The bioBakery help forum

Microbiome influences on infection

Hi, I am trying to test if my samples microbiome is predictive of my infection severity. Another way of saying this is I am wanting to know which bacteria are associated with an increasing infection integral (continuous value). I am worried the math would not make sense if I put infection integral as a fixed effect-as the microbiome should be influences the infection not the other way around.

I have the “pre-infection microbiome” of my 16s samples (n=40 samples) those samples were than infected with a pathogen and I have resulting “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?