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

The Gut-Kidney Connection

In this series we examine the comprehensive gut restoration protocol used to as a foundational approach to heal gut integrity. 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. 

In our previous blogs, we discussed the impact of exposure to food and environmental triggers that impact the gut lining (or mucosa)integrity and microbiome balance leading to intestinal permeability (aka “leaky gut”)

So far we have looked at how the first and second steps of the 5R protocol, Remove and Replace, help to address the underlying factors associated with leaky gut that include a combination of factors like exposure to food and environmental triggers causing local and systemic inflammation, disruption of digestion and nutrient absorption, altered bowel motility, and dysbiosis.

Below, we will explore step 3, Reinoculate. Let’s first review the five steps of the comprehensive gut restoration protocol. The 5R Protocol addresses leaky gut as a foundational approach to reduce the risk of progression of CKD. The five areas of GI mucosal integrity are: 

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 basic premise of the third stage of gut restoration is to foster an environment that allows beneficial microflora (aka good bacteria) to thrive in the gastrointestinal (GI) tract. This is achieved by leveraging diet, supplementation, and lifestyle modification.

In previous blogs, we have explored the connection between dysbiosis and kidney health. An increasing number of studies have demonstrated a significant relationship between the health of the microbiome and the progression of kidney disease, a relationship referred to as gut-kidney axis.

Those with a healthy microbiome, abundance of good bacteria and no overgrowth of bad bacteria, are less likely to develop chronic kidney disease. In fact, the presence of certain strains of bacteria in the gut can actually slow the progression of chronic kidney disease and even reduce the need for dialysis. 

Where to start?

Prebiotics (aka Fiber)

Most Americans fall significantly short of the recommended fiber intake of 30+ g/day. High fiber intake is associated with reducing the risk of heart disease, obesity, diabetes, and even certain kinds of cancers like colorectal cancer. These benefits are linked to to improved bowel movements, neutralizing and removing toxins, and “feeding” gut bacteria contributing to a favorable microbiome balance. 

Research even suggests that dietary fiber-intake may be one of the most significant predictors not only of gut health, but overall health and risk of disease!

Remember to always choose whole, fresh, fiber-rich fruits and veggies whenever possible to maximize nutrients and prebiotics simultaneously. Whole grains and legumes make good fiber sources as well, but always avoid processed foods that claim to have “added fiber”. They are usually packed full of fillers, sugars, grains, cereals and artificial ingredients.

High-sugar diets can be a major disrupter of your gut microbiome, primarily because it feeds bad bacteria and yeast overgrowth. This is one of the proposed mechanisms contributing to metabolic diseases like diabetes and heart disease, two conditions associated with KD.

Prebiotic supplementation might also be necessary in some cases. Supplemental powders and capsules of resistant starch, arabinogalactan, and mastic gum, among others, might be useful in many situations. Your integrative or functional medicine provider can help you determine which, if any, are appropriate for your unique situation. 


Supplementation with high intensity probiotics may be very useful in the Reinoculation phase of the 5R protocol. There are a variety of strains of bacteria and even beneficial yeast that are used to help to “seed” the gut (though technically more recent studies suggest the benefit is transient, it can still be helpful). Depending on your individual needs, your integrative and functional medicine provider may choose a particular strain or opt for a broad-spectrum formulation. Either way, the quality and potency of the probiotic is important to consider (not all brands are created equal). 

That said, research seems to support that the best long-term strategy is to increase the intake of probiotics coupled with prebiotic fiber intake through diet. Traditionally fermented foods are a great source of naturally found probiotics, these include non-pasteurized traditionally made kefir, sauerkraut, kimchi, miso, and pickled vegetables.

Other factors impacting the microbiome

Interestingly, exercise impacts microbiome balance and promote changes that improve gut health. Aim for at least 20 minutes of exercise daily at a level appropriate to your physical fitness and make it priority to get up and move – you and your kidneys are worth it! 

Furthermore, stress has been found to negatively alter the balance of the microbiome by reducing the presence of friendly flora and promote the growth of bad bacteria. Although we know that stress cannot always be avoided, everyone can find a stress management practice to reduce its negative impact. Breathing exercises, meditation, long walks, listening to music, adult coloring books – the options are endless. Find what works best for you!

Bottom Line

The third step in an individualized comprehensive gut restoration protocol involves promoting microbiome balance. This is often done after the Remove step but might be simultaneous to the Replace step. Sequencing the steps of the protocol is case-by-case dependent. It’s important to work with an integrative or functional medicine provider trained in the comprehensive gut restoration protocol to help you navigate this successfully.

Next, we will tackle the fourth “R” in the gut restoration protocol: Repair.