Longitudinal Analysis for Alpha and Beta Diversity

I am new to qiime and could use assistance to determine the best way to due longitudinal analysis.
I have a study with 4 different treatment groups and stool samples at 3 different time points 0 (baseline), 14, and 28 (washout). I was able to do alpha and beta diversity for the treatment groups, but i need to do it at each time point to determine if there really is an effect. How do you suggest i do this analysis?


Hi @RossMaltz,
It sounded like you were on the right track here, using an ANOVA to look at differences in alpha diversity between treatment and time:

You could also check out the q2-longitudinal tutorial for other ideas, e.g., use pairwise-differences or pairwise-distances or linear-mixed-effects so that you could control for variation across individuals when looking at temporal change:

Well that works too: you can use qiime feature-table filter-samples to isolate individual timepoints and then, e.g., run an ANOVA on each time point individually.

Good luck!