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You may be surprised to know, that most of your body’s immune system is housed in your gut. So, if you have a digestive system problem such as Crohn's disease that is related to dysfunctional immunity, you’ll find this paper to be life changing.

Crohn’s mainly manifests as a gastrointestinal discomfort.  This should come as no surprise, since I’ve said before that the gastrointestinal system is central to mind-gut-immunity.  Why? Because it hosts over a Trillion, immune cells.  Yeah…. you read that right…. It is an enormous number.

So in this article, I will describe to you how you can retrain your immune system, and reclaim healthy function, by using your intestines. This is a form of biohacking, or microbiome hacking more specifically.

I have broken down the techniques that I use to treat my patients into three main axioms: and In my opinion, if you master these three concepts, you will be able to fix over 90% of your problems related to gut health and Crohn’s.

These are:

  1. complex protein theory 
  2. intestinal transit time
  3. Probiotic Concepts

Complex protein theory 

We get protein in our diet from a variety of sources including in both plants and animals. A protein is basically a bunch of amino acids connected together. When the protein enters our digestive system, enzymes in our intestine, called Proteases break it up into individual components called amino acids, which then get absorbed.  

The reason this is important is, sometimes the proteases don’t get the job done, and we are left with large particles of protein that remain in our intestines and blood stream for prolonged periods of time. 

Why does this Occur? 

Certain types of protein are hard to break down, also there may not be enough protease to break down the proteins. Protease enzymes are produced by our bodies, but can also be found in many types of plants. So these incompletely digested proteins register as a foreign threat, and generate an immune response.  Basically, the body thinks it’s under attack, by these undigested proteins.  So, then it secretes immune chemicals which cause inflammation.  

Here are some examples.

1) Bovine Serum antibodies and auto-immune disease. In many people the serum protein from cows is not broken down completely and you may end up with antibodies. These antibodies are 10x more common in immune disease. Here is a link to a famous study that looked at the human body’s response to beef, and cow’s milk. 

2) Casein/ Whey. Many people cannot break down the casein in milk protein. Some people also have a difficulty with whey. Its best to avoid Casein altogether, and probably also most whey products including dairy milk, and cheese If you are dealing with immune inflammation,. Also check your protein powder to make sure its not causing you problems. I prefer a plant-based protein, but if you decide to use whey, I recommend Whey isolate not Whey concentrate which contains casein in it. There is some person-to-person variations on this, so if you are just starting the protocol its best to avoid this altogether, but once you have mastered the process you will begin to see how things evolve.  There is a type of casein called A2 that’s a bit easier to digest, but its hard to find, and you have to specifically be looking for A2 cows milk (affiliate link). 

3) Gluten- It’s estimated that nearly a third of the population has an issue with this. This is a multi-factorial problem. But to summarize, I tell most people to limit their contact with gluten containing products in general. Including wheat flour and its products.

4) Egg protein- Many people who give up meat, rely on eggs as a source of protein. Some nutritionists would disagree with me on this, but there is a lot of misinformation.  The data from several studies show that egg protein can potentially trigger a strong immune response in the body, specifically in people with inflammatory conditions. My suggestion is to cut this out for a few months and see if it makes an overall difference. Egg whites can sometimes be re-introduced when the time is right. 

Generally--I’m not saying these foods are bad. What I’m saying is that when you are trying to decrease inflammation in the body, and you intend to do it quickly, it’s best to limit these types of proteins in the diet.  It’s also highly important to consider taking a protease enzyme supplement (link) with your largest meal. I personally use one that’s all natural and derived from plants. And its something that I’ve had good results with. The company should have a very good track record of compliance and safety and should be trustworthy to source their enzymes.

You can also get protease from plant sources

Bonus: Best dietary sources of Digestive enzymes: Must Read 

Since your stomach is acidic, your small bowel is alkaline, and your blood is neutral to slightly basic, ideally you need an enzyme blend that functions across all three.  If you cannot get it from your diet, then you may also consider a supplement. 

Intestinal transit time

Intestinal transit time is the amount of time it takes for food to travel through the GI tract.  Normally, food will travel through the small intestine in 4-6 hours, and the large intestine in about 12.  But when constipation occurs, and you have bacterial overgrowth then sometimes it can take several days or up to a week to get through. 


Lingering Foods 

Lingering foods is a term I came up with to describe any type of food that lingers in the intestinal tract for too long.  

This list includes meats, cheeses, sugar, and simple carbohydrates.

