Colon Cleansing: How to Do It Properly

Colon Cleansing: How to Do It Properly

Colon Cleansing

Periodically colon cleaning is extremely important for digestive health. Colon cleansing is performed so that you can reduce opportunistic bacteria, toxins, undigested fecal matter, and restore proper intestinal MMC function. Proper diverse fiber intake, magnesium intake, water intake, regular light exercise, and using a Squatty Potty should be all the average person needs to keep their bowels regulated.1

Some alternative medicine experts recommend colonics or even coffee enemas for colon cleansing. I believe that both of these types of colon cleansing should be performed sparingly, if even used at all. Both of these commonly recommended forms of colon cleansing may create electrolyte imbalances, reduction of intestinal mucosa (which protects our gut from microbes and inflammation), and imbalances of gut flora as well.2

I believe that everyone should at least do one of my colon cleansing protocols at least once a year to keep the digestive system running smoothly.


Fiber’s job in the body is to help bulk up stools, properly regulate colonic transport time, absorb toxins, reduce opportunistic bacteria, feed probiotic bacteria for them to produce SCFA’s, improve the integrity of the mucosa, and regulate colonic pH. Not all fiber is good for the digestive tract, and some types of fiber should be reduced for certain digestive conditions and situations.

There are two different types of fiber soluble and insoluble.3

Soluble Fiber

Sources: oatmeal, lentils, apples, oranges, pears, oat bran, strawberries, nuts, beans, peas, blueberries, psyllium, cucumbers, carrots, sweet potatoes, chia seeds4 5

Soluble fiber attracts water and forms a gel, which can slow down digestion. Soluble fiber delays the emptying of the stomach and can help you feel full. Soluble fiber also has been indicated in helping reduce oxidized cholesterol absorption in the intestine.

Soluble fiber is fermented in the colon there it is considered prebiotic. Soluble fiber is fermented into short chain fatty acids that can help rebuild a healthy colon by nourishing colonocytes, lower colonic pH, and help improve the integrity of the intestinal mucosal barrier. Depending on the state of the microbiome in your gut, the production of SCFA’s in the gut from the ingestion of soluble fiber will differ. Probiotic bacteria produce more of the SCFA’s, acetate, and butyrate, where opportunistic bacteria seem to produce more propionate.

If you have increased opportunistic bacteria, in your small intestine (SIBO), soluble fiber may increase bloating by feeding opportunistic organisms. Soluble fiber might need to be limited to people with severe symptoms that have digestive issue, but it should not be limited forever, because of its importance in feeding a probiotic microbiome as well.6

Insoluble Fiber

Sources: legumes, nuts, seeds, potato skin, vegetable fiber (green beans, cauliflower, zucchini, and celery), avocado, unripe bananas, kiwi, grapes, tomatoes, cellulose. Whole grain foods are high in insoluble fiber. Brown rice and organic corn are an “ok” source of whole grains, wheat, and oats should be limited in our diet.7 8

Insoluble fiber does not dissolve in water and is used to absorb water in the intestines to bulk up the stool. It also helps the intestines eliminate waste, faster and efficiently. It helps properly regulate the pH of the intestines. Unlike, soluble fiber, some types insoluble fiber do not ferment in the intestines. Since it does not ferment, it does not feed opportunistic bacteria greatly. The types of insoluble fiber that do not ferment in the colon are nuts, seeds, some types of vegetable fiber, and cellulose (any insoluble fiber that is not a FODMAP). Insoluble fiber helps promote regular bowel movements and helps prevent constipation. Finally, people diagnosed with diverticulosis may need to limit ingestion of certain types of insoluble fiber including nuts and seeds, because ingestion of these foods may inflame the digestive tract.9

Is Fiber Even Needed?

There are some people that argue that fiber is not important to ingest for digestive health. 10 I do believe that there is merit to this in some people, types of fiber might need to be limited possibly in people suffering from SIBO and diverticulosis. For the average person, some fiber ingestion is important for regulating digestive health. It all depends on where you are getting your fiber. Is it from whole wheat bread? The fiber in whole wheat bread is one of the worst forms because it his heavily fermentable, hard to digest, and full of inflammatory protein like gluten. Alternatively, is the source of your fiber intake nuts, rice, sweet potatoes, vegetables, or fruits? These sources of fiber are better for your digestive system.

