Studying Intestinal Microbiomes by Nanopore Sequencing

The microbiome -- the commensal microbes that colonize the human skin, mouth, gut, and urinogenital tract -- play an important but poorly characterized role in human health and disease. Microbial communities in the gut are of particular interest: they impact not only digestion, but also our immune systems and even our mental health! Part of the challenge in characterizing this role is the immense diversity of these microbial communities -- the microbes present in an individual's large intestine seem to be impacted by heredity, environment, diet, disease, and other factors. Thus, simply surveying these communities from healthy individuals to determine which microbes are present, and in what proportions, provides useful data as to community structure and may allow us to infer the metabolic activity of these communities. Ultimately, understanding the structure and function of these commensal microbial communities may allow us to alter them rationally, leading to better health outcomes.