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ou may be surprised to know that most of your body’s immune system is housed in your gut. So, if you have a problem such as lupus, which is related to dysfunctional immunity, chances are, you have problems with your gut. And believe it or not, if you fix your gut health and function, you will be able to completely resolve what was until now deemed a “chronic” disorder. The best part? This all natural method targets the root causes of lupus through a dietary approach that arguably works better than the medications prescribed to “control” these diseases. That’s because this isn’t a way to just put a band-aid on lupus. It is an actual way to get rid of lupus entirely, and live a healthy, pain-free lifestyle.

So, in this article, I will describe exactly how you can retrain your immune system, and reclaim healthy function, simply by fixing the functionality of your intestines. This is considered a form of biohacking, or more specifically, microbiome hacking, and I constantly employ these techniques when treating my patients. 

I have broken this down into three main concepts, and in my opinion, if you are able to master all three concepts, you will be able to fix over 90% of problems related to gut health and lupus. 

The three concepts are:

  • Complex protein theory
  • Intestinal transit time
  • Probiotic concepts

Complex Protein Theory

Protein is a major part of our diet, coming from both plant and animal products. In simple terms, a protein is just a bunch of amino acids connected together. When the protein enters our digestive system, enzymes in our intestines break these up into individual components called amino acids, which then get absorbed. These intestinal enzymes are called proteases. 

The reason this is relevant is because if the proteases don’t get the job done, we are left with large particles of protein that linger in our intestines and blood stream for long periods of time.

Why does this happen? Certain types of proteins are harder to break down than others, and sometimes, there just may not be enough protease available to successfully accomplish this. Protease enzymes are produced by our bodies, but can also be found in many types of plants. As you already know, the gut is just one giant immune organ— 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, causing it to secrete a bunch of immune chemicals which in turn cause inflammation.

Let me give you some examples: 

  1. Bovine Serum Antibodies and Autoimmune disease.

There are some very famous studies that looked at the human body’s response to beef and cow’s milk. 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 people with an immune disease.

  1. Casein/Whey

Many people cannot break down the casein in milk protein. Some people also have difficulty with whey. If you are dealing with immune inflammation, it is best to avoid casein altogether, and probably also most whey products (ex: dairy milk and cheese). Also, check your protein powder to make sure it's not causing you problems. I prefer a plant based protein, but if you decide to use whey, I would recommend whey isolate instead of whey concentrate, as concentrate contains casein in it.
There is a type of casein called A2 that’s a bit easier to digest, but it's hard to find and you have to specifically be looking for A2 cow’s milk [aff link].

  1. Gluten

This one is very famous because it's estimated that nearly a third of the population has an issue with this. This is a multi-factorial problem.  However, to summarize, I tell most folks to limit their contact with gluten containing products entirely. This includes anything to do with wheat flour. If you would like to read more about this, I have linked a study here. 

  1. Egg protein

This is a tough one because 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 in this field.  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. In some cases, egg whites can slowly be re-introduced when the time is right.

I want to be clear - 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 is best to limit these types of proteins in the diet.  It is also very important to consider taking a protease enzyme supplement [link] with your largest meal. I personally use an all natural one derived from plants, and it’s something that I’ve had very good results with. Whatever company you decide to use, they should have a very good track record of compliance and safety, with their enzymes being responsibly sourced. 

You can also get protease from plant sources.

Bonus: Best dietary sources of digestive enzymes; Must Read

With your stomach being acidic, your small bowel being alkaline, and your blood being neutral to slightly basic, it is ideal to incorporate an enzyme blend that functions across all three. If you cannot get it from your diet, then you may want to consider a supplement (link).

Intestinal Transit Time

I want to introduce you to a concept called intestinal transit time. This is the amount of time it takes for food to travel through the GI tract.  Usually, food will travel through the small intestine in 4-6 hours, and the large intestine in about 12. This means that you should be having a bowel movement within 16 to 18 hours after eating, typically resulting in 2-4 bowel movements for most individuals on any given day. However, if you are constipated or have bacterial overgrowth, this process can take several days or up to a week.

Lingering Foods

There are certain types of foods, which I have termed “lingering foods”, that have been found to stay (or linger) in the intestinal tract for too long. These include meats, cheeses, sugars, and simple carbohydrates. 

But how long is too long?

The answer is anything surpassing 12-18 hours, meaning that you should aim to produce stool multiple times per day. Although it may sound crazy to some, 2-4 bowel movements per day is ideal and normal around the world; In our own human history, when we were foraging for food, our ancestors went 2-4 times a day. Nowadays, in developed countries, we are lucky to even go once. In fact, some of my clients who suffer from bacterial overgrowth, irritable bowel syndrome (IBS), and constipation sometimes only go a couple of times per week. All of these folks have problems with inflammation, fatigue, and stress. 

Thus, it’s no wonder that 60-70% of people with lupus have digestive issues.

So, why do these foods linger?

Remember, the list includes meat, dairy, processed grains, and sugars; all foods with a very minimal amount of fiber. 

