What is a microbiome (and why are they important)?

What is the gut microbiome?

The gut microbiome is a microscopic ecosystem that runs off the work of microbes in the digestive tract. These workers make getting energy from food possible. What and how that energy manifests depends on what building blocks these microbes have to work with, meaning their composition and functions are strongly influenced by diet. Gut microbes have their own genes, which affect how a person's genes act.

How the microbiome affects your health

The gut microbiome is so influential to overall human health that some researchers consider it a separate organ. Its conditions, influenced by environmental and lifestyle factors such as medication and exercise, contribute to immunity, metabolism, inflammation, medical treatment efficacy, brain development and function, and the development of disorders and diseases, including asthma, depression, inflammatory bowel disease, and Alzheimer's.

The gut microbiome—a complex community of up to 100 trillion microbes—has a changing composition, influenced by our life stage, diet, medications, environment, and other factors.

A technical review of what researchers know about the gut microbiome

This overview from the National Institutes of Health provides a deeper (but still accessible) look at the different bacteria in the gut, how the microbiome develops through life, its purpose, and more.

There are up to 100 trillion microbes in the gut, and maintaining the relative balance in this ecosystem is important for our health.

Trillions of bacteria, viruses, fungi, protists, and archaea live in our guts, producing a wide range of molecules, hormones, and more—underscoring the immune system's pivotal role in the microbiota-gut-brain axis.

Some animals, including certain tropical ants, have little or no microbial populations in their gut, upending the idea that all animals rely on this ecosystem to help maintain their health and proper functioning.

Gut bacteria are evolving and can acquire as many as 100 new genes per year, on average. (Paywall may apply.)

What's next for gut microbiome science?

A Stanford microbiologist explores what we don't yet know about the gut microbiome—such as whether we can engineer the bacterial species within it—and the current scientific advances in the field.

Researchers generally group gut bacteria into six different categories, with varying amounts of these microbes residing in different parts of the digestive tract.

What happens when the gut microbiome is out of whack?

An imbalance in gut microbiome flora can lead to a condition known as dysbiosis. This condition is typically characterized by a drop in microbiota diversity and an increase in harmful unicellular and acellular organisms, such as viruses, that can negatively impact the host's immune system and overall health. Genetics, infections, dietary choices, antibiotics, food additives, artificial sweeteners, and other lifestyle and environmental factors can cause dysbiosis.

What constitutes a 'healthy' diet?

A natural diet, typically high in plant-based foods and low in processed foods, appears to be the main contributor to a healthy, diverse gut microbiome.

The reason some people love exercise may be because of their microbiome

Certain gut microbes in mice trigger dopamine release and drive motivation to exercise more. Scientists are investigating whether humans carry similar microbial patterns that influence our natural inclination towards movement, exploring how unseen microbial ecosystems may shape mammalian fitness behavior and reinforce innate reward pathways. (Some users may experience a paywall.)

In 2026, University of Cambridge researchers reported that a group of gut bacteria called CAG-170 may be a key marker of good health, occurring far more often in healthy individuals and less commonly in people with chronic diseases.

Some dementia cases may be linked to microorganisms in the brain

Researchers now know that, much like the gut, the brain is home to an ecosystem of microorganisms—the brain microbiome. While this area of study is still new, some scientists believe 50% of bacteria-caused dementia cases could be treated. (Some users may encounter a paywall.)

Gut microbiome experiments involving transfers of gut microbes from depressed people to rodents indicate that the rodents may then display depression-like symptoms.

Listen to how the gut microbiome influences your emotions

The gut-microbiome connection may involve the enteric nervous system, a collection of hundreds of millions of neurons throughout the gut that transmit signals up the vagus nerve to the brain.

Specific gut microbiome 'fingerprints' are associated with cancer recurrence, with up to 94% accuracy.

Exercise causes diet-independent changes in the gut microbiome

Cardiovascular exercise has been found to boost the gut's population of beneficial bacteria, and exercise overall decreases the likelihood of developing a "leaky gut," a condition in which a porous gut lining allows bacteria to leak into the bloodstream and cause inflammation.

Research links the gut microbiome and rheumatoid arthritis

Arthritis is a potentially disabling joint condition that currently affects nearly one in five adults across the globe. Doctors still don't know what causes rheumatoid arthritis, but the answer may be partly determined by chemicals produced by bacteria in the gut.

Can the gut microbiome drive addiction?

New research suggests an imbalance of gut microorganisms may influence the likelihood of addiction and addictive behaviors by increasing the severity of withdrawal symptoms, triggering brain inflammation in regions of impulse control, and more.

The gut microbiome may play a major role in autoimmune disease and symptom flare-ups

Certain unhealthy foods can promote gut bacterial growth and inflammation in the lining of the gut, potentially disrupting its lining—leading to a leaky gut that may allow pathogens to dribble out into the bloodstream, fueling further inflammation that can both cause disease flare-ups and set the stage for future disease development.

Microbes are essential to creating the many varieties of cheese, influencing texture and taste

Microbes break down proteins and fats and produce compounds with distinct tastes. These microbes can include bacteria (like the one used to give Swiss its trademark holes), molds (like the ones that give blue cheese its distinctive veining), and countless other tiny organisms.

Gut microbiome rewrites may help reduce allergies

Researchers are investigating different strategies to determine if one day they could give people a combination of gut microbes to set them up for fewer allergies. In animal research, scientists have already prevented severe allergic responses in allergy-prone mice—supplying them with gut microbes from healthy, non-allergic human babies.

The gut microbiome's community of viruses is collectively known as the virome, but most of its viruses remain unidentified.

Bacteria in our intestine influence the brain via the gut-brain axis. (Paywall may apply.)

Scientists have found that the Great Barrier Reef's microbiome includes an estimated 362,802 distinct viruses and 876 distinct bacterial and archaeal species—584 of which had never been documented before 2026.

See how the gut and the brain communicate through a bundle of nerves running from the brain to the digestive tract, serving as both a physical and chemical link.

Probiotics, which are living bacteria and yeasts, are not recommended for most patients.

The secret lives of cells

Cutting-edge microscopy has revealed previously unseen interactions of biological molecules within their cellular environment, enabling scientists to observe and analyze the molecules in a holistic view. This podcast explains the minute advancements made over the last few decades in observing cells, revealing how scientists have come and what the future holds for the field.

Farts are tiny status reports from our gut microbiome, with American adults typically passing gas more than 30 times daily.

Supplements ahead of exertional heatstroke helped protect mice against brain damage

In the lab, mice dosed with probiotics prior to inducing exertional heatstroke, had better cognitive outcomes. This evidence underscores the links between the gut microbiome and the brain, at least in rodents.

Microplastics 101: What we know about the contaminants invading our bodies

Fifty-one trillion particles of microplastics float in our oceans. Yet there is very little science of how this affects our health. This quick 2-minute video explains the dangers of microplastics.