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.

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.

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.

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 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.)

Bacteria in our intestine influence the brain via the gut-brain axis.

Gut bacteria are evolving and can acquire as many as 100 new genes per year, on average.

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.

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.

Some dementia cases may be linked to microorganisms in the brain.

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

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.

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.

How depression affects the brain

Treatment for depression has historically hinged on the theory that the condition was caused by underactive or abnormal neurotransmitters, specifically serotonin and norepinephrine. This four-minute video by Yale Medicine details how these neurotransmitters didn't explain the symptoms of depression but, two other neurotransmitters involved in regulating mood and emotion did. GABA and glutamate, some of the brain's most plentiful neurotransmitters, may possibly be the source of depressive symptoms.

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.

These areas of the brain are hard-hit in depression—but the changes are reversible

Depressed brains can have certain characteristic changes, including an overactive amygdala, reduced hippocampus size, and changes to the thalamus and neuromodulating chemicals in the brain.

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.

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 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.

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.

Can microdosing improve mental health?

Animal studies involving microdoses of psilocybin, the psychoactive component in magic mushrooms and ketamine, found it helped to alleviate anxiety and inflammation, an immune response that can cause damage when chronically active. Human studies are ongoing. In at least one double-blind study, where researchers and patients don't know who got a placebo versus the real thing, about half of the participants incorrectly guessed they had been given placebos.

Inflammation appears to cause specific symptoms of depression

A large analysis of existing studies published in 2021 found that systemic inflammation is associated with fatigue, appetite changes, and sleep disruption, rather than some of depression's broader symptoms including hopelessness about the future, or feeling fearful. This may suggest that inflammation influences specific symptoms of the condition, rather than the disease as a whole.

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

JJ Schildkraut theorized depression is linked to brain chemical imbalances—in 1965

Schildkraut was one of the first to put forward this idea, which stemmed from lab animal research. A decade later, researchers published the first landmark paper on fluoxetine—better known by trade name Prozac—which increases serotonin levels in the brain.

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.

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

Mixed reality technologies may help treat depression

A study led by a team from Stanford University showed that MR can help people with depression by providing pathways to engage in activities such as digital board games and dancing. Participants saw reduced symptoms of depression that made their overall treatment plans more successful.

Exercise causes diet-independent changes in the gut microbiome.

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.

What rodent cars can tell us about human joy

Neuroscientist Kelly Lambert and her colleagues taught rats to drive in a mini car. She writes her findings from this unconventional experiment, sharing that positive and fun experiences can sculpt the brain just as powerfully as stressful ones. Click to learn more about how the apparent joy of these rodents seemed to enhance their neuroplasticity.

Model organisms like yeast, mice, and flies help scientists decode the human body

Some species are used to quickly study the effects of human diseases and treatments because they are short-lived and have similar systems to those found in humans. Bacteria, like E. coli, have been used as human proxies given their rapid growth and ease of genetic manipulability.

Neural replays in mice help explain food aversions

Princeton University scientists published research in 2025 analyzing how mice learn to associate certain foods or flavors with feeling ill—even when there’s a time gap between eating something and feeling sick. The work, performed with grape Kool-Aid and injections of a substance that made mice sick, traced the literal “gut reaction” of how gut distress signals are linked to neural replays of what the mouse ate.

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

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.

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.

Psychedelics interact with neurotransmitter systems to alter one's perception

LSD, psilocybin, and MDMA can suppress the brain's default mode network and enhance connectivity. Research shows that, when paired with therapy, psychedelics may help treat mental health conditions, including depression, addiction, and PTSD.