Dysbiosis - A Gut Reaction

What do stool transplants, Irritable Bowel Syndrome, gluten sensitivity, and probiotics have in common? They are all related to a phenomenon that is known as Dysbiosis, a condition where the normal, healthy balance of bacteria, fungus, and other micro-organisms in the gut are out of balance. Evidence is mounting that anything that disturbs the normal balance of micro-organisms in the gut could have profound health consequences. These can be very severe, as in Clostridium difficile Enterocolitis, which can be life threatening, or they can be subtle, as in vague symptoms of fatigue, bloating, allergies, intermittent abdominal pain and/or diarrhea (often diagnosed as irritable bowel syndrome). How is it that so many problems can be caused by a just a few abnormal micro-organisms?



It turns out that we rely on our intestines (specifically our intestinal bacteria) for myriad functions that our body requires. Astonishingly, there are estimated to be anywhere from 500 to 1,000 different species of bacteria living in the human gut. Though members of the gut micro-flora are found on all surfaces exposed to the environment (on the skin and eyes, in the mouth, nose, and small intestine), the vast majority of these bacteria live in the large intestine. These gut microorganisms perform a host of useful functions such as training the immune system, preventing growth of harmful species of microorganisms, regulating the development of the gut, producing vitamins for us (such as biotin and vitamin K), digesting carbohydrates, and producing hormones to direct our bodies to store fats. Because the effects of these micro-flora are so varied and essential to us, many scientists refer to them collectively as a “forgotten organ”.

Basically, we just wouldn’t do too well without the help of all these microorganisms working in concert with us. We have evolved to work together for mutual benefit. Research has shown that, in normal animals, some typical resident bacteria secrete substances called bacteriocins that prevent the overgrowth of other, potentially pathogenic, bacteria and other organisms (fungi, parasites) in the gut. This ability to protect the body from pathogenic organisms is called “the barrier effect”.

The problem is that humans have been changing the game on the micro-organisms, especially over the last few hundred years. As modern man has changed diets (more refined and processed foods), added toxins to our environments (think pesticides or synthetic chemicals and pollution), and discovered antibiotics and their myriad uses, we have been messing with a system that has evolved over millions of years. We are undermining a very sophisticated and evolved symbiosis between bacteria and human and expecting our health to stay unaffected. The fact is, that when this system falters we may start to have difficulties with metabolizing our food, creating the vitamins we require, and our immune system may even start to over or under react to our environment causing allergies or even auto-immune disorders, as well as suffering abdominal symptoms like pain and diarrhea or constipation.

How do problems arise?

Antibiotics:

After taking antibiotics, bacteria in your gut are killed just as they are in other places you may be trying to target for treatment. This kills many of the bacteria which secrete substances (bacteriocins) that keep colonies of potentially harmful bacteria, fungi, and parasites check. When these helpful bacteria are wiped out by antibiotics, other micro-organisms are able to start to dominate our gastro-intestinal tract. These can be harmful and cause us to develop symptoms.

One example of this acute form of dysbiosis is the overgrowth of fungus such as Candida albicans (one of the types of fungus that torments us with yeast infections. Since most fungi thrive in warm, moist environments,we can be left with the very unpleasant symptoms of yeast/fungal infections in all the places that tend to make us generally miserable (e.g. vaginal yeast infections, crotch rot, etc.).

This is why doctors often prescribe ‘probiotics’ in an effort to reestablish a healthy balance of micro-flora to control this overgrowth of unwelcome micro-organisms. By depositing and encouraging beneficial bacteria cultures to grow in our bodies, probiotics can mitigate the symptoms and problems of killing off beneficial bacteria with antibiotics.

