Question about metabolic pathway prediction using only DNA sequencing data

Question

[Mark]

Hi,

Our group has a strain of a rare microbe that produces a strange volatile compound. The chemistry team in the lab have done some analytical chemistry and determined what the chemical is that's producing this scent, but our group wants to correlate phenotype data and genotype data. I ran a ONT sequencing on this bacteria and I got a good de novo genome reconstruction, but I'm puzzled as to where to go from here. RNA sequencing data seems to be the next logical step, but I'm wondering if anyone has any suggestions for doing pure metabolic predictions using just this assembly reconstruction.

[GenoMax]

You may get a specific answer from someone, here is a solution you could explore. You are looking for something specific so if you know what that compound is your job may be a bit easier or difficult (since you may end up looking at a class of enzymes). It is not clear if you are looking for the specific step that does the ultimate conversion or are looking to reconstruct the entire pathway.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02295-1

Answer 1

[hakimbazol]

I just assume you got the WGS dataset by using ONT and then you would like to obtain metabolic pathways based on the WGS. You may want to see CarveMe or ModelSEED that can assist you to obtain metabolic pathways for entire pathways based on your WGS result. This publication may help you to do that, since they provide the entire pipeline from WGS to obtain metabolic model.

https://doi.org/10.1002/bit.28492

Hope it helps!