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The Healthy Human Microbiome

Researchers have mapped the normal bacteria that live in and on the healthy human body. The accomplishment sets the stage for better understanding how bacterial communities affect human health and disease.

The human body is host to trillions of microbes. These microbes outnumber the body’s cells by 10 to 1. Most of the time they are beneficial to human health, but sometimes they can cause illness. Scientists are using new genomic techniques to study these microbial communities and their genes, which collectively are known as the microbiome.

The Human Microbiome Project (HMP) was launched by NIH in 2007 to characterize the microbes found in different regions of the body, including the nose, mouth, skin, digestive tract and vagina. Researchers from almost 80 universities and scientific institutions described 5 years of research in a series of coordinated reports published online on June 13, 2012, in Nature and several journals in the Public Library of Science.

The scientists studied the microbes of 242 healthy adult volunteers by collecting tissue from 15 body sites in men and 18 in women. The sites included the nose, mouth, skin, stool from the lower intestine, and 3 vaginal sites in women. Bacteria were identified by extracting DNA from each sample and then analyzing a bacteria-specific gene called the 16S ribosomal RNA gene. The researchers also did more complete sequencing for about 800 reference strains.

The scientists found that more than 10,000 microbial species occupy the human body. They estimated that the microbiome provides more genes that contribute to human survival than the human genome itself provides (8 million vs. 22,000). Humans need bacterial genes to aid in basic processes such as digestion.

A surprising finding involved microbial metabolism. “It appears that bacteria can pinch hit for each other,” says Dr. Curtis Huttenhower of Harvard School of Public Health and lead co-author for one of the papers in Nature. “It matters whether the metabolic function is present, not which microbial species provides it.”

Several clinical studies using project data have been completed. Researchers at the Baylor College of Medicine, for example, compared changes in the vaginal microbiome of 24 pregnant women with 60 women who weren't pregnant. They found less species diversity in the pregnant women. This suggests that the vaginal microbiome may have evolved to make a healthier passage for the newborn.

In another study, researchers at the Washington University School of Medicine explored the human virome, the viral component of the human microbiome. They analyzed viruses in the blood and nasal swabs of children with unexplained fevers, a common problem in children under 3. Feverish children had nasal samples with up to 5 times more viral DNA than children without fever. This suggests that a quick test for viral load may help children avoid potentially harmful antibiotic treatment for a fever caused by viruses. 

“Enabling disease-specific studies is the whole point of the Human Microbiome Project,” says Dr. Barbara Methé of the J. Craig Venter Institute, lead co-author for one of the Nature papers. “Now that we understand what the normal human microbiome looks like, we should be able to understand how changes in the microbiome are associated with, or even cause, illnesses.”