What is the Best Gut Cleanse Diet?

Written by Dr. Ruscio on September 7, 2022

Written by Dr. Ruscio on September 7, 2022 — Reviewed by Heidi Turner

How a Gut Cleanse Diet Can Jump Start Your Gut Healing

What is a Gut Cleanse?|
Signs You Need a Gut Cleanse Diet|
Choosing Your Diet|
Option 1|
Option 2|
Elimination Diets|
Why a Customized Diet is Best|
Adding Probiotics|
Simplify Your Gut Cleanse Diet|

Key Takeaways:

Despite its name, a “gut cleanse diet” does not literally clean your gut, but it can help it rest, reset, and heal while stabilizing the gut microbiome for better digestive health.
A gut cleanse diet that resets the gut can be a great option for people who have tried many different diets and supplements but are still experiencing gastrointestinal symptoms.
There are two options for a gut cleanse diet: intermittent fasting plus an elimination diet, or, an elemental diet for a few days followed by an elimination diet.
Most gut cleanse formulas found in health stores are not proven to improve gut health or symptoms, and most have additional fillers and large amounts of fiber, which can aggravate symptoms.

You are probably considering a gut cleanse diet due to persistent digestive symptoms such as pain, bloating, diarrhea, and/or constipation. Or you might be simply looking for ways to clean up your diet and improve your overall health. Giving your gut a reset with a gut cleanse diet can be a great way to improve your digestive system so you can start to feel better.

Research-backed gut cleanse diets are great for giving the digestive tract a temporary “rest” from your normal diet. These protocols can balance the gut microbiome, lower inflammation, and heal the lining of the gut, which all help to eliminate toxins and your symptoms.

There are two gut cleanse diet options — fasting plus an elimination diet or an elemental diet followed by an elimination diet. In this article, we will look at what a gut cleanse diet actually is, when you might want such a diet, and two options for gut cleanse diets you can do at home.

What is a Gut Cleanse?

When talking about gut cleanse diets, we are not referring to gut cleanse protocols you might find on the shelves of a health food store, but rather whole foods that are anti-inflammatory and help to heal the gut lining and balance the gut microbiome.

These protocols often include some type of fasting, to let the gut rest from its digestive processes and take some time to repair. It’s often accompanied by a diet rich in vegetables, healthy fats, and quality protein that removes processed foods.

The term “gut cleanse” is not a medical term, but is often used in alternative medicine to describe any protocol or technique that is designed to help remove toxins, accumulated fecal matter, and parasites from the digestive system. One of the proposed benefits of a gut cleanse is to resolve symptoms such as diarrhea, bloating, and abdominal pain [1].

This concept is based on the medical term “detoxification”, which is a natural body process that removes toxins from the body and converts toxins into less toxic metabolites [2, 3]. Natural detoxification happens every day through sweating, urination, defecation, our skin, and the functioning of the lungs, liver, and kidneys [4]. It’s important to understand that your body is constantly eliminating toxins on its own, and you don’t need a gut cleanse to accomplish this.

However, there are many methods that people use to support their body’s natural detox process, such as supplements, herbs, colon cleanses, saunas, fasting, and dietary changes [3, 5]. A gut cleanse diet, which is the focus of this article, falls under the fasting and dietary changes that can help with detox and gut healing.

As gut cleanses are related to detoxification, you may hear the term used interchangeably with “gut detox.” I previously took a deep dive into the research surrounding the benefits of gut detox protocols, such as the box protocols you often see in the health food store. For this article though we are going to look at how a gut cleanse diet can help heal the gut and improve your well-being.

How Do Gut Cleanse Diets Work?

As the idea of a gut cleanse is based on an outdated theory, it’s likely that these products and diets aren’t directly removing “toxins” from the body. But the truth remains that people continue to report feeling better after trying these protocols. What is more likely occurring, is that many gut cleanse diets are actually reducing inflammation levels in the digestive tract, which helps the body naturally detoxify (along with many other benefits).

So while these diets aren’t actually “cleansing” or directly eliminating toxins from your gut, they can still offer you many health benefits. To steer away from the idea of a “gut cleanse” we prefer the term “gut reset.” A gut reset allows for the gut to take a break from constantly having to break down the food that we consume.

Giving the gut a rest is important for gut healing. If the gut is digesting foods from you eating every few hours, it’s continuously working with no time to rest and repair. This is similar to strength training when we take 1-2 days off after a hard workout of lifting weights. This allows for the muscles to properly repair and rebuild.

