The gut microbiome may play a major role in autoimmune disease and symptom flare-ups

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

Autoimmune disease prevalence and incidence are on the rise—but no one knows why

Researchers theorize that environmental factors, including shifts to less healthy diets, air pollution, infections, stress, climate change, and exposures to xenobiotics—substances like pesticides, plastics, and toxins that incite immune responses—may all be fueling epigenetic changes to our bodies that make people's immune responses go awry.

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.

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.

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.

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.

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.

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

Exercise causes diet-independent changes in the gut microbiome.

There's no specific anti-inflammatory diet, but certain foods increase the chance of inflammation

Research suggests humans can reduce inflammation by limiting foods that are already known to be unhealthy for the human body—because they alter gut bacteria and stress the immune system—such as highly-processed foods, deep fried foods, sugary drinks, trans fats, red meats, and foods made with white flour. Foods that help the body include fatty fish such as salmon, legumes, fruits, and vegetables.

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

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.

Chronic inflammation can cause cellular damage and could lead to cancer

Over time, this cellular defense system can inadvertently damage cells and tissues when it's in this heightened alarm mode over a prolonged period. This occurs because, when immune cells are sent somewhere without a true target, they may attack healthy cells and tissues.

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.

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

Women typically have more robust immune responses than men

This difference helps women better combat infectious diseases, but this more turbo-charged response may also make women more vulnerable to autoimmune diseases by potentially priming their immune systems to overreact to their own cells and tissues and label them as invaders that must be destroyed. Roughly 80% of American women have autoimmune conditions.

Almost 80% of people diagnosed with autoimmune diseases are women

Yet it's still unanswered what may account for that difference. To better understand this disparity researchers are exploring factors including hormonal changes that occur around puberty, pregnancy, and menopause, as well as gut microbe differences, and aspects of X-chromosome protein-coding genes. (Some users may encounter a paywall.)

Autoimmunity is when the body attacks itself, causing inflammation

Inflammation is the body's way of healing itself, and acute inflammation saves our lives when we have injuries or infections. It increases blood flow to the affected areas to bring immune cells to fight off invaders. This often results in short-term swelling, redness, and pain.

How one autoimmune disease patient is questing for inflammation cures

This article's writer, who has Hashimoto's Disease and characteristic symptoms from her body attacking her thyroid—like exhaustion, hair loss, and brain fog—shares big take-aways from an anti-inflammatory retreat in Italy. The writer suggests that a holistic approach to eating, sleeping, and stress management, are the only sustainable ways to lower inflammation.

Many patients with psoriasis develop other autoimmune diseases, too

A small study published in 2024 found that nearly three-quarters of patients with psoriasis—a condition in which the body attacks healthy skin cells—also developed autoimmune disorders including thyroid diseases, connective tissue diseases, and more, suggesting such connections between these autoimmune disorders warrant further exploration.

How autoimmune diseases, which attack your own tissues and cells, work in the body

These diseases remain some of medicine's thorniest problems because the immune system can mistakenly attack almost any tissue in the body, resulting in myriad diseases, including lupus (numerous tissues affected), Hashimoto's (thyroid), and MS (the nervous system).

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

Autoimmune diseases affect between 5% and 10% of people worldwide, but their causes remain unknown

Autoantibodies—which attack the body—may be detectable in the body years before a patient develops symptoms, but some people may have detectable levels yet never go on to develop an autoimmune disease. This video discusses this and other unsolved mysteries with autoimmune disease.

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.

GLP-1s are netting interest for treating autoimmune diseases, but are considered experimental

Already used to treat type 2 diabetes, the novel medications are showing some early promise in experimental studies at reducing inflammation and treating autoimmune conditions including rheumatoid arthritis and inflammatory bowel conditions. But researchers caution that side effects are still under investigation—rarely the medication has caused lupus, an autoimmune disease.

