Millions of people suffer from dysbiosis, yet it often goes undiagnosed. An unhealthy imbalance in the microbes that live in the body—dysbiosis can affect nearly every aspect of health. Its wide-ranging symptoms and lack of standardized testing make it difficult to identify and easy to overlook.

Microbial disruption associated with dysbiosis triggers chronic inflammation, contributing to a range of chronic health conditions, including gastrointestinal, mental, neurodegenerative, autoimmune, and metabolic diseases.

Even one course of antibiotics or a poor-quality diet can disrupt microbial balance. Fortunately, with the right approach, dysbiosis can be identified and corrected. Targeted nutrition, lifestyle changes, and natural therapies can help rebalance the microbiome and improve overall health.

Dysbiosis results from a disruption in the normal composition or function of the microbiota. The three primary features of dysbiosis, which may occur individually or together, are:

• A decrease in microbial diversity


• A loss of beneficial microbes


• An overgrowth of harmful or opportunistic microbes

These shifts can lead to very different effects depending on where they occur. For example, a loss of microbial variety in the gut may affect the brain, contributing to mood changes or memory issues, while an overgrowth of bacteria on the skin might trigger eczema. Each body system connected to the microbiome can experience its own type of microbial imbalance.

Dysbiosis can also occur when microbes end up in places where they do not belong. In people with liver disease such as cirrhosis, oral bacteria may migrate into the gut and disrupt its microbial balance. Another example is small intestinal bacterial overgrowth, where bacteria normally found in the colon begin to multiply in the small intestine. While these microbes are not harmful in their usual location, their presence in the wrong area can cause symptoms like bloating, abdominal pain, and impaired nutrient absorption.

The relationship between dysbiosis and disease is often bidirectional. Changes in the microbiome may contribute to disease development, as seen in conditions like Type 1 diabetes and Parkinson’s disease. However, dysbiosis can also emerge in response to changes in the body’s internal environment caused by disease.

Various factors can alter the microbiome, contributing to dysbiosis, including:

• Viral or bacterial infections, including SARS-CoV-2


• Underlying health conditions such as inflammatory bowel disease, obesity, and chronic liver disease


• Lifestyle habits such as smoking, alcohol consumption, unprotected sex, lack of physical activity, and sleep deprivation


• Physical or emotional stress—including trauma, surgery, or chronic tension


• Poor hygiene or excessive sanitization


• Poor diet—high in animal protein, unhealthy fats, sugars, and processed foods, and low in fiber


• Food additives such as antimicrobial preservatives, sulphates and sulphites, emulsifiers, and artificial sweeteners


• Antibiotics and other drugs, including statins, proton pump inhibitors, nonsteroidal anti-inflammatory drugs, and antidepressants

Additionally, the following factors may increase the risk of developing dysbiosis:

• Genetics may play a small role in susceptibility.


• Cesarean birth—frequently paired with antibiotics—can delay healthy microbial colonization. The benefits of swabbing the infant’s mouth with vaginal fluid appear to last less than a month.


• Formula feeding lacks breastmilk’s prebiotics and probiotics, reducing microbial diversity.


• A poor maternal diet or dysbiosis during pregnancy can increase the baby’s risk.


• Environmental toxins like pesticides, air pollution, and endocrine disruptors alter gut pH and microbial function.


• Hormonal changes during puberty, pregnancy, or menopause.


• A leaky gut allows bacteria and other substances to enter the bloodstream, fueling inflammation that worsens microbial imbalance.


• Low production of butyrate—a compound made when gut bacteria break down fiber—weakens gut wall protection and changes oxygen levels in the intestines.

Many people associate dysbiosis with gut issues, but the body’s microbiome stretches beyond the gut. Microbial communities—including bacteria, viruses, fungi, and more—also reside on the skin, in the mouth, and in the vagina. Bacterial cells in the body nearly match human cells in number, and their collective genome outweighs the human genome by nearly 100 times.

When these communities are out of balance, symptoms can emerge in unexpected ways. The imbalance might impair nutrient absorption, disrupt immune signals, weaken protective linings in the gut or skin, or trigger widespread inflammation. These disruptions can lead to a wide range of symptoms that may appear unrelated, depending on the affected area and the nature of the imbalance.

Sometimes, dysbiosis presents without obvious symptoms, silently affecting health and increasing the risk of developing various conditions.

The initial indicators of dysbiosis often present as gastrointestinal disturbances.

