Creating and characterizing communities of human gut microbes in gnotobiotic mice

Microbiology laboratories are laden with flasks, plates, and freezer stocks containing axenic cultures and their products. In contrast, virtually every other habitat on Earth is filled with microbial communities of varying degrees of complexity. In this context, microorganisms are interdependent components of ecosystems; deciphering this dynamic requires a move from microbial organisms studied in isolation to model microbial communities studied under conditions that mimic those encountered by their members in their native habitats. Here, we focus on model communities consisting of microbes that inhabit the human body habitat containing our largest collection of organisms—the gut.