The Human Microbiome consists of all the organisms that comprise the many distinct microbial communities found on and in the human body. Early individual studies and the concerted initial steps of the Human Microbiome Project (HMP) have begun to define the extent of the diversity within these communities and the importance of their structure and temporal variation on human health. To establish the necessary foundation to measure the variation of communities and the functional consequences, we must: i) establish baseline measurements of these communities, including cataloging both the presence and prevalence of specific organisms and their gene content;ii) determine the physiological capabilities of each organism in the community by elaborating their gene content, to be able to interpret the functional significance of changes in community structure;iii) continue to develop new methods to characterize microbial communities and the organisms therein;and, iv) promote research in human metagenomics by engaging the research community and creating publicly available data and resources. We will take advantage of the explosive advances in new sequencing technologies to rapidly create a catalog of over 400 reference microbial genome sequences, including those of bacteria, eukaryotes, and viruses, as well as generate extensive community profiles from a number of human body sites with a focus on the oral and vaginal microbiome. We will also aggressively develop and apply new methods and technologies to further reduce the cost and expand the reach of the HMP. These data will be rapidly released to the public and, along with those of our collaborating partners in the HMP network, will define the Human Microbiome communities and provide baseline measurements for a wealth of subsequent experimental research.

Public Health Relevance

The ultimate goal of the HMP is to understand how microbial community structure and function determine normal human health, development, and disease, and can contribute to new diagnostic or therapeutic tools. To do this we must first generate large, public data sets that define the organisms commonly found in healthy human subjects, and measure the extent to which they vary and the reasons for this.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54HG004969-04
Application #
8266494
Study Section
Special Emphasis Panel (ZRG1-GGG-J (52))
Program Officer
Proctor, Lita
Project Start
2009-07-30
Project End
2014-04-30
Budget Start
2012-05-01
Budget End
2014-04-30
Support Year
4
Fiscal Year
2012
Total Cost
$639,871
Indirect Cost
$345,771
Name
Broad Institute, Inc.
Department
Type
DUNS #
623544785
City
Cambridge
State
MA
Country
United States
Zip Code
02142
Liu, Chaoyue; Wright, Benjamin; Allen-Vercoe, Emma et al. (2018) Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions. Genome Biol Evol 10:2255-2265
Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali et al. (2017) Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 550:61-66
Ward, Doyle V; Scholz, Matthias; Zolfo, Moreno et al. (2016) Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants. Cell Rep 14:2912-24
Sizova, Maria V; Chilaka, Amanda; Earl, Ashlee M et al. (2015) High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. Stand Genomic Sci 10:37
Franzosa, Eric A; Huang, Katherine; Meadow, James F et al. (2015) Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A 112:E2930-8
Taft, Diana H; Ambalavanan, Namasivayam; Schibler, Kurt R et al. (2015) Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants. PLoS One 10:e0130604
Blekhman, Ran; Goodrich, Julia K; Huang, Katherine et al. (2015) Host genetic variation impacts microbiome composition across human body sites. Genome Biol 16:191
Huang, Katherine; Brady, Arthur; Mahurkar, Anup et al. (2014) MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res 42:D617-24
Cuomo, Christina A; Rodriguez-Del Valle, Nuri; Perez-Sanchez, Lizaida et al. (2014) Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251). Genome Announc 2:
Coyne, Michael J; Zitomersky, Naamah Levy; McGuire, Abigail Manson et al. (2014) Evidence of extensive DNA transfer between bacteroidales species within the human gut. MBio 5:e01305-14

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