• Halitosis or bad breath


• Gas


• Bloating


• Food intolerances or sensitivities


• Abdominal cramping


• Diarrhea


• Mucus in the stool

Beyond the digestive system, dysbiosis can trigger a variety of symptoms that might not seem connected at first.

• Genitourinary symptoms, such as vaginal itching or discharge


• Dermatological signs, including skin rashes or redness


• Oral health issues, such as cavities or bleeding gums


• Systemic symptoms like persistent fatigue

Dysbiosis can also significantly affect mental well-being, contributing to depression, anxiety, and cognitive difficulties such as memory issues or brain fog.

Dysbiosis can be classified in several ways—by location, cause, or interconnected pathways called axes, which link the gut to other organs like the gut-brain axis or gut-liver axis. Through these pathways, dysbiosis in one area can affect other areas.

Gut Dysbiosis

The most common and well-researched type of dysbiosis involving imbalances in the gut microbiota that contribute to inflammatory bowel disease, irritable bowel syndrome, and other gastrointestinal disorders.

Oral Dysbiosis

Occurs in the mouth and can lead to conditions such as gingivitis, periodontitis, and other oral health issues.

Vaginal Dysbiosis

Involves imbalances in the vaginal microbiota, most notably bacterial vaginosis.

Skin Dysbiosis

This condition involves imbalances in the skin microbiota, which can contribute to conditions such as eczema and acne.

A lack of diagnostic guidelines and a clear clinical definition of dysbiosis make it difficult to diagnose. Laboratory methods also vary, making it hard to compare results across different labs. Dysbiosis involves complex interactions between microbes, their by-products (metabolites), and the human host. Identifying dysbiosis often requires specialized testing and expert interpretation. As a result, some health care practitioners may be unaware of available tests or unsure how to use them effectively.

Basic Tests 

• Stool culture: Detects harmful bacteria but often misses the broader microbial picture


• Breath test: Helps identify bacterial overgrowth, particularly small intestinal bacterial overgrowth


• Endoscopy/colonoscopy: Offers direct visualization of the gut, but doesn’t assess microbial balance

Functional Medicine Tests

• Comprehensive stool analysis: Assesses bacterial balance, inflammation markers, and digestive function


• Intestinal permeability tests: Measures “leaky gut” through blood or stool samples


• Organic acids test: Indicates microbial activity based on metabolites in urine


• Food sensitivity testing: Identifies foods that may contribute to gut dysfunction

These specialized tests can help detect imbalances in the gut bacteria that standard tests may miss.

Dysbiosis contributes to a variety of complications by promoting chronic, low-grade inflammation, weakening mucosal barriers, and disrupting immune and metabolic function. When harmful microbes override beneficial ones, disease can develop or worsen.

While not always the root cause, dysbiosis can intensify symptoms, accelerate progression, or interfere with recovery. Some complications arise locally, while others reflect systemic effects throughout the body.

The following conditions have also been associated with dysbiosis:

• Oral: Gingivitis, periodontitis, dental caries, oral candidiasis


• Gastrointestinal: Ulcerative colitis, Crohn’s disease, irritable bowel syndrome, gastroenteritis


• Neurodevelopmental and neuroinflammatory: Meningitis, stroke, Parkinson’s disease, autism spectrum disorder


• Cardiovascular: Atrial fibrillation, endocarditis


• Respiratory: Cystic fibrosis, pneumonia, lung infection, sleep apnea


• Kidney: Chronic kidney disease, uremia (excess urea in the blood)


• Bladder and reproductive tract: Pelvic inflammatory disease, urinary incontinence, interstitial cystitis, bladder pain syndrome


• Psychiatric: Dementia, depression, anxiety, bipolar disease, schizophrenia


• Skin: Rosacea, psoriasis, dermatitis


• Metabolic: Insulin resistance, Type 2 diabetes, obesity, dyslipidemia (unbalanced blood lipids)


• Autoimmune conditions: Rheumatoid arthritis, systemic sclerosis, Sjögren’s syndrome, antiphospholipid syndrome, Type 1 diabetes, multiple sclerosis


• Cancer: Gynecological, colorectal, skin, and lung cancers

Other Systemic Complications

Endotoxemia: A condition in which bacterial toxins such as lipopolysaccharide leak into the bloodstream due to a compromised gut barrier, triggering widespread inflammation.

Bone resorption: Inflammatory cytokines and reduced nutrient absorption may increase bone breakdown and contribute to bone loss over time.

