This is part of a series of blogs discussing an individualized comprehensive gut restoration protocol in chronic kidney disease.

The Gut-Kidney Connection

Researchers have established a relationship between gut integrity and microbiome diversity with various chronic diseases, including kidney disease. Increased intestinal permeability, also known colloquially as “leaky gut” has been shown to be at the root of this connection. This gut-kidney relationship is the result of complex biochemical and immune mechanisms. 


Past studies have attempted to explore the impact of dietary changes shifting the gut microbiome to help restore the lining of the gut and reduce the resulting inflammation. However, many of the studies in the literature looking at the use of probiotics to reduce uremic load show some limited benefit in reducing the chronic kidney disease (CKD) burden. 

But these studies failed to present a comprehensive approach that reveres damage to the gut while simultaneously inoculating the necessary bacteria. This single dimensional approach does not acknowledge all the different factors involved in the gut-kidney Axis.

To assure that the patient is getting a comprehensive gut restoration protocol, all the mechanisms that underlie probiotic use should be addressed. These include modification of microbiota, competitive adherence to the mucosa and epithelium, strengthening of gut barrier and modulation of the immune system. 

The 5R gut restoration program addresses these gaps and help reduce the risk of progression of CKD.

This program is designed to address five areas of GI mucosal integrity repair: 

1) Remove potential triggers, including polypharmacy, pathogenic organisms, food intolerances, sensitivities and allergies, or toxic exposure.  

2) Replace digestive aid to support improved nutrient absorption and metabolism, including digestive enzymes, or agents that promote improved motility and regular bowel movements.  

3) Reinoculate provide an environment where good bacteria can thrive and where bad ones cannot. 

4) Repair support of the cellular repair process through the above, as well as by providing specific nutritional support for the regeneration of the GI protective barrier. 

5) Rebalance lifestyle factors that influence the gut bacteria such as stress, sleep, exercise and relationships and assure ongoing gut health.


The first step of this protocol focuses on removing any exposures that may be contributing to increase inflammation in the gut. This includes food exposures, toxins, as well as screening for and treating pathogenic bacteria, fungi, parasites, or viruses that maybe disrupting the normal microbiota balance, which may require antimicrobial treatment to eradicate. 

First, food known to cause sensitivities and allergies should be eliminated as part of an elimination diet. There are multiple categories of foods that contribute to inflammatory response that disrupts the lining of the gut. For example, gluten has been found to be associated with the development of leaky gut and IgA nephropathy. At the same time, we should be emphasizing the inclusion of key nutrient-dense foods that help to restore gut integrity and reduce inflammation, including antiinflammatory fats, organic fiber and phytonutrient-rich vegetables and fruit. 

Typically, an elimination diet  removes common food triggers like gluten, dairy, eggs, and soy. Depending on the root of the food reactivity, sometimes the removal or reduction of grains, legumes, FODMAPS, or night-shade vegetables is also necessary. 

A nutritionist or clinician trained in implementing the elimination diet can help guide on which foods to eliminate or reduce. The decision may be done empirically, using symptom monitoring to guide the progress. Alternatively, the program can be personalized by using specialized testing for immune response against food can help guide this process. 

Second, exposure to environmentally derived toxic substances should also be minimized, this includes mercury, arsenic as well as pesticides and other environmental pollutants whenever possible. We are exposed to toxic chemicals on a daily basis including pesticides in conventionally-farmed food, non-stick cookware, plastic use, and flame retardants and off-gassing released from furniture. 

Addressing this aspect involves focusing on consuming organic produce and animal products and addressing environmental sources of toxicity. This topic is covered in more detail in this blog here.

Lastly, remove also entail identifying potential microbial triggers that might be contributing to inflammatory response. As mentioned above this may be “bad” bacteria, viruses, candida, and/or parasites. The presence of these offenders can be detected through symptoms as well as through advanced stool testing that employs a technique called PCR. Once identified, your practitioner can use antimicrobials to help eradicate the pathogenic organism, using prescriptive antibiotics or even herbal antimicrobials if appropriate.    

Where to start?

Inflammatory foods

Some foods can be inflammatory or induce allergic reactivity. Furthermore, they may provide an environment that allows for the growth of pathogenic microbes, including low-fiber diets and high sugar diets. Furthermore, depending on your genetics, some foods can even lead to autoimmune conditions that may affect the kidneys. Eliminating food that is known to cause sensitivities varies dependent on the individual and their genetic predisposition. 

An elimination diet can help with identifying what food an individual should avoid. This diet involves the removal of foods commonly associated with food sensitivities or immune reactivity. There are many variations of the elimination diet, and it’s very important to work with a nutritionist who can ensure you’re doing the protocol correctly and not missing any essential nutrients.  

After a period of removal lasting at least 4 weeks, and assuming improvement in symptoms that suggests improved gut integrity, your integrative or functional medicine provider will work with you on gradual and careful reintroduction of foods to assess if tolerance has improved. 

Decrease/Eliminate Exposure to Toxins

It is very hard to eliminate all sources of toxin exposure, but these steps can help minimize it:

1.    Water filtration: we discussed options for water filtration in a previous blog.

2.    Cookware: gradually eliminate all toxic non-stick cookware from your kitchen.

3.    Avoid plastic containers or utensils: gradually switch from plastic to non-plastic containers and utensils.

4.    Eat organic when possible: we know that choosing organic food can be expensive. If you are on a budget, there are certain fruits and vegetables that you should buy organic because of their high toxic burden. Visit the Environmental Working Group website to learn about their “Dirty dozen” T. This list gets updated yearly depending on their tests.

5.    Be careful of processed drinks and juices. Not only do these contain excessive amounts of sugar, but they can also be a source of heavy metals and toxins because of poor regulations.

More on this topic here

Eliminate Pathogens

As discussed above, laboratory analysis of the patient’s stool and serum can help give insight to the extent of intestinal permeability (leaky gut), as well as the status of microbiota. Establishment of baseline status is essential for measuring outcomes at designated milestones to give quantifiable outcomes. A comprehensive stool analysis can be a good start. In addition, a good dietary intake can help identify issues that could be related to food intake to guide this process. 

Depending on the results of the individual’s comprehensive stool analysis, certain bacterial or yeast overgrowth can be detected. Also, parasites can sometimes be identified. Any of these should be treated by various medications, dietary changes, and/or herbal supplements as indicated and advised by an integrative or functional medicine provider.

Remove stress

Stress can have a bad influence on digestion and absorption. People who are stressed tend to eat too fast, make poor choices, and may eat too much at various intervals. This can lead to food choices that can lead to feeding the bad bacteria in the gut and poor digestion causing nutritional deficiencies. Furthermore, stress itself can influence epigenetic changes that impact dysbiosis as well as disease expression in general.

Bottom Line

The first step in an individualized comprehensive gut restoration protocol involves the removal of food sensitivities, environmental toxins, pathogenic organisms, stress. It’s important to work with an integrative or functional medicine provider trained to guide patients with elimination diets can help you navigate this successfully.

Next, we will tackle the second “R” in the gut restoration protocol: Replace.