A technical review of what researchers know about the gut microbiome

The gut microbiome, explained

This video from 1440 takes a high-level look at what populates the gut microbiome, its purpose, how it affects our health, and much more.

Chemicals from the gut have complex interactions with the rest of the body

Trillions of bacteria live in our guts, producing a wide range of molecules, hormones, and more. This review underscores the immune system’s pivotal role in the microbiota–gut–brain axis. Gut microbes influence immune cells and metabolites, which in turn modulate neurodevelopment, neural signaling, mood, and neuroinflammation—highlighting immune pathways as central mediators in gut‑brain communication.

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.

Researchers generally group gut bacteria into six different categories

The trillions of bacteria in the gut microbiome can be grouped into six categories: firmicutes, actinomycetota, pseudomonadota, fusobacteriota, bacteroides, and a broad miscellaneous category. The functions of each are complex but range from breaking down food and producing vitamins to fighting pathogens.

How to maintain a healthy gut

Approximately 40 trillion microbes reside in the human gut, forming a unique microbiome, containing hundreds of millions of neurons in what is often called a "mini-brain". A healthy gut is characterized by an effective mucus-lined barrier that prevents unwanted substances from entering the bloodstream. So how do you attain such an ideal gut? This guide outlines a healthy approach to protecting your gut.

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 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.

What is the gut virome?

The gut microbiome's community of viruses is collectively known as the virome. It has been found to affect immune system development—important to the gut-brain axis—and has been implicated in the development of inflammatory bowel disease and Type 2 diabetes. As of early 2023, less than half of the viral sequences in the gut had been identified. Further study is needed to understand the virome's influence and therapeutic potential.

Some animals have little or no bacterial populations in their gut

Gut microbiomes are essential to human health, but many animals have a much smaller, transient, or even nonexistent microbiome. The discoveries have advanced our understanding of the evolution of the human microbiome.

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.

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.

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.

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.

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

The American Gastroenterological Association in 2020 concluded that although almost 4 million American adults have taken some form of probiotics, health claims about them are not backed in strong evidence. They only recommend their use for a few specific situations: to prevent Clostridioides difficile infection in people taking antibiotics that kill gut bacteria, to prevent necrotizing enterocolitis in preterm infants, and for the management of a complication of inflammatory bowel disease called pouchitis.

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.

See why food poisoning makes you feel nauseous

Scroll through these illustrations to learn what’s happening behind the scenes with bacterial foodborne illnesses, including why we sometimes vomit and how the body reacts to toxins secreted by bacteria.

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.

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.

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...

Learn about the more than 100 known autoimmune diseases

Explore this resource with summaries and related resources for the dozens of autoimmune diseases defined in the medical literature. Many of these disease write-ups also have interviews with a patient with the disorder—offering a personal take about challenges, advice, and lifestyle effects.

Each scientific study adds incremental knowledge to existing understanding

On its own, no study serves as a source of truth or solves an existing problem indefinitely, though many can be analyzed collectively in a systematic review to build more confidence—the result of more data—in a conclusion. Studies can explore knowledge gaps or test an existing theory, which is always subject to refinement and improvement.

Read a deep dive on the 'all-purpose healing' peptide BPC-157.

Thoughts from an anonymous Michelin inspector

An anonymous Michelin inspector answers the most common questions about their job and explains how reviewing and awarding stars works. Covering everything from how they decide what to order to advice for young chefs, get a peek into the details of one of the most influential restaurant reviewing jobs.

An overview of bioremediation, which can help clean up oil spills, mining waste, and some plastics

The umbrella term refers to a variety of techniques that use organisms to remove harmful substances from an environment or break them down into nontoxic compounds. Because the availability of certain resources can limit the growth of these organisms and impair bioremediation efforts, nutrients such as fertilizers can be deployed to accelerate cleanup.

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.

Visualize how CRISPR-Cas9—a type of immune system used by single-celled organisms to attack invasive viruses—targets and makes precise changes to a gene's DNA.

Hookworm infection, though risky, may help fight certain autoimmune conditions by tamping down the immune system's inflammatory response.

See how each of the more than two million known species relates to each other—and to common ancestors—in this zoomable tree of life.

At the beginning of the 20th century, a group of young men ate standard American food—replete with food additives like borax and formaldehyde—as part of government research to better understand food safety.

Listen to an in-depth conversation on the links between Parkinson's disease and herbicide exposure and the challenging pace of scientific investigation.

As of 2025, the most cited papers in science include a review of graphene, methods to improve image recognition, streamlining electron density calculations, and optimizing protein studies.

Learn how your body is, scientifically, like a firework with its own slow, controlled burn.

Studies suggest when you sleep is as important as how much you get, and syncing with your circadian rhythms may lead to less fatigue and improved long-term health outcomes

Learn how to read a prospectus, the juicy document that any company must file with the SEC before going public.

Explore an interactive map built from more than 100,000 survey responses on where people find joy in their lives

Tattoos remain visible on your skin thanks to immune cells called macrophages

The syncytiotrophoblast is the outer layer of the placenta and the largest human cell, spanning an area about twice that of a king-sized bedsheet.

Alzheimer's can lead to brain shrinkage, with an average of around 2% of volume reduction per year

The American cockroach is actually from Africa, an apparent hitchhiker aboard ships carrying enslaved people, with evidence suggesting the bug may have arrived in the New World as early as the 1600s.

Explore what it's like inside a patient isolation unit, used in situations such as treating a patient or suspected patient with Ebola.

Hear about the 250-year history of the United States Postal Service, complete with some of its strangest deliveries, important innovations, and the figures that made it an American institution.

Fish populations in the Great Barrier Reef have increased after installing waterproof speakers on the ocean floor that played recordings of sounds from healthy coral reefs.

The US Constitution is widely regarded as the longest-standing written national constitution still in force—see how it has influenced rights worldwide.

In 1963, a basement renovation in Turkey revealed a passageway to a hidden, multilevel underground city that once housed as many as 20,000 people

A researcher recently discovered an interview from 1967 between groundbreaking journalist Joan Didion and the Grateful Dead, years before the band became an institution.

Most of the observable universe's volume consists of voids and supervoids—enormous regions of space with little to no galaxies, stars, or light.

Scientists can determine Earth's past climate conditions by analyzing air trapped in microscopic bubbles within ice cores—columns of compressed snow layers that build up over hundreds of thousands of years.

The price of gas is a composite made up of several different factors, with the federal gas tax making up less than 20% of what drivers pay at the pump.

The Brothers Grimm were lawyers before they were storytellers, but became interested in fairy tales as they began investigating how rules and customs had been passed down through cultures.