NIH Human Microbiome Project Defines Normal Bacteria Makeup of the Body

VCU researchers contribute to scientific reports in Nature and PLoS

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The National Institutes of Health’s Human Microbiome Project Consortium, which includes more than 200 investigators from nearly 80 multidisciplinary research institutions – including Virginia Commonwealth University – has mapped, for the first time, the normal microbial makeup of healthy humans.

The findings will be shared in a series of coordinated scientific reports published tomorrow in the journal Nature and several Public Library of Science publications. Read the NIH news release at

The project has enabled researchers to gain a more complete picture of the community of microorganisms inhabiting the human body and advance knowledge about health and susceptibility to a number of diseases. Ultimately, this may help researchers develop strategies for new therapies that manipulate the human microbiome and improve human health in the future.

“Like 15th century explorers describing the outline of a new continent, HMP researchers employed a new technological strategy to comprehensively define, for the first time, the normal microbial makeup of the human body,” said NIH director Francis S. Collins, M.D., Ph.D.

“Human Microbiome Project created a remarkable reference database by using genome sequencing techniques to directly detect microbes in healthy volunteers. This lays the foundation for accelerating infectious disease research previously impossible without this community resource.”

For the past three years, researchers at VCU have been studying how microorganisms found in the vagina influence health and disease in women.

The VCU project is one of eight across the country that were launched in 2009 as part of the Human Microbiome Project, a $153-million, five-year effort started in 2008 as part of the NIH Common Fund’s Roadmap for Medical Research.

“Through this research, we ultimately hope to more clearly understand the impact of the microbiome and how we may be able to ultimately change the course of disease or provide improved treatment strategies to help patients,” said Gregory Buck, Ph.D., director of the VCU Center for the Study of Biological Complexity and the principal investigator for the microbiome project at VCU.

The VCU team, which includes women’s health experts, physicians, pathogenic microbiologists, geneticists, epidemiologists, biostaticians and systematic biologists, has been working to determine the contribution of human genetics to defining the composition of vaginal microorganisms, and how changes in the vaginal microbiome are associated with disease or common physiological states such as pregnancy and menopause, or abnormal conditions such as pre-term labor and diabetes.

One unique component to the project is that the group has been using twin research to examine the vaginal microbiome. Currently, the team is recruiting participants for the study through the VCU Mid-Atlantic Twin Registry and women’s clinics of the VCU Medical Center and the Virginia Department of Health. 

As a part of the Human Microbiome Project, NIH funded a number of studies to look for associations of the microbiome with diseases, and several PLoS papers include medical results. In addition to the vaginal microbiome being studied at VCU, other institutions are studying and collecting data on the microbiota inhabiting the gastrointestinal tract, oral cavity, naso-pharyngeal tract and skin as part of the NIH Human Microbiome Project.

Below is a sample of some of the earliest results from clinical studies using microbiome data to study their role in specific illnesses.

For example, researchers at VCU have collected vaginal samples from more than 4,000 women visitors to local women’s clinics and found an unexpectedly large diversity of bacterial species in an environment once thought to be largely homogeneous. Many of these species have never before been observed, cultured or characterized.

As some of these bacteria have pathological implications, the team is using advanced never-before applied technologies to characterize their genomes and metabolic and pathogenic potentials. In parallel, they are associating these specific bacterial species and the overall microbiome profiles with specific abnormal physiological and infectious disease states, including but not limited to bacterial vaginosis, sexually transmitted diseases, preterm birth, diabetes and obesity. One of the bacterial species they have characterized was on the list of the “100 most wanted” human microbes.

Findings published in the Nature and PLoS journals from other institutions include:

  • The Baylor College of Medicine in Houston compared changes in the vaginal microbiome of 24 pregnant women with 60 healthy controls and found that the vaginal microbiome undergoes a dramatic shift in bacterial species in preparation for birth, characterized by decreased species diversity. A newborn is a bacterial sponge as it populates its own microbiome after leaving the sterile womb. Passage through the birth canal gives the baby its first dose of microbes, so it may not be surprising that the vaginal microbiome evolved to make it a healthy passage.
  • Researchers at the Washington University School of Medicine in St. Louis examined the nasal microbiome of children with unexplained fevers, a common problem in children under three years old. Nasal samples from the sick kids contained 1.5- to 5-fold more viral DNA than children without fever, and from a wider range of virus species. Scientists know that viruses have ideal temperature ranges to reproduce. Fevers may be part of the body’s defense against pathogenic viruses and rapid tests for viral load may help children avoid treatment with useless antibiotics which don’t actually have any effect on viruses and that may actually disrupt their healthy microbiome.
  • The microbiome may also play a role in inflammatory bowel diseases such as Crohn’s disease. Researchers at University of Maryland School of Medicine in Baltimore compared the microbiomes of twins with and without Crohn’s disease. The results suggest that the microbiome does mediate, at least in part, the effects of genetic and environmental factors on irritable bowel disease.

The cross-disciplinary cluster of researchers at VCU is more than 40-people strong and from across campuses. Co-principal investigators on the grant at VCU are Jerome F. Strauss III, M.D., Ph.D., dean of the VCU School of Medicine; Cynthia Cornelissen, Ph.D., from the Department of Microbiology and Immunology; and Lindon Eaves, Ph.D., from the Department of Human and Molecular Genetics.

For more information about Human Microbiome Project, visit