Hi @saatkinson
That looks interesting. Yes you can compare multiple groups with this method, since the linear regression boils down to ANOVA for categorical variables.
As noted at the end of the gneiss tutorial, there are a few possibilities that could explain the shift in the log ratios - notability the numerator could be increased in D36_Cntrl, D36_Risp compared to D15_Cntrl, or the denominator could be decreased in D35_Cntrl, D36_Risp compared to D15_Cntrl.
Concerning D0 and D15_Risp, it would appear that these taxa are not commonly observed in these samples (since like you noted above, log(1)=0). Of course, the raw counts of these taxa within D15_Risp and D0 will need to be sanity checked.
Concerning the taxonomy summaries – those don’t change, because you have already define the balances before running the regression (I’m assuming that you either ran correlation-clustering or gradient-clustering).
Once the balances are constructed, the taxonomies for each balance are set in stone – if you have defined 2 Firmicutes in the numerator and 5 Bacteroides in the denominator, then that log ratio is fixed.
The boxplots may change, when you specify different categories, since you will specify different groupings – you can think of it like coloring different categories in a PCoA plot in Emperor.
Does this help?