The Human Microbiome Project (HMP) is a United States

United States

The United States of America is a federal constitutional republic comprising fifty states and a federal district...

 National Institutes of Health

National Institutes of Health

The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...

 initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and disease

Disease

A disease is an abnormal condition affecting the body of an organism. It is often construed to be a medical condition associated with specific symptoms and signs. It may be caused by external factors, such as infectious disease, or it may be caused by internal dysfunctions, such as autoimmune...

d humans (their microbial flora). Launched in 2008, it is a five-year project, best characterized as a feasibility study, and has a total budget of $115 million. The ultimate goal of this and similar NIH-sponsored microbiome projects is to test if changes in the human microbiome are associated with human health or disease. This topic is currently not well-understood.

Important components of the Human Microbiome Project will be culturing-independent methods of microbial community characterization, such as metagenomics

Metagenomics

Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures...

 (which provides a broad genetic perspective on a single microbial community), as well as extensive whole-genome

Genome

In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

 sequencing

DNA sequencing

DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....

 (which provides a "deep" genetic perspective on certain aspects of a given microbial community, i.e., of individual bacterial species). The latter will serve as reference genomic sequences

Genomics

Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...

 — 600 such sequences of individual bacterial isolates are currently planned — for comparison purposes during subsequent metagenomic analysis. The microbiology

Microbiology

Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell , cell clusters or no cell at all . This includes eukaryotes, such as fungi and protists, and prokaryotes...

 of five body sites will be emphasized: oral

Oral microbiology

Oral microbiology is the study of the microorganisms of the oral cavity and the interactions between the oral microorganisms with each other and with the host. Of particular interest is the role of oral microorganisms in the two major dental diseases: dental caries and periodontal disease.The mouth...

, skin

Skin flora

The skin flora are the microorganisms which reside on the skin. Most research has been upon those that reside upon the 2 square metres of human skin. Many of them are bacteria of which there are around 1000 species upon human skin from 19 phyla. The total number of bacteria on an average human has...

, vaginal

Vaginal flora

The bacteria that colonize the vagina, collectively referred to as the vaginal microbiome, were discovered by the German gynecologist Albert Döderlein in 1892. The amount and type of bacteria present have significant implications for a woman's overall health...

, gut

Gut flora

Gut flora consists of microorganisms that live in the digestive tracts of animals and is the largest reservoir of human flora. In this context, gut is synonymous with intestinal, and flora with microbiota and microflora....

, and nasal

Nasal cavity

The nasal cavity is a large air filled space above and behind the nose in the middle of the face.- Function :The nasal cavity conditions the air to be received by the other areas of the respiratory tract...

/lung

Lung

The lung is the essential respiration organ in many air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located near the backbone on either side of the heart...

. The project also financed deep sequencing of bacterial 16S rRNA sequences amplified by PCR from human subjects.

Context and importance of HMP

Total microbial cells

Cell (biology)

The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....

 found in association with humans may exceed the total number of cells making up the human body

Human body

The human body is the entire structure of a human organism, and consists of a head, neck, torso, two arms and two legs.By the time the human reaches adulthood, the body consists of close to 100 trillion cells, the basic unit of life...

 by a factor of ten-to-one. The total number of genes associated with the human microbiome could exceed the total number of human genes by a factor of 100-to-one. Many of these organisms have not been successfully cultured

Microbiological culture

A microbiological culture, or microbial culture, is a method of multiplying microbial organisms by letting them reproduce in predetermined culture media under controlled laboratory conditions. Microbial cultures are used to determine the type of organism, its abundance in the sample being tested,...

, identified, or otherwise characterized. Organisms expected to be found in the human microbiome, however, may generally be categorized as bacteria

Bacteria

Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

 (the majority), members of domain

Domain (biology)

In biological taxonomy, a domain is the highest taxonomic rank of organisms, higher than a kingdom. According to the three-domain system of Carl Woese, introduced in 1990, the Tree of Life consists of three domains: Archaea, Bacteria and Eukarya...

 Archaea

Archaea

The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...

, yeasts, and single-celled eukaryotes

Protozoa

Protozoa are a diverse group of single-cells eukaryotic organisms, many of which are motile. Throughout history, protozoa have been defined as single-cell protists with animal-like behavior, e.g., movement...

 as well as various helminth parasites

Parasitism

Parasitism is a type of symbiotic relationship between organisms of different species where one organism, the parasite, benefits at the expense of the other, the host. Traditionally parasite referred to organisms with lifestages that needed more than one host . These are now called macroparasites...

 and virus

Virus

A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...

es, the latter including viruses that infect the cellular microbiome organisms (e.g., bacteriophages, the viruses of bacteria).

