The Human Microbiome Project is a five-year research collaboration between 200 scientists at 80 universities and scientific institutions, all funded with $153 million by the National Institutes of Health (NIH) with the aim of, “characterizing the microbial communities found at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract, and to analyze the role of these microbes in human health and disease.”

The project began in 2007 and has just been “completed,” with the publication of 14 scientific papers in medical journals this past week. By completed, I mean that the discoveries made by this group, although immense in scope due to the amount of data garnered, only begin to scratch the surface of what we know about the human microbiome and how it functions in relation to health and disease.

The findings of this latest research, which I will begin to summarize here, set the foundation for what will be a fascinating quest, through research and yet more discovery, of the depths of complexity that is our microbiome. As Dr. Barnett Kramer, director of the division of cancer prevention at the National Cancer Institute stated, “we may just serve as packaging” for our microbiome. Our microbes are truly in control.

The Human Microbiome Project sampled up to 18 different body sites from five different areas of the body—airways, skin, oral cavity, digestive tract, and vagina—in 242 healthy humans aged 18 to 40 years.1 Traditionally, microbes have been identified using culture-based methods, a process that requires organisms to remain alive in the laboratory, thus greatly limiting the wide range of microbial species identified. Instead, the researchers utilized relatively new DNA sequencing techniques to identify the full array of bacteria present. They say they have identified between 81 and 99 percent of all microbial genera in healthy Western adults.

The microbial communities were found to be remarkably diverse. Not only did the diversity differ substantially from body site to body site, it also differed greatly from person to person. The greatest similarities between people were seen in those with similar ethnic/racial backgrounds, and, interestingly, in the saliva of people living in the same communities.2 Also, the greatest diversity was found in the oral cavity, and the least diversity was found in the vagina (thought to be due to the tight regulation of vaginal conditions required for health).

Not only did the researchers study microbial composition, but they also examined functional status of the microbes based on the protein coding of the microbial DNA. As it turns out, our bacteria contribute far more genes responsible for human survival than do our own DNA—360 times more, to be exact. “Humans don’t have all the enzymes we need to digest our own diet,” said Lita Proctor, PhD, Human Microbiome Project program manager at the National Human Genome Research Institute. “Microbes in the gut break down many of the proteins, lipids, and carbohydrates in our diet into nutrients that we can then absorb. Moreover, the microbes produce beneficial compounds, like vitamins and anti-inflammatories that our genome cannot produce.”

As it turns out, the greatest similarities were found regarding these functions of the microbes. That is, certain functions are always needed in certain areas of the body, like carbohydrate digestion in the gut, but different microbes can perform these same functions. “It appears that bacteria can pinch hit for each other,” said Curtis Huttenhower, Ph.D., of Harvard School of Public Health and lead co-author for one of the papers in the journal Nature. “It matters whether the metabolic function is present, not which microbial species provides it.”

The studies also looked at certain conditions under which microbial communities change, such as after antibiotic therapy, just before birth, or in children with fevers. These initial studies are only the beginning. “Enabling disease-specific studies is the whole point of the Human Microbiome Project,” said Barbara Methé, PhD, of the J Craig Venter Institute, Rockville, MD, and lead co-author of the Nature paper on the framework for current and future human microbiome research. “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.”

Kudos to these tenacious scientists for their groundbreaking work that will serve as a stepping stone to the discovery of a whole new universe—the microbiome: changing the face of medicine as we know it. I look forward to the ride.


  1. The Human Microbiome Consortium, “Structure, function and diversity of the healthy human microbiome.” Nature. 2012 June 14;486:207–214.
  2. K Li, et al., “Analyses of the Microbial Diversity across the Human Microbiome.” PLoS One. 2012 June;7(6):e32118.