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Working on >Human Microbiome Project
Freeman.all/sandbox (HMP) | |
---|---|
Owner | US National Institutes of Health |
Launched | 2008 |
Closed | 2017 |
Website | hmpdacc |
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,[1] 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.[2]
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.[3]
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.[4] 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.[4][5] 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").[6][7]
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.[8]
The HMP has been described as "a logical conceptual and experimental extension of the Human Genome Project."[8] In 2007 the HMP was listed on the NIH Roadmap for Medical Research[9] 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.[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.[11]
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.
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:[12]
The HMP1 closed in 2012.
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