The human intestinal microbiota is composed of hundreds of microbial species and strains and is one of the densest microbial ecosystems on Earth. Despite the heightened interest in the intestinal microbiota, investigations into the dynamic microbial interactions that occur within this ecosystem are still in their infancy. Little is known about how bacterial species become established in the mammalian intestine, the interactions that occur between strains and species, and the factors that influence microbial stability and diversity in the ecosystem.

Our lab studies the biology of a predominant order of bacteria of the human intestine, the Bacteroidales. These are the most abundant Gram-negative bacteria of this ecosystem and establish mutualistic relationships with their hosts in that they both receive and provide beneficial properties. We study properties and molecules of these bacteria that allow them to survive and thrive in the human gut. We are also very interested in population and community dynamics of the intestinal microbiota, community stability, and how these bacteria interact with other members of the intestinal microbiota. A main focus of the lab is the study of competitive or antagonistic interactions among gut Bacteroidales species mediated by the production of molecules that directly harm other members.

We have identified antimicrobial toxins or toxin delivery systems in more than half of human gut Bacteroidales strains and we have shown that many of these genes are encoded on conjugative elements that are readily transferred to other co-resident Bacteroidales members in the human intestine. As the Bacteroidales toxins we have identified are new types of antibacterial molecules, we are elucidating their mechanisms of intoxication of target cells as well as their role in shaping gut microbial communities.

By understanding the bacterial factors that contribute to compositional changes in this ecosystem, we will eventually be able to use these data to manipulate the microbial community in select individuals to improve health outcomes. We are also studying other translational aspects of these antibacterial molecules including their use to combat bacterial pathogens.