What Is the Microbiome?

Where microbes live

The US National Institutes of Health supported the Human Microbiome Project from 2007 to 2016, which mapped the normal bacteria living in and on the healthy human body. [3] Its main paper studied the largest group of healthy people and body sites at the time, including the gut, skin and vagina. [4] Each body site is a different habitat with its own typical microbes. See the separate guides on the gut and the skin.

How many microbes are there?

A widely repeated claim says bacteria outnumber human cells ten to one. A 2016 calculation for a 70 kg "reference man" estimated about 38 trillion bacteria and about 30 trillion human cells, so the numbers are of the same order, and the bacteria weigh about 0.2 kg in total. [5] These are estimates for an average adult, not measurements of any one person.

It is different in every person

The Human Microbiome Project found that even healthy people differ remarkably in the microbes they carry, and that ethnic or racial background was one of the strongest associations with both microbes and metabolic pathways in its data. [4] Researchers have also observed that the same person's community stays fairly steady over time: in 37 US adults followed for up to five years, most bacterial strains looked like residents for decades. [6]

It also changes

The microbiome is dynamic and changes with exercise, diet, medication and other exposures. [1] Two examples from small human studies:

• Antibiotics. In three people given a course of the antibiotic ciprofloxacin, diversity dropped and the community shifted within three to four days. A week after each course it began to return, but the return was often incomplete. [7]
• Diet. In a short feeding study, a diet made entirely of animal products or entirely of plant products changed community structure within days. [8]

These studies are small and show that the community responds. They do not show whether any change is good or bad for health.

How scientists measure it

Most studies read DNA from a sample, often stool or a skin swab. Results depend on the choices made along the way. In a blinded comparison across 15 laboratories, variability depended most on the type and origin of the sample, followed by DNA extraction, sample handling and computer analysis. [9] That is one reason two tests on the same sample can disagree. See Microbiome Tests for what consumer tests can and cannot tell you.

What the microbiome is not

• It is not a single organ you can "reset", and it is not the same thing as a probiotic. Probiotics are live bacteria and yeasts promoted as having health benefits. [10]
• Describing the microbes in a body site is not the same as showing that changing them treats a condition. That step needs trials in people. [3]

For ingredient guides on probiotics, see Probiotic Supplements Explained. For everyday digestion, see How Digestion and the Microbiome Work.