Your body carries a huge population of microbes, and the community living in your gut does jobs your own cells can't, from breaking down fibers you can't digest to helping train your immune system.
What the word means
The National Institute of Environmental Health Sciences (NIEHS) defines the microbiome as the collection of all microbes, such as bacteria, fungi and viruses, and their genes, that naturally live on and inside our bodies. The gut microbiome is the part of that collection living in the digestive tract. You'll also see the word microbiota, which refers to the microbes themselves; in everyday writing the two are used almost interchangeably.
The numbers are large, and the estimates have changed over time. Cleveland Clinic describes trillions of microorganisms in the gut, including more than a thousand species of bacteria along with viruses, fungi and parasites. A review in the Biochemical Journal by Elizabeth Thursby and Nathalie Juge puts the number of microbes in the digestive tract at more than 100 trillion. An older estimate held that bacterial cells outnumber human cells ten to one, but a more recent one puts the ratio closer to one to one, which matches the NIEHS description of about as many microbes as human cells. Their genes are another matter: the same review describes the microbes' combined genetic content as more than 100 times that of the human genome.
Where gut microbes live
There are some microbes in the stomach and small intestine, but most gut microbes live in the large intestine, or colon. The small intestine is a harder place to settle. It typically has high levels of acid, oxygen and antimicrobial substances, and food moves through it relatively quickly. The colon supports a dense, diverse community made up mainly of anaerobes, bacteria that need a low-oxygen environment to survive. Some float freely inside the intestine, and others attach to the mucous lining of the intestinal wall.
The material that reaches them includes fibers and complex carbohydrates the body can't break down by itself. (For the full route food takes before it gets there, see how your digestive system works.)
What gut microbes do for digestion
Gut bacteria ferment what we can't digest. They have enzymes that break down certain complex carbohydrates and dietary fibers, and the byproducts of that fermentation include short-chain fatty acids, mainly acetate, propionate and butyrate. Cleveland Clinic describes short-chain fatty acids as an important nutrient that feeds the cells of the gut lining, and Thursby and Juge single out butyrate as a particularly important energy source for the cells lining the colon.
Gut bacteria also provide enzymes needed to make certain vitamins, including B1, B9, B12 and K. Vitamin B12 is a striking case: according to Harvard's Nutrition Source, the key enzymes needed to form it are found only in bacteria, not in plants or animals. And gut bacteria help metabolize bile in the intestines. In the colon they convert bile acids that weren't reabsorbed earlier into different compounds, known as secondary bile acids.
What they do for the immune system
According to Cleveland Clinic, the gut is the body's largest immune system organ, containing up to 80% of the body's immune cells. Beneficial gut microbes help train the immune system to tell them apart from harmful, disease-causing types.
Resident bacteria also compete with would-be invaders for nutrients and for places to attach, and they produce antimicrobial substances, all of which makes it harder for harmful microbes to take hold. Cleveland Clinic notes that short-chain fatty acids have anti-inflammatory properties in the gut and help maintain the gut barrier, which keeps bacteria and bacterial toxins inside the intestine rather than letting them into the bloodstream.
Thursby and Juge describe germ-free mice, raised without any microbes, as having an extremely thin layer of mucus lining the colon, and trouble renewing the cells of the gut lining, a problem that reverses once gut bacteria are introduced. Germ-free animals also have immune deficiencies, notably a failure to expand an important population of immune cells called CD4+ T cells. The review notes that the gut microbiota matters for the development of both the gut's own immune defenses and the immune system throughout the body.
The gut-brain connection
Gut microbes can also affect the nervous system through the gut-brain axis, the network of nerves and chemical signals linking the digestive tract and the brain. Cleveland Clinic explains that certain bacteria produce, or stimulate the body to produce, neurotransmitters such as serotonin that send chemical signals to the brain. Short-chain fatty acids appear to have positive effects on nerves, while some bacterial toxins might damage them.
How much this matters for health is still being worked out. Researchers are investigating whether the gut microbiome is involved in various neurological, behavioral, nerve pain and mood disorders, and some of the evidence so far comes from animals. In one line of mouse research described by Thursby and Juge, wiping out gut bacteria with antibiotics changed how serotonin was processed in the colon and slowed the movement of the gut. That's a finding about gut function in mice, and a long way from showing that gut bacteria shape mood in people.
Metabolism and hormones
The gut lining also contains hormone-producing cells, called enteroendocrine cells, and gut microbes and their products interact with them. Cleveland Clinic notes that these cells make the gut the body's largest endocrine organ, and the hormones they release help regulate blood sugar, hunger and fullness. Researchers are exploring how the microbiome might be involved in obesity, insulin resistance, type 2 diabetes and excess fat storage in the liver. These conditions do have some relationship with certain gut microbes, but exactly what that relationship is isn't clear yet.
Balance, dysbiosis and the limits of what's known
Harvard's Nutrition Source describes most gut microbes as symbiotic, meaning both they and their human host benefit, with a smaller number that can promote disease. In a healthy body, the two kinds coexist without problems. Cleveland Clinic compares a healthy microbiome to a thriving native garden in which different types of microorganisms support one another, and notes that a community lacking a healthy variety is more vulnerable to being overrun by invasive types.
When that balance is disturbed, by an infection, certain diets or prolonged use of antibiotics, for example, the result is called dysbiosis. (Those influences are covered in what shapes your gut microbiome.) Clinicians use the term for a gut microbiome that has lost beneficial bacteria, has an overgrowth of potentially harmful ones, or has lost its overall balance. Small intestinal bacterial overgrowth (SIBO) is one specific form: dysbiosis in the small intestine.
An international consensus statement on microbiome testing, published in 2024, concluded that there is no common definition of dysbiosis that can be used in clinical practice, and not enough information to set strict healthy reference ranges for how abundant particular species should be. Thursby and Juge also point out that when a disease is linked with dysbiosis, it is often unclear whether the microbial changes are driving the disease or resulting from it. Even the basic question is open: a 2024 review in the journal Gut was titled "What defines a healthy gut microbiome?"
Cleveland Clinic lists gas, bloating, poor digestion, lower abdominal pain, diarrhea and constipation as typical symptoms of gut dysbiosis, but symptoms like these are also shared by many digestive disorders, according to the clinic's overview of the digestive system. If they persist, get them checked rather than assuming your microbiome is to blame. How your digestive system works explains when that's worth doing.
This article is for general education only and isn't medical advice, so please talk to a doctor or other qualified clinician about any symptoms or health concerns.
Sources
- Microbiome, National Institute of Environmental Health Sciences
- Gut Microbiome, Cleveland Clinic
- Introduction to the human gut microbiota, Thursby E, Juge N. Biochemical Journal, 2017
- The Microbiome, The Nutrition Source, Harvard T.H. Chan School of Public Health
- International consensus statement on microbiome testing in clinical practice, Lancet Gastroenterology & Hepatology, 2024
- What defines a healthy gut microbiome?, Van Hul M, Cani PD, Petitfils C, et al. Gut, 2024
- Digestive System, Cleveland Clinic