Signs You Need a Gut Cleanse Diet

You may benefit from a gut cleanse diet if you have recurring gastrointestinal symptoms such as diarrhea and/or constipation, abdominal pain, and bloating that don’t seem to fully respond to any diets or other treatments.

Perhaps you have tried every diet or protocol out there, from increasing fiber and prebiotics to a low histamine diet to boxed gut cleanse protocols. If this sounds familiar, it can feel overwhelming to know what to do next. We are here to simplify your next steps and give you a targeted gut cleanse diet.

For many people with digestive symptoms, their gut microbiome is imbalanced and/or the lining of their gut is inflamed. Sometimes even eating a low-inflammatory diet isn’t enough to bring on relief. It’s at this point where the gut needs more of a rest and is why I recommend combining some type of fasting with a low-inflammatory diet to give the gut some more time to heal.

There are a few ways to do this, so let’s take a look at the two options that I have found work best for the patients at our clinic and how to know which one is right for you.

Choosing the Right Gut Cleanse Diet for You

Gut cleanse diets aren’t one-size-fits-all, and the goal is to find the right one for you. In order to do that, let’s look at the two main gut reset protocols that benefit many of my patients:

Intermittent fasting plus an elimination diet
An elemental diet followed by an elimination diet

In both of these options, you will want to choose the elimination diet that is right for you. In a moment, will discuss four different elimination diets and who they are best for so you can make an informed decision.

Option 1: Fasting Plus Elimination Diet

This option is where I like to start with patients who still have symptoms, even after removing common problematic foods like dairy and gluten. In these cases, starting with intermittent fasting (not eating for 14-18 hours per day) a few times a week, while also following an elimination diet can be a great gut reset.

The combination of intermittent fasting to allow the gut to rest, plus an elimination diet that reduces inflammation is a powerful healing combination for many people.

Benefits of Intermittent Fasting

Intermittent fasting allows the body to take a complete (but temporary) break from the high-energy process of digestion, so the gut can rest and repair.

Intermittent fasting has been shown to:

Improve symptoms of IBS [6]
Balance the gut microbiome [7, 8, 9]
Repair the lining of the gut [10]
Improve mental health, lower inflammatory markers, and decrease symptoms in people with inflammatory bowel disease (IBD) [11]
Promote autophagy, which is a natural cellular detoxification process that removes damaged cells and encourages new cell growth [12, 13]

The easiest way to add intermittent fasting into your life is to stop eating a few hours before bed and wait to eat your first meal an hour or two after you wake up. That way you can reach a 14-hour fast, mostly while you sleep [13].

While intermittent fasting has many benefits, you could reverse or lessen those benefits by eating inflammatory or irritating foods during your eating window. This is why we use intermittent fasting with an elimination diet. It’s best to combine intermittent fasting with an elimination diet for at least a month before reintroducing foods back into your diet.

Intermittent fasting is so beneficial that I still recommend fasting a few days a week for good gut health if you have seen benefits — even after you reach the maintenance phase of your elimination diet (more on that later).

Before we cover the four most common elimination diets I recommend for my patients, let’s look at your second option for a gut cleanse diet. This one also includes an elimination diet but starts out a bit differently.

**Option 2: Elemental Diet Followed By an Elimination Diet**

Sometimes gastrointestinal distress is so severe and the gut is so inflamed that intermittent fasting with an elimination diet may not provide your gut with enough rest. This is because it is still digesting whole foods, which can irritate a highly inflamed gut.

Option two might be the right gut cleanse diet for you if you are in an acute flare of gastrointestinal symptoms, such as experiencing bloating, diarrhea, constipation, and/or abdominal pain for multiple days in a row every week.

In this gut cleanse diet, we start with 2-4 days of an elemental diet before moving you to an elimination diet. During those 2-4 days, the only thing you consume is this meal replacement diet, which really gives the gut time to rest, reset, and heal.

An elemental diet is a liquid diet that’s anti-inflammatory, provides all essential vitamins and macronutrients, and is a full meal replacement (meaning you don’t need to supplement with additional food while on the elemental diet). It was created to provide those with severe GI issues complete nutrition that the gut can readily absorb, as all of the proteins are in their most broken-down form.

Elemental diets have been shown to help to heal and repair the gut in many medical conditions:

Preliminary data shows that elemental diets can improve celiac disease and IBS [14, 15, 16].
In one study, patients with IBS who tested positive for small intestine bacterial overgrowth (SIBO) used an elemental diet for 14 days, and 80% achieved a normal SIBO breath test by day 15 [14].
Elemental diets improve symptoms in people with IBD, such as Crohn’s and colitis, showing a remission of symptoms in many cases [17, 18].
Studies have shown elemental diets to be as effective as prednisone (an anti-inflammatory drug) in promoting IBD remission [18, 19].

