Lessons from the model gut Bacteroidales Bacteroides fragilis and Bacteroides thetaiotaomicron and future opportunities

ABSTRACT Bacteroidales is an order of bacteria that includes members that colonize the human gut, oral cavity, cow rumen, and other host-associated environments. Most humans become colonized with gut Bacteroidales species relatively soon after birth and later become colonized at high density with numerous diverse species. Bacteroidales strains often persist in the human gut for decades where they extensively evolve, acquiring point mutations, prophage, mobile plasmids, and integrative conjugal elements, making each person’s gut Bacteroidales strains highly personalized. Much of what we have learned about basic biological properties of gut Bacteroidales comes from analyses of two species, Bacteroides fragilis and Bacteroides thetaiotaomicron , which were studied for different reasons. Three decades ago, there was only one human gut Bacteroidales genus recognized, the Bacteroides , into which all human gut Bacteroidales species were classified. Today, the human gut Bacteroidales number over 50 species with more than 14 genera and at least seven families. Studies of B. fragilis and B. thetaiotaomicron have provided a wealth of information of basic processes of these gut symbionts, many of which are generally applicable to other species of gut Bacteroidales. In this review, I provide a historical perspective as to why these two species have served as models, as well as some of the biological processes learned from studies of these two species. Finally, I discuss why present and future analyses of the gut Bacteroidales have expanded beyond these two model organisms.