Hello everyone,
I want to find out how the co-culture of two anaerobic bacteria influences each other in order to find competition and cross-feeding relations between them. My first approach is to use RNA seq to find the differential expression of important genes, but this method uses one library (I asume that from only one microorganism). I found about dual RNA seq, but it's commonly used for host-pathogen interactions. Could I use it for my two bacteria?
Thanks in advance
In short, yes this is possible!
You will need control samples of bacteria A and bacteria B separately and then AB together for comparison.
RNA can be extracted and sequenced as normal.
The trick is with the bioinformatics analysis.
You should create a hybrid reference genome consisting of both species. In the coculture you will get reads from both species which can be separated prior to differential analysis using the pure culture as the control.
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