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.

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.

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

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.

Exercise causes diet-independent changes in the 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.

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.

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.

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

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

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.

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

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.

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.

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.

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...

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.

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.

The marvels of mucus

Mucus—otherwise known as snot or phlegm—has a gross reputation, but the substance is actually of vital importance, lining the moist surfaces of our nose, intestines, lungs, and more. It plays a constant role in keeping our tissues from drying out and acts as a line of defense, but if it gets too sticky or thick, it can cause problems. Read about the marvels of mucus here.

What is the immune system? A quick 101

Your body’s immune system is designed to protect you from infection. Find out more about how the immune system works with this quick overview and set of diagrams.

Fungi can cause disease, but they’re also our planet’s key decomposers

Fungi are their own taxonomic kingdom separate from flora and fauna, acting as the key decomposers and nutrient recyclers for our planet. Watch this video to understand the diverse types of fungi and the stages of the fungal life cycle. This video illustrates how fungi species may spread, eat nematode worms, damage nearby plants, and much more.

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.

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.

Microforests in urban environments may help combat climate change

Areas of densely packed native trees and drought-tolerant plants within cities can pull carbon dioxide from the air, cool surrounding neighborhoods, and support local wildlife. The idea behind microforests traces back over 50 years to Japanese ecologist Dr. Akira Miyawaki, who promoted planting whole ecosystems to restore degraded land.

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.

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.

The history of germ theory, which explains that illnesses are caused by microorganisms

For centuries, the miasma theory, which held that illnesses were caused by clouds of "bad air" produced by decaying organic matter, was the accepted explanation for the spread of disease. The development of microscopes and the subsequent technology to isolate bacteria and test disease spread in mice greatly contributed to contagionists overturning miasmatists.

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.

From soil to beer, microplastic pollution is all around us

Marine plastic pollution has been studied for decades, but the extent and effects of plastic pollution elsewhere is only just beginning to be explored.

What happens when the population grows faster than the food supply?

Human history is shaped by our ability to feed ourselves. See how population growth is tied to farmland, and how food production’s profound environmental effect shows us the need for change.