Hello Razieh, you may want to have a look at the methods of biochemical characterization presented in there publications:
Colorimetric method for determination of sugars and related substances. M Dubois, Ka Gilles, Jk Hamilton, Pa Rebers, F Smith . 1956. Anal Chem 28 350-356.
Protein Measurement with Folin-Phenol Reagent. Lowry et al. 1959. Biochemistry 193(1)
You can apply these to your substrate as well as your reactor effluent. It gives you an idea of how much carbohydrates and proteins have been consumed. But please keep in mind the biomass growth of the microbial consotria.