One of our patients, Randy, used an elemental diet for just three days to finally recover from ongoing SIBO, fatigue, reflux, inflammation, and joint pain. This was after he had tried many other diets, medications, and supplements. You can hear more about his story on our YouTube channel.

Often elemental diets are prescribed by a doctor, though there are a few options that can be purchased without a prescription. In general, non-prescription elemental diets have been shown to be either just as effective or even better, than prescription diets [20, 21].

I am happy to report that our elemental diet formula is a fully elemental diet available without a prescription. While many people who are sensitive to dairy tolerate the original formula well, we do have a completely hypoallergenic and lactose-free option.

After you start your elemental diet, use that as your only nutrition source for 2-4 days. Most taste best cold, and our patients like to blend our Elemental Heal powder with ice and water and sip it throughout the day.

After you have finished your 2-4 days of an elemental diet, you can start phase 2 — your individualized elimination diet. This will continue to support further gut healing that you started with the elemental diet.

What You Need to Know About Elimination Diets

Now that you know your two options, let’s get into the details of choosing and following an elimination diet.

Benefits of Elimination Diets

Though research is lacking on using intermittent fasting or an elemental diet alongside an elimination diet, these interventions on their own have shown positive benefits in the literature. I see that the above gut reset options are often very beneficial for our patients in the clinic who are dealing with gut-related issues.

Elimination diets can improve a wide variety of gastrointestinal issues and other markers of overall health as well. They have been shown to:

Decrease levels of inflammation [22]
Improve symptoms of IBS and IBD [23, 24, 25, 26, 27]
Decrease brain fog [28]
Lower blood sugar [29]
Reduce signs and symptoms of leaky gut [30, 31]
Lessen the chronic pain associated with fibromyalgia [3 2]

There are several elimination diet options — we will get into that in a minute. First, let’s cover how to complete an elimination diet protocol.

How to Follow An Elimination Diet

Depending on the type of elimination diet you choose, the foods that you temporarily remove will vary. I recommend starting with the least restrictive diet first (Paleo), then moving on to the next tier if you see little to no improvement.

Once you have eliminated the recommended foods for 3-4 weeks (the elimination phase) and have seen significant improvement in your symptoms, you can move on to the reintroduction phase. You can start to add foods back in one at a time to see if any trigger your symptoms.

Try to choose just one new food to reintroduce every 2-3 days so you can be sure as to which foods are worsening your symptoms. If you add in two new foods or try multiple new foods day after day, you will not be able to tell which of the foods you are sensitive to.

Once you have completed this process for all of your eliminated foods, you should have your list of foods that work for you and can enter your maintenance phase. The maintenance phase is all about eating the most diverse and nutrient-dense diet that maintains symptom relief.

If you experience minimal improvement, you may need to try a more restrictive version of your current elimination diet (like AIP) or try a different type of elimination diet altogether, as there could be another hidden cause for your symptoms.

There are many types of elimination diets, so how do you choose which one is right for you? For most people, I suggest starting with a Paleo diet because it is the least restrictive and easiest to complete. It cuts out many of the most common inflammatory foods such as wheat and other grains, dairy, legumes (beans and lentils), and processed foods.

The Paleo diet is a great option for controlling inflammation in the gut (and the rest of the body), which helps promote a balanced and healthy gut microbiome and overall wellness [22, 33, 34, 35].

But what if you have tried a Paleo diet and you are still not feeling well?

That is when you might want to try one of the other diets below. This chart shows you other options such as an autoimmune protocol (AIP) Paleo diet and a low FODMAP diet, a short description of each diet, and who it might be best for.

Elimination Diet	Description	Who it Can Help
Paleo Diet	Eliminates common inflammatory foods such as whole grains, legumes, and dairy. A low-carb, whole-foods diet high in veggies, healthy fats, and healthy proteins.	People who have not tried a more structured elimination diet and/or who have intermittent stomach distress, brain fog, fatigue, or other symptoms.
Low FODMAP Diet	Eliminates fermentable carbohydrates and fiber that often cause bloating and diarrhea due to a gut bacteria imbalance.	Good for people who have tried Paleo but still have symptoms. Often helpful also for people with IBS and IBD [24, 25 26, 27, 36]. Particularly good for people who often have symptoms of bloating, gas, and/or diarrhea after meals.
Autoimmune Protocol (AIP) Paleo Diet	A Paleo diet that also removes additional foods that can be inflammatory such as nightshades (ex: peppers, eggplant, and tomatoes), nuts, seeds, and eggs.	A good fit if you have tried Paleo but still have symptoms like gut distress, brain fog, skin rashes, and fatigue. Has been helpful for people with IBD [37] and Hashimoto’s thyroiditis [38]
Low Histamine Diet	Eliminates foods that are high in histamines. Some of these are fermented foods like sauerkraut, kimchi, apple cider vinegar, kombucha, and kefir. It also avoids leftover foods, which can develop histamine over time.	Often helpful if you have tried all the above diets and not found relief [39, 40]. People with histamine intolerance frequently have itchy skin, flushing, respiratory allergies, bloating, diarrhea, and stomach pain