Colon Cleansing Protocol

Support and Restore Your Gut Health:

Binding and Reduction of Toxins and Heavy Metals (Do Not Follow If You Have Mercury Toxicity)

  • Sonne’s No. 7 Detoxification – follow supplement recommendations
  • Sun chlorella – chew ten tablets daily with meals, do not use if you have Th1 dominance.
  • Unifiber – one tablespoon, three times daily, mixed well with a glass of filtered water before consuming.
  • Ingest a raw carrot salad to help reduce estrogen and endotoxin build up in the gut. Grate one raw organic carrot, and mix with one tablespoon of extra virgin olive oil, one tablespoon of extra virgin coconut oil, and one tsp of apple cider vinegar. Use with caution if you have histamine or fat malabsorption issues.

Facilitate Proper MMC Function

  • Himalaya triphala – take one capsule twice daily, right before meals
  • Drink a cup of organic ginger tea with breakfast daily.
  • Proper magnesium supplementation, use magnesium malate or peroxide.
  • Drink up to ten glasses of filtered water, each with 1/8 tsp of Real Salt to help speed up elimination.
  • Use a squatty potty and perform light exercise daily (walking for thirty minutes at a brisk pace is a good idea).

Coconut oil ingestion will help reduce any yeast overgrowth. 11

L-glutamine and NAG are important for GALT (gut associated lymphatic tissue) health and preventing leaky gut. 12 13

GOS and collagen will act as prebiotics, to help increase endogenous probiotic growth including Bifidobacteria and Lactobacillus. 14 15

Carrots, unifiber, and bentonite clay will help bind to excess endotoxins produced in the gut and eliminate them. 16 17

Ginger increases bile production, which aids in digestion and elimination of toxins.

Bentonite clay and chlorella will bind to most heavy metals that are released from bile and eliminate them.18 19

Triphala, magnesium, salt, and proper hydration increases motility and MMC function. 20

  1. Hi John,
    How long these protocols should be followed?

  2. John, thanks for this very comprehensive article. I wrote up a “Colon Cleansing protocol” program for me based on this. You mention at the introduction that you recommend one to “do this once a year.” I’m confused: can I continually take these in the proper dosages regularly throughout the year, like I would supplements?
    – chlorela
    – L-glutamine
    – N-Aceetyl Glucosamine
    – Mg

    Much thanks,

  3. My body literally loves L-glutamine but it does constipate when taking higher doses. Is there a reason for this? My colon hurts after a bowel movement. Will L-glutamine heal it?

  4. This article was very informative, thank you for SHARING your knowledge

  5. Why is it that you say use L-glutamine with caution if you have severe leaky gut? I thought it’s one of the best things for this condition?

    • For me L Glutamine ruins me, racing heart and anxiety leading to severe insomnia and physical pain. It’s not for many sick people…

  6. I would value your opinion on if a supplement like Thorne Moducare which is suppose to regulate autoimmune diseases by balancing Th1 and Th2 could decrease anti viniculin autoimmune response or could it do the opposite . I read the research on their product but can’t figure out if this could work to decrease anti viniculin antibodies and if this could decrease Th1 and Th2 .

  7. I don’t see how you can not mention cellulose (which is what insoluble fiber IS!) and its effect on worsening methane which worsens IBS-C when caused by methanogen overgrowth.

    Increasing fiber cannot be the answer for these people, when that fiber is insoluble.

    “The digestibility of cellulose and hemicellulose are strongly related to methane production, more so then soluble carbohydrate” In other words, animals and people who digest cellulose more completely have more methanogens in their guts.

    And “digestion of cell wall fiber increases methane production” Cell wall fiber is insoluble fiber. Hello, so why are you and other well meaning people recommending more of this kind of fiber to people with methanogenesis? We are tired of hearing advice that is only good for IBSD people, NOT for us.


    There are many other references out there to this, this is just one.

  8. John, I was wondering between your choices of options with OR supplements can we do both if it is a severe case like autism or we really do not want to double up and either or is a must and not both or all of the option.

  9. What about microbiolgists finding that deity fiber and more spefically that different types of dietary fiber feed different benefical bacteria?
    How The Gut Microbiota Affects Our Health with Dr. Erica & Dr. Justin Sonnenburg

  10. Hi! what kind of elemental diet should I follow? I cannot find one that
    doesn’t contain scary ingredients. Also, can I eliminate the chia seeds
    or fiber compounds? I get completely stopped up with fiber!

  11. John: is any fat loss expected after this protocol? Thanks in advance!

  12. John: is any fat loss expected after this protocol? Thanks in advance!

    • Possibly, but all “fat” loss with most colon cleansing techniques is water weight and build up fecal matter. The best way to lose weight is to change your lifestyle like the bulletproof diet. paleo diet, or perfect health diet.

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