hi there,

I think you could try to quantify your bacterial DNA by a quantitative PCR approach. By using universal 16S rDNA targeted approach, you can have an idea of the amount of bacterial DNA in your sample. I can suggest you te read this article (http://www.ncbi.nlm.nih.gov/pubmed/14607398) that give an overview of PCR primers available for this kind of work. But indeed this approach is not perfect, because some bias exist, but it could be a first approach to evaluate the amount of bacterial DNA.

Hope it'll help!

Good luck for your work

I confirm this is but suggest also the following reading:

http://www.ncbi.nlm.nih.gov/pubmed/24594623

That adress your special case, most notably because authors are trying to study symbiosis eukaryote-bacteria symbiosis.