Dysbiosis: What It Is, Causes, Symptoms, Diagnosis and Treatment

Oct 8

9 min read

Updated: 5 days ago

Medically reviewed by Dr. Baraa Alnahhal, MD · Last reviewed: October 2026

Dysbiosis is an imbalance in the community of microorganisms, called a microbiome, that live in your body [1]. When one type of bacterium, virus or fungus dominates and variety drops, these microbes can stop working for you and start working against you [1]. It can affect your gut, mouth, skin or genitals [1]. Gut dysbiosis is directly tied to several digestive diseases, and it may be indirectly involved in conditions as wide-ranging as mood disorders and fatty liver disease [1]. Treatment targets the cause, and most microbiomes can recover with the right environmental and dietary conditions [1].

Quick Answer: What is dysbiosis, and how is it treated?

Dysbiosis is an imbalance within one of the body's microbiomes, the communities of bacteria, viruses and fungi living in the mouth, skin, gut or genitals. Causes include antibiotics, smoking, alcohol, stress, chronic disease and diet. In the gut, it is involved in infections, SIBO and inflammatory bowel disease. Treatment targets the cause and includes diet changes, especially plant-rich eating. [1]

What the research says

Antibiotics can leave a long-lasting imprint on the gut microbiome. In 12 healthy men given a 4-day course of three last-resort antibiotics, the gut microbiota recovered to near-baseline composition within 1.5 months, but 9 common species that every participant had before treatment remained undetectable in most of them after 180 days (Palleja et al., Nature Microbiology, 2018 [2]).
Plant-based, high-fiber diets are linked to a healthier microbiome. A systematic review of 30 clinical trials in people with chronic inflammatory diseases found that high-fiber plant-based diets were consistently more effective than other diets and fiber supplements at reducing pathogenic bacteria and increasing microbiome diversity and short-chain fatty acid-producing bacteria. The trials had a moderate to high risk of bias (Wagenaar et al., Nutrients, 2021 [3]).

What Is Dysbiosis?

Dysbiosis is an imbalance within a community of microorganisms living together, which is called a microbiome. Your body is host to several distinct microbiomes, which are communities of microorganisms that live with you and assist you in various ways [1].

A balanced microbiome is one where there's a healthy variety of microorganisms and no single bacterium, virus or fungus dominates. Dysbiosis means there's an imbalance in the types of microorganisms, and it changes how they function in your body [1]. For a broader look at how this community works, see our guide to the gut microbiome.

How Does Dysbiosis Affect You?

In any microbiome, reduced variety and balance can pave the way for one type of microorganism to take over. Dysbiosis makes you more vulnerable to infections from germs living inside and outside of your body. It can also interfere with other important services that your microbiomes normally provide [1].

Your gut microbiome provides many services by interacting with your body in a multitude of ways, and it talks to your other systems [1].

What Can Gut Dysbiosis Lead To?

Bacterial dysbiosis in your gut is directly involved in various gastrointestinal (GI) diseases affecting your digestive system, including [1]:

Bacterial infections: H. pylori and C. difficile
Bacterial overgrowth: small intestinal bacterial overgrowth (SIBO)
Inflammatory bowel diseases: ulcerative colitis and Crohn's disease
General digestive difficulties: diarrhea, constipation and gas

Your gut microbiome also interacts with your brain and with many of your other body systems, including your immune system, nervous system and endocrine system. Gut dysbiosis may be indirectly involved in a variety of other conditions [1]:

Nutrition: malnutrition and malabsorption
Digestion: food intolerances and irritable bowel syndrome (IBS)
Metabolism: atherosclerosis, fatty liver disease and metabolic syndrome
Whole-body effects: chronic inflammation, chronic fatigue and mood disorders

Symptoms and Causes

Dysbiosis can affect your gut, skin, mouth or genitals [1].

Signs and Symptoms

You might have dysbiosis in your mouth, on your skin, in your intestine or in your urinary system if you have signs or symptoms of a bacterial, viral or fungal infection or overgrowth there [1]:

Mouth: bleeding gums, tooth decay and cavities
Skin: atopic dermatitis or acne
Intestine: bloating, gas and poop changes
Urinary system and genitals: painful urination, genital discharge or itching

Intestinal dysbiosis, in particular, may have broader effects, though it's hard to tell when symptoms outside your gut relate to your gut microbiome. If you've recently developed intestinal symptoms together with other symptoms, like mood changes or weight changes, they might be related [1].

What Causes Dysbiosis?