In the most severe cases of overgrowth of harmful bacteria, patients may suffer a dangerous bacterial infection (Clostritdium difficile) that has the potential to cause a life threatening infection of your small intestine and colon. Stool transplants, a kind of extreme version of probiotics, show promise as a treatment. In a stool transplant procedure, the colonies of bacteria from a healthy person’s stool are used to colonize the gut of someone suffering from C. difficile. Early experimentation with transferring stool from healthy individuals to those suffering chronically with C. difficile seems to help restore a healthier balance of micro-organisms in the gut, thus helping to keep the dangerous C. difficile bacteria in check and the patient asymptomatic.

Food Senstivities:

The intestines essentially function as a barrier between our bodies and the outside world. Like tightly interlocked fingers, the cells of the small intestinal lining fit together to prevent large objects from passing into the bloodstream. However, the cells do have tiny gaps between them that are designed to only let the smallest of particles and nutrients through to the blood stream. When the intestinal lining is damaged by irritation, the gaps get larger and allow large, potentially harmful particles through, which can cause the body to react adversely. This is sometimes called ‘leaky gut syndrome’. In addition to widening the gaps between the finger-like cells of the small intestines, damage to the gut can destroy the cells of the small intestines themselves. Because these cells are responsible for absorbing vital nutrients, this kind of damage reduces the body’s ability to absorb the nutrients it needs to function properly.

Essentially, letting too much across the intestinal barrier might allow toxic substances to reach the blood stream, while not letting enough across could result in vitamin, mineral, and nutrient deficiencies. Furthermore, irritation or damage anywhere along the small or large intestines increases the likelihood of creating an abnormal balance of micro-organisms in the gut. This imbalance of micro-flora then has the potential to cause a wide range of symptoms (discomfort, pain, allergies, fatigue, diarrhea, constipation, autoimmune disorders, or even serious life threatening infections).

In addition, some foods require certain bacteria to be properly digested. This is why most people are lactose intolerant. As people age, they lose the population of bacteria that digests lactose (the sugar in milk).

The Immune System and Dysbiosis:

Dysbiosis even has the potential to exacerbate symptoms of, or hinder recovery from, other illnesses. For example, because dysbiosis can contribute to allergies and other immune system problems, dysbiosis could aggravate symptoms in individuals already predisposed to having these issues. The same goes for anyone with digestive health problems, vitamin or nutrient deficiencies, or any other illness related to digestive health. Most importantly, recovery from injuries and chronic illnesses such as cancer can be jeopardized if the body does not get enough energy and nutrients from the foods we eat.

There is also evidence to suggest that proper functioning of the immune system is heavily influenced by gut micro-flora. In some animal studies, animals were bred in sterile environments to specifically have significantly lower levels of immune cells circulating in their blood. These animals were not exposed to bacteria and therefore did not have a normal population of gut microorganisms, and they were observed to develop abnormal allergies to their environment. These animals were also shown to be highly susceptible to infection. This is attributed to a lack of competition for surface area in the gut, where in normal animals the resident micro-flora would compete with pathogenic bacteria, keeping them in check. In germ-free animals, however, these pathogenic bacteria can grow and multiply virtually unchecked.

Exposure to Foreign Micro-organisms:

Ingesting harmful foreign organisms (such as bacteria, fungus, or parasites that might hitch a ride on our favorite foods) can possibly cause dysbiosis. Many types of cheese contain bacteria and mold which can populate your gut. Food that is spoiled, stale, or old can also contain harmful micro organisms which, when ingested, can make your gut their home and alter the balance.

The progression of intestinal disorders (like Celiac Disease) can lead to
a damaging of the cells responsible for absorbing nutrition and keeping
out toxins.

Many medical conditions involving the gastro-intestinal tract may be caused or worsened by dysbiosis. These include disorders like Irritable Bowel Syndrome, gastro-intestinal ulcers (caused by H. pylori), and Celiac Disease (where simply eating gluten causes damage to the intestinal lining, leading to malnutrition). More confusing for patients and health practitioners alike, many symptoms and disorders that don’t seem to be directly related to the gut may, in fact, be caused or aggravated by dysbiosis. Unexplained symptoms including fatigue, rashes, bloating and allergies may show improvement or be cured completely by taking steps to normalize gut micro-flora.


