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The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbial flora involved in human health and disease. Launched in 2008, the first phase (HMP1) was a five-year project that focused on identifying and characterizing human microbial flora. The second phase, known as the integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016, with the iHMP closing in 2017.

Important components of the HMP were culture-independent methods of microbial community characterization, such as metagenomics (which provides a broad genetic perspective on a single microbial community), as well as extensive whole genome sequencing (which provides a "deep" genetic perspective on certain aspects of a given microbial community, i.e. of individual bacterial species). The latter served as reference genomic sequences — 3000 such sequences of individual bacterial isolates are currently planned — for comparison purposes during subsequent metagenomic analysis. The project also financed deep sequencing of bacterial 16S rRNA sequences amplified by polymerase chain reaction from human subjects.

Introduction
Prior to the HMP launch, it was often reported in popular media and scientific literature that there are about 10 times as many microbial cells and 100 times as many microbial genes in the human body as there are human cells; this figure was based on estimates that the human microbiome includes around 100 trillion bacterial cells and an adult human typically has around 10 trillion human cells. In 2014 the American Academy of Microbiology published a FAQ that emphasized that the number of microbial cells and the number of human cells are both estimates, and noted that recent research had arrived at a new estimate of the number of human cells at around 37 trillion cells, meaning that the ratio of microbial to human cells is probably about 3:1. In 2016 another group published a new estimate of ratio as being roughly 1:1 (1.3:1, with "an uncertainty of 25% and a variation of 53% over the population of standard 70 kg males").

Despite the staggering number of microbes in and on the human body, little was known about their roles in human health and disease. Many of the organisms that make up the microbiome have not been successfully cultured, identified, or otherwise characterized. Organisms thought to be found in the human microbiome, however, may generally be categorized as bacteria, members of domain Archaea, yeasts, and single-celled eukaryotes as well as various helminth parasites and viruses, the latter including viruses that infect the cellular microbiome organisms (e.g., bacteriophages). The HMP set out to discover and characterize the human microbiome, emphasizing oral, skin, vaginal, gastrointestinal, and respiratory sites.

The HMP will address some of the most inspiring, vexing and fundamental scientific questions today. Importantly, it also has the potential to break down the artificial barriers between medical microbiology and environmental microbiology. 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.

The HMP has been described as "a logical conceptual and experimental extension of the Human Genome Project." In 2007 the HMP was listed on the NIH Roadmap for Medical Research as one of the New Pathways to Discovery. Organized characterization of the human microbiome is also being done internationally under the auspices of the International Human Microbiome Consortium. 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.

Contributing Institutions
The HMP involved participation from many research institutions, including Standford Univeristy, the Broad Institute, Virginia Commonwealth University, Washington University, Northeastern University, MIT, the Baylor College of Medicine, and many others. Contributions included data evaluation, construction of reference sequence data sets, ethical and legal studies, technology development, and more.

Phase One (2008-2012)
The HMP1 included research efforts from four institutions: the Broad Institute, the Baylor College of Medicine, Washington University School of Medicine, and the J. Craig Venter Institute, as well as contributions from the NIH Data and Analysis and Coordination Center (DACC). The HMP1 set the following goals:


 * Develop a reference set of microbial genome sequences and to perform preliminary characterization of the human microbiome
 * Explore the relationship between disease and changes in the human microbiome
 * Develop new technologies and tools for computational analysis
 * Establish a resource repository
 * Study the ethical, legal, and social implications of human microbiome research

The HMP1 closed in 2012.

Integrative Human Microbiome Project
In 2014, the NIH launched the second phase of the project, known as the Integrative Human Microbiome Project (iHMP). 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. 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."The project encompassed three sub-projects carried out at multiple institutions. Study methods included 16S rRNA gene profiling, whole metagenome shotgun sequencing, whole genome sequencing, metatranscriptomics, metabolomics/lipidomics, and immunoproteomics. The key findings of the iHMP are due for publishing in 2018.

Pregnancy & Preterm Birth
The Vaginal Microbiome Consortium team at Virginia Commonwealth University led research on the Pregnancy & Preterm Birth project with a goal of understanding how the microbiome changes during the gestational period and influences the neonatal microbiome. The project was also concerned with the role of the microbiome in the occurrence of preterm births, which, according to the CDC, account for nearly 10% of all births and constitutes the second leading cause of neonatal death. The project received $7.44 million in NIH funding.

Onset of Inflammatory Bowel Disease (IBD)
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. Research participants included cohorts from Massachusetts General Hospital, Emory University Hospital/Cincinnati Children's Hospital, and Cedars-Sinai Medical Center.

Onset of Type 2 Diabetes (T2D)
Researchers from Standford 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. T2D affects nearly 20 million Americans with at least 79 million pre-diabetic patients, and is partially characterized by marked shifts in the microbiome compared to healthy individuals. The project aimed to identify molecules and signaling pathways that play a role in the etiology of the disease.