Drug delivery systems for delivering agents capable of reducing the quantity of residual antibiotics reaching the colon following oral or parenteral antibiotic therapy, and for delivering metallo-dependent enzymes, and methods of using the drug delivery systems, are disclosed. The drug delivery systems include pectin beads that encapsulate the active agent (which can be a metallo-dependent enzyme), where the pectin is crosslinked with zinc or any divalent cation of interest and the pectin beads are coated with Eudragit®-type polymers. The drug delivery systems are orally administrable, but can deliver the active agents to the colon. In some embodiments, they can administer the agents to various positions in the gastro-intestinal tract, including the colon. One metallo-dependent enzyme is the β-lactamase L1 from Stenotrophomonas maltophilia, and agents that inactivate macrolide, quinolone, fluoroquinolone or glycopeptide antibiotics can also be used. The delivery of the active agent can be modulated to occur at various pre-selected sites of delivery within the intestinal tract by gelling/crosslinking a mixture of the active agent, such as a metallo-dependent enzyme, and pectin, with divalent metallic cations such as Ca+2 or Zn+2. A stable metallo-dependent enzyme formulation can be delivered to the lower intestine or colon. The use of zinc cations to crosslink the pectin is particularly preferred when specific metallo-dependent enzymes, which are Zn2+ dependent, could interact with other cationic species if they were used to gel the pectin beads and thus adversely affect the activity of such metallo-dependent enzymes.