hi @Ray4
The coefficients that MaAsLin2 outputs represent the estimates in a general linear model. In a simple model with a single binary covariate the coefficient will represent the difference in means between the two groups after any normalization or data transformation.
In your case it looks like you are apply CLR transformation so the coefficient would represent the difference in means of CLR abundance between the groups of interest.
To get fold change you would need to either log transform your data and then do some back calculations as shown here: Trying to understand coef column (and how to convert it to fold change) - #4 by mrgambero. Logging the data allows you to more easily compute the fold change because log(a/b)= log(a) - log(b).
Hope that’s helpful.
Thanks,
Jacob