Bacterial signal in metatranscriptome data

Question

[cook284]

Hi all. I have some RNA-Seq data from the sequencing of a green algae in co- culture with a bacterium. The bacterial cell numbers were reported to be in a 50:1 ratio with the green algae. However, only ~7% of the reads are ascribed to bacteria, the rest are algae/ plant. I have argued myself silly around this matter but this seems a low ratio of bacterial to algal signal but I can think of no way of knowing. Ultimately the aim is to publish a comparison of functional activity amongst based on metatranscriptomic reads from both algae and bacteria. I'm concerned about what would be an expected (publishable) signal from the bacterial population for this kind of study.