"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."http://www.nature.com/nature/journal/v449/n7164/full/nature06244.html

The HMP has been described as "a logical conceptual and experimental extension of the Human Genome Project

Human Genome Project

The Human Genome Project is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional...

"http://www.nature.com/nature/journal/v449/n7164/full/nature06244.html. In 2007 the Human Microbiome Project 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

Canadian Institutes of Health Research

Canadian Institutes of Health Research is the major federal agency responsible for funding health research in Canada. It is the successor to the Medical Research Council of Canada. It aims to create new health knowledge, and to translate that knowledge from the research setting into real world...

, 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 its potential alteration during chronic disease state.

Distributed computing initiative

The distributed computing

Distributed computing

Distributed computing is a field of computer science that studies distributed systems. A distributed system consists of multiple autonomous computers that communicate through a computer network. The computers interact with each other in order to achieve a common goal...

 project World Community Grid

World Community Grid

World Community Grid is an effort to create the world's largest public computing grid to tackle scientific research projects that benefit humanity...

 now operates a human microbiome application, which can be run as background software on home computers with World Community Grid installed.

Related entries

• Bacterial disease
• Body odor
  Body odor
  Body odor or body odour, sometimes colloquially abbreviated as B.O., is the smell of bacteria growing on the body. The bacteria multiply rapidly in the presence of sweat, but sweat itself is almost completely odorless to humans....
  
  
• Environmental microbiology
  Environmental microbiology
  Environmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas...
  
  
• Genome project
  Genome project
  Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features...
  
  
• Genomics
  Genomics
  Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
  
  
• Gut flora
  Gut flora
  Gut flora consists of microorganisms that live in the digestive tracts of animals and is the largest reservoir of human flora. In this context, gut is synonymous with intestinal, and flora with microbiota and microflora....
  
  
• Human flora
• Infectious disease
  Infectious disease
  Infectious diseases, also known as communicable diseases, contagious diseases or transmissible diseases comprise clinically evident illness resulting from the infection, presence and growth of pathogenic biological agents in an individual host organism...
  
  
• List of Archaea genera
• List of Bacteria genera
• List of clinically important bacteria
• List of infectious diseases
• List of human diseases associated with infectious pathogens
• List of sequenced archaeal genomes
• List of sequenced prokaryotic genomes
• List of sequenced eukaryotic genomes
• List of viruses
• Medical microbiology
  Medical microbiology
  Medical microbiology is both a branch of medicine and microbiology which deals with the study of microorganisms including bacteria, viruses, fungi and parasites which are of medical importance and are capable of causing infectious diseases in human beings...
  
  
• Metagenomics
  Metagenomics
  Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures...
  
  , links to references follow…
  • …of bodies
  • …of extreme environments
  • …of marine ecosystems
  • …of sediments
• Microbial ecology
  Microbial ecology
  Microbial ecology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses....
  
  
• Microflora
• Oral microbiology
  Oral microbiology
  Oral microbiology is the study of the microorganisms of the oral cavity and the interactions between the oral microorganisms with each other and with the host. Of particular interest is the role of oral microorganisms in the two major dental diseases: dental caries and periodontal disease.The mouth...
  
  
• Skin flora
  Skin flora
  The skin flora are the microorganisms which reside on the skin. Most research has been upon those that reside upon the 2 square metres of human skin. Many of them are bacteria of which there are around 1000 species upon human skin from 19 phyla. The total number of bacteria on an average human has...
  
  
• Superorganism
  Superorganism
  A superorganism is an organism consisting of many organisms. This is usually meant to be a social unit of eusocial animals, where division of labour is highly specialised and where individuals are not able to survive by themselves for extended periods of time. Ants are the best-known example of...
  
  
• Vaginal flora
  Vaginal flora
  The bacteria that colonize the vagina, collectively referred to as the vaginal microbiome, were discovered by the German gynecologist Albert Döderlein in 1892. The amount and type of bacteria present have significant implications for a woman's overall health...
  
  

External links

• Data Analysis and Coordination Center
• Human Microbiome Project
• The CIHR Canadian Microbiome Initiative
• The International Human Microbiome Consortium
• 2008, Request for applications, Human Microbiome Demonstration Projects (UH2/UH3) (May 22, 2008 = deadline for submission)
• 2008, Request for applications, Metagenomic Analyses of the Oral Microbiome (R01)
• 2007, Article, "The Human Microbiome Project", as published in Nature
• 2006, Lay summary of colon microbiome study (the actual study: Gill et al., 2006)
• 2006 (or 2005), Proposal, Human Gut Microbiome Initiative (HGMI)
• Olivia Judson Microbes ‘R’ Us New York Times 22 July 2009