I don't think this is a correct question. One cannot study metabolomics by transcriptomics. If it was possible, there would not be a separate field for that. Only inferences about metabolism can be made by using transcriptomics.
You can conduct RNA-Seq analysis (only in host or dual in both pathogen and host) to get the DEGs between infected and non-infected conditions and get a bit of idea regarding the genes and metabolic pathways which might be involved in inciting the disease response