In general, the following suggestions are helpful for prevention of dysbiosis:

Dietary changes can reduce not only your chances of developing dysbiosis, but also aid in the treatment as well. Avoiding many types of food will aid in maintaining a healthy balance of micro-flora in the gut. Sugary foods and refined carbohydrates can allow certain microorganisms like fungi and bacteria to reproduce quickly, reaching numbers that disrupt the overall balance of micro-flora in the gut.

• Avoid antibiotic medications unless absolutely necessary. Ask your doctor about alternatives to antibiotics in the form of natural products that have an anti-microbial activity. These may provide relief from infections or boost your immune system, and will likely have less chance of causing dysbiosis.

• Recognize that some pharmaceutical medications (e.g., opiate analgesics) may decrease the normal motion of digestion in your small intestines. This motion is essential for moving food through and cleaning the gut of excess or unwanted micro-organisms. If you suffer from dysbiosis ask your health care practitioner if any of your medications could be of concern.

• If you suffer from food sensitivities or allergies, avoid these foods or ask your doctor about treatments that may be able to decrease these sensitivities or allergies.

• Consider avoiding those foods that are highly sensitising in many individuals. Two examples include gluten and dairy products. Gluten is found in wheat, rye, spelt, or triticale and many individuals are sensitive to these grains even if they do not have Celiac Disease. Dairy includes casein and whey which are both components of all dairy products. If you are sensitive to these foods (or any other foods), they may cause irritation to the lining of the small intestine, even if you do not have an official diagnosis of Celiac Disease.

• Avoid toxins (such as pesticides) in your food and your environment. Toxins can damage even a healthy gastrointestinal tract and cause “leaky gut” by themselves. Eating organic foods will lower your body’s intake of pesticides that contribute to many problems in the gut, including dysbiosis.

• Be aware of mold issues in your environment. Moisture is mold’s best friend, so a home with water damage or even a geographic area with a lot of moisture may expose you to mold in your environment.

• Handle your food safely to avoid food poisoning and only eat in restaurants that you trust will be doing the same.

• Eat foods with fiber to maintain proper flow in the gastrointestinal tract. Organic vegetables, organic fruits, organic gluten-free whole grains (organic brown rice, organic quinoa, organic oats, organic amaranth, organic corn), organic legumes and peas (organic black beans, kidney beans, etc.), organic oat bran, organic inulin, and organic ground flax seeds are all options that will provide plenty of fiber. 

• Regular exercise and drinking enough clean water are important in maintaining the normal flow and environment in the gastrointestinal tract.

• If you or someone in your family is diagnosed with Dysbiosis, it is important to have other members of your family assessed, including any pets with whom you have regular physical contact. Wash your hands regularly and consider a water filter for your home.

• If you suffer from chronic symptoms of illness that are otherwise unexplained you may want to consider having a consultation with a physician experienced in the assessment and treatment of dysbiosis. See below for organizations which may be able to refer you to qualified health care professionals in your area. 

Health care practitioners who may have expertise with dysbiosis include: Internal Medicine Physicians with sub-specialization in Gastroenterology and/or Infectious Diseases, Naturopathic Physicians, Integrative and/or Holistic Medicine Physicians, Functional Medicine Physicians, Environmental Medicine Physicians, Chiropractors who have specialised in Applied Kinesiology and Nutrition.

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The following organizations may help you find a qualified health care practitioner:

American Academy of Environmental Medicine
The Institute for Functional Medicine
American Assosciation of Naturopathic Physicians
International College of Applied Kinesiology
International Society for Infectious Diseases
American Board of Integrative Holistic Medicine

For more information on the causes of dysbiosis:

The Causes of Intestinal Dysbiosis: A Review

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Researched and written by Dr. Rebecca Malamed, M.D. with assistance from Mr. Malcolm Potter and Ms. Alexandra Hill.