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Writer's pictureDanielle

Current Research on CKD and the Gut Microbiome

This post is part two of Danielle Starmer RD, LDN's talk at the 2024 AL Renal RD conference. For part one, click here!



Last time we talked about general nutrition recommendations for gut health. Let's now dive into the gut microbiome!



What is the Gut Microbiome???

You might have heard about the gut microbiome, but what exactly is it, and how does it affect our health, particularly for those with chronic kidney disease (CKD)? Let's dive in and explore this fascinating aspect of our bodies.

The gut microbiome, often referred to as the "second human genome," consists of all the bacteria, viruses, fungi, archaea, and eukaryotes that live within our bodies, with a significant portion residing in our digestive system. There are roughly 100 trillion microbes representing as many as 5,000 different species in our gut alone, weighing approximately 2 kilograms!!!

The Gut microbiome power point slide

A balanced microbiome is crucial for maintaining good health, as it ensures a healthy diversity of microorganisms with no single bacteria, virus, or fungus dominating. When imbalanced, it can impact the way microorganisms function within our bodies, potentially leading to health problems.


The gut microbiome can be disrupted by factors such as environmental exposures, heavy or long-term antibiotic use, poor dietary habits, excessive stress, and certain illnesses. This disruption, known as dysbiosis, can have severe consequences on our overall well-being, including:

  1. Bacterial infections like H. pylori and C. difficile.

  2. Small intestinal bacterial overgrowth (SIBO).

  3. Inflammatory bowel diseases like ulcerative colitis and Crohn's disease.

  4. General digestive difficulties like diarrhea, constipation, and gas.


For those with CKD, dysbiosis can further complicate matters by increasing the production of uremic toxins, including indoxyl sulfate (IS) and p-cresyl sulfate (PCS), which have been linked to disease progression. PCS is also difficult to remove through dialysis and poses a cardiovascular burden.


Constipation and longer colonic transit time can cause elevated bacterial fermentation of protein, potentially leading to an overgrowth of proteolytic (protein-loving) bacteria in the human colon. This can result in decreased beneficial byproducts of fermentation, known as short-chain fatty acids (SCFAs), which have been shown to slow CKD progression.

Ultimately, an increase in uremic toxins and a decrease in beneficial byproducts can lead to increased gastrointestinal distress for CKD patients. By understanding the importance of maintaining a balanced gut microbiome, healthcare providers can develop targeted treatments to support overall health and improve quality of life for those living with CKD.


Diet significantly impacts the composition of our gut microbiome, particularly in individuals with chronic kidney disease (CKD). A healthy colon microbiota mainly comprises saccharolytic or "carb-loving" bacteria, while proteolytic or "protein-loving" bacteria predominate in those with CKD. Saccharolytic bacteria primarily ferment carbohydrates, producing beneficial short-chain fatty acids (SCFAs) like acetate, butyrate, and propionate. On the other hand, proteolytic bacteria metabolize proteins, generating various end products, some of which have toxic properties.


To reduce the production of harmful metabolites like p-cresyl sulfate and indoxyl sulfate, shifting gut metabolism to favor saccharolytic bacteria is essential. This can be achieved by increasing dietary complex carbohydrates and fibers while decreasing protein intake. Although research on this topic is still emerging, a study has shown that increased dietary fiber intake in hemodialysis (HD) patients resulted in lower free plasma uremic toxin levels.


However, strict protein restriction for CKD and HD patients is not the best solution to diminish uremic toxins, as inadequate dietary protein intake can contribute to malnutrition. Additionally, patients with CKD are often prescribed diets to prevent fluid overload, hyperphosphatemia, and hyperkalemia, limiting their intake of fruits, vegetables, and high-fiber products. This dietary restriction can alter fermentation, favoring a proteolytic profile and increasing unwanted toxic compounds.


Omega-3-rich diets have also been associated with increased SCFA-producing bacteria, emphasizing the importance of consuming foods rich in these essential fatty acids.

Incorporating prebiotics and probiotics can help foster a saccharolytic environment. Research indicates that supplementation with Lactobacillus and Bifidobacteria can improve inflammation, iron status, and intact parathyroid hormone levels, with potential cardiovascular benefits when administered early.


For instance, in one study, Lactobacillus supplementation restored SCFA-producing bacteria, increasing SCFA levels in the gut, circulation, and kidney. Bifidobacterium animalis administration decreased toxin-producing bacteria, serum levels of uremic toxins, creatinine, and urea, while reducing renal fibrosis and glomerulosclerosis.


Prebiotics, or fermentable fibers, also show promising results. One study showed that administration of prebiotics like lactulose or oligofructose-enriched inulin (OF-IN) in healthy humans led to a significant reduction of uremic toxins in urine. Synbiotics, a combination of pre- and probiotics, have also recently gained interest for their potential benefits. Long-term synbiotic administration decreased serum p-cresol levels in non-dialyzed CKD patients according to one study.


In conclusion, fostering a saccharolytic gut environment can positively impact CKD management by reducing toxic metabolites. A well-planned, balanced diet incorporating complex carbohydrates, prebiotics, probiotics, and omega-3-rich foods can help restore microbial balance and promote overall health in CKD patients. As always, consult with your healthcare provider before making any significant dietary changes to ensure the best possible outcomes.




Stay tuned for our next post in the series, where we will talk about complex digestive issues in CKD such as IBS and GERD!


Want to work with Danielle? Schedule a FREE 30-minute discovery call to talk about your goals and find out more here.


Sources for the presentation can be found in the PDF below.



DISCLAIMER: This post is purely informational and is not a substitute for professional medical advice. Please consult your doctor or qualified health care provider with any medical concerns or questions you may have regarding a medical condition or treatment and before undertaking a new health care regimen. Never disregard professional medical advice or delay in seeking it due to information found online.

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