Symposium 4.2 – Microbiome in CKD

Symposium Summary

Written by Jasna Trbojevic-Stankovic
All the speakers reviewed and approved the contents

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Personalized targeting of the microbiome

Laetitia Koppe, France

Current research findings have enough evidence to suggest that intestinal microbiota is a new organ system made up of several billion microbial cells with a total weight of over 1kg. This system is important for the regulation of multiple functions, such as the immune system, inflammation, weight regulation, etc. Nevertheless, gut microbes also produce uremic toxins such as p-cresyl sulfate (pCS) and indoxyl sulfate (IS), which are normally excreted by the kidneys. Patients on dialysis with an intact colon exhibit higher plasma levels of these uremic toxins compared to patients with normal renal function. Interestingly, hemodialysis patients who underwent colectomy have levels of these uremic toxins similar to healthy volunteers.

Many studies point to the fact that the modulation of the intestinal microbiota is an appealing target for reducing the production of uremic toxins that can improve CKD outcomes. One study found that Fusobacterium nucleatum and Eggerthella lenta are enriched in CKD patients and strongly correlate with the production of uremic toxins. Authors also demonstrated that CKD rats without intestinal microbiota exposed to these bacteria had greater CKD progression and higher levels of uremic toxins and that the probiotic strain of Bifidobacterium animalis reduced levels of uremic toxins and the severity of the disease.

Figure 1. Characterizing the gut microbiota in CKD

Another reasonable strategy to decrease the production of uremic toxins by the microbiota is dietary modification. For instance, the selective decrease in dietary tyrosine, tryptophan, and phenylalanine intake, which are the precursors of phenols and indoles, decreases pCS and IS levels in CKD mice. These beneficial changes are similar to those found in low protein diets. On the other hand, increased intake of sulphur-containing amino acids (e.g. methionine and cysteine) can regulate indole, ammonia, and urea production by Escherichia coli. This occurs through inhibition of enzyme tryptophanase by S-sulhydration and can decrease IS production and CKD progression. Targeted drug therapies also make sense. One study demonstrated that the use of a specific inhibitor of the bacterial enzyme tyrosine phenol lyase decreases the production of phenols and IS and slows the progression of CKD in mice. Another interesting solution is the use of transgenic bacteria. In one study, the IS production in mice was reduced when researchers replaced the bacteria of the Bacteroides family with genetically modified Bacteroides which do not contain enzyme tryptophanase. Finally, completely or partially replacing the microbiota during CKD is also an interesting therapeutic target. Faecal transplantation in mice proved to be effective in improving dysbiosis and decreasing pCS production.

Finding individualized strategies to reduce the production of uremic toxins is important for improving the health of CKD patients. Exploring the intestinal microbiota is fascinating and opens up new innovative therapeutic targets for CKD.

Microbiota in CKD: how promising are gut-targeted approaches?

Carmela Cosola, Italy

High urea concentration in CKD leads to alterations in the intestinal flora that can increase the production of gut-derived uremic toxins and negatively affect the intestinal epithelial barrier. In ESRD patients, the presence of dysbiotic gut microbiome is characterized by the reduction of short-chain fatty acids production by beneficial bacteria and the abundance of “bad” bacteria as well as urease, uricase, and tryptophanase enzymes. Such a state leads to increased production of gut-derived uremic toxins such as indoxyl sulphate (IS), p-cresyl sulphate (PCS), indole-3 acetic acid (IAA), trimethylamine N-oxide (TMAO), and phenylacetylglutamine. Dietary restrictions and CKD-associated medications (antibiotics, phosphate-binders, iron-containing compounds) further worsen gut microbiota dysbiosis, intestinal permeability, and constipation in these patients. Moreover, the disruption of colonic epithelial tight junctions subsequently leads to translocation of bacteria and endotoxins across the intestinal wall to the systemic circulation, which additionally contributes to uremic toxicity, local and systemic inflammation, progression of CKD, and associated cardiovascular disease.

Figure 2. Intestinal permeability in CKD

Recent studies showed that the addition of butyrate promotes colonic mucin and tight junctions’ proteins expression, strengthens the gut wall, and reduces the intestinal epithelial barrier permeability in CKD rats. Furthermore, very low protein vegan diets (VLPD) increase the number of the main butyrate-producing bacteria families, Lachnospiraceae and Ruminococcaceae, and this is probably correlated with a reduced intestinal permeability in CKD patients, as recently observed by Di Iorio et at. (doi: 10.3390/jcm8091424).

Altered gut microbiota and uremic toxins production can also lead to aggravated constipation in CKD patients, which is associated with the growth of Bacteroidetes phylum and reduction in Bifidobacterium and Lactobacillus phyla. Constipation status and severity are associated with a higher risk of incident CKD and ESRD and with progressive eGFR decline, independent of known risk factors. Circulating uremic toxins accumulate more as the patient becomes constipated. Constipation may also be involved in the pathogenesis of atherosclerosis through lipopolysaccharide/uremic toxins-induced chronic inflammation, contributing to adverse cardiovascular outcomes in the CKD population.

