NIH announces complete mapping of microorganisms that infect humans

Robin Wulffson MD's picture
infection, bacteria, viruses, Human Microbiome Project , DNA

The human body is home to trillions of microorganisms. On June 13, a consortium of researchers affiliated with the National Institutes of Health (NIH) announced that they had mapped the normal microbial makeup of healthy humans.

The human body is home to trillions of microorganisms; they inhabit the skin, the mouth, the entire intestinal tract, and the nasal passages. Sometimes, they case illnesses ranging from mild to severe; however, most of the time they live in harmony with their human host and some provided functions necessary for human survival. On June 13, a consortium of researchers affiliated with the National Institutes of Health (NIH) announced that they had mapped the normal microbial makeup of healthy humans.

The mapping has yielded a wealth of information. For example, the investigators found that nearly everyone routinely carries pathogens, microorganisms known to cause illnesses. In these healthy individuals, the pathogens cause no disease; rather, they simply coexist with the rest of the human microbiome (the collection of all microorganisms living in the human body). This discovery presents a challenge: the researchers must now determine why some pathogens turn deadly and under what conditions. The knowledge is likely to revise current concepts of how microorganisms cause disease.

The Human Microbiome Project (HMP) Consortium is comprised of scientists from nearly 80 universities and scientific institutions report; the current project is the result of five years of research. “Like 15th Century explorers describing the outline of a new continent, HMP researchers employed a new technological strategy to define, for the first time, the normal microbial makeup of the human body,” noted NIH Director Francis S. Collins, MD, Ph.D. He added, “HMP created a remarkable reference database by using genome sequencing techniques to detect microbes in healthy volunteers. This lays the foundation for accelerating infectious disease research previously impossible without this community resource.”


To delineate the normal human microbiome, the researchers sampled 242 healthy US volunteers (129 male, 113 female); they collected tissue samples from 15 body sites in men and 18 body sites in women. They collected up to three samples from each volunteer at sites such as the mouth, nose, skin (two behind each ear and each inner elbow), and lower intestine (stool), and three vaginal sites in women; each body site can be inhabited by markedly different organisms.

Historically, physicians studied microorganisms in their patients by swabbing a body area and growing them in culture. According to the NIH, this process typically identifies only a few microbial species; because they are hard to grow in the laboratory. For example, Neisseria gonorrhoeae , the organism responsible for gonorrhea requires specific nutrients and a high level of carbon dioxide to grow. In the HMP project, the investigators purified all human and microbial DNA in each of more than 5,000 samples and analyzed them with DNA sequencing machines. With the aid of computers, researchers sorted through the 3.5 terabases of genome sequence data to identify specific genetic signals found only in bacteria: the variable genes of bacterial ribosomal RNA called 16S rRNA. Bacterial ribosomal RNA helps form the cellular structures that manufacture protein and can identify the presence of different microbial species. This allowed the researchers to ignore material of human origin and analyze only the bacterial DNA. They were also able to evaluate the metabolic activity of the organisms.

Of interest, the researchers also found that the microbes inhabiting the human body are more responsible for human survival than humans are. The human genome carries some 22,000 protein-coding genes; however, the researchers estimate that the human microbiome contributes approximately 8 million unique protein-coding genes or 360 times more bacterial genes than human genes. The presence of these bacteria is critical for human survival. For example, genes carried by bacteria in the gastrointestinal tract allow humans to digest foods and absorb nutrients that otherwise would be unavailable. The investigators were surprised to discover that the distribution of microbial metabolic activities is more important than the species of microbes providing them. In the healthy gastrointestinal tract, for example, there will always be a population of bacteria needed to help digest fats; however, it may not always be the same bacterial species performing this function. When an individual is sick or takes antibiotics, the species that comprise the microbiome may shift substantially as one bacterial species or another is affected; however, eventually, the microbiome returns to a state of equilibrium, even if the previous composition of bacterial types does not.

The researchers note that by understanding how microorganisms are modified by individual lifestyle, environmental exposure, as well as interaction with human genes and disease is likely to lead to new strategies, medicines, and foods to maintain health and treat disease. For example, by determining which microbes in the intestinal tract regulate functions such as the digestion of fat or proteins could help in the fight against obesity. A better understanding of the bacteria Clostridium difficile, which attacks hospital patients, could provide better tools to treat and prevent hospital infections

Reference: National Institutes of Health