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Causes of Gut Dysbiosis

By now, many of us are aware of the importance of gut health and how much of an impact it has when it is out of balance, physically, mentally, and emotionally. Furthermore, gut issues, such as irritable bowel syndrome have become a major concern worldwide and the interest in understanding more about the gut has grown proportionally. In this article we want to shed some light on what exactly gut dysbiosis is, some of the symptoms, most probable causes, and even some tips on how to balance your gut.

Meaning of gut dysbiosis

Dysbiosis, from the medical perspective, means “an unhealthy change in the normal bacterial ecology of a part of the body, e.g., of the intestines or the oral cavity1.” In this case, gut dysbiosis, or intestinal dysbiosis, refers to an imbalance of bacterial ecology in the gastrointestinal (GI) tract.  

This term can also be used to refer to a shift from a healthy state, called eubiosis (microbial balance), to an imbalanced state, dysbiosis. But before we go deeper into what gut dysbiosis really means and its real implications, let’s first approach the concept of our gut as being the “house” of trillions of bacteria and microbes.

The human gut

The human body contains between ten to one hundred trillion bacteria and microbes, called the human microbiota, and the gastrointestinal (GI) tract is unquestionably the most populated organ2,3. The GI tract alone is the residence of trillions of microorganisms, including bacteria, archaea, fungi, and viruses. It is estimated that the adult human gut contains about 1014 bacterial cells with up to 100 genera and more than 1000 different bacterial species4,5. Within the GI tract, the colon is the most populated area, colonized by more than 70% of the microorganisms2

Compared to the more than 100 bacterial phyla found on the planet Earth, the human gut houses only a few major divisions: Firmicutes, Bacteroidetes, Proteobacteria, Verrucomicrobia, Actinobacteria and Fusobacteria. From these, four are dominant groups in the gut microbiota; Firmicutes and Bacteroidetes accounting for about 99% of the identified species and between 70-90% of the total population and Actinobacteria and Proteobacteria accounting for less than 1–5%2,5,6.

The colonization of the human body by these microorganisms starts immediately after birth, and recent studies even found the existence of microorganisms in the intrauterine environment6. This early colonization is essential for human health, since a good microbiota composition is a great adjuvant in “educating” the immune system in which microorganisms are pathogenic and nonpathogenic, developing appropriate responses. Contrarily, a poor microbiota composition can lead to a variety of health conditions, from metabolic disorders to autoimmune diseases, to increased vulnerability to infectious diseases, and even play a role in neuropsychiatric disorders.

Human-Microbiota interaction

Most of these bacteria are protective and beneficial, co-existing in harmony with the human host, but there are also some bacteria that could be potentially harmful5. Despite the preconceived idea that bacteria are bad, in actuality the great majority of the gut microbiota exert permanent essential functions for the host, such as promoting food digestion, metabolization of xenobiotic (substances that are foreign to the body) materials, production of vitamins such as B12 and K, and regulation of innate and adaptive immunological processes, among many other tasks. Furthermore, the influence of microbiome activity is not limited to the gut, since proteins, peptides and metabolites released both locally and at distant sites trigger many cell signaling and pathways4,6. For more information on Gut Health and why it is so important for human health, check our article Why is Gut Health So Important.

Causes of Dysbiosis

The host impacts the microbiota through genetics and lifestyle factors, including diet, antibiotic and other drugs, and exposure to the natural environment6,7. In turn, the microbiota affects the health of the host through modulation of interrelated physiological systems, like immune system development and regulation, endocrine pathways, metabolism regulation, brain function and even epigenetic modification of the host’s genome6,7. When there is a balanced relationship in the human-microbiota, the benefit is mutual; “the bacteria thrive in the rich environment of the gut while the host benefits from multiple functions provided by the bacteria5.”

However, when this balance is disrupted or altered, causing human microbiota imbalance or dysbiosis, problems start to ensue. Dysbiosis is more common in the GI tract (gut dysbiosis), however this imbalance can also occur in other parts of the body colonized by microorganisms, such as the genital organs or skin. 

The most common causes of gut dysbiosis, which can also act in combination, are:

  • Antibiotics and antibacterial medications and other drugs
  • Bacterial, yeast, or fungal overgrowth
  • Presence of harmful chemical substances in the food (pesticides, herbicides, etc.) 
  • Toxicants from the environment (mold in the house, use of glyphosate in nearby fields, etc.)
  • Unhealthy and proinflammatory diet: high consumption of processed foods, refined starches, and sugars, and also food additives, such as preservatives, emulsifiers and artificial sweeteners
  • Food sensitivities
  • Excessive alcohol consumption
  • Poor dental health and hygiene, which can lead to the overgrowth of harmful bacteria
  • Poor bile flow and low stomach acid
  • Psycho Emotional factors, such as depression and anxiety, elevated or chronic stress, which affect the immune system 

Symptoms of Gut Dysbiosis

Many of the major symptoms are related with the gut, including digestive disorders, such as diarrhea or constipation, but alterations in gut microbiota affect many parts of the human body, and therefore may translate into diverse symptomatology.

