A Beginner’s Guide to Gut Bugs & Dysbiosis

Did you know that your gastrointestinal tract is over 9 meters long with a surface area that covers the space occupied by a tennis court?

It comes into daily contact with a huge variety of environmental factors including the food we eat and the air we breathe. It is affected by everything from stress to hormonal cycles and environmental toxins.

Keeping this tube working properly and efficiently is probably the number one thing we can do to stay healthy and prevent chronic disease.

You gut is inhabited by trillions of bacteria. Yes, trillions. In fact, the bacteria that live in your body outnumber your cells 10 to 1! You could honestly say that you are more bacteria than human… Weird thought, eh?

The weight of this microbe “organ” is approximately 1.5 kg or 3-4 pounds. It might be crazy to think about, but science is finding that the balance of these little microbes within your body can greatly determine your bodies ability to fight disease, manage weight and regulate mood. It could be the biggest breakthrough in medicine since vaccines and penicillin!


What happens when the balance is disrupted?

Otherwise known as dysbiosis, when a negative change happens to balance of microflora it can produce harmful effects to the host (a.k.a. YOU). Dysbiosis is believed to play a role in many chronic and degenerative disease that include rheumatoid arthritis, ankylosing spondylitis, IBS, IBD, atopic eczema, kidney stones, obesity and autism.


What causes dysbiosis?

Modern diet and lifestyle, as well as the use of pharmaceutical drugs, has led to a disruption of the normal intestinal flora and leads to dysbiosis in many individuals.

Other causes may include:

  • Antibiotic use
  • Chemotherapy
  • Stress (both physical and mental)
  • Caesarean section deliveries
  • Birth location (infants born vaginally at home have a better composition of gut bacteria than those born in a hospital)
  • Formula feeding (exclusively breastfed infants have a better gut flora)
  • Standard American Diet (specifically those that are on a low fiber diet and high in refined grain or excessively high in fat and/or protein)
  • Sulphate or sulphite ingestion (common foods with sulphur compounds include dried fruits, dehydrated vegetables, shellfish, white bread, packaged fruit juices, baked goods, and most fermented alcoholic beverages)
  • Artificial sweetener consumption


What are the symptoms of dysbiosis?

Symptoms do vary, but common signs include abdominal pain, abdominal bloating, excessive flatulence, constipation and/or diarrhea, decreased mental concentration, joint pain and unexplained fatigue to name a few.

How to we treat it?

The treatment of intestinal dysbiosis includes the use of both food and supplemental forms of prebiotics, probiotics, and colonic foods. Your medical health care provider may also advise taking an antimicrobial herb as well. It’s important that you follow his or her instruction when taking any of these things in supplemental form.

A metaphor that helps explain the treatment of dysbiosis is “weed, seed, and feed”. In treatment, we are effectively “weeding” out the bacteria that have gone out of balance while simultaneously “seeding” the more beneficial bugs back into the gut. As a means to keep those good bugs happy and alive, we then have to “feed” them with specific foods that support their existence.


What are probiotics?

Simply put, probiotics are the seed. They are the good bugs that help restore balance to your digestive tract and help you feel better. They prime your immune system and help the network of bugs in your system work more efficiently. The type of probiotic strain is extremely important and it’s unadvisable to buy a product off the internet or from a health food store without knowing exactly what it contains. Different probiotic strains have different therapeutic effects, so if you take any brand or variety, you are not guaranteed it will do good for your specific ailment. Instead, it’s important that you follow the advice of your nutritionist or doctor who will be able to identify the exact species and strain of probiotic to fit your condition or ailment.

