Bilophila wadsworthia 3.1.6 was cultivated with 2,3-dihydroxypropanesulfonate, or inorganic sulfite, each provided with L-lactate as the electron donor. Distinct enzymatic pathways are required for the respective respiratory processes, i.e., sulfite respiration versus organosulfonate respiration. Comparative proteomic analysis of B. wadsworthia 3.1.6 grown under these different conditions allows the identification and assessment of enzymes specifically involved in each type of respiration.