I have a marine aerobic bacteria, belong to phylum Bacteroidota, which can degrade laminarin.

I want to understand the molecular mechanism of this procedure by exploring the expression of genes which contribute to degrade laminarin from polysaccharide size to oligomer and monomer for glycosylation.

As I read from other related studies of other bacteria in same phylum which also could degrade marine polysaccharides, they cultivated their target bacteria on the same basal medium and added different substrates (eg. xylan or glucose) and then compared their transcriptomic profile to find the upregulated genes related to xylan degradation for example.

I tried to cultivate my strain on laminarin or xylose. I found that both substrates could support growth of the strain and the cells harvested from each culture could degrade laminarin in enzyme reaction test to produce reducing sugar (detected by DNS assay).

I tried to analyse their hydrolytic products on TLC plate. I found that cell grown on laminarin could produce not only glucose as final product, but also other oligosaccharides. While, cell grown on xylose could degrade laminarin into glucose only.

In my case, if I compare their transciptomic profile, may be the gene responsible for endo-acting enzyme could be detectd, but the gene respondible for exo-acting enzyme could be same.

So I want to ask whether I can apply transcriptomic analysis to find the whole set of genes which contribute to laminarin degradation when the cell grow on medium containing laminarin or not? Whether I can design the experiment like this:

- (1) The strain is grown on medium contain laminarin, and medium (marine broth) without any mono-, oligo-, or polysaccharides.

- Then do transcriptomic analysis for both type of cells.

- Compare the upregulated genes between 2 profiles and using 16S rRNA as internal standard gene and as normalized factor to compare 2 different profile.

- Then concluted the the co-upregulated genes which contribute to laminarin degradation.

From the view of science or from your experience. Could you give me some advise please?

Thank you in advanced.