How can I identify differential Taxon for paired design experiment?

My data is about effect of anti-cancer treatment for gut microbiota.

5 peoples were treated using same anti-cancer medicine and we produced before and after

gut metagenome data for each individual.


In the tutorial, using linear-mixed model in longitudinal, I can identify the effect of treatment.

on alpha diversity and etc. However, I also want to know what taxa were significantly effected

by anti-cancer treatment. I tried to find the tutorial about this case but I cannot find it.

I need some help.

Hi @Kaspy,
Good question. You could run LME or paired-difference tests on individual taxa, but this is only useful if you have specific taxa in mind. Sounds like you want an exploratory analysis — check out q2-gneiss.

I hope that helps!

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