Gut Dysbiosis: Symptoms, Causes, and How to Treat It
Gut dysbiosis symptoms, including chronic bloating, fatigue, digestive discomfort, and even mood changes, are signals that the balance of microorganisms in your gut has been disrupted. Gut dysbiosis occurs when harmful bacteria, fungi, or other microbes overpopulate relative to beneficial bacteria, disrupting the microbiome ecosystem that governs digestion, immune function, inflammation, and mental health.
The gut microbiome contains trillions of microorganisms, and maintaining their balance is central to overall health. When dysbiosis develops, whether from antibiotics, diet, chronic stress, or other triggers, the resulting symptoms can be wide-ranging and persistent. Understanding what causes gut dysbiosis, how to recognize the symptoms, and what treatment approaches actually address the root cause is the starting point for restoring gut health.
What is gut dysbiosis?
“Your gut is home to more than 100 trillion bacteria—and that is a LOT,” says Sarah Steinberg, MD, PhD, a former physician at Parsley Health in New York City. Together, the bacteria and other microbes in your gut make up your gut microbiome. In recent years, we’ve learned a lot about how this microbiome works and how it influences aspects of our health, including not just our digestion but also our immune systems, inflammatory response, and even mental health. “The field of microbiome science has really exploded in the last 10 years,” Dr. Steinberg explains.
“Dysbiosis” is a term used to describe a maladaptation or imbalance inside the body, and a “gut dysbiosis” occurs when there is an imbalance in the number and diversity of your gut microflora. This can impact your health in various ways; in fact, as the authors of a 2018 study wrote: “Studies in animal models and humans have shown that a persistent imbalance of gut’s microbial community, named dysbiosis, relates to inflammatory bowel diseases (IBD), irritable bowel syndrome (IBS), diabetes, obesity, cancer, cardiovascular and central nervous system disorders.”
As you can see, gut health plays a major role in our long-term health and ability to fend off disease.
The health research your doctor didn't mention.
Functional medicine insights from Parsley's clinical team, written for people who want to understand their body, not just manage symptoms.
Gut dysbiosis treatment works best when it addresses the specific imbalances driving your symptoms rather than applying a one-size-fits-all approach. A functional medicine provider can run comprehensive stool testing to identify which bacteria are overgrown or depleted, which pathogens are present, and which aspects of gut function are most affected, giving a much clearer roadmap for treatment than symptom management alone.
Probiotics and prebiotics: Targeted probiotic supplementation can help restore beneficial bacterial populations. The most evidence-supported strains for dysbiosis include Lactobacillus and Bifidobacterium species for general microbiome support, and Saccharomyces boulardii for antibiotic-associated dysbiosis. Prebiotics, non-digestible fibers that feed beneficial bacteria, include foods like garlic, onion, leeks, asparagus, and oats, as well as supplemental inulin and FOS.
Dietary changes: An anti-inflammatory, whole-food diet reduces the substrate for harmful bacterial growth while supporting microbial diversity. This typically means reducing refined sugar and processed carbohydrates (which feed dysbiotic species), increasing diverse plant fiber, and adding fermented foods like sauerkraut, kimchi, kefir, and yogurt. Some people with significant dysbiosis benefit from a temporary low-FODMAP or specific carbohydrate diet (SCD) while gut healing is underway.
Antimicrobial herbs: For cases involving specific pathogens or significant bacterial or fungal overgrowth, herbal antimicrobials, such as berberine, oregano oil, allicin, and caprylic acid, can reduce overgrown populations before rebuilding beneficial flora. These are typically more gentle than pharmaceutical antibiotics and less disruptive to the broader microbiome.
Addressing root causes: Sustainable gut dysbiosis treatment requires identifying and addressing what caused the imbalance in the first place, whether that's a history of antibiotic use, a high-sugar diet, chronic stress (which directly alters gut microbiome composition via the gut-brain axis), or an underlying condition like hypothyroidism or autoimmunity. Parsley Health providers run advanced stool, gut permeability, and inflammatory marker testing to build an individualized treatment plan.
What causes gut dysbiosis?
As Dr. Steinberg explains, “It seems like every day we’re learning new things about factors that contribute to imbalances in the bacteria in the gut.” According to her, some of the main factors that set people up for gut dysbiosis are:
1. Medications
This includes antibiotics, acid-reducing medications, over-the-counter pain relievers, steroids, and oral contraceptive pills. All these medications, “cause a discreet insult to the gut flora that can lead to dysbiosis,” Dr. Steinberg explains. A 2020 multi-drug metanalysis in Nature Communications found that 18 commonly used drug categories extensively impact the gut microbiome composition, with proton pump inhibitors (PPIs), laxatives, and antibiotics having the largest effect. Each drug has a slightly different effect, causing things like an increase in population of certain harmful bacterias and an increase in fatty acid production. These types of changes are related to multiple health conditions.
