A technical review of what researchers know about the gut microbiome

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'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.

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.

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.

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

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

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…

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.

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.

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.

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.

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.

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

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 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.

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

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

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

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.

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.

Western babies often lack a gut microbe common elsewhere.

An overview on germ theory, the crucial framework developed by Louis Pasteur

Germ theory of disease is based on the concept that many diseases are caused by infections with microorganisms, typically only visualized under high magnification. Read this general overview to understand the basic framework which allowed for development of vaccines.

A doctor answers the internet's burning questions about the gut

Gastroenterologist Dr. Ugo Iroku answers the internet's burning questions about digestion and bowel movements. Get the lowdown on what it means when your stuff is super dark, the impact of coffee on evacuating bowels, and much more.

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

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.)

Visualize the different parts of the digestive tract, a roughly 30-foot tube which runs from our mouths to our rear.

A gallery of medical illustrations from NIH

The National Institutes of Health provides educational materials for broad use. The institute hosts a Flickr account with many different image galleries, including this one (with over 70 images to date) that illustrate and annotate curious phenomena, from the life cycles of a malaria parasite to the comparison of male and female bladders. Explore the gallery here.

Vitamin B1 is linked to gut motility—helping fight constipation—in 2026 research

A study published in early 2026 found a link between vitamin B1 and the successful movement of food through your GI tract, known as gut motility. The work incorporated genetic and survey data about poop frequency to identify genes associated with gut motility and then separately linked poop frequency data with how much vitamin B1 people ingested, theorizing that the vitamin supports the production of acetylcholine, a neurotransmitter that stimulates GI system contractions.

Exercise causes diet-independent changes in the gut microbiome.

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

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.

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.

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.

Search this citation-heavy database of nutrition and supplement research

Explore a reference site that aggregates and summarizes peer-reviewed studies on hundreds of supplements and dietary interventions. It is ad-free and funded by subscriptions, making it a health resource without a financial stake in what you buy.

Explore these images to better understand why food poisoning makes you feel nauseous.

A quick video on how your immune system works

Explore how your immune system's vast network of cells, tissues, and organs coordinate your body's defenses against bacteria, viruses and toxins with this 5-minute TED talk video.

An interactive dive into the immune system

Our bodies are equipped with an incredible system able to fight off invasive pathogens to protect us from illness. The complicated system includes lymph nodes, the spleen, bone marrow, and even the tonsils. But this same system can turn against itself, a condition known as autoimmune disorders. Follow along with this thorough, engaging explainer on the human body's defense system.

Take a 360-degree look at biochemical activity from within a human cell

In this tour, users can observe the dynamic processes that occur within the basic units of the human body, including the production and transport of proteins and the assembly and disassembly of microtubules—thin, cylindrical structures that provide structural support and a means of moving material within the cell.

Scientists seeking gut insights are attaching flatulence sensors to volunteers' underwear

This fart-tracking device detects gas generated in the gut, providing insights about gut microbial activity. The underwear sensors measure a component of what is technically called flatus—digestive system gas.

The promises and perils of using at-home genetic tests for your health

A primer on genetic testing, personalized medicine, and the promise of pharmacogenomics–the use of genetics to predict an individual's response to a drug.

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.

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.

How epigenetics blurs the line between nature and nurture

An exploration of the study of how behaviors and environment affect the way genes work — and how that complicates the nature-versus-nurture debate.

My experience with biohacking

A general approach that employs technology to enhance the functioning of the human body, biohacking enthusiasts are continuously seeking new ways to optimize their performance. Martin Kremmer, an entrepreneur who became interested in the topic after experiencing burnout, explores his own experiences in biohacking his own diet and lifestyle in pursuit of a longer, healthier life.

Meet six commercially available synbio products

An article exploring the science behind synbio products currently on the market, and projecting the products that can be expected over the next 10 years.

The ABCs and FAQs on GMOs from the WHO.

GMOs (or genetically modified organisms) are a subject of great debate in the food world…but how come? GMOs are organisms whose genetic materials have been altered in a way that does not occur naturally in order to create a product that has a...