Oral-intestinal microbial translocation and colonization - PROJECT SUMMARY Small-intestine microbes play pivotal roles in human health, and can affect (and be affected by) factors such as probiotics, diet, drugs, supplements, and botanicals. Probiotics, including engineered probiotics, act in the small intestine and may support or compete with commensals and pathogens, as well as improve micronutrient absorption. In contrast, an altered SI microbiota has been implicated in impairing the efficacy of supplemental nutrition. Despite these important roles, studies of the human small-intestine microbiome are challenging because this region of the gut is difficult to access and because the sequencing tools used to analyze stool microbiomes are inappropriate for host-dominated mucosal samples. Critical gaps include knowing which microbes colonize the human small-intestine mucosa, where those colonizers originate from, and which microbial genes and/or environmental features enable them to persist there. These gaps must be addressed in humans because mouse models of the small-intestine microbiome are severely hampered by coprophagy. One long- standing hypothesis is that microbes from the oral cavity transit the acidic gauntlet of the stomach and colonize the small intestine. However, this hypothesis remains contentious and unproven because it is difficult to differentiate colonizers from dead microbes and endoscopies are known to introduce oral contaminants. The primary goal of this R21 exploratory study is to document the first definitive observation of oral microbes translocating and colonizing the SI. To accomplish this goal, we will utilize a combination of two innovative technologies we have optimized for studying host-rich microbiomes: (1) quantitative sequencing for measuring the absolute abundances of microbial taxa and differentiating it from contamination and (2) a microbial enrichment method that enables the construction of high-quality microbial metagenome-assembled genomes directly from host-rich samples. Identifying a definitive example of live oral-derived microbes colonizing the SI will open new avenues for more complete characterization of human intestinal microbes and a framework for further study of the relationship between oral and small-intestine microbial communities. For example, prebiotics intended to nourish beneficial small-intestine microbes and probiotics can be rationally designed to not inadvertently promote growth of oral pathobionts. Similarly, probiotic strains can be engineered to better compete with the oral pathogens capable of colonizing the small intestine and also take advantage of administered prebiotics. Ultimately, the findings from this R21 will improve the microbiome field’s understanding of how oral microbes can affect interventions such as specialized diets, drugs, prebiotics, probiotics, dietary supplements, and botanicals.