Conventional medical approaches to treating dysbiosis primarily focus on addressing severe imbalances or infections.

Treatment strategies typically include:

Removing Harmful Strains

Antibiotics are prescribed for bacterial infections, with selection based on the infection’s type and location. Antifungals are used for fungal overgrowth, such as Candida infections.

Fecal Microbiota Transplantation (FMT)

FMT is highly effective and approved for treating recurrent Clostridioides difficile infections, also known as C. diff, which can cause severe diarrhea and inflammation of the colon. FMT involves transferring fecal matter from a healthy donor to the patient’s gut via colonoscopy, enema, or oral capsules.

Addressing Medication-Induced Dysbiosis

If a medication is suspected of causing dysbiosis, practitioners may recommend discontinuing or modifying treatment until microbial balance is restored.

Microbial Metabolic Pathway Therapy

This emerging approach uses pharmaceuticals to influence microbial activity—enhancing beneficial effects and suppressing harmful ones. Drugs are used to block the metabolic pathways of harmful microbial by-products.

Probiotics

Conventional medical practitioners use probiotics, but limited clinical guidance and a lack of U.S. Food and Drug Administration regulation restrict their application. Effectiveness varies by strain—a distinction not all clinicians may recognize—so strain selection, formulation, and dosing should be guided by a knowledgeable professional and personalized based on stool analysis, genetics, and medications.

While conventional treatments—such as using antibiotics—can be effective for acute infections or severe dysbiosis, they often fail to address underlying causes or support long-term microbial balance. This limitation underscores the need for a more holistic approach to managing dysbiosis.

Eliminating dysbiosis requires more than simply removing harmful bacteria or replacing the microbiome. Without changes in diet and lifestyle, improvements may be temporary. The most effective natural strategies focus on restoring balance by creating an environment in which beneficial microbes can thrive—starting with the food we eat.

The Dietary Pathway to a Healthy Microbiome

Diet provides a primary source of microbial flora in the body—a principle emphasized by traditional medicine systems such as Chinese medicine and Ayurveda. Modern research confirms that changes in macronutrient intake, like protein, fat, and carbohydrates, can rapidly alter the gut microbiota. Diets high in simple sugars are especially disruptive, as they can damage the intestinal barrier, trigger inflammation, and impair metabolism. These effects contribute to dysbiosis by altering microbial activity and interactions.

Simple dietary changes can meaningfully influence the microbiome. Both the Mediterranean and alkaline diets are supported by research. While they differ in structure and scientific depth, they share core features that promote microbial balance.

The Mediterranean Diet

Known for its anti-inflammatory benefits and positive influence on gut health, research has shown the Mediterranean diet increases microbial diversity, promotes beneficial bacteria, and decreases harmful strains. It emphasizes:

• High intake of fruits, vegetables, whole grains, nuts, seeds, and olive oil


• Moderate consumption of fish, poultry, and dairy


• Limited intake of red meat and processed foods


• Healthy fats, particularly monounsaturated fats from olive oil and omega-3s from fatty fish

The Mediterranean diet is rich in fiber, which feeds microbes that break down complex carbohydrates. This process boosts the production of short-chain fatty acids, which support gut health. Polyphenols in foods like olive oil and wine also act as prebiotics, feeding beneficial microbes. In addition, these healthy fats have anti-inflammatory properties and help promote microbial balance.

The Alkaline Diet

The alkaline diet focuses on foods that create alkalizing substances, reducing acidity in the body. Although blood pH is tightly regulated by the body, urinary pH can change based on diet and is tested using pH strips.

Research on the alkaline diet’s direct effects on the microbiome is more limited than research on the Mediterranean diet, and its influence on specific bacterial strains appears mixed. However, some evidence suggests that alkaline environments support a healthier microbial balance, while harmful bacteria are more likely to thrive in acidic conditions.

The alkaline diet’s anti-inflammatory foods also align with dysbiosis management by emphasizing:

• High intake of fruits, vegetables, nuts, and seeds


• Limited intake of acid-forming foods such as meat, dairy, and refined grains


• Plant-based fats from sources such as nuts, seeds, and avocados

The 5 Rs of Functional Medicine

While nutrition plays a central role in microbial health, restoring full-body balance often requires additional support. Functional medicine practitioners commonly use a flexible framework called the “5 Rs” to guide this process. The 5 Rs framework targets the root causes of dysbiosis and promotes long-term balance through five key steps: remove, replace, reinoculate, repair, and rebalance.

