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Dysbiosis

What Is It, Causes, and More

Author: Nikol Natalia Armata

Editors: Alyssa Haag,Emily Miao, PharmD,Kelsey LaFayette, DNP, RN

Illustrator: Abbey Richard

Copyeditor: David G. Walker

Modified: 25 Aug 2022


What is dysbiosis?

Dysbiosis refers to an imbalance of microbial species and a reduction in microbial diversity within certain bodily microbiomes (i.e., the collection of microorganisms existing in a specific part of the human body). As a result, beneficial bacteria (e.g., Firmicutes) are usually minimized, whereas other bacteria that may be harmful (e.g., Proteobacteria) increase in number. Dysbiosis is commonly linked to impaired gut barrier function and immune-mediated inflammation, which is a result of an excessive immune response. Therefore, there has been a potential association between intestinal dysbiosis and certain conditions, including inflammatory bowel disease (IBD), diabetes mellitus, and colorectal cancer

The gastrointestinal (GI) tract is home to trillions of microorganisms, including bacteria, fungi, and viruses. The collective genetic information of the whole microbial community combines to form the gut flora. The intestinal microbiota can be viewed as an actual body organ contributing to the well-being of the organism: the human. Gut dysbiosis may influence local and systemic processes, such as nutrient transformation, vitamin supply, immunity, gut-to-brain communication, and even tumor progression. Nonetheless, dysbiosis may occur in other microbiomes, such as on the skin, vagina, and oral cavity

Two Petri dishes with various types of microorganisms.

Is dysbiosis contagious?

Dysbiosis is not contagious. However, certain infections can later, under certain circumstances, cause an imbalance in their natural microbiome and cause dysbiosis.

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What causes dysbiosis?

The main factors influencing the composition of the microbiota that may cause dysbiosis include medications, specifically antibiotics; dietary changes; as well as psychological and physical stress. Antibiotic use is the most common and significant cause of major alterations in the body’s natural microbiota. The potential of an antimicrobial agent to influence the microbiome is related to its spectrum of activity, dosage, and length of administration. For example, antimicrobial agents against both gram-positive and gram-negative organisms (e.g., ceftriaxone, meropenem) can cause almost all beneficial bacteria of the body to disappear, reducing the microbial diversity and suppressing the immune system. They typically have a greater impact on the intestinal flora but may also affect the skin and vaginal flora. Additionally, the greater the dosage and length of administration, the more significant their impact on the microbiota. 

Consumption of foods rich in sulfur compounds (e.g., beef, spinach, broccoli, nuts, chickpeas), protein, and sugar may produce detrimental effects on the gut microbiota by altering the microbial balance and leading to mucus disruption and inflammation. Similarly, stress can induce significant alterations in the skin microflora (which may cause atopic dermatitis) and the GI tract microflora (which may cause a significant decrease in beneficial bacteria, such as Lactobacilli and Bifidobacteria, and an increase in potentially pathogenic microorganisms, such as E. coli). These changes may be caused by the growth-enhancing effects of norepinephrine on gram-negative microorganisms or by stress-induced changes to GI tract motility and secretions. 

Moderate shifts in microbial composition can provide a window of opportunity for other aggravating factors to escalate changes and cause an imbalance. Increased oxidative stress, as seen in immune-mediated inflammation, bacteriophages (i.e., viruses that destroy the bacteria they infect), and bacteriocins (i.e., toxins produced by bacteria to inhibit the growth of other bacteria), are common exacerbating factors known to cause shifts of the microbiota, leading to dysbiosis. 

Often, a single factor is not sufficient to cause dysbiosis. The microbiota has natural resilience and a unique capacity to adapt to variations in nutrient availability and changing environmental conditions. By contrast, the combined actions of several factors can eventually trigger pathologically significant shifts in microbiota. The threshold required to trigger dysbiosis largely depends on the bacterial groups affected. Broad shifts in the main phyla, Bacteroidetes, and Firmicutes may remain without pathologic consequence. On the other hand, increased amounts of marginal groups (i.e., microbes that pre-exist in the GI system but in smaller quantities), like Clostridium perfringens, may disturb the normal intestinal function. 

What are the signs and symptoms of dysbiosis?

