The small intestine microbiome: composition, host interactions and therapeutic potential

The human microbiome, the collection of microorganisms that inhabit the human body, has been extensively studied over the past two decades and has been shown to play a critical part in health and disease. These research efforts renewed interest in developing microbial therapeutics to promote human health and treat disease. However, the vast majority of human gut microbiome research has been focused on fecal microbial strains and communities, leaving most of the gastrointestinal tract understudied. The dynamic environment of the small intestine provides distinct opportunities for microorganisms to interact with the host and diet. In this Review, we discuss the current state of research on the microbiome of the small intestine, how interactions between the small intestine and its microbiome influence host physiology, and we posit that small intestinal microorganisms are a unique source of novel therapeutics for treating human disease. Next-generation microbial therapeutics that emerge from the small intestinal microbiome are anticipated to be relevant to improving small intestinal diseases as well as systemic human health.