production of bread, cheese, yogurt, chocolate, coffee, beer); soil production and regeneration; pollutant and toxin degradation; oxygen production; and plant, animal, and human health. Lita Proctor remarked, “Every living thing on this planet has a microbiome … associated microbes that maintain health and well-being.” She defined the microbiome as the full complement of microbes (bacteria, viruses including bacteriophages, fungi, protozoa) and their genes and genomes in or on the human body.
That there are beneficial microbes living in and on the human body is not a new concept. Proctor traced the notion as far back as van Leeuwenhoek. “Four centuries ago,” she said, “we realized that there are lots of microbes associated with our bodies. But it has taken four centuries for us to really look at these microbial communities in any depth and to consider them not just as pathogens.” While advances in sequencing and other technologies are no doubt contributing to this burgeoning research, Proctor acknowledged the significant contributions of other scientific disciplines. Notably, environmental microbiology and microbial ecology and evolution “really set the conceptual framework for … recognition that the vast majority of microbes that live in and on us are not germs or pathogens but belong there and actually help maintain our health and well-being.”
The Human Microbiome Project
The HMP was initiated by the National Institutes of Health (NIH) in the fall of 2007, with the majority of funding ($153 million of the $173 million to date2) coming from the NIH Common Fund. The Common Fund is designed to catalyze new and emerging areas of science. The HMP used sequencing to examine the microbes associated with the human body. Its main purpose is to create resources for the research community, with a focus on building a “healthy cohort” reference database of human microbiome genome sequences (known as metagenomic sequences), computational tools to analyze complex metagenomic sequences, and clinical protocols for sampling the human microbiome. Other resources include the suite of demonstration projects that provide data on the association of microbiomes with disease. The “healthy cohort” project is a sequencing study of the microbiome based on sampling from 5 major body sites (18 subsites): nasal passages, oral cavities, skin, gastrointestinal (GI) tract, and urogenital tract. The body sites were selected by a panel of experts in human microbiology. The study recruited 300 adults (of whom half were women and half were men) who were clinically verified to be free of overt disease. About 20 percent of the study participants self-identified as a racial minority and 10 percent as Hispanic. Each participant was sampled up to three times
2 As of February 2012 (i.e., at the time of the workshop).