Different things in your internal and external environment can affect your microbiomes [1]:

Antibiotics and antimicrobial agents: these kill helpful and unhelpful microbes alike.
Other drugs and medications: these can shift the microbial balance.
Smoking and alcohol use: these harm some types of microorganisms while encouraging others.
Environmental toxins: these also favor some types and harm others.
Physical and psychological stress: long-term stress can cause significant changes.
Chronic inflammation and chronic diseases: these alter the environment that microbes live in.
Food choices: your diet shapes which microbes thrive.

Microbiomes are resilient overall, but heavy or long-term exposure to one of these factors, or a combination of several, could cause significant changes. Environmental factors can harm some types of microorganisms while encouraging others, leading to an imbalance. Helpful types might not be able to do their jobs well enough, while the unhelpful types might do more damage [1].

How Dysbiosis Is Diagnosed

Healthcare providers can diagnose infections with various lab tests. They might take a sample of your blood, poop or urine, or take a swab from your skin, mouth or genitals to test for infection or overgrowth [1]:

Blood, stool or urine sample: tests for infection or overgrowth.
Swab of the skin, mouth or genitals: tests for infection or overgrowth at that site.
Pathologist lab examination: makes the diagnosis from the sample.
Breath test: for gut dysbiosis, shows which bacteria dominate in your gut.

Treatment Options

Treatment for dysbiosis depends on the cause. If an underlying disease or condition causes it, you'll need specific treatment for that condition. If environmental and lifestyle factors contribute, your provider will work with you to change these factors. Environmental and lifestyle changes can usually benefit anyone with dysbiosis, regardless of other causes involved [1].

If you have an infection or overgrowth, your provider might need to target it directly with antibiotics, antivirals or antifungals. These medications can diminish the infection or overgrowth, but they can also diminish the helpful types of microorganisms. Some microbiomes will bounce back after treatment, but others might need more follow-up care to restore their healthy composition [1].

Treat the underlying condition when a disease or condition is the cause.
Antibiotics, antivirals or antifungals to target an infection or overgrowth directly.
Environmental and lifestyle changes, which benefit anyone with dysbiosis, regardless of cause.
Probiotics and targeted nutrition as follow-up care to restore healthy composition.
Fecal microbiota therapy in rare cases, to restore the microbiome.

Living With Dysbiosis

Can You Fix Gut Dysbiosis Naturally?

With the right environmental conditions in place, most microbiomes can recover from dysbiosis naturally. You can help it along with long-term lifestyle changes [1]:

Reduce substance use: less smoking and alcohol.
Change medications if necessary, with your provider's guidance.
Reduce exposure to environmental toxins.
Manage stress and its causes, both physical and psychological.
Feed your gut microbiome healthy foods, such as a plant-rich, whole-food diet.
Use probiotics or supplements if recommended to support gut health recovery.

A healthcare provider can help you isolate the factors influencing your microbiome and what it might need to recover, including specific probiotics or supplements [1].

What Kind of Diet Helps Heal Gut Dysbiosis?

The simplest way to improve your gut health naturally is to make sure you're feeding it a plant-rich diet. Different types of gut bacteria need different types of plant fibers and micronutrients to thrive, so variation in your diet helps support a healthy balance. Whole foods, like plants, also tend to be anti-inflammatory, which makes conditions in your gut friendlier to the friendly bacteria [1].

Foods to include:

A variety of whole fruits and vegetables, which are rich in prebiotic fiber that feeds good bacteria
Fermented foods such as yogurt, pickles, miso soup and sauerkraut, which are rich in probiotics
Healthy fats such as fish, nuts and plant oils, which are anti-inflammatory

Foods to avoid:

Fast and fried foods, which are high in inflammatory saturated fats
Candy, soda and sweets, which are high in added sugar
Packaged and convenience foods, which are high in additives and preservatives

Is Dysbiosis Related to Leaky Gut Syndrome?

Leaky gut syndrome isn't yet a recognized medical diagnosis. But the theory does involve bad bacteria in your gut. Certain types of gut bacteria attack and erode your gut lining, weakening your gut barrier, and certain types produce toxins as byproducts. If these toxins leaked through your weakened gut barrier into your bloodstream, theoretically they might cause an inflammatory response [1]. Read more in our article on leaky gut syndrome: theory vs. medical fact.

Bottom Line

Dysbiosis is a word for a simple idea: your body's microbial communities are out of balance. In a healthy state, variety reigns and no single microbe dominates. When that balance tips, microbes that used to work for you can start working against you, across your gut, mouth, skin and genitals [1].

