Taxonomy names confusion


I have used the greengenes2-qiime2 non-v4-16s plugin for taxonomy as follows

qiime greengenes2 non-v4-16s --i-table table.qza --i-sequences rep-seqs.qza --i-backbone 2022.10.backbone.full-length.fna.qza --o-mapped-table gg2.biom.qza --o-representatives gg2.fna.qza|

qiime greengenes2 taxonomy-from-table --i-reference-taxonomy 2022.10.taxonomy.asv.nwk.qza --i-table gg2.biom.qza --o-classification gg2.taxonomy.qza

The classification in one of the ASVs is as follows......

MJ010-1-barcode30-umi139474bins-ubs-6 d__Bacteria; p__Firmicutes_A; c__Clostridia_258483; o__Peptostreptococcales; f__Peptostreptococcaceae_256921; g__; s__Eubacterium tenue 1.0

Genus is empty but species is present, also, I looked around but I have not come across the order Peptostreptococcales, is it another name for Eubacteriales since the family Peptostreptococcaceae comes under Eubacteriales.

And why is genus empty when species is defined as Eubacterium tenue.

Please help.

Thanks & Regards

Just came to say I've had the same issue and made an issue on the github page although I've also just realised that the lead author is active on this forum!

@wasade I don't know if this is intentional or not, do you have any thoughts?

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Thanks! I followed up on the github issue. It is not intentional, and very helpful to spot! I'm puzzled as gaps are intended to be part of the automated assessment, but it's possible those checks are not properly accounting for some of the changes made to tax2tree to support Greengenes2.

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Hi @Alka_Srivastava,

Thank you for flagging this record, this is very helpful. The gap should not happen (please see reply to @Micro_Biologist). Eubacterium in general have undergone a lot of changes in GTDB, and I suspect there are inconsistencies arising in how we reconciled GTDB and LTP. I've noted this issue on our github tracker.

Note this species bears a lot of similarity in 16S to other records, more information can be found here


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