When I say fiber, most people think of metamucil, or this thick powdery stuff we mix into water and drink. However, when I’m talking about fiber, and particularly insoluble fiber, I’m talking about that chewy fibrous material found in plants and vegetables. For example, celery. Despite how long or hard you chew, you are left with this material that you can’t really break up, and just end up swallowing. The same thing is true with broccoli, kale, and carrots. As it turns out, this fibrous material is not digested in the intestines, but it does two very important things: 1) it pulls in extra water, making the bowel movements nice and soft, and 2) it prevents the growth of bad bacteria in the small intestine and colon. This is why you hear so many people talk about fiber as being a good “prebiotic”, as it basically sets your intestines up for success by harboring good bacteria.

It’s important to note that there is nothing special or profound about prebiotics, so don’t get tricked by marketing. All prebiotics are basically just fiber, and you should be getting them from your diet. I think fiber is very under-rated and should be considered an essential nutrient. And because it's only found in plants, fiber is considered an essential phytonutrient.

Examples of high fiber foods:
High Fiber Foods
These foods should comprise 75% of your daily caloric intake in order to make sure you are getting enough fiber every day.

The FDA thinks that 28 grams per day is enough, but I personally believe 40-50 grams should be your target. Keep in mind, even that is just half of what our ancestors used to intake when foraging for food, so you can never really have too much.

After about 4 hours, there is very little digestion taking place.

Most of the time, food waste is just sitting there, slowly getting metabolized by gut bacteria. Yet, this is where it gets interesting. The reason that sluggish foods are a problem is because they create secondary metabolites in the body, which are deadly. 

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

By the way, you can test this out yourself. There are these blue colored muffins you can buy which will turn your stool blue. 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 probably good. If it takes any longer, like 2 days or more, then you are probably dealing with an excessive amount 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 magnesia works well. A typical starting dose is 30ml twice daily, but some people use it more than that (up to 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 magnesia, you can try these natural alternatives (link).  However you do it, you should aim for 2-4 bowel movements every day in order to get rid of the bad bacteria and replace their occupancy with that of good bacteria. Also, remember that certain medications and medical conditions can cause severe constipation, so check to see if any of these are part of the problem.

Probiotic Concepts

When it comes to probiotics, 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.  There are even companies that will now 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 Lactobacillus, Saccharomyces, and Bifidobacterium, with Lactobacillus and Bifidobacterium being the most important with the best scientific evidence.


Next, it's important that you introduce good microbes into your system at least twice a day, but ideally four times a day.  This means that taking probiotics just once daily is not enough. Additionally, as you introduce good microbes into your system, you need to get rid of the old microbes. The best way to do this is by having 2-4 bowel movements every day. Turnover is important. Most people just assume that 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 just once in a while, sufficient results are unlikely to be observed. And 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.

Some people opt for yogurt or fermented foods when it comes to their probiotic intake. Others prefer oral probiotics, but with the countless choices of brands that are out there, it may be hard to decide which one is best. I have 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 the FREQUENCY of administration. 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 per day). You want to constantly introduce good microbes into your system, so that as your body gets rid of the old microbes, the new microbiome has a chance to flourish and populate.

Remember, I told you that there is scientific data backing this up. I will link it here.

If you are looking to solve the inflammation caused by lupus, then probiotics may be helpful.

Before I conclude this section, there is one more thing I want to discuss: yogurt. If you are a vegan, this is obviously a no go. If you have a dairy allergy, or simply can’t tolerate it, then this might not apply to you either. However, if your only issue is lactose intolerance, or fear of dairy, then hear me out…

  1. Lactose content in yogurt is lower than milk.
  2. Yogurt contains bacteria that help break up lactose.
  3. Fat free yogurt is great, but make sure it doesn’t have any thickeners or sweeteners. If you like full fat yogurt, then a grass-fed source is probably best.
  4. Yogurt 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 yogurt, just keep those four things in mind. Otherwise, just take a supplement capsule. I have clients that do both, and many of them do fine with adding a bit of yogurt.  As you probably know by now, I usually recommend avoiding all dairy—but yogurt does have its benefits, especially if you choose wisely. It's easy and 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 (link).  It's 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 lupus, naturally, without medications in my practice. Typically, lupus manifests in the integumentary, haematological, and musculoskeletal systems, but is usually tied to a multifaceted problem affecting mind-gut-immunity.  All areas need to be addressed to successfully solve lupus. You must fuel the mind and properly heal the gut to reset immunity.

Here, we discussed how to heal the gut. 

  1. Get rid of the bad
  2. In with the new
  3. Rinse 
  4. Repeat. 

And this cycle keeps going so that you can maintain a favorable microbiome.

  • Aim for 2-4 bowel movements daily. (Consider taking a laxative, such as milk of magnesia)
  • 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 yogurt)
  • 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 can undergo the necessary digestion, and efficiently 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)


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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.

Writer:  Kaloyan Momchilov

Editor: Chanu R. Dasari MD

May 25, 2022

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