Computational methods for microbiome epidemiology
Human microbiome research at population scale is now capable of achieving the molecular detail needed to integrate gut microbial community profiles with biochemical, environmental, and human regulatory and immunological responses. This has been driven by the development of computational and experimental platforms that can reliably apply multi'omic profiling of the microbiome to tens of thousands of individuals with dietary, pharmaceutical, infectious, or chronic disease phenotypes of interest. I will discuss the methods that have made prospective microbiome epidemiology research possible at the Harvard Chan Microbiome in Public Health Center (HCMPH) and their application to inflammatory bowel disease during the "HMP2" IBD Multi'omics Database (IBDMDB) study and the Human Microbiome Bioactives Resource (HMBR). Together, these represent a community and research platform able to assess the gut and body-wide microbiome in large human populations and link individual microbial gene and biochemical products to pathway-specific mechanisms of inflammation and disease.