Illuminating the dark matter of the human small intestinal microbiota - Progress in translational microbiome science has been slow, despite the clear importance of the gut microbiome on human health and tremendous investment. Lack of understanding of the small intestinal microbiota is a primary obstacle—the small intestine (SI) is where nutrients are absorbed, the interface for interaction between microbes and the mucosal immune system, and the site for rising disorders such as Crohn’s and small intestine bacterial overgrowth (SIBO). The SI is a highly distinct environment from the colon, yet the human SI microbiota is poorly characterized due to our reliance on analyzing feces, which is easily accessible but inadequately represents the SI. The natural hypothesis that SI regional specificity arises from distinct microbial physiologies remains untested due to lack of SI-focused resources. Here, I lay out an ambitious roadmap to close this knowledge gap and enable engineering of therapies to improve human health through the SI microbiota. These efforts include a comprehensive species atlas that deconstructs the regional specificity and function of SI-resident microbes, a synthetic community that resists pathogen colonization in the SI, and capabilities for engineering the SI microbiota using phage editing and location-specific delivery. Our recent work has successfully reduced the major obstacles to studying the SI microbiota: regional sampling, microbial and phage isolation, and synthetic community design strategies. We have developed a revolutionary capsule device for safely and non-invasively collecting luminal samples from specific gut regions of humans during normal digestion. Our findings highlight the frontier nature of the SI: the microbiome, virome, metabolome, and host proteome differed dramatically from that of feces, and bile acids displayed region- specific signatures correlated with the abundance of specific species. To reduce the labor of strain isolation, we developed a cell sorting protocol to assemble personalized isolate libraries that is fast, inexpensive, and effective for even strict anaerobes. Finally, we used an iterative, ecology-based “backfill” process to develop a near-complete defined community as a model of the fecal microbiota. Using these tools, we aim to generate comprehensive strain libraries of bacteria from specific regions of the intestinal tract across donors with a wide range of diets and disease states. These personalized strain libraries will enable systematic functional characterization, genetic engineering, and utilization in therapies such as fecal microbiota transplants. We will construct diverse synthetic communities that capture microbiota function in both healthy and diseased humans throughout the intestines, not just the colon. Finally, we will generate phage libraries to enable precise editing of SI communities, and devices that enable precision delivery of specific microbes targeted locations. These efforts will refocus my lab’s expertise in bacterial physiology, imaging, systems biology, and big data toward a major scientific and societal challenge and lead to a new therapeutic paradigm: knowledge-based and probiotic solutions centered on SI-specific microbes.