Inflammation appears to cause specific symptoms of depression

A large analysis of existing studies published in 2021 found that systemic inflammation is associated with fatigue, appetite changes, and sleep disruption, rather than some of depression's broader symptoms including hopelessness about the future, or feeling fearful. This may suggest that inflammation influences specific symptoms of the condition, rather than the disease as a whole.

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.

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

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.

Twin studies suggest celiac disease is among the more genetically-linked disorders

Genetics appear to play a larger part in this condition's development than many other autoimmune disorders. Research shows a roughly 60-75% genetic probability that if one identical twin has it, the other will too. Celiac triggers a small intestine attack when people eat gluten, a protein commonly found in wheat, barley, and rye.

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

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.

Addressing lifestyle factors, which influence inflammation, can cure some chronic diseases

In this video, a physician claims that he reversed a patient's Type 2 diabetes in six weeks by addressing inflammation drivers such as diet. More broadly, he argues that society needs to better consider and address numerous disease factors that are modulated by inflammation, such as stress, sleep, diet, and movement.

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.

Inflammaging is chronic low-level inflammation as we age, and it may be a key disease driver

The term refers to the idea that largely invisible but consistent low-level inflammation as humans age fuels chronic diseases and cellular aging. Inflammaging, this article says, is due to lifestyle factors like poor sleep, low levels of activity, and poor diet, acting in concert to cause cellular damage and trigger inflammation.

Lengthy incubation periods are why it's tough to link foodborne illness to specific foods.

Short-term cortisol spikes can boost the immune system

Elevated acute levels can enhance the immune system's ability to fight off infection or respond to injury. Chronic heightened cortisol levels, however, can lead to inflammation that harms cells and tissues over time.

More than 5 million Americans have more than one autoimmune disease

Overall, about 4.6% of the US population—15 million people—have an autoimmune condition. Some common examples include rheumatoid arthritis, psoriasis, type 1 diabetes, Grave's disease, and autoimmune thyroiditis.

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

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.

Learn how colorectal cancer is linked to the American diet and chronic inflammation

A University of South Carolina colon cancer researcher offers insights from his own research and notes that more exercise, social support, and eating fruits, vegetables, legumes, and foods like fish and olive oil—often called the Mediterranean diet—are associated with better health—and could improve our colons.

Hookworm infection, though risky, may help fight certain health conditions.

The science of food allergies

Why do certain substances trigger an immune response while others don't? Listen to researchers explain the science in this five-minute video. Food allergies affect around 8% of children and 2% of adults in the US, and—unlike sensitivity or intolerance—they involve the immune system mistaking certain harmless proteins in foods as dangerous invaders, triggering a rapid and sometimes severe defense response.

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.

Why are women more likely to suffer autoimmune diseases than men?

A majority of Americans with autoimmune diseases have more than one X chromosome, a typical marker of the female biological sex, according to a study published in February of 2024. During fetal development, cells side with one X chromosome over the other, preventing the overproduction of X-chromosome-specific proteins and shutting down the twin chromosome. This article explores how this X-chromosome inactivation can lead to autoimmune disorders by generating antibodies to the body's own tissues.

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.

Our ancient fight-or-flight response may contribute to modern ailments

Many common modern diseases humans struggle with may in fact have their origins in our ancient fight-or-flight stress response. Long-term effects of the stress hormones cortisol and adrenaline—in this case, triggered by things like workplace stressors—can wreak havoc on the delicate internal balance of our organ systems.

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.

Inflammaging appears to differ across global populations

Chronic, low-grade inflammation linked to aging is a byproduct of our industrialized lifestyles, according to recent research. The work compared two industrialized populations with two Indigenous, non-industrialized populations in Bolivia and Malaysia, and found that inflammation levels in the Indigenous groups—unlike the industrialized ones—did not seem to differ by age.

Autoimmune disorders are one of the top 10 killers of young and middle-aged women

Studies in the US and the UK, though conducted decades ago, have underscored that autoimmune diseases, when grouped together, are a top killer of women.