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)
[1] "Intercept"                         "Sex_M_vs_F"                        "SubjectGroup_E.cig_vs_Non.smoker" 
[4] "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!

For interactions, even though the column is labeled "logFold2Change", that's not what it is. Edit: It's the log of the ratio of the fold changes.

I found this site helpful

https://rpubs.com/ge600/deseq2

Look down to the header "The different response in genotypes (interaction term)"