1. Remove

The first step in restoring balance is eliminating microbial disruptors that contribute to dysbiosis. These include pathogenic microbes, inflammatory triggers, environmental toxins, and personal care products that damage local microbial ecosystems. Common disruptors of the microbiome and how to remove them are:

• Harmful microbes: Natural remedies like garlic, pomegranate peel, or green tea extract may be options for removal. Seek professional guidance before using stronger herbs.


• Dietary triggers: Limit processed foods, additives, and alcohol.


• Medications: Talk with your health care provider about reducing medications that affect gut bacteria.


• Environmental toxins: Minimize exposure to air pollution, pesticides, and smoke. Consider an indoor air purifier and choose organic produce.


• Disruptive skin products: Avoid harsh soaps and overuse of sanitizers. Choose gentle, fragrance-free options.


• Mouth care: Antiseptic mouthwashes kill both harmful and beneficial bacteria. Replace with microbiome-friendly rinses containing xylitol, essential oils, or botanical extracts such as green tea or clove. Oil pulling with coconut oil may also help reduce harmful biofilms and support microbial balance.


• Feminine hygiene products: Avoid douching and scented or chemical-laden menstrual products. Opt for organic, unscented products to protect the vaginal microbiome.

2. Replace

This step focuses on restoring missing elements that support digestion and microbial nourishment. Dysbiosis often develops—or persists—when digestive function is impaired or key nutrients are lacking. Replacing digestive secretions, supportive nutrients, and healing compounds helps create an internal environment where beneficial microbes can thrive.

• Digestive enzymes and bile support: Low stomach acid, insufficient digestive enzymes, or sluggish bile flow can impair digestion and contribute to microbial imbalance. Supplemental enzymes or bile support, such as ox bile or digestive bitters, may improve digestion when needed.


• Nutrients potentially depleted in dysbiosis: Deficiencies in zinc, magnesium, vitamin A and D, omega-3 fatty acids, and iron may impair barrier function, alter microbial composition, and disrupt immune regulation. Nutrient testing can help identify individual needs.


• Gut-healing foods: Bone broth provides collagen, glutamine, and minerals that support gut lining integrity.


• Plant compounds to enhance digestive secretions: Bitter herbs such as gentian, dandelion, and artichoke can stimulate stomach acid, bile, and pancreatic enzymes, aiding food breakdown and supporting microbial balance.

3. Reinoculate

Reintroduce beneficial microbes through food or supplementation.

Probiotics and fermented foods: While probiotic supplements can be helpful, dietary sources also play a valuable role. Fermented foods—such as sauerkraut, kimchi, and pickled carrots or beets—offer a broad spectrum of live microbes and prebiotic fibers that help nourish beneficial bacteria. These microbes can also promote the production of short-chain fatty acids and organic acids that support gut health.

Prebiotics: While probiotic strains often do not colonize the gut long-term, prebiotics feed the beneficial microbes already present. This approach can be highly effective, as it supports the existing microbial ecosystem. Prebiotic sources include dietary fiber and supplements such as inulin, flax meal, psyllium husk, fructooligosaccharides, and galactooligosaccharides.

4. Repair

Restore barrier integrity and reduce inflammation.

• Nutrients that support cells in the gut lining include L-glutamine, zinc carnosine, omega-3s, collagen, and vitamins A and D.


• Herbs such as camellia sinensis from black tea, deglycyrrhizinated licorice, marshmallow root, and ginger may soothe inflammation and promote mucosal healing.


• Short-chain fatty acids such as butyrate, propionate, and acetate may be used as supplements to reduce inflammation and support epithelial repair, especially if butyrate-producing bacteria are depleted.


• Polyphenols such as resveratrol, quercetin, curcumin, and epigallocatechin gallate may support gut healing. Resveratrol may also help reduce trimethylamine N-oxide, a compound linked to cardiovascular risk.

5. Rebalance

Address lifestyle factors that influence the microbiome, such as stress management and sleep. Time outdoors and physical activity can increase exposure to diverse microorganisms. Contact with natural elements—like soil and plants—may introduce beneficial microbes to the skin and enhance the diversity of the skin microbiome. Research shows that time spent in urban green spaces can improve skin and nasal microbial diversity and influence the overall makeup of the human microbiota.