Natural food sources: Many probiotics are found naturally in foods. Getting a variety of bacteria from these foods is helpful in creating diversity in your digestive system for long-term health. Below is a list of common, traditional foods that contain a wide variety of beneficial bacteria for your gut:

  • Raw sauerkraut
  • Kimchi
  • Natto
  • Kefir
  • Vinegar (also a great source of acetate, a great energy source for your body and immune system)
  • Yogurt (only selected brands are medicinal)
  • Tempeh and Miso may also be consumed but are not always a reliable source of probiotics due to the heat and processing that they sometimes are exposed to

Supplemental sources: As mentioned before, taking the appropriate strain of probiotics is essential in creating a therapeutic healing effect in your body. Supplemental forms of probiotics should ideally be obtained directly through your health care provider or another reputable source recommended by a professional.


What are prebiotics?

As mentioned above, prebiotics are the food that feed the more beneficial bugs in your gut. The specifically feed the good bugs and change the microflora ecosystem of your body toward a healthier composition and promote your health. They are widely found in natural food sources but may be prescribed in supplemental form for a temporary time period to ensure the good bugs are happy. There are many forms of prebiotics, but the most widely researched are fructooligosaccharides (FOS), galactooligosaccharides (GOS), and lactulose.

Natural food sources: Supporting your healthy gut bacteria with real food is the best way to go. We evolved on these foods and will benefits from incorporating more of them into our diets. This is a short list of prebiotics rich foods:

  • Jerusalem artichoke
  • Onion
  • Garlic
  • Leeks
  • Asparagus
  • Barley
  • Dandelion
  • Rye flour
  • Banana
  • Wheat
  • Chicory
  • Burdock

Supplemental: The most commonly available types of prebiotics are fructooligosaccharides (FOS), lactulose and galactooligosaccharides (GOS). Your doctor or nutritionist will help you determine which prebiotic will be most effective and in what dose.


What are colonics?

Like prebiotics, colonics are good at feeding the bacteria in the gut. The difference is that they lack specificity in the kinds of bugs they feed. In a simple sense, you can think of them as “prebiotic-like foods”. A few examples are listed below and are worth adding to your diet as tolerated.

  • Oat bran
  • Spirulina
  • Resistant start
  • Green Tea
  • Almonds
  • Pomegranate husk
  • Carrots
  • Brown rice
  • Dark cocoa or cacao


How do we “weed” the gut of the bad guys?

In addition to seeding and feeding the microflora, you may also need to do some “weeding” to help reduce the number of potential pathogenic bugs so that you heal more quickly. You’ll need a doctor or nutritionist specializing in herbs and dysbiosis to help you with this part. An herbal blend needs to be clinically researched to help rebalance your digestive system in an efficient and safe way.

It is very important to follow your doctor or nutritionist’s directions when taking an herbal broad spectrum supplement. If you take it too long or in an inappropriate dose, you could further disrupt the fine balance of your gut in a negative way.


Closing Comments

The factors leading to dysbiosis of your intestinal tract take time, often years, to develop. The healing process is also expected to take time. Every individual is different when it comes to the length of treatment and support needed from supplements to heal. Age, preexisting disease, and stress can all affect the healing curve. Learning to expand and grow from the process is part of the healing.



  1. Hawrelak JA. Prebiotics. In: Pizzorno JE, Murray M (eds). Textbook of Natural Medicine (4th ed). Elsevier. 2013. Pages 966-978.
  2. Hawrelak JA. Probiotics. In: Pizzorno JE, Murray M (eds). Textbook of Natural Medicine (4th ed). Elsevier. 2013. Pages 979-994.
  3. Marteau P. Evidence of probiotic strain specificity makes extrapolation of results impossible from a strain to another, even from the same species. Annals of Gastroenterology & Hepatology. 2011.
  4. Hawrelak JA, Myers SP. Intestinal Dysbiosis: A review of the literature. Alternative Medicine Review. 2004; 9(2):180-197.
  5. Jernberg C, Lofmark S, Edlund C, Jansson JK. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology. 2010;156:3216-3223.
Attributions: Top image courtesy of the Lewis Lab at Northeastern University, created by Anthony D’Onofrio, William H. Fowle, Eric J. Stewart and Kim Lewis. Second image created by Shanna Trim from here. Both used with permission. No changes made to images.

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