In CKD patients the gut also becomes important in maintaining potassium balance. However, constipation can enhance intestinal potassium absorption and provoke hyperkalaemia. Non-pharmacological measures including fibre, water, good fats intake, and physical activity along with prebiotics and probiotics are recommendable options in reducing constipation in CKD patients. Animals’ studies also proved that laxatives such as lubiprostone, linaclotide, and lactulose can positively modulate gut microbiota, increase expression of intestinal tight junction’s proteins, and reduces uremic toxins and inflammation. Finally, a recent study found that VLPDs are effective in the beneficial modulation of gut microbiota, reducing IS and PCS serum levels, and restoring intestinal permeability in CKD patients.

Exploring functional interactions between microbiota and host

Alessandra Perna, Italy

There are currently many proposed uremic toxins, all of which exhibit characteristic biological and/or biochemical activities. They can be classified according to their molecular weight and their protein-binding ability (i.e. small water-soluble, middle, or protein-bound molecules) or according to their origin (i.e. dietary, mammalian metabolism, or microbial metabolism).

One of the first experimental studies on the interaction between the gut microbiome and kidney function of the mammalian host was the observation that germ-free mice that underwent bilateral nephrectomy lived longer than control mice. Over the years, several uremic toxins derived from microbial metabolism were identified including IS, PCS, and TMAO. It has also been shown that CKD substantially alters intestinal microbial flora causing a reduction of SCFA-generating bacteria such as Bifidobacterium spp and Streptococcus spp, and an increase in aerobic bacteria including Enterobacteriaceae and E.coli. Additionally, more frequent haemodialysis cannot effectively clear protein-bound azotemic uremic toxins derived from the gut microbial metabolism. Likewise, a low protein vegetarian diet can counter-attack the production of uremic toxins and increase their excretion in CKD patients.

Recent findings also suggest that alterations in sulphur metabolism characterized by low hydrogen sulphide (H2S) levels produced by sulfate-reducing and fermentative bacteria and high levels of lanthionine (a novel sulphur-containing uremic toxin) are prominent features in CKD, and are strictly linked to changes in the microbiota composition and function. A recent study demonstrated that H2S is significantly lower in the plasma of haemodialyzed uremic patients than in control subjects. Another study confirmed that plasma H2S runs progressively lower in stages CKD stages, eventually reaching a third of the level found in control subjects. Nevertheless, the CSE gene, one of the most important H2S producing enzymes, is down-regulated in uraemia.

Figure 3. Schematic representation of the metabolic pathways related to H2S production and relevant alterations in uraemia

On the other hand, one in vitro study showed that lanthionine inhibits H2S production. This finding represents the basis for a hypothesized mechanism purporting that lanthionine can induce at least in part the alterations of sulphur compounds seen in CKD patients, supporting the concept that lanthionine is a new uremic toxin. In Zebrafish, for instance, lanthionine can induce heart tissue fibrosis and trigger alterations of regulatory RNA molecules involved in cardiovascular and kidney diseases. However, the exact contribution of the microbiota to lanthionine increase in CKD patients still needs to be elucidated.

Further reading

Aronov PA, Luo FJ, Plummer NS, et al. Colonic contribution to uremic solutes. J Am Soc Nephrol. 2011;22(9):1769-1776. doi:10.1681/ASN.2010121220

Wang X, Yang S, Li S, et al. Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents. Gut. 2020;69(12):2131-2142. doi:10.1136/gutjnl-2019-319766

Lobel L, Cao YG, Fenn K, Glickman JN, Garrett WS. Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function. Science. 2020;369(6510):1518-1524. doi:10.1126/science.abb3763

Barba C, Soulage CO, Caggiano G, Glorieux G, Fouque D, Koppe L. Effects of Fecal Microbiota Transplantation on Composition in Mice with CKD. Toxins (Basel). 2020;12(12):741. Published 2020 Nov 24. doi:10.3390/toxins12120741

Devlin AS, Marcobal A, Dodd D, et al. Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota. Cell Host Microbe. 2016;20(6):709-715. doi:10.1016/j.chom.2016.10.021

Wong J, Piceno YM, DeSantis TZ, Pahl M, Andersen GL, Vaziri ND. Expansion of urease- and uricase-containing, indole- and p-cresol-forming and contraction of short-chain fatty acid-producing intestinal microbiota in ESRD. Am J Nephrol. 2014;39(3):230-237. doi:10.1159/000360010

Rysz J, Franczyk B, Ławiński J, Olszewski R, Ciałkowska-Rysz A, Gluba-Brzózka A. The Impact of CKD on Uremic Toxins and Gut Microbiota. Toxins (Basel). 2021;13(4):