The Human Microbiome Project (HMP) Fundamentally Changed Our Perspective on the Human Microbiome

The Human Microbiome Project (HMP) was a research program funded by the U.S. National Institutes of Health (NIH) to investigate and characterize the microorganisms associated with healthy humans.¹

One of its goals was to establish a reference framework for future research into the human microbiome.

Microbial communities from different body sites were studied, including the gastrointestinal tract, oral cavity, skin, nasal passages, and urogenital tract. Advanced sequencing and genomic technologies were used throughout the project.

One of the most important publications was the 2012 Nature paper “Structure, function and diversity of the healthy human microbiome.” The study demonstrated:

substantial individual variation in the microbial communities of healthy people; and pronounced site-specific specialization of microbial ecosystems throughout the body.

In addition, the project generated extensive genomic and functional datasets that became important reference resources for subsequent microbiome research.

What exactly was studied?

Baseline characterization: Mapping the normal microbiota across five major body regions—the oral cavity, nasal cavity, skin, gastrointestinal tract, and urogenital tract—in hundreds of healthy adults.

Reference genomes: Sequencing more than 3,000 bacterial reference genomes to build robust databases for culture-independent metagenomic analysis.

Disease correlations: Investigating how changes in microbial populations correlate with specific clinical conditions.

Technology & ethics: Developing advanced computational bioinformatics tools and assessing the ethical, legal, and social implications (ELSI) of microbiome research. What was the major shift brought about by the HMP's findings?

Rather than searching for a single, universal composition of a “normal” microbiome, it became increasingly clear that the microbiome is a dynamic ecosystem with substantial individual variation and partially shared functional capabilities.

This distinction remains highly important today when interpreting commercial microbiome tests.

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