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. 2019 May 29;569(7758):641–648. doi: 10.1038/s41586-019-1238-8

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — The ten-year NIH Human Microbiome Project (HMP) program, organized into two phases (HMP1 and HMP2), developed reference sequences, multi-omic data sets, computational and statistical tools, and analytical and clinical protocols as resources for the broader research community. The HMP1 focused on the characterization of microbial communities from numerous body sites (oral, nasal, vaginal, gut, and skin) in a baseline study of healthy adult subjects, and included a set of demonstration projects that focused on specific diseases or disorders. The HMP2 expanded the repertoire of biological properties analysed for both host and microbiome in three longitudinal cohort studies of representative microbiome-associated conditions: pregnancy and preterm birth (vaginal microbiomes of pregnant women), inflammatory bowel diseases (gut microbiome) and prediabetes (gut and nasal microbiomes). These studies followed the dynamics of these conditions through multi-omic analyses of multiple measurement types over time, including changes in microbial community composition, viromics, metabolomic profiles, gene expression and protein profiles from both host and microbiome, and host-specific properties such as genetic, epigenomic, antibody, and cytokine profiles, along with other study-specific features. All sequences and multi-omic data, clinical information, and tools from both HMP1 and HMP2 are housed in the HMP Data Coordination Center (DCC) or referenced public or controlled-access repositories to serve as a central resource for the research community.