Good morning,

I am working on a microbiome longitudinal study. There are two groups (treated/untreated) over a course of n months. I am interested to identify which ASVs are expressed at different levels between the two groups, over the course of time.

I used ANCOM-BC2 as it suits perfectly the longitudinal design (linear mixed model), and it accounts for individuals as random effect. I've set the model as this :

fix_formula = Time + Group
rand_formula = (1 | Subject_ID)

To account for similarities between samples from same subject.

From the res object, I get the logFC at the different times, but I am not sure how to interpret the logFC. They seem to be calculated between the n time point and the first time point (which is a reference), is the Group effect taken in account ?

If anyone is using ANCOMBC, it would be of a great help.

Best regards