I have a question about longitudinal microbiome analysis, in which microbiome data (alpha, beta diversities, and taxa abundance) are considered independent variables. I looked at the current example in Docs, and"Linear Mixed Effect models" and "Volatility analysis" have been suggested for conducting the longitudinal analysis. In those examples, microbiome data have been considered a dependent variable; however, I want to conduct an analysis in which microbiome data (e.g., alpha diversity) is considered an independent variable. Here is an example: Fatigue ~ alpha diversity + age + time
So, I wonder if you could please let me know which longitudinal model best fits my purpose.
Whether the microbiome data is independent or dependent depends on your experiment design. In the Q2 Longitudinal tutorial it is a dependent variable because we are sampling from subjects over time. If your microbiome data is not sampling a subject over time or does not include replicates, then it could be considered an independent variable.
Can you please elaborate more on the example you provided and the data you are working with? That will help me answer your question.