How and Why to Cleanse the Gut

How and Why to Cleanse the Gut

For anyone who’s been reading my cleansing series (you can find the first five articles on our site), sorry for leaving you hanging without this final article. The good news is: I’ve been on vacation. You may wish to do a brief happy dance on my behalf. Now for the last installment: your intestines.

The intestines – tubes about 25 to 30 feet long in an adult – are where the nutrients from your food are absorbed, so they are vital to all bodily functions. Furthermore, they house about 100 trillion microbes – your gut flora – known communally as your gut microbiome. We’re still learning about the complex role they play in our health. They keep the intestinal lining healthy, they assist in nutrient absorption, they protect us from infections, and they help regulate metabolism.

Emerging research shows that gut health is connected to the health of the skin, brain, lungs, and immune system (and likely more systems). Many autoimmune diseases (where the immune system is attacking one’s own body), respiratory problems, joint pain, chronic skin rashes, and mood disorders are antagonized by, or even caused by, a problem with the gut and its microbiome.

Even though it seems that the intestines are just a long simple tube, the intestinal environment is rather complex – too complex to cover in depth in this article. So, the nutshell version is this: although, ideally, only nutrients should be absorbed through the intestinal lining, we know that this isn’t really the case. Toxins produced by bacteria in the gut, and ingested through foods and chemicals we’re exposed to, can also be absorbed into the blood stream. Actually, we give patients medicines in suppository form because they pass very efficiently from the rectum into the blood stream. In addition, the activities of our gut flora are able to activate immune and hormonal mechanisms that can be both beneficial and destructive to our health.

Some of the most common gut disorders include: (1) insufficient removal of waste (from constipation or retained pockets of stool) (2) unhealthy population of gut flora (too much of the harmful species and not enough of the beneficial species – known as “dysbiosis”) (3) inflammation and excessive permeability (leakiness) of the intestinal lining. Remodeling the gut environment can have dramatic effects on a wide range of diseases. For some reason (maybe because they’ve been so beleaguered by the mainstream medical establishment), I feel that it’s worth mentioning that naturopathic physicians have known this stuff for years, and it’s a cornerstone of ancient medical systems such as Traditional Chinese Medicine and Ayurveda.

One of my nutrition professors, Satya Ambrose (who co-founded Oregon College of Oriental Medicine and is a brilliant doctor), teaches what she calls the “Five R’s” of restoring healthy gut function. (1) REMOVE. Remove the offenders: toxins, inflammation, infection, harmful microbes, unhealthy foods, foods you’re sensitive or allergic to, etc. (2) REPLACE. Replace the nutrients that have been missing due to poor gut health. Consume healthy, easy-to-absorb, you-appropriate foods. (3) RE-INOCULATE. Seed the gut with beneficial microorganisms through probiotics and cultured foods. (4) REBUILD. Rebuild the damaged lining of the gut with herbs (such as slippery elm, marshmallow, and licorice) and nutrients (such as l-glutamine, coenzyme Q10, and omega-3 fatty acids). (5) REST. Resting more during this process will allow the body to devote more energy and resources to the healing process.

Since this series is about cleansing, we’re really only covering the first R – removal. If you have significant health problems, I urge you to see a practitioner who can guide you through the process in a more comprehensive way. But if you feel mostly healthy and want to occasionally support clean, calm intestines, taking measures to promote removal can be useful sometimes.

The best strategy for ongoing cleaning of the intestines is to eat a high fiber diet, possibly supplementing with additional fiber as an extra cleanser. This is especially important if you experience constipation on a regular basis. There’s lots of fiber in most fruits and vegetables, and a good amount in beans and whole grains, too. As a fiber supplement, you can try psyllium seed husk powder in some water or juice. Start with a small dose, like half a teaspoon, take with lots of liquid, and increase the dose gradually over several days. Flax seed and chia seeds are also very high in fiber and can be ground and eaten in cereal or stirred into water or a smoothie.

Another way to ensure more complete evacuation of the bowels is by squatting on the toilet. Here’s a video I made about the benefits and logistics of the practice:

The health benefits of squatting with Dr. Peter Borten

Posted by The Dragontree on Tuesday, May 17, 2016


If you’re having lots of gas or foul smelling stools, activated charcoal can be useful to carry out the gas and toxins from the intestines. You can take six capsules at a time, apart from food. Activated charcoal particles are covered with millions of tiny nooks and crannies that serve as adsorption sites – they bind up whatever is there. For this reason, drinking a slurry of activated charcoal in water is a common treatment for poisoning.

Another popular gut detoxifier is bentonite clay. Ingesting clay has gotten some fad status recently due to some celebrity talking about it, but it has been used in Traditional Chinese Medicine (TCM) and other traditional healing systems for a couple millennia. In TCM we use a red clay called kaolin, which also happens to be one of the original ingredients in the diarrhea product Kaopectate (the other main ingredient was pectin – hence the name, “kao” + “pect” – nowadays they use neither).

Besides being a useful source of minerals, clay binds up toxins and certain viruses and bacteria. Due to its ability to stop diarrhea and firm up the stool, it’s really important to consume clay in small amounts, combined with lots of water. Otherwise it can be constipating. It’s recommended to start with just ¼ to ½ of a teaspoon of (food grade) clay. Put it in a jar of water, seal it, shake it thoroughly, and let it sit for several hours. When you’re ready to drink it (between meals), shake it again, then consume. One caveat on this stuff: a brand called Best Bentonite was recently found to contain a lot of lead, which is obviously something you don’t want to put in your body. I suggest you look for a brand that has gone through third-party lab analysis for heavy metals. 

As indicated by the “pect” part of Kaopectate, pectin can also solidify stools. In addition, it can bind up toxins in the gut. If you feel like trying pectin, one of my favorite ways is by blending an entire lemon in water. It works best if you have a really powerful blender, like a Vitamix. I also like to quarter and freeze the lemon beforehand. Then I liquefy it in the Vitamix with about a pint of water (I often add some greens and a bit of stevia). If that’s too complicated, you can just get modified citrus pectin in capsule or powder form. Pectin has been shown to enhance the excretion of mercury, cadmium, arsenic, and lead from the body. And many marijuana users claim that consuming it enables them to pass drug tests, so it seems likely that it facilitates detoxification in numerous ways.

Finally, if you tend to be constipated, magnesium is an excellent natural laxative. There are numerous natural herbal laxatives, but many, like senna, cascara, and buckthorn, are stimulating to the gut in a way that can be habit forming, so they’re best used only occasionally. Magnesium is usually a better option because so many people are deficient in it anyway. Over 50% of Americans don’t get the Recommended Daily Allowance – and that’s not even an optimal dose. If you could use some bowel assistance, feel free to take magnesium citrate (or malate, or ascorbate, or an amino acid chelate, or even oxide). You can start with 200 milligrams a day, and increase it by 200 milligrams until it has the desired effect. If you’re like me, though, and you don’t want it to give you loose stools, you should take it as magnesium glycinate or magnesium bisglycinate.

Thanks for reading. I’d love to hear your experiences – both positive and negative – with cleansing.

Be well,

Dr. Peter Borten


1 Comment
  • Flora Rudolph
    Posted at 07:19h, 17 June Reply

    Hello Peter,

    I have been blending and drinking the lemon since I read your article. How often are we supposed to do this? Is it a daily thing? I have lots of diarrhea and love to get the bad bugs. I am doing many good things for my gut, but did not have this link until your article.

    I cannot use clay or charcoal and don’t want antibiotics.
    Thank you!

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