The HMP set out to discover and characterize the human microbiome, emphasizing oral, skin, vaginal, gastrointestinal, and respiratory sites.

It is hoped that the HMP will not only identify new ways to determine health and predisposition to diseases but also define the parameters needed to design, implement and monitor strategies for intentionally manipulating the human microbiota, to optimize its performance in the context of an individual's physiology.

[10] The Canadian Institutes of Health Research, through the CIHR Institute of Infection and Immunity, is leading the Canadian Microbiome Initiative to develop a coordinated and focused research effort to analyze and characterize the microbes that colonize the human body and their potential alteration during chronic disease states.

The goal of the iHMP was to produce resources to create a complete characterization of the human microbiome, with a focus on understanding the presence of microbiota in health and disease states.

[14] The project mission, as stated by the NIH, was as follows: The iHMP will create integrated longitudinal datasets of biological properties from both the microbiome and host from three different cohort studies of microbiome-associated conditions using multiple "omics" technologies.

[18] The Inflammatory Bowel Disease Multi'omics Data (IBDMDB) team was a multi-institution group of researchers focused on understanding how the gut microbiome changes longitudinally in adults and children suffering from IBD.

IBD is an inflammatory autoimmune disorder that manifests as either Crohn's disease or ulcerative colitis and affects about one million Americans.

[20] Researchers from Stanford University and the Jackson Laboratory of Genomic Medicine worked together to perform a longitudinal analysis on the biological processes that occur in the microbiome of patients at risk for Type 2 Diabetes.

[51] The announcement was accompanied with a series of coordinated articles published in Nature[52][53] and several journals including the Public Library of Science (PLoS) on the same day.

[57] From 242 healthy U.S. volunteers, more than 5,000 samples were collected from tissues from 15 (men) to 18 (women) body sites such as mouth, nose, skin, lower intestine (stool) and vagina.

Other studies using the HMP data and techniques include role of microbiome in various diseases in the digestive tract, skin, reproductive organs and childhood disorders.