What happens when the gut microbiome is out of whack?

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

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.

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.

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.

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.

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.

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.

Exercise causes diet-independent changes in the gut microbiome.

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

Artificial sweeteners may disrupt gut health, throwing off the balance of beneficial bacteria in the gut and shifting the composition of the microbiome.

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.

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.

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

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

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

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.

Researchers are investigating how altering the gut microbiome may influence the development of rheumatoid arthritis, which is an autoimmune disease.

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

Jump to: What is the microbiome? How microbiota benefit the body The role of probiotics Can diet affect one’s microbiota? Future areas of research What is the microbiome? Picture a bustling city on…

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.

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.

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

Western babies often lack a gut microbe common elsewhere.

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.

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.

Fecal transplants can help treat infections by transplanting healthy gut bacteria from a donor into a patient's gastrointestinal tract using samples of human waste, which are turned into a liquid mixture and often delivered via a colonoscopy procedure.

Fake sugars may disrupt metabolic health.

Some dementia cases may be linked to treatable microorganism infections in the brain.

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

The risks of bioremediation, from intermediate products to ecological disruption

A step in the series of complex biochemical reactions involved in the implemented bioremediation process may produce dangerous molecules—sometimes more toxic than the initial pollutants—that require ongoing monitoring to ensure optimal conditions for processing these intermediates toward the eventual, safe outputs. Introducing non-native nutrients or species, including GMOs, may alter existing food webs and gene pools.

Research suggests the cleanliness of the ISS may make astronauts unhealthy

The International Space Station's sterile conditions deprive astronauts of the opportunity to strengthen their immune systems through microbial exposure. To address this problem, future missions may use probiotic-based cleaners and foster diverse microbes in space habitats.

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

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.

Invasive species may harm new ecosystems via the spread of disease

Besides damaging native species through direct interactions such as competition for resources and predation, invasive species may come from environments with greater biodiversity than the new environment. This makes them more likely to carry pathogens unfamiliar to native species, increasing the risk of biodiversity loss.

Microbial research suggests shifts in diverse populations may help an invasive species establish itself

In 1958, English ecologist Charles Elton suggested that diverse ecosystems should be more resistant to invasive species because gaining a foothold would be more challenging when resources are more thinly spread. However, in lab-grown microbial ecosystems with greater biodiversity, population volatility opened more ecological roles that invasive species could easily fill.

Fungi make people sick when they invade and survive in otherwise healthy human tissue

We breathe in airborne spores frequently, but they often don't make us sick. This video details how certain concerning fungal changes can occur and discusses the role of mycologists—scientists who study fungi—in helping to improve human health.

Some research suggests that the gut microbiome influences our risk of heatstroke, with elevated exercise levels raising body temperature to unsafe levels and increasing gut permeability—causing a "leaky" gut.

Autoimmune disease prevalence and incidence are on the rise—but no one knows why

Researchers theorize that environmental factors, including shifts to less healthy diets, air pollution, infections, stress, climate change, and exposures to xenobiotics—substances like pesticides, plastics, and toxins that incite immune responses—may all be fueling epigenetic changes to our bodies that make people's immune responses go awry.

Lengthy incubation periods are why it's tough to link foodborne illness to specific foods.

During coral bleaching, corals sacrifice their food source and expel colorful microorganisms to protect themselves, a phenomenon that resembles an organism's immune system attacking itself.

Artificial sweeteners are considered safe for most people, but researchers are investigating their effects on gut microbiome health.

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.

Microgravity can alter the evolution of viruses and bacteria

Experiments conducted on the International Space Station have shown that microgravity environments can delay viral and bacterial infections and induce mutations not seen on Earth. These mutations could have implications for long-term space missions and human health and suggest space can serve as a testing ground for developing new therapeutic approaches.

Microplastics are infiltrating the human body with unclear but concerning effects

Scientists have linked microplastics to immune system damage, hormone disruption, inflammatory diseases, and even cancer—yet most of their health impacts remain unknown due to limited research. Studies suggest we ingest about a credit card's worth of plastic weekly.

Benign species can become invasive if introduced into predator-free habitats

Most ecosystems contain organisms that, over many generations, have evolved into a stable balance with one another and their surroundings. In a new environment, a species may no longer be restricted by the limiting factors it is used to, and the native organisms in the area may not adapt quickly enough to the invader to establish a new balance.

Learn how cholera bacteria sicken humans

Once a person has ingested large amounts of the bacteria, typically through contaminated water, cholera bacteria begin producing and releasing a toxin inside their host. It attacks the mucosal lining of the intestine, making it hard to absorb liquids. This process leads to cholera's characteristic symptoms, like voluminous, watery diarrhea.

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.)

Modern conveniences may be contributing to allergy increases

A combination of genetics and how the environment changes our genes are likely contributing to the rise in allergies. But daily conveniences, such as dishwashers and packaged baby food, also change the level of bacterial exposures in early life, with potential implications for allergy development, experts from Mount Sinai Health System state in this video discussion.

Candida albicans is a natural body-dwelling yeast, but it can cause yeast infections

This fungus is naturally occurring on the body, but C. albicans can become a problem when the natural balance of bacteria on the body is off-kilter, allowing this yeast to spread. It can cause anything from diaper rash to a yeast infection in the throat or vagina. It’s typically treated with doctor-prescribed antifungal medications.

Learn how environmental conditions are optimized to increase bioremediation efficacy

Through biostimulation, Indigenous microbes are provided with moisture, nutrients, or oxygen to prevent their death and ensure optimal progression of their biochemical reactions. Bioaugmentation can introduce new microbial cultures to target specific compounds not natively found in the environment, while landfarming can spread or aerate contaminated soil to improve access to contaminants.