Hi,

We are studying intestinal microbiome dynamics and are currently looking at a dataset consisting of 75 individuals, where each individual is sampled at four time points. I realize that shotgun metagenomics is not what DESeq2 was designed for, but I'm curious to know if you think it might still be useful to help provide assessments of the within-individual and/or between-individual variability of all observed microbial taxa in the samples. The data consists of a number of read counts per taxa per sample

I have never used DESeq2 before, and looking through the documentation, I don't see any clear indications of whether measures of these two types of variability are even computed. However, I saw that coef can be used to extract standard errors of the model, but I'm not entirely sure what these standard errors would mean in our case (would they correspond to the between-individual variabilities for each taxa?). I'd love some input on how I can proceed to assess these two components.

I might be missing something obvious or thinking about this in a wrong way. Thankful for any help!

DESeq2 uses a GLM and so you compare eg within condition and across condition variability with a LRT of ~condition vs ~1. Because of the GLM this is an analysis of deviance, not variance. The deviance for the two models is saved in the metadata columns.