Eukaryotic organisms are, in part, defined by their associated microbiota, composed of a complex series of relationships between species. Bacteroides fragilis is a ubiquitous anaerobic bacterium in the mammalian intestinal tract. The range of symbiosis and pathogenic factors produced by this organism provide a fascinating window into host-microbe interactions. Non-toxigenic B. fragilis (NTBF) strains are symbiotic in the intestinal environment, providing protection from inflammatory disease while Enterotoxigenic B. fragilis (ETBF) strains induce colitis through a toxin called B. fragilis toxin (BFT). This dichotomy allows for detailed study of the interactions between these bacteria and their effect on the environment in which they live. The studies contained herein explore the relationships between a virulence factor, molecular cues and bacterial competition in the context of the mammalian intestine. We find that toxigenic strains of B. fragilis transcriptionally regulate production of BFT in response to environmental and growth conditions, partially mediated by a two-component system response regulator. Additionally, we demonstrate that a host factor protects from lethal BFT-dependent ETBF infection, illustrating the close relationship between these species and the role of bi-directional signaling molecules in maintaining homeostasis. The effect of colonization with NTBF differs drastically from that of infection with ETBF. We found strain-specific exclusion of ETBF by NTBF from the microbiota in a type VI secretion system-dependent manner. A putative type VI secretion effector/immunity pair confers protection against pathogen exclusion, increasing host disease burden. Resistance against acquisition of a second non-toxigenic strain was also observed, indicating a potential function of type VI secretion systems in microbiota composition. This resistance did not apply across species, however, suggesting a complex environment- and regulation-dependent interaction in the colon. Our studies demonstrate a novel role of type VI secretion systems in host-protective colonization resistance against a pathogen. This understanding of bacterial competition may be utilized to define a molecularly targeted probiotics strategy.