 Common symptoms include:

  • GI issues: upset stomach, cramps, constipation and diarrhea, acid reflux or heartburn, gas and bloating, nausea, bad breath
  • Food intolerances
  • Appetite change
  • Weight gain and insulin resistance
  • Fatigue
  • Vaginal or rectal infections or itching
  • Difficulty urinating
  • Poor immune function 
  • Inflammation
  • Chronic pain
  • Muscle and joint pain
  • Headaches and migraines
  • Skin rash or redness, acne, psoriasis
  • Depression, anxiety, irritability, mood issues
  • Difficulties concentrating and thinking, brain fog 
  • Poor memory
  • Sleep disorders: trouble sleeping or insomnia

Some symptoms of gut dysbiosis might be mild and temporary, however if the underlying issue contributing to gut dysbiosis is not addressed it can lead to more serious conditions and even chronic disease.

Gut Dysbiosis and Chronic Conditions4,6,8

Gut dysbiosis, if left untreated, can lead to more severe and chronic conditions: 

  • auto-immune conditions such as asthma and arthritis and diabetes type I
  • inflammatory bowel conditions (IBD), which includes Crohn’s and ulcerative colitis
  • metabolic and cardiovascular conditions  like obesity, diabetes, atherosclerosis, and liver dysfunctions
  • cancer
  • Alzheimer’s disease 
  • irritable bowel syndrome (IBS)
  • leaky gut syndrome
  • psycho emotional disorders like depression, stress, anxiety, autism
  • central nervous system disorders, neurological issues and memory disorders
  • rheumatism and muscular dystrophy
  • problems in blood coagulation due to lack of vitamin K
  • disturbances in the transfer of nerve cells due to lack of vitamin B12
  • thyroid issues
  • hormonal imbalance
  • compromised immune health

Having in mind that gut dysbiosis may lead to some very serious illnesses, may prompt you to make changes in your lifestyle and approach to your gut health. But what are those changes?

Strategies to Restore Gut Balance and Improve Overall Health

As we have discussed, gut dysbiosis may be the consequence of several factors, including lifestyle, diet, environment, and health issues. And although there might not be a “one answer fits all” type of approach to treat this condition, there are certainly some strategies you can adopt to help you restore the balance in your gut microbiota.

Since the problem starts in the gut, addressing your nutrition and other factors, like exposure to harmful chemicals, might be the easiest and most important step to take.

Which factors might be contributing to the imbalances in your gut and how do you solve them?

Going back to our list of most common causes of gut dysbiosis, let’s outline some possible solutions:

  • Antibiotics and other drugs – try to reduce drug consumption and get advice from your Doctor regarding antibiotic medication
  • Bacterial, yeast, or fungal overgrowth – consult your doctor for possible treatments to control abnormal growth of microorganism and what is causing it
  • Presence of harmful chemical substances in the food – consume organic foods
  • Toxicants from the environment – study the environment around you, evaluate possible exposure to toxicants and try to remove them or yourself from that environment
  • Unhealthy and proinflammatory diet – adopt a healthy diet
  • Food sensitivities – eliminate foods that cause symptoms of intolerance, like bloating
  • Excessive alcohol consumption – reduce consumption of alcoholic beverages
  • Poor mouth health and dental hygiene – go to a specialist in dentistry and follow a careful dental hygiene plan
  • Poor bile flow and low stomach acid – consider testing your stomach acid and bile flow and address those issues with your doctor
  • Psycho Emotional factors – identify and develop tools to help manage stress levels, and other psychological or emotional issues, not hesitating to consult with a specialist for proper follow up 

Regarding the diet and your nutritional approach, adopt a low inflammatory diet that is also gut friendly. In our blog you can find two amazing articles on Best Foods for Gut Health ( and Top Foods to Fight Chronic Inflammation. 

Foods to support gut health and lower inflammation:

  • Fermented foods, with live probiotics: sauerkraut, tempeh, miso, natto, kimchi, kombucha, raw nut cheese (fermented), coconut kefir, probiotic coconut yogurt, pickles
  • Prebiotics rich foods: chicory root, dandelion greens, Jerusalem artichoke, garlic and onion, leeks, asparagus, green bananas, konjac root, cacao, burdock root, flaxseed, yacon root, jicama root, seaweed, and microalgae 
  • Cruciferous vegetables and dark, leafy greens
  • Mushrooms
  • Spices and herbs
  • Berries

Foods to avoid:

  • Processed and ultra-processed foods, including meats (deli meat and salted or canned meat) and refined carbohydrates (pasta, pizza, crackers, cookies, etc.)
  • Foods rich in gluten: wheat, barley, rye
  • Dairy: yogurt, milk, and cheese
  • Sugar and foods high in sugar: syrups (corn syrup, maple syrup, etc.), cane sugar, coconut sugar, etc. 

How is your gut feeling? Have you ever wondered why it’s called “gut feeling”? Because the composition of your gut says a lot about yourself, and maybe this article can help you understand how to maintain a more balanced and healthy gut for a more balanced and healthy self 😊


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