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Old 09-03-2019, 02:21 AM   #1
uloeber
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Location: Germany

Join Date: Mar 2013
Posts: 40
Question 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.

Cheers,
Ulrike
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16s, greengenes, lotus, microbiome analysis, taxonomic classification

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