Repeat Taxonomies in Taxa Barplot

[UnevenCuttlefish]

Hi All!

I'm using the Silva 138 classifier for my 16S sequences and I have created a summed barplot for my two species but I've noticed something odd, and that is there repeats in certain Classes!

There are two representation of class Gammaproteobacteria, but one is represented by Domain and the other Kingdom. This pattern holds even further down into the taxonomy

I would like any information you may have about a) why this might be happening, b) how to possibly fix this and, c) what this might mean for my analyses.

Thanks in advance!

-UC

[SoilRotifer (Mike Robeson)]

Hi @UnevenCuttlefish,

It appears that two different taxonomy databases were used and combined by accident. That is some databases will use k__Bacteria (e.g. Greengenes v1), and others will use d__Bacteria (e.g. Greengenes v2, SILVA, GTDB).

Can you send the QZV file so that I can look at the provenance.

[UnevenCuttlefish]

This makes sense! This was originally two different analyses that were combined together and I had control over the Silva.

Hopefully I understand which files you're wanting, if it's the taxonomies themselves here are the files.

for TAGR
vis_taxonomy.qzv (1.4 MB)

for TATO
vis_TATO_taxonomy.qzv (1.7 MB)

That would make sense as to why it would be coming up different visually. Any idea what this would mean for analyses?

[SoilRotifer (Mike Robeson)]

@UnevenCuttlefish

Any idea what this would mean for analyses?

The different databases use different taxonomic labels for different organisms and different ranks. Making taxonomic summaries, and any taxonomy-based analysis potentially spurious. I'd suggest re-classifying all of the features with the same reference database.