While many of these approaches can be implemented at home, some steps should be guided by a qualified practitioner to ensure safety, tailor interventions to individual needs, and improve outcomes.

Just as fertile soil determines whether seeds thrive or wither, the body’s inner terrain—the biochemical environment—influences which microbes thrive, struggle, or become harmful. Mindset helps shape this terrain by turning thoughts into biochemical signals like hormones and neurotransmitters that affect microbial balance. Persistent negative thoughts or emotional tension contribute to psychological stress—the body’s response to perceived threats or pressures.

Psychological stress activates a hormone called corticotropin-releasing factor (CRF), which can disrupt the gut microbiome. CRF raises levels of cortisol, a hormone that weakens the tight junctions between intestinal cells. As a result, the gut becomes more permeable, allowing bacteria and other substances to leak through. Stress also reduces microbial diversity, lowers levels of beneficial bacteria such as Lactobacillus and Bifidobacterium, and decreases short-chain fatty acids, creating a terrain that promotes dysbiosis.

Stress further compromises the gut’s defenses by reducing mucin production and suppressing secretory IgA (sIgA) levels in the gut and mouth. Mucin is part of the protective mucus layer that prevents harmful microbes from adhering to the gut lining. sIgA binds to pathogens and prevents them from colonizing. By weakening these protective barriers, stress reshapes the inner terrain, making it easier for certain microbes to adhere, become pathogenic, and contribute to dysbiosis.

The gut, brain, and microbiome are deeply interconnected, forming a dynamic feedback loop in which each influences the others. Stress and mindset can alter gut function, while changes in the microbiome can affect mood, behavior, and cognitive health. Research suggests that certain probiotics may help reduce the effects of stress, support the repair of the intestinal lining, and improve central nervous system function—a promising approach to addressing dysbiosis.

While targeted probiotics offer one path to help rebalance the microbiome, mindset remains a powerful tool for recovery. A calm, steady mindset fosters resilience, helping restore and protect the inner terrain—even during ongoing stress. Research has shown that practices like mindfulness-based cognitive therapy and breathwork can reduce inflammation, support microbial diversity, and improve vagal tone—a measure of the vagus nerve’s role in linking gut and brain communication.

Mindset also affects digestion, another key player in microbial balance. Chronic stress or emotional tension can disrupt the nervous system’s regulation of stomach acid, enzymes, and gut motility. In contrast, a relaxed state supports efficient digestion, nutrient absorption, and elimination, influencing the health of the microbiome.

Over time, shifting from a chronically stressed state to one of greater calm and resilience creates a more hospitable inner terrain—one where beneficial microbes can thrive and dysbiosis can begin to resolve.

While the causes of dysbiosis are numerous and complex, many are easily preventable. Taking proactive steps throughout life can help preserve microbial balance, maintain a protective gut barrier, and reduce inflammation to support long-term health. Below are practical strategies to support a healthy microbiome across different life stages:

Pregnancy and Birth

The earliest steps toward prevention begin before birth. A mother’s microbiome shapes her child’s microbial foundation.

• Focus on a nutrient-dense, whole-food, fiber-rich diet to support the maternal microbiome.


• Incorporate probiotics or prebiotics during pregnancy when appropriate.


• Choose vaginal delivery, if possible, and prioritize immediate skin-to-skin contact.


• Extend exclusive breastfeeding for six months or longer when feasible.

Infancy and Childhood

Early life is a critical window for microbiome development, setting the stage for lifelong health.

• Limit antibiotic use to medically necessary situations.


• Encourage outdoor play and exposure to pets to boost microbial exposure.


• Reduce intake of processed foods with added sugars.


• Use fragrance-free soaps and minimize antimicrobial products.

Adolescence to Adulthood

As independence and lifestyle habits form, so do long-term microbial patterns.

• Maintain consistent oral hygiene, including brushing and flossing.


• Practice safe sex using barrier methods such as condoms.


• Adopt dietary patterns that align with Mediterranean and alkaline principles.


• Limit alcohol intake, avoid smoking, and reduce exposure to secondhand smoke.

Throughout Life

Regardless of age, some habits are universally protective.

• Incorporate stress-reducing practices like prayer, mindfulness, deep breathing, or time in nature.


• Prioritize sleep hygiene and aim for seven to nine hours of restful sleep each night.


• Opt for targeted antibiotics when appropriate, and consult with a provider about alternatives to broad-spectrum medications.


• Evaluate and limit the use of medications known to disrupt the microbiome.