Most individuals with dysbiosis present with localized symptoms depending on the microbiome affected. When the microbiome of the GI tract is disrupted, symptoms are usually mild and may include tooth decay, cavities, and sore and bleeding gums in the setting of oral dysbiosis. Bloating, abdominal discomfort, belching, nausea, and changes in bowel movements (e.g., constipation, diarrhea) can occur in the setting of gut dysbiosis. Accordingly, changes in the microbiota of the urogenital region may cause painful urination, unusual vaginal or penile discharge, rashes, or itching of the genitalia and rectum. Skin dysbiosis can also present as skin rashes that may present as atopic dermatitis (i.e., eczema), psoriasis, or acne. In more severe cases, when the immune system is weakened, symptoms may become systemic and may include fatigue, difficulty concentrating, mood changes, irritability, anxiety, and depression

How is dysbiosis diagnosed?

Initially, an assessment of the individual’s medical history followed by a thorough physical examination is performed in order to identify the cause of the symptoms. After dysbiosis is identified as a potential cause, a series of tests will be required to confirm the diagnosis. A blood test called complete blood count (CBC) can provide information concerning the overall health of the individual and can reveal signs of inflammation or disturbances in coagulation. Additionally, a complete metabolic panel (i.e., a series of blood tests used to evaluate the function of critical organs, such as the liver and kidneys) as well as an evaluation of vitamin levels (e.g., B-complex vitamins, vitamin D) can help determine the severity of the dysbiosis. Blood tests can also reveal conditions associated with dysbiosis, like type 2 diabetes (e.g., elevated glucose and hemoglobin A1C levels).

In order to confirm the diagnosis, more specific tests will be required. A hydrogen breath test is a diagnostic tool for small intestine bacterial overgrowth. After drinking a solution with high levels of glucose or lactose, also known as an oral glucose tolerance test, individuals will be asked to breathe into a plastic bag. The breath sample taken will be analyzed for its hydrogen or methane content to determine if there is bacterial overgrowth. Alternatively, the organic acid test is a urine test that can be performed to measure the amount of organic compounds produced by microorganisms in the body and, specifically, the intestinal microbiome. The Comprehensive Digestive Stool Analysis (CDSA) is an advanced stool test that provides immediate, precise clinical information on the overall health of the GI tract. Lastly, if areas of infection are suspected, biopsies can reveal the extent and the underlying cause of the disease. For instance, biopsies can confirm the diagnosis of Crohn disease or ulcerative colitis, which may be caused by dysbiosis. 

How is dysbiosis treated?

Treatment of dysbiosis should be based on the results of the diagnostic tests and tailored to the individual's needs. Studies show that a combination of dietary changes, probiotic supplements, and lifestyle modifications (e.g., healthy diet, exercise, smoking cessation) are usually sufficient to create optimal conditions for beneficial gut bacteria to thrive. Daily administration of supplements high in vitamin A; vitamin B complexes; vitamin C; vitamin D; vitamin E; calcium; magnesium; as well as omega three, six, and nine are suggested additions to the diet of affected individuals. Both probiotics and prebiotics can help enhance the natural microbiome. Probiotics are live microorganisms that offer health benefits by restoring health to the gut microbiome, whereas prebiotics are food components used by the natural microbiome and, therefore, act as a health benefit as well. Notably, gut dysbiosis is associated with many other conditions, including Crohn disease, ulcerative colitis, and type 2 diabetes and, therefore, should be treated when diagnosed. Lastly, Fecal Microbial Transplant (FMT), when stool is taken from healthy individuals and transferred into individuals with dysbiosis, is suggested only after more conservative treatment has been exhausted and under medical advice. This treatment option is preferred mainly for individuals with recurrent disease or other gastrointestinal disorders and constipation

Can dysbiosis be cured?

Yes, dysbiosis can be cured. This usually occurs with minor lifestyle alterations and the aforementioned treatments. 

What are the most important facts to know about dysbiosis?

Dysbiosis refers to the imbalance of microbial species due to a reduction in microbial diversity within certain bodily microbiomes. Beneficial bacteria are usually minimized, whereas other harmful bacteria increase in number. The main factors influencing the composition of the microbiota include medications, dietary changes, as well as psychological and physical stress. Most individuals with dysbiosis present with localized symptoms depending on the microbiome that is affected. In combination with the clinical presentation, a series of tests (including blood tests and biopsies as well as the hydrogen breath test, the organic acid test, and the Comprehensive Digestive Stool Analysis) can confirm the diagnosis. Treatment of dysbiosis is typically based on a combination of dietary changes; prebiotic and probiotic supplements; lifestyle modifications; and less frequently, fecal microbial transplantation.

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Related links

Prebiotics and probiotics
The oral microbiota and systemic health

Resources for research and reference

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Shaw, K. A., Bertha, M., Hofmekler, T., Chopra, P., Vatanen, T., Srivatsa, A., … Kugathasan, S. (2016). Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease. Genome Medicine, 8(1). DOI: 10.1186/s13073-016-0331-y   

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