I know there are a lot of options for elimination diets, and hopefully, the above chart helps you discern which one might be best for you.

In addition to choosing your elimination diet, don’t forget to plan your meals! If you need help with meal plans, How to Build an Elimination Diet Meal Plan for Healing is a great resource to make meal planning less daunting.

Why a Customized Gut Cleanse Diet Is Best

Many gut cleanse diets aren’t fit for everyone as they contain foods that may actually worsen symptoms in some people.

High-fiber foods have been reported to worsen symptoms in people with IBD, such as Crohn’s and colitis, as well as irritable bowel syndrome (IBS) [41, 42]. Prebiotics are also fiber, and supplementation with fiber/prebiotics was shown in one randomized clinical trial to worsen gastrointestinal symptoms [36].

Worsening of your symptoms with fiber can be a sign that you have an underlying gut bacteria imbalance, and will likely benefit from a gut cleanse diet and/or elimination-based diet like a low FODMAP diet.

We do not want to completely discount fiber though, as fiber can be beneficial in certain cases. In some people, increasing fiber can improve IBS and IBD symptoms, decrease the risk of colon cancer, and increase the levels of beneficial bacteria in the gut [43, 44, 45, 46].

Additionally, an elimination diet will look different for everyone, as we all have unique food triggers and/or underlying gut imbalances that provoke an inflammatory response in our gut. For example, not everyone will have a sensitivity to gluten or histamine, and it’s not necessary for everyone to avoid them.

Healing your gut is all about doing what’s best for you as an individual — there are really no hard-and-fast rules.

Adding Probiotics

I would be remiss if I talked about a gut reset and did not mention probiotics. Part of the purpose of a gut cleanse diet is to improve the makeup of microbes in the gut, eliminating the bad bacteria and getting a good balance of beneficial bacteria.

Your gut cleanse diet will help do this, but adding probiotics to either diet you choose will help aid in this process.

In fact, one study found that adding six weeks of probiotics after a week of a liquid diet increased the number of beneficial bacterial species in the gut [8]. Adding probiotics to your gut cleanse diet protocol is easy and can be highly effective.

Probiotics can also help people whose gut flora feeds off of fiber causing gas, bloating, and abdominal pain by decreasing the number of harmful bacteria or an overgrowth of good bacteria in the gut.

They promote a healthy immune system (about 70% of our immune system is in our gut) and decrease inflammation [47, 48, 49]. This can make it easier for you to digest foods and improve your natural detoxification.

We don’t want to complicate this process — just find a good quality probiotic supplement and take it daily. There is no one best type of probiotic for any one health condition, and studies have shown that in general, a multi-strain probiotic can offer better results for certain digestive conditions.

Simplifying Your Gut Cleanse Diet

We covered a lot of information in this article, so let’s quickly outline the process so you can get started and start feeling better.

There are basically four parts to your gut cleanse diet:

Choose your gut reset option: intermittent fasting plus an elimination diet or an elemental diet followed by an elimination diet. Most people will start with fasting plus an elimination diet.
After your elimination phase, reintroduce one food back into your diet every three days, record any symptoms you have, and simply maintain the diet that feels good. This is your customized healthy gut diet that you will use going forward.
If you don’t see benefits with one type of elimination diet, try another.
Lastly, consider adding in a good daily probiotic during your gut cleanse diet.

Remember, a gut cleanse diet is not forever and is meant to help you get to a place where you can have a wide-variety, whole-foods diet. Following the process as best as you can gives your gut the greatest chance of really repairing its lining and improving its microbiome so you can feel better, consistently.

I hope this article has helped you discern what gut cleanse diet will best help you reset your gut. However, if you are seeking medical advice or guidance, you can become a patient at the Ruscio Institute for Functional Health so we can help you on your journey.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

Dr. Michael Ruscio is a DC, Naturopathic Practitioner, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.

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