Performing "taxon specific scaling" with only MTX data

Downstream analysis and statistics
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I currently have MTX data (only MTX without paired shotgun metagenomic sequencing) from cultured fecal samples exposed to different conditions. I using humann3.9 to regroup my table from CAZymes to uniref90 counts per million (CPM) mapped reads. If I want to perform CAZyme DE analysis between conditions, how should I go about applying taxon specific scaling to my table to run downstream DE analysis? Can I apply taxon specific scaling directly to my CPM CAZyme table or do I need to apply it to the Uniref90 table then regroup back to CAZyme families?

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Scaling within-taxon among just the CAZymes should work. The key is that you don’t want the total depth of the taxon to influence the apparent expression of any individual within-taxon feature, and within-taxon scaling helps to solve that. It might be more convenient to do the scaling at the UniRef90 level so that you can regroup from UniRef90s to other features (including CAZymes) and/or to test individual UniRef90s if you don’t see a lot of signal at the CAZyme level.

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Thank you so much Dr. Franzosa!