We describe the inhibition of the starch utilization system (Sus) belonging to various strains of Bacteroides dorei in a non-lethal manner using the small molecule probe, acarbose. Concentrations of acarbose as low as 5 μM significantly impede the growth of B. dorei and increase the doubling time of cultures. The successful inhibition of this species of Bacteroides is relevant to several disease states including type I diabetes mellitus. This method continues to explore a new, potential route to intervene in illnesses associated with aberrant changes in the composition of the human gut microbiota through the strategic manipulation of its constituents.