Antimicrobial compositions for oral delivery, and administration to the colon, distal ileum, or other portion of the gastrointestinal tract other than the stomach, of bacteriophage, phage proteins, antimicrobial peptides, or antimicrobial aptamers, are disclosed. In one embodiment, the active agent is capable of lysing the bacterial cell wall. In another embodiment, the active agent is capable of interacting with a receptor or enzyme in the bacteria. In some embodiments, the active agents selectively act on one or more harmful bacteria, such as Clostridium difficile, and either do not act, or act to a lesser extent, on helpful bacteria, such as bifidobacteria. When the agents are not delivered directly to the colon, they active agents ultimately enter the colon and affect the bacteria that are present in the colon. The compositions can include beads of pectin in the form of a cationic salt enclosing the active agent, or other types of drug delivery systems designed for targeted delivery to the desired portion of the gastrointestinal tract.