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

Trillions of bacteria 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 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.

The gut microbiome—a complex community of up to one 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 bacterial populations in their gut, upending the idea that all animals rely on such microbes to help maintain their health and proper functioning.

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.

Gut microbiome experiments involving transfers of gut microbes from depressed people to rodents indicate that the rodents may then display depression-like symptoms, underscoring that gut microbes may influence behavior and personality more than previously known.

Bacteria in our intestine influence the brain via the gut-brain axis. (Paywall may apply.)

The gut microbiome's role in chronic diseases

Research shows that the microbial makeup of one's gut microbiome is associated with chronic diseases ranging from asthma to schizophrenia. Understanding these associations may reveal new ways to prevent or treat chronic diseases. In the meantime, nutritional changes—such as including more dietary fiber and unsaturated fat—appear to be the "most obvious, noninvasive, and immediate" way to alter the gut's microbiota makeup and functions.

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.

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.

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…

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.

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.

Western babies often are missing a key gut microbe common elsewhere

Studies show infants in Europe and North America often lack Bifidobacterium infantis, a microbe widespread in babies in Africa and South Asia that helps digest breast milk and train the immune system. Researchers link the gap to antibiotics, formula use, and sanitized spaces.

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.

Some dementia cases may be linked to microorganisms in the brain

Researchers now know that, much like the gut, the brain is home to an ecosystem of microorganisms—the brain microbiome. While this area of study is still new, some scientists believe 50% of bacteria-caused dementia cases could be treated. (Some users may encounter a paywall.)

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.

Exercise causes diet-independent changes in the gut microbiome

Cardiovascular exercise has been found to boost the gut's population of beneficial bacteria, and exercise overall decreases the likelihood of developing a "leaky gut," a condition in which a porous gut lining allows bacteria to leak into the bloodstream and cause inflammation.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Bacteria use chemical signals to communicate and coordinate with one another

Through a system called quorum sensing, bacteria produce and absorb compounds from their environment to identify allies or competitors and adjust their behavior accordingly. Some bacteria produce food-digesting enzymes only in the presence of similar bacteria, thereby preventing competitors from consuming their meal.

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.

We're breathing microplastics

White blood cells can't fight off microplastics and that sparks inflammation and bigger health risks. They're in our food, water, even the rain. What does that mean for us?

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.)

Corynebacterium species are particularly responsible for our funky smell

Myriad bacteria contribute to our body odor, but research suggests that Corynebacterium species are strongly associated with the bad smells emanating from adults. Staphylococcus and Cutibacterium genera may also play leading roles.

Why bacterial bioremediation may help counter the negative effects of past chemical solutions

Molecules such as DDT, a synthetic insecticide, and PFAS—"forever" chemicals used to make products resistant to heat, water, and grease—have historically been used across various industries but are now known to be harmful. Microbes that can convert some of these substances into nontoxic products, such as water and carbon dioxide, have already been identified, with ongoing research to find others.

Neglected tropical diseases affect more people than the population of Europe

This group of conditions, which includes hookworm, sickens roughly one in seven people on the planet—a tally which dwarfs Europe's population of roughly 450 million. International cooperation and donations are helping to control some of these illnesses, which can be caused by parasites, viruses, and bacteria. They're all treatable or preventable, but primarily occur among poor, isolated communities that may not receive adequate care.

Explore the history of antibiotics with 'This Podcast Will Kill You'

The show blends medical history with storytelling and science. In Episode 50, the hosts trace the dramatic origins of antibiotics—from Fleming’s moldy petri dish to Florey’s wartime labs—and explore their lasting impact on health.

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.

Fake sugars may disrupt metabolic health

Alternative sweeteners such as stevia and sucralose are 100 times sweeter than common table sugar. New research suggests these "high-intensity" sweeteners significantly disrupt the composition of the gut microbiome, affecting overall health. (Some users may encounter a paywall.)

'Gram-negative' bacteria: Bugs with extra defenses along their cell walls

The term 'Gram-negative' bacteria refers to bugs which react a certain way under a Gram stain test. These bacteria are harder to kill due to their double-layer cell walls with a thin peptidoglycan layer in between. This structure makes the delivery of drugs into the bacterial cell substantially more difficult.

Some mosquitoes are key pollinators—and eat disease-carrying mosquitoes

​​There are more than 3,500 species of mosquitoes, and only a small fraction of them bite humans. They also play vital roles in the ecosystem: One young elephant mosquito, for example, can eat dozens of smaller mosquitoes that bite humans in just one day. Sometimes mosquito-gobbling species are released by humans to control other mosquitoes.

1 in 6 Americans get food poisoning each year

The US federal government estimates there are about 48 million cases of foodborne illness in the country annually, resulting in as many as 3,000 deaths and 128,000 hospitalizations. Food poisoning puts those with weakened immune systems, the elderly, pregnant people, and young children at particularly high risk. This chart of common disease-causing pathogens highlights common threats and details about them, including likely food sources.

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.

Explaining the physical connection between the gut and brain

This video overview from Duke University helps visualize the gut-brain axis—a physical connection of nerves running from the brain to digestive tract that acts as a physical and chemical link.

Cells cannot grow forever due to escalating inefficiency in transporting chemicals

As cells get larger, their volume grows much faster than the surface area through which nutrients and waste products pass, creating a bottleneck that eventually causes cells to die. This forces nearly all organisms visible to the naked eye to comprise enormous numbers of smaller cells, such as the approximately 30 trillion found in the average adult human.

The biology of stress in your body

Stress is a normal human response that has evolved over millions of years to handle changes or threats in our environment. This article is a helpful overview of the biological basics of this response. While it is not harmful to our physiology in the acute setting, chronic stress can lead to damaging changes in the human body over many years.

One-third of the world’s food supply relies on pollinators

By supporting crop production and farmland ecosystems, these animals contribute over $200B to the global economy. A 3% to 5% decrease in this production may result in as many as 427,000 deaths due to nutritional deficiencies.

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.

Most people breathe fungal spores daily without getting sick

Most people breathe in hundreds of Aspergillus fumigatus spores daily without getting sick—it’s a common microscopic fungus in our environment. But people who are severely ill, including those who have undergone an organ transplant, are at risk of developing infections from these spores.

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.

Increasing contact between humans and wild animals is driving zoonotic threats

Zoonotic diseases, which spread from animals to humans, present one of the most significant emerging threats worldwide. Scientists have identified around 200 viruses capable of infecting humans, and unfortunately, the number of such diseases are on the rise—at least 60% of all emerging infectious diseases are zoonotic in origin.