Hi, I am trying to test if my samples microbiome is predictive of my infection severity
I have the “pre-infection microbiome” of my samples and I have the pathogen load over course of infection or “infect integral”. I am wondering what variables I should put into Maaslin.
In MaAsLin2, can I place “infection integral” as fixed effects, or would that imply it was causing the community difference?
Hi @Rachael_Kramp - if I understand correctly, you have a variable (or a set of variables) named infection severity (let’s call it Y) and pre-infection microbiome samples (X) and you want to test whether X is predictive of Y? Could you share more details such as how many Y features and sample size? Depending on the question and data dimensions, MaAsLin 2 may or may not be appropriate for this task.
You are correct I am trying to see if microbial community before infection is correlated with severity. We used 16s metabarcoding and have around 40 microbiome samples (X) and their corresponding (Y) values. The infection severity is a continuous value generally between 0-1200.
OK - in that case, you can use infection severity as a fixed effect to identify individual features statistically significant with respect to infection severity. Note that, if you are interested in community-level inference instead, PERMANOVA is a better approach for that purpose. Hope this helps!