The Human Microbiome

On almost every surface of the human body, both inside and out, are thriving ecosystems of microorganisms: bacteria, fungi and archaea. In fact, there are so many of them that they outnumber our own body cells ten to one, enough to collectively form one to three percent of the body mass of an average human adult. But that’s no reason to go and repeatedly scrub down your body with soap — the vast majority of these microorganisms coexist in harmony with the human body, even aiding in vital functions for human health. Simply put, we could not live a comfortable life without them.

Perhaps the most diverse hub of human microbiota lies in the gut, where a vibrant community of bacteria thrives. These organisms boost human health by undertaking a wide variety of digestive and immune tasks. For example, the human body by itself is unable to digest certain carbohydrates, including some fibers and starches. Bacteria come in to fill this gap: Prevotella bacteria ferment the carbohydrates into smaller products that our gut is then able to absorb. As an added bonus, they even synthesize vitamins such as biotin and folate. Other bacteria can stimulate growth of our intestinal lining by altering the expression of cell surface proteins. This thickens the protective layer of mucosa, reducing the risk of injury to our insides. And if that weren’t enough, bacteria such as Bacteroidetes and Firmicutes play a protective role by preventing harmful organisms from colonizing our guts. Through a process known as competitive exclusion, the harmful organisms aren’t able to grow due to competition from the helpful bacteria.


Microbes colonize every area of our bodies, playing crucial roles in digestion, immunity, and many other physiological functions.

When the normal makeup of our gut microbiota is thrown out of equilibrium, there can be some very severe health consequences. For example, if normal gut bacteria aren’t present, an invasion of Clostridium difficile may cause severe diarrhea and colitis (inflammation of the large intestine). The course of treatment is clear: restore the normal gut microbiota to crowd out the harmful pathogens. The way doctors are actually reintroducing these protective bacteria, however, may seem peculiar at first. The process is known as fecal bacteriotherapy, or more crudely, a stool transplant. This is exactly what it sounds like: fecal matter from a healthy donor is introduced, through whatever route, into the diseased recipient’s body. The helpful bacteria in the transplant colonize the gut, in the process displacing and thus eradicating the C. difficile. Several studies have found fecal transplants to be highly effective, in addition to being much cheaper and simpler to administer than antibiotics. The FDA even regulates human feces as an experimental drug.

Given the enormous importance of our bodies’ microbial residents, scientists have taken an ever greater interest in their diversity, metabolism and genomes. In 2008, the National Institutes of Health launched the Human Microbiome Project with the goal of identifying and sequencing the genomes of the microbiota found in the human body. With this information, scientists hope to develop a greater understanding of how changes in the human microbiome affect human health and disease. Some important findings have already been made. One study looked at the genetic sequences of gut microbiota taken from lean and obese twins. It was found that obesity is associated with a heightened expression of digestive enzymes that increases the efficiency of calorie harvest. Another study found that children with type I diabetes had microbiomes that were significantly less diverse and more unstable than healthy peers. This discovery suggests both a novel method for early diagnosis and a method for preventing disease progression by restoring the balance of microbiota.

As our understanding of the human microbiome grows, it has become increasingly clear that we cannot separate human genetics from the wider context of its microscopic residents. These microbiota do more than just take advantage of the warm environment of the human body — they fundamentally shape the type of people we are.

About The Author

Daniel Liu
Editor-in-Chief emeritus

Hailing from the quiet suburbs of Potomac, Maryland, Daniel is the former editor-in-chief of Innovation. He studies molecular biology at Princeton, with a particular research interest in cancer stem cell biology and the molecular pathways governing metastasis. Outside of academics, Daniel also enjoys painting and drawing in his free time.