I usually study eukaryotes but I've started working on a microbiome project. I am wondering about the utility of DNA sequencing vs RNA sequencing.
I know that RNA sequencing tells me about expression levels of specific genes while DNA sequencing simply reveals the presence of those genes in the microbiome. I am familiar with analysis of eukaryotic cells, where the presence of a specific gene is basically a given and, ultimately, expression has to be investigated by RNAseq. Expression levels between any two genes can vary nearly infinitely, so DNAseq tells you almost nothing about expression.
So, I am wondering if it is the same situation for the microbiome. If I do DNA sequencing and find one million copies of gene A and only 20 copies of gene B. that means there are more species/organisms that contain gene A. Can I assume that gene A is more highly expressed in my sample? Are there some genes that are "silenced" in the bacterial genome?
Any advice or papers that deal with this would be greatly appreciated!