21 The Integrative Human Microbiome Project
The Integrative Human Microbiome Project is an open access article published in Nature under the Creative Commons: By Attribution 4.0 License (http://creativecommons.org/licenses/by/4.0/).
The Integrative Human Microbiome Project
The Integrative HMP (iHMP) Research Network Consortium
Abstract
The NIH Human Microbiome Project (HMP) has been carried out over ten years and two phases to provide resources, methods, and discoveries that link interactions between humans and their microbiomes to health-related outcomes. The recently completed second phase, the Integrative Human Microbiome Project, comprised studies of dynamic changes in the microbiome and host under three conditions: pregnancy and preterm birth; inflammatory bowel diseases; and stressors that affect individuals with prediabetes. The associated research begins to elucidate mechanisms of host–microbiome interactions under these conditions, provides unique data resources (at the HMP Data Coordination Center), and represents a paradigm for future multi-omic studies of the human microbiome.
Main
Although the ’omics era has accelerated all aspects of biological research, its effects have been particularly apparent in studies of microbial communities and the human microbiome. In the 18 years since the publication of the first human genome, studies of the microbiome have grown from culture-based surveys of the oral cavity and gut to molecular profiles of microbial biochemistry in all ecological niches of the human body1,2,3. Epidemiology and model systems have been used to identify associations between changes in the microbiome and conditions ranging from autism4 to cancer5,6,7, and microbial and immunological mechanisms have been identified that affect, for example, the efficacy of drugs used to treat cardiac conditions8 or survival during graft-versus-host disease9.
Contemporary studies of the human microbiome have also been a source of basic biological and translational surprises, exposing a compelling range of novel findings and open questions. Every human being appears to carry their own, largely individual, suite of microbial strains10,11, which are acquired early in life12,13,14, differ between environments and populations15,16, and can persist for years17 or undergo relatively rapid transitions18. Microbial diversity manifests differently in different ecological niches of the body; for example, greater diversity is generally expected in the gut, but can be associated with dysbiotic states and risk of adverse events in the female reproductive tract. The microbiome can be perturbed by conditions such as inflammatory bowel disease and diabetes, but a variety of microbiome-linked health states, and the underpinnings of these links, remain unexplored. How dynamic is the microbiome during processes such as pregnancy or viral infection? Which changes in the microbiome represent causes rather than effects of changes in health? Which molecular elements