2. Diet
According to Dr. Steinberg, “the American diet tends to be higher in bad fats and lower in vegetables, which can negatively impact our gut flora.” Why? Because vegetables provide a lot of the roughage and fiber that allow good bacteria to grow. The standard American diet also contains a lot of carbohydrates, which can allow bad bacteria to overgrow and crowd out the good ones. This can, sadly, cause you to crave more sugar, setting you up to eat more sugar and possibly even develop a blood sugar issue, like pre-diabetes or diabetes.
Unfortunately, the use of medications, a diet of more processed foods, and a stressful lifestyle are all extremely common for most people, which means many of us are at higher risk of developing a gut microbiome imbalance and dealing with the impacts it can have.
Gut dysbiosis symptoms
Some of the signs that unhealthy stress levels, medications, and a poor diet have impacted your gut microbiome are clear cut; others, not so much. “For the majority of people, the symptoms of dysbiosis are very obvious and include things like include diarrhea, constipation, gas, bloating, belching, and abdominal pain,” says Dr. Steinberg.
But these aren’t the only symptoms to look out for. According to Steinberg, a microbiome imbalance can also be a contributing factor in harder-to-pin-down issues like sugar cravings and carbohydrate cravings. There are also people with dysbiosis who do not present with digestive symptoms at all. “Instead, dysbiosis may be the root cause of issues like rashes, rosacea, and recurrent hives,” she explains.
So while dysbiosis isn’t anything to panic about, it is something that you should address. “If left untreated, it can become a root cause of a multitude of different diseases,” says Dr. Steinberg. And many of these diseases also require medications and cause stress, which makes dysbiosis worse. “It becomes a matter of imbalanced gut flora propagating the risk factors that caused it,” she continues. That’s why it’s important to get early gut dysbiosis treatment and support your gut health.
Probiotic
Professional Grade
493REVIEWS
Happier belly, happier you! Your gut microbiome impacts everything from your digestive and immune systems to your brain function and mood.
If you suspect that you have gut dysbiosis, give a primary care doctor a call. They can order the proper tests and lab samples, help interpret the results, and create a treatment plan.
Typically, they will order blood tests to diagnose gut dysbiosis. Other times, they will order a comprehensive digestive stool analysis that will be tested in a lab. The latter may make it easier to assess the gut microbiotas. In some cases, a gut dysbiosis diagnosis may be possible with a breath test, though this isn't as common.
See what your labs actually reveal.
Parsley's Longevity Labs tests 80+ biomarkers, with live clinician review. Use code LABS25 for $25 off.
Parsley Health takes a holistic, personalized point of view in treating dysbiosis and improving gut health. Typically, this means creating a treatment plan tailored to the individual patient based on their symptoms and lifestyle. But according to Dr. Steinberg, when it comes to dysbiosis, many of those treatment plans have the following things in common:
1. Decreasing sugar and carbohydrates
“One thing that has always been very clear is that glucose transport is a huge mediator of dysbiosis,” says Dr. Steinberg. In other words, the amount of sugar you’re consuming has a tremendous negative impact on your gut flora. The good news is that by shifting gut flora to a healthier balance, your cravings for sugar will decrease because your gut will start to favor healthier bacteria over the unhealthy, sugar-eating ones.
2. Increasing fiber intake
Fiber is another big piece of the healthy gut puzzle. That’s because fiber is a source of prebiotics, which is essentially the food that healthy gut bacteria like to eat. According to Dr. Steinberg, the goal when it comes to consuming fiber is diversity. “We often get stuck in a rut in terms of what we eat. When we approach gut healing, we want to aim to create a diverse ecosystem,” she says.
She recommends eating diverse vegetables that provide all different types of roughage. “Inulin powder is also a great prebiotic supplement to add to your routine to feed beneficial bacteria,” she continues.
3. Getting serious about stress relief
If you want to heal dysbiosis in the gut, getting stress under control is critical. “I’m a big believer in meditation and I’ve been practicing yoga for over 25 years,” says Dr. Steinberg. That said, any kind of mindfulness exercise will do the trick. “Each person has to find their own access point,” she says, “Some people need to tire themselves out with a sweaty yoga class; others like to do balance exercises.”
