The human intestinal microbiota is comprised of more than 100 bacterial species that provide numerous benefits to their host. The production of antibacterial toxins (bacteriocins) by minor members of the gut microbiota such as Escherichia coli, Lactobacilli and Bifidobacteria, have been known and studied for years. It is only recently that the production of pore-forming antibacterial protein toxins have been shown to be produced by the numerically abundant gut Bacteroides species. Pore-forming toxins with MACPF domains are produced by numerous gut Bacteroides species and target diverse surface molecules of sensitive cells that are necessary for the organism’s colonization of the mammalian intestine. These toxins do not require cognate immunity proteins to protect the producing cell, but rather the toxin producing cells have altered surface molecules that render them resistant. The ecological aspects of toxin production in contributing to the composition of the gut microbiota and the application of these pore-forming proteins to strategically alter the gut microbiota are currently being investigated.