Beta diversity longitudinal analysis (3 time points or more)


I am trying to find an appropriate command for running beta diversity data (Bray-Curtis) over time. Currently, the command in the Qiime2 tutorial covers just two-time points. Would you please let me know if there is any command that can handle beta diversity data more than two-time points (three or more time-points)?


Hello @Barandouzi,
I am not sure what tutorial you are referring to but beta-group-significance can be run on any number of "Groups"(In this case time points). However you might be able to use beta-correlation if your timepoint metadata is numeric.

Hope that helps!

Thanks for your answer. I looked at the link you sent, but there is no option that we can put time or timepoints as a variable in the commands. I am interested in knowing how beta diversity changes among groups (not paired) over time (e.g., T1, T2, T3).

Hey @Barandouzi,
I think I misunderstood your goal. So you have groups that you are tracking over time? I think that the longitudinal plugin is what you are looking for. The parkinson's mouse tutorial(specifically the longitudinal section) might be a good example to work off of if you want a tutorial: longitudinal — QIIME 2 2022.2.0 documentation

Also we have youtube videos walking through that tutorial if that is helpful. Here is a video for more general background on longitudinal analysis and a video walking through the tutorial.

Hope that answer is alittle bit more on target for what you need! Let me know