Comparing Relative Abundance according to a metadata category

[Nicholas_Bokulich]

Hi @fstudart,

@fstudart

Just wondering if there is a way of comparing the relative abundance of a specific genus (e.g. Haemophilus) according to a metadata category

Yes! After you collapse your feature table to the taxonomic level of interest, you can input the resulting feature table to ANCOM to test for taxa that are differentially abundant between groups (e.g., survivor/non-survivor). There are no QIIME2 actions that allow you to test a single taxon at a single time point.

There are a bunch of forum posts discussing interpretation and troubleshooting of ANCOM if you run into trouble with ANCOM during your analysis or have trouble interpreting the output, e.g., here.

@fstudart

I’m also interested in creating plots (boxplots) with these kinds of comparisons.

QIIME2 has no such action for a single taxon at a single time point. However, ANCOM outputs median/quartile abundance data for each group, which can be used to easily generate plots in R, Excel, or whatever external program you favor.

I hope that helps!