A community inside the gut
The human digestive tract is home to a huge community of microorganisms, mostly bacteria, along with archaea, fungi and viruses that infect bacteria. Together they are called the gut microbiome, or sometimes the gut microbiota. The term microbiome can also refer to their collective genes. The great majority live in the large intestine, where conditions are slow-moving, warm and low in oxygen.
The number of microbial cells is often described as being of the same order of magnitude as the number of human cells in the body, with figures in the tens of trillions mentioned. Estimates vary and have been revised over time, so it is best to treat any exact number with caution. What is clear is that the community is large and diverse, and that each person’s mix differs from anyone else’s.
Where the microbes come from
Babies are thought to pick up their first microbes during and after birth, from the mother, from other people and from the environment. The community changes during infancy, as feeding shifts from milk to solid foods, and tends to settle into a more stable pattern by early childhood. It continues to shift through life with diet, age, illness, medicines and location.
What gut microbes are known to do
Much of the research is recent and ongoing, but several functions are reasonably well established.
- Breaking down fiber. Humans lack enzymes for digesting many plant fibers. Bacteria in the colon ferment them and produce short-chain fatty acids, some of which the cells lining the colon use as fuel.
- Making some vitamins. Certain gut bacteria produce vitamins such as vitamin K and some B vitamins, though how much this contributes to the human body’s needs is debated.
- Training the immune system. Early exposure to microbes helps the immune system develop and learn what to tolerate. Gut bacteria also compete with harmful microbes for space and nutrients, which makes it harder for pathogens to take hold.
- Interacting with medicines and food compounds. Gut microbes can chemically alter some drugs and food components, which may affect how they work.
You can think of the gut as a kind of internal ecosystem, with ideas such as ecosystem balance and species biodiversity applying in a loose way. In general, researchers consider a varied gut community to be a sign of a more resilient one, though what counts as “healthy” is not precisely defined.
What disrupts it
Antibiotics can reduce the number and variety of gut bacteria, sometimes for weeks or longer, and can occasionally allow harmful species to flourish. The infection caused by the bacterium Clostridioides difficile is a well-known example. For recurrent cases of it, transplanting stool from a healthy donor, called fecal microbiota transplantation, has proved effective and is an accepted treatment in appropriate patients. It is one of the clearest examples of the microbiome being used as medicine, and it shows how some modern medicine has moved in this direction. Other uses of the approach remain under study.
Diet, illness and some medicines can also change the community.
What is not yet understood
The microbiome has attracted enormous interest, with studies linking it to conditions such as obesity, diabetes, inflammatory bowel disease, allergies, and even mood and brain health. Many of these links are based on associations, meaning a difference in gut microbes is seen in people with a condition. An association does not show cause. A disease might change the gut microbes, as opposed to the other way round, or both could be affected by a third factor such as diet or medication.
Experiments in animals, such as mice raised without microbes, have given useful hints, but results in mice do not always carry over to people. Researchers are still working out which microbes matter, how they act and whether changing them can reliably improve health.
The idea of a gut-brain connection is an active area of study. The gut and the brain communicate through nerves, hormones and immune signals, and stress response and mood can plainly affect digestion. How much gut microbes influence the human mind is much less settled.
Probiotics, prebiotics and diet
Probiotics are live microorganisms sold as supplements or found in some fermented foods, and prebiotics are food components that gut bacteria can use. Evidence for benefits depends on the specific product and condition. Some have been shown to help in certain limited situations, such as certain kinds of diarrhea, while for many other claims the evidence is weak or mixed. Products differ widely, and the same bacteria do not suit everyone.
A diet containing a variety of plant foods and fiber is generally associated with a more diverse gut community, but the link from diet to long-term health through the microbiome is not fully mapped out.
Caution about claims
Because the science is young, marketing sometimes runs ahead of the evidence. Claims that a particular product will “reset” or “fix” your gut deserve skepticism. This article is general educational information, not medical advice. Individual cases differ, and a qualified health professional should be consulted about digestive symptoms, special diets or supplements.