The gut connection deserves the most attention. Gut dysbiosis is directly tied to infections, SIBO, inflammatory bowel disease and everyday digestive trouble, and it may reach even further, into mood, metabolism and chronic inflammation. The science is still evolving, but the practical takeaway is well established: diet and lifestyle have a major impact on your gut microbiome [1].

The number to remember: a plant-rich, varied diet is the simplest lever. Prebiotic fiber from fruits and vegetables, probiotics from fermented foods and anti-inflammatory fats feed the microbes that feed you, while ultra-processed, sugary, fried foods do the opposite [1].

Your next step: if you have persistent symptoms, from bloating and bowel changes to recurring mouth or skin issues, a healthcare provider can test for infection or overgrowth and help you isolate the factors tipping your microbiome out of balance.

Frequently Asked Questions

What is dysbiosis?

Dysbiosis is an imbalance within one of your body's microbiomes, the communities of bacteria, viruses and fungi that live with you. A balanced microbiome has a healthy variety where no single microbe dominates; dysbiosis means that balance is lost and function changes.

Is dysbiosis a disease?

Not exactly. It's an imbalance state rather than a disease on its own. But gut dysbiosis is directly involved in several gastrointestinal diseases, and it may be indirectly involved in many chronic conditions.

Where can dysbiosis occur?

Dysbiosis can affect your gut, skin, mouth or genitals. Signs appear as infection-like symptoms at each site: mouth (bleeding gums, cavities), skin (dermatitis, acne), intestine (bloating, gas, poop changes) or urinary and genital area (painful urination, discharge, itching).

What causes dysbiosis?

Antibiotics and other medications, smoking and alcohol use, environmental toxins, physical and psychological stress, chronic inflammation, chronic diseases and food choices. Heavy or long-term exposure to one factor, or a combination of several, can cause significant changes.

What diseases is gut dysbiosis directly linked to?

Bacterial infections (H. pylori, C. difficile), small intestinal bacterial overgrowth (SIBO), inflammatory bowel diseases (ulcerative colitis, Crohn's disease) and general digestive difficulties like diarrhea, constipation and gas.

Can gut dysbiosis cause mood changes or weight changes?

The gut microbiome interacts with your brain, immune, nervous and endocrine systems, and gut dysbiosis may be indirectly involved in mood disorders, chronic fatigue, metabolic syndrome and other conditions. New gut symptoms appearing together with mood or weight changes might be related.

How is dysbiosis diagnosed?

Providers test blood, stool or urine samples, or swab the skin, mouth or genitals, and a pathologist examines them in the lab. For gut dysbiosis, a breath test can show which bacteria dominate in your gut.

How is dysbiosis treated?

Treatment depends on the cause: specific treatment for underlying conditions, antibiotics, antivirals or antifungals for overgrowth, and environmental and lifestyle changes. Antibiotics can also diminish helpful microbes, so follow-up care may be needed.

Can the gut microbiome recover after dysbiosis?

Yes. With the right environmental conditions, most microbiomes can recover naturally. Follow-up care may include probiotics, targeted nutrition and, in rare cases, fecal microbiota therapy.

What diet helps heal gut dysbiosis?

A plant-rich, varied diet. Include whole fruits and vegetables (prebiotic fiber), fermented foods like yogurt, pickles, miso soup and sauerkraut (probiotics), and healthy fats like fish, nuts and plant oils. Avoid fast and fried foods, added sugars and packaged convenience foods.

Is leaky gut syndrome the same as dysbiosis?

No. Leaky gut syndrome isn't yet a recognized medical diagnosis. The theory involves bad gut bacteria eroding the gut lining and producing toxins that might leak into the bloodstream and trigger inflammation. It is related to dysbiosis but not the same thing.

References

Cleveland Clinic. Dysbiosis. Cleveland Clinic. April 16, 2024. https://my.clevelandclinic.org/health/diseases/dysbiosis
Palleja A, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology. 2018;3(11):1255-1265. PMID 30349083. https://doi.org/10.1038/s41564-018-0257-9
Wagenaar CA, et al. The effect of dietary interventions on chronic inflammatory diseases in relation to the microbiome: a systematic review. Nutrients. 2021;13(9):3208. PMID 34579085. https://doi.org/10.3390/nu13093208

Medical disclaimer

This article is based on clinical reference sources current as of April 16, 2024. Medical information changes over time — this content is for general education and is not a substitute for professional medical advice. Always consult a licensed clinician for diagnosis and treatment.