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.

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.

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.

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.

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

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.

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

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.

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.

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

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.

Exercise causes diet-independent changes in the gut microbiome.

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…

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.

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

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.

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.

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.

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.

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

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.

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.

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

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

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.

Antimicrobial resistance is responsible for 1.3 million deaths each year

Antimicrobial resistance is a global health threat, driven by the misuse and overuse of antimicrobials in humans, animals, and more. Estimates suggest superbugs could lead to $1T in healthcare costs by 2050, and the world faces a shortage of new drug development to meet the challenge.

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.

Bacteriophages—viruses that infect bacteria before multiplying within them—exist on Earth in numbers greater than all other living organisms combined.

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

Western babies often lack a gut microbe common elsewhere.

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

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.

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

Lining up every microbe on Earth would stretch to about 105,000 light-years

There are about 10²⁷ such organisms on the planet, many of which are adapted to produce energy through uncommon reactions in unconventional environments, such as within rocks or near volcanoes on the ocean floor. Studies of these organisms have reframed astrobiologists' search for life beyond Earth by broadening the parameters under which life can exist.

Superbugs could claim 1.9 million lives per year by 2050

The increased use of antibiotics combined with an aging population, is projected to result in an almost 50% increase in global deaths from antimicrobial resistance each year. At the same time, antibiotic use for livestock is expected to increase by 30% over the same time frame.

An estimated 1% of DNA mutations in bacteria can produce more dangerous strains

Researchers have developed a technique to monitor these mutations in real time. Using this technology, scientists found that mutations occur at a steady rate, with 1% leading to potentially deadly changes.

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.

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

A macrophage can eat 100 bacteria, on average, before it's exhausted

These specialized immune cells are first responders during inflammation, responding to a threat or injury and then performing other inflammatory response tasks, including summoning neutrophils to help attack invaders.

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.

Superbugs are pathogens that have proved resistant to medications designed to combat them, rendering standard treatments ineffective.

Scientists from the frontline discuss the future of antibiotics and superbugs

Superbugs are a very real problem, but researchers around the world are working to advance our understanding of these pathogens and develop new medicines. This podcast talks with several scientists on the frontier of superbug research, offering insight into what we know—and what the future of medicine may look like.

Tips for reducing the risk of antimicrobial resistance

Antimicrobial resistance is bad news. But there are lots of things you can do to both protect yourself from superbugs and help keep the problem of antimicrobial resistance from getting worse. This page from the CDC offers clear, straightforward guidelines that can help keep you—and your loved ones—healthy.

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.)

Antibiotic resistance is a growing global health problem

Over decades, bacteria have grown increasingly resistant to antibiotics. This resistance now causes an estimated 1.27 million deaths each year and is associated with nearly 5 million deaths worldwide, according to the World Health Organization.

Overuse of antibiotics gives bacteria more opportunity to evolve their defenses

The overuse and misuse of antibiotics are significant contributors to the rise of antibiotic resistant bacteria. Experts say antibiotics should only be used for specific medical problems, and patients need to be sure to take antibiotics exactly as prescribed in order to reduce the risk of antibiotic resistance.

Roughly 80% of US antibiotics sold each year go to agricultural use

Antibiotics have long been used in agriculture to treat diseases in animals and plants. However, antibiotics are also often misused, to treat non-bacterial diseases, to encourage growth in animals, and more. This expansive use of antibiotics has become one of the primary sources of the emergence of new superbugs.

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.

Superbugs evolve defenses against medication, then share them with neighbors

One reason antibiotic resistance spreads so quickly is that bacteria have multiple mechanisms allowing them to share genetic material. This short video offers a concise explanation for each of these mechanisms, and animation that helps viewers understand how antimicrobial resistance can quickly spread from one organism to another.