I am collecting tissue samples and will be extracting total RNA from them for sequencing. However, I'm only interested in the metatranscriptome of the bacterial members within my samples. The kits and procedures that I've seen so far primarily remove ribosomal RNA and that's about all. This seems to only enrich the bacterial transcripts within the total RNA from about 1% to 10-16% of the total transcripts sequenced. What methods have anyone used/know of?

I am trying to multiplex as many samples into a single sequencing run as possible however, I have not been able to determine ways to estimate the sequence coverage that would be useful in drawing inferences. Does anyone know ways to estimate needed sequence depth for the metatranscriptome? I think that the differences in our samples will be subtle however, I do not have any evidence to suggest one way or another.

I'm looking for any advice and experience on metatranscriptome sequencing and analysis.