information, or how would you judge this:
158718 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__

186714 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__[Paraprevotellaceae]; g__[Prevotella]; s__

What does the parenthesis mean? Anyways, unfortunately, this results in one genus on different nodes, retrieved from one database!

Looking much forward for a fruitful discussion with you.


asorbie 09-09-2019 01:31 AM

Greengenes hasn't actually been updated since 2013. Personally, I just wouldn't use it at all. Stick to Silva, RDP or GTDB if possible.

uloeber 09-09-2019 04:50 AM

Really? I used version 13-5 released this year 2019-05-01

asorbie 09-09-2019 04:53 AM

I think they may have changed some minor things this year but not the entire database. 13-5 is the May 2013 release.

uloeber 09-10-2019 05:17 AM

Thank you!

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