Hello, I am working on analyzing 16S microbiome sequencing data using DESeq2. I am very new to this type of work, so apologies if this question has a very obvious answer. I have data from three subject groups (E-cig, non-smoker, smoker), and two sexes (male and female). I am interested in the effect of sex on changes in the microbiome in the different subject groups and I have modeled this using the following code:
deseq_data <- phyloseq_to_deseq2(data, ~ Sex + SubjectGroup + Sex:SubjectGroup)
Which returns these possible results:
> resultsNames(deseq_data)  "Intercept" "Sex_M_vs_F" "SubjectGroup_E.cig_vs_Non.smoker"  "SubjectGroup_Smoker_vs_Non.smoker" "SexM.SubjectGroupE.cig" "SexM.SubjectGroupSmoker"
What I am confused about (and have tried reading the help pages/vignettes) is what exactly the interaction terms are in comparison to. For example, when I graph the results of "SexM.SubjectGroupE.cig," what is the log2FoldChange data in comparison with? Male non-smokers? I understand that using an interaction term tests for microbes that respond differently to exposure across sexes, but I am struggling the most with the meaning of the log2FoldChange. Any help would be greatly appreciated! Thanks!