Testing differential abundance based on multiple metadata categories

Hello,
I found this forum post (Comparing Relative Abundance according to a metadata category) clarifying that you can’t use ANCOM to test for differential abundance of a specific taxon at a specific time point, but I was wondering if it is possible to somehow test for differential abundance of any taxa based on two separate metadata categories (i.e. at a specific time point between two pre-defined groups of subjects)?

Thank you,
RIley

Hi @Riley, I believe ANCOM2 can support this – @Mehrbod_Estaki posted the zip file here: ANCOM: 'low W taxa identified as significant' issue's workaround, ANCOM2 code/instructions.

Gneiss can also do this, but won’t give you information about individual taxa, only their ratios.

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Hi @mortonjt, thank you for this resource! Just to confirm though, currently there is no capability to do this sort of analysis within Qiime2?

ANCOM2 is not yet available in QIIME2 (but we are working on it, so stay tuned). You will need to run in R.

However, it is not entirely clear if you need to run ANCOM on multiple metadata categories, based on your description:

“specific time point” sounds more like you are filtering your samples to a specific time point, and then testing for the influence of a single metadata column.

I apologize, you’re correct. I was able to filter the samples to include only the relevant time point and then compare the two groups. Still great to have the ANCOM2 resource though and can’t wait to see that incorporated into QIIME2. Just to reiterate the forum I referenced in my first post, would also love to see the ability to query individual taxa incorporated soon as well! Thank you for your help!

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