The key is to get out of your head and into your body. “All these exercises bring all the activity in your brain out of the frontal lobe (the part of the brain that regulates decision making, judgment, and memory) and into the cerebellum (the part of the brain that regulates muscle movement),” says Dr. Steinberg.
4. Improving sleep quality
Last but not least, sleep is a crucial part of healing gut dysbiosis. This may seem strange at first. What does sleeping have to do with the bacteria in your gut? Well, research shows that sleep and gut bacteria are actually intricately connected. For example, a 2023 study suggest sleep deprivation may be a direct cause of gut dysbiosis.
To improve your sleep without drugs, Dr. Steinberg recommends getting sunshine and fresh air first thing in the morning, “I’m a huge believer in getting sunlight to reset circadian rhythm,” she says.
Frequently Asked Questions About Gut Dysbiosis
What is gut dysbiosis?
Gut dysbiosis is an imbalance in the composition of the gut microbiome, the community of bacteria, fungi, viruses, and other microorganisms that live in the digestive tract. A healthy gut microbiome is diverse and dominated by beneficial species that support digestion, immune function, and overall health. Dysbiosis occurs when this balance shifts: harmful or opportunistic microbes overpopulate, beneficial species decline, or microbial diversity decreases. This imbalance can disrupt virtually every system influenced by the gut, including immunity, inflammation, hormone metabolism, and mood.
How do you treat gut dysbiosis?
Gut dysbiosis treatment typically includes a combination of dietary changes (reducing sugar and processed foods, increasing plant diversity and fermented foods), targeted probiotic and prebiotic supplementation, and in some cases herbal antimicrobials to address specific overgrowths. The most effective approach is individualized based on stool testing that identifies the specific imbalances present. A functional medicine provider can run advanced microbiome testing and design a protocol that addresses both the dysbiosis itself and the root causes driving it.
How long does it take to heal gut dysbiosis?
Recovery from gut dysbiosis varies depending on the severity of the imbalance, how long it has been present, and how consistently treatment is followed. Mild dysbiosis may improve noticeably within four to eight weeks with dietary changes and probiotics. More significant dysbiosis, particularly cases involving pathogen overgrowth or significant microbiome depletion, may take three to six months or longer to fully resolve. Addressing the root causes (diet, stress, medication history) alongside direct gut healing protocols is essential for durable results rather than temporary symptom relief.
How do I know if I have dysbiosis?
If you suspect that you have gut dysbiosis, it's best to give a primary care doctor trained in functional medicine a call. They can order the proper tests and lab samples, help interpret the results, and create a treatment plan.
How do you fix gut dysbiosis?
Often, the most successful gut dysbiosis fix is tailored to an individual's lifestyle and symptoms. However, many treatment plans involve increasing fiber intake, improving sleep quality, eliminating sugars and carbohydrates, and finding ways to relieve stress.
What triggers gut dysbiosis?
Gut dysbiosis is usually triggered by medications or certain lifestyle choices, such as eating a diet high in carbohydrates and sugar or not getting enough sleep (7-9 hours a night for most of us). More and more evidence points to stress' role in triggering gut dysbiosis too.
What are the symptoms of gut dysbiosis?
Common gut dysbiosis symptoms include chronic bloating and gas, diarrhea or constipation (or both alternating), abdominal pain or cramping, food sensitivities, fatigue, brain fog, skin conditions like eczema or acne, and recurring yeast or bacterial infections. In more systemic cases, dysbiosis has been linked to mood disorders including anxiety and depression, as well as autoimmune conditions, because of the microbiome's central role in immune regulation. Symptoms often develop gradually and can be attributed to many other conditions, which is why dysbiosis is frequently underdiagnosed.
At Parsley Health, we believe better health starts with trusted information. Our content is accurate, accessible, and compassionate—rooted in evidence-based research and reviewed by qualified medical professionals. For more details read about our editorial process.
But these aren’t the only symptoms to look out for. According to Steinberg, a microbiome imbalance can also be a contributing factor in harder-to-pin-down issues like sugar cravings and carbohydrate cravings. There are also people with dysbiosis who do not present with digestive symptoms at all. “Instead, dysbiosis may be the root cause of issues like rashes, rosacea, and recurrent hives,” she explains.
The key is to get out of your head and into your body. “All these exercises bring all the activity in your brain out of the frontal lobe (the part of the brain that regulates decision making, judgment, and memory) and into the cerebellum (the part of the brain that regulates muscle movement),” says Dr. Steinberg.