As Many Microbes as Body Cells
Your body is not just you. It hosts an estimated 38 trillion bacterial cells. Your own human cells number around 30 to 40 trillion. In other words, you carry roughly as many bacteria as body cells. Those bacteria also carry about 2 million genes, some 100 times the roughly 20,000 human genes.
This hidden crowd is called the human microbiome. It includes bacteria, archaea, fungi, protists and viruses living on the skin and in the mouth, gut, lungs and many other places. Many of these microbes are commensal, living with us without helping or harming us. Others are mutualistic, and both sides benefit.
People often call these microbes "flora," but that is technically wrong, because the word root flora refers to plants. Scientists now prefer microbiota, although the old word is still widely used. Some microbes do useful jobs for us, but the role of most of them is still not well understood.
Counting the Invisible Guests
Studying the microbiome means working out who lives there. Scientists do this mainly by reading DNA. One tricky part is keeping the host's own human DNA out of the results. A common approach targets a marker gene called 16S rRNA, which helps identify bacteria and archaea.
On 13 June 2012, the Human Microbiome Project reached a major milestone. National Institutes of Health director Francis Collins announced the results, alongside a set of papers in Nature and other journals on the same day. Researchers had collected more than 5,000 samples from 242 healthy volunteers in the United States. They sampled 15 body sites in men and 18 in women, including the mouth, nose and skin.
The team calculated that more than 10,000 microbial species live in the human ecosystem. They also built a reference map of what normal looks like in healthy people. A big open question is whether most humans share a "core" set of microbes. The answer matters, because a core would make it possible to link certain microbe mixes to disease.
Every Body Part Has Its Own Crowd
Each part of the body has its own community. The mouth and gut hold the most variety, while the skin shows less. An estimated 500 to 1,000 species of bacteria live in the gut, yet they belong to just a few major groups. Even in the mouth, bacteria of the same species come in subtypes that prefer different spots.
The skin is a world of its own. One study of 20 skin sites on ten healthy people found 205 genera of bacteria. Yeasts called Malassezia live there too, feeding on oils from the skin's glands. The eye has its own guard: tears contain lysozyme, which makes it hard for microbes to survive and settle.
The gut also hosts archaea, mostly methanogens. Only about half of people have easily detectable numbers of them. Some places once thought empty turned out to have residents. The esophagus was once thought to lack a microbiome, but since the 1980s it has been known to host a diverse one. In January 2024, biologists even reported "obelisks," a new class of viroid-like elements, in the human microbiome.
Partners in Digestion
Some gut microbes do real work for us. They ferment dietary fiber into short-chain fatty acids, such as acetic acid and butyric acid, which the body then absorbs. Gut bacteria also help make B vitamins and vitamin K. The compounds they produce act a lot like hormones, so the gut flora itself seems to work like a hormone-making organ.
This partnership starts early. A baby's gut microbiome forms during birth and matures into an adult version within the first few years. How a baby is born matters. Babies born vaginally get helpful gut microbes similar to the mother's, while babies born by C-section need more time to build up helpful gut microbes.
The mix keeps changing through life, with diet and with health. Microbes pass between mothers and children, and between people who share a home. Moving to a new country can shift them too, as studies of Thai immigrants in the United States found. And people who live to 100 or older have a distinct gut microbiome, rich in microbes that make special bile acids that may support healthy aging.
When the Balance Tips
Trouble can start when microbes grow beyond their usual numbers, or reach places that are normally sterile, such as the blood. A disturbed gut microbiome, called dysbiosis, shows up in inflammatory bowel disease. In the mouth, bacteria such as Streptococcus mutans form sticky plaque and release acids that dissolve tooth enamel.
Antibiotics can wipe out helpful gut bacteria, which normally keep harmful ones in check. That opens the door to the bacterium C. difficile. Treating that infection with more antibiotics works only 20 to 30% of the time on average. So researchers turned to fecal microbiota transplant, which gives patients stool from a healthy donor to restore a normal gut. It is about 85 to 90% effective in people for whom antibiotics failed.
The idea of a link between gut and skin is old. In the early 20th century, eating baker's yeast was sold as a treatment for acne. Today, studies point to a two-way connection between gut microbes and skin health. Microbes are also implicated in some 20% of human cancers, though finding microbes at a tumor does not prove they caused it.
