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Taxonomy tree conflicts in Greengenes V 13.5

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  • 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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