Anything more than 12-18 hours is usually considered too long, which means, you should aim to produce stool multiple times a day. 2-4 bowel movements a day, is ideal and normal around the world, and in our own human history, when we were foraging for food, out ancestors went 2-4 times a day.  Nowadays, in developed countries, we are lucky to have one a day. Some of my clients who suffer from bacterial overgrowth IBS and constipation sometimes only go a couple times a week.  All of these folks have problems with inflammation, fatigue, stress. 

It’s also no wonder that many people with Crohn’s have other digestive issues. 

So why do foods linger?  

Recall that the list includes meat, dairy, processed grain, sugar.  This is directly related to the amount of fiber in these foods.  

When I say fiber, most people think of Metamucil, or this thick powdery stuff we mix into water and drink.  But when I’m talking about fiber, and particularly insoluble fiber, I’m talking about that chewy fibrous material in plants and vegetables.  For example, celery, when you chew it and chew it, you are left with this material that you can’t really break up, and you just end up swallowing it.  Same thing with broccoli and kale, and carrots. It turns out… this fibrous material is not digested in the intestines, but it does two things. 1) it pulls in water, making the bowel movements nice and soft. and 2) it prevents the growth of bad bacteria in the small intestine and colon. This sets up your intestines for success, by harboring good bacteria. That’s why you hear a lot of people talk about fiber as being a “prebiotic” 

And by the way, there is nothing special or profound about pre-biotics, so don’t get tricked by marketing, all prebiotics are basically fiber, and you should basically be getting them from the diet. I think fiber is very under-rated and should be considered an essential nutrient. And because it’s found only in plants, it’s considered an essential phytonutrient.

So, what are some examples of high fiber foods:

Download the list

These foods should comprise 75% percent of what you eat, so that you know you are getting enough fiber every day

The FDA thinks that 28 grams per day is enough. But You can never really have too much fiber. I think 40-50 should be your target. Keep in mind, that’s still basically one half of the fiber that our ancestors used to eat when they foraged for food. 

After about 4 hours, there is very little digestion happening. 

Most of the time, the food waste is just sitting there getting metabolized by gut bacteria. The reason sluggish foods are a problem is they create secondary metabolites, and these secondary metabolites are deadly.   

Primary metabolites are formed when food gets metabolized the first time. These primary metabolites become food for a second population of bacteria, which then create secondary metabolites.  And so on… and so forth.   This first set of bacteria, the ones doing the primary metabolism; these are good bacteria- they keep our intestines healthy.  This second population of bacteria is problematic- because the secondary metabolites are what cause, bloating, inflammation, weight gain, depression, and even cancer. Think about when you feel bloated or inflamed, the colon is usually just storing and holding on to the feces before expelling.

By the way, you can test this out at home using blue colored muffins. You can also eat an entire beet or two and see how long it takes for your stool to turn red.  If it happens within 12-24 hours, you are usually good. If it takes any longer, like 2 days or more, then you are probably in trouble, and probably deal with a lot of bacterial overgrowth and inflammation. You can impact this by eating a lot of fiber, and taking magnesium supplements when you are constipated.  Milk of magnesium works well. A typical starting dose is 30ml twice daily, but some people use it more than that, like 4-5 times a day. The goal is to titrate and adjust it so that you are having 2-4 liquid bowel movements a day.  Eventually when you eat foods that contain a lot of fiber, you won’t need the magnesium.  If you do not like milk of magnesium, you can try these natural alternatives.  However you do it, you should aim for 2-4 bowel movements a day, so that you know for sure the bad bacteria are being let go, making room for some good bacteria to move in and setup shop. Also remember, that certain medications and medical conditions can cause severe constipation, so check to see if any of these are causing a problem.

3. Probiotics Concepts

Now onto the third concept, A lot of people spend an inordinate amount of time talking about colony forming units, number of strains, types of strains etc.  Some even talk about buying refrigerated versions vs soil-based spore forms.  And there are even companies now that will take a stool sample from you, analyze it, and send you custom designed blends. 

I can tell you, that as a physician, I have studied over 300 scientific articles on this subject and my findings can be summarized as the following:

The three main bacteria in a good probiotic are Lactobaccilus, Sacchromyces, and Bfidobacterium. And of these three, Lactobaccilus and Bfidiobacterium are the most important with the best scientific evidence.

Next, its important that you introduce good microbes into your system at least twice a day, but ideally four times a day.  So even once a day is not enough.

Also, as you introduce good microbes into your system, you need to get rid of the old microbes. The way you do this, is to have bowel movements, ideally 2-4, a day.  

Turnover is important. Most people just assume if they take a probiotic they will be fine.  But if they are not constantly expelling waste, and only taking a probiotic once a day or once in a while, they won’t be able to benefit from the full potential of this technique. in my opinion, they may be missing out on the full potential of these beneficial microbes. So don’t get too obsessed over the number of strains or colony forming units and don’t waste your money on expensive probiotic supplements, which are generally not useful. The frequency of probiotic intake matters the most.

So which probiotic is the best?

 Download Dasari MD’s Crohn’s Supplement guide 

Some people have yoghurt or fermented foods. Others prefer oral probiotics, but have countless choices and don’t know where to start.  I put together a helpful guide to supplements for my clients to use when tackling these questions. I tend to keep things simple and favor reputable brands that are affordable. 

Just remember, the most important factor is not usually the number of strains, but rather how many times you take the probiotics. And this is the one thing that most people miss.   You want to keep introducing good microbes into your system throughout the day, not just once, but 2-4x day in fact. You want to constantly introduce good microbes into your system, so that as your body excretes the old microbes, the new microbiome have an opportunity to flourish and populate. 

So, as promised here is a link to a scientific data

If you are looking to solve Crohn's, then probiotics may be helpful.

Okay, before I conclude this section, there is more thing to talk about, and that’s the topic of yoghurt. If you are a vegan, obviously this is a no go.  And if you have a dairy allergy, or can’t tolerate it, then fine.   But…. If your only issue is lactose intolerance, or fear of dairy, then hear me out.  

  1. Lactose content in yoghurt is lower than milk
  2. Yoghurt contains bacteria that help break up lactose. 
  3. Fat free yoghurt is great, but make sure it doesn’t have any thickeners or sweeteners. If you like full fat yoghurt, then a grass-fed source is probably best
  4. Yoghurt still has casein milk protein which can cause allergies in some people. This is prevented by getting a specific type of cows milk yoghurt called A2, or switching to goats milk yoghurt.

So if you strongly desire traditional milk yoghurt, just keep in mind these four things. Otherwise, just take a supplement capsule. I have clients that do both, and many of them do fine with adding a bit of yoghurt.  As you probably know by now, I usually recommend avoiding all dairy altogether—but yoghurt does have its benefits, especially if you choose wisely.  Its easy and its helpful for getting probiotics, and all you need is a spoonful, 2-4 times a day.  

If you want to go into detail with this, I have a blog post called Decoding Milk & Dairy.  Its part of a larger series that describes the nutritional profiles of controversial food groups, like eggs, fish, and meat in general. I realize that there are very strong opinions regarding the healthiness of foods, So I try to stick with the facts, and give you what I think is a safe zone for functioning every day.  


I have had much success treating Crohn's, naturally, without medications in my practice.  Typically, Crohn’s manifests in the digestive system but is typically a three-part problem affecting mind-gut-immunity.  All three areas need to be addressed to successfully solve Crohn's. You must fuel the mind, heal the gut, to reset immunity. 

Here we discussed how to heal the gut. Get rid of the bad In with the new🡪 rinse🡪 repeat. And this cycle keeps going so that you can maintain a favorable microbiome

Summary here

Aim for 2-4 bowel movements daily. (Consider taking laxative)

Limit complex proteins  (until inflammation decreases)

Consider a Protease Enzyme Supplement

Eat Fiber-rich foods, Green and Leafy vegetables contain lots of Insoluble fiber. 40-50 grams daily if possible

Limit sluggish foods like Sugars, Carbs, Meat, Dairy (perhaps with the exception of yoghurt)

Take Probiotics 2-4x daily. My favorites are listed here 

Drink Lots of water, a gallon a day, unless you have kidney or heart problems

Avoid medications that cause constipation 

Your goal should be to decrease your intestinal transit time, so that the food you eat will undergo the necessary digestion, then exit your system without creating opportunities for harmful metabolites to form from bacterial overgrowth.  


There are a whole host of conditions associated with dysfunctional microbiome, the list includes: Eczema, Allergies, UTIs, IBS, IBD, Crohn’s/Colitis, SIBO, Candida, GERD, Viral illnesses (including Flu and COVID), Autism, Multiple sclerosis, Lupus, Rheumatoid

“Fuel the Mind, Heal the Gut, Reclaim Immunity”

Chanu Dasari MD (@DasariMD)

Have Crohn’s]? Want to stop INFLAMMATION for good?

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Top Picks

Protease Enzyme Supplement: PhytoZyme Protease by Physicians Trust

Probiotic Supplement: Jarrow’s Brand

Stool Softener: Milk of Magnesia, Dulcolax

Show Notes:

Although I am a licensed, and practicing surgeon, the presented material is intended for educational purposes only and should not be construed as medical advice. Please use your best judgment and consult with a healthcare professional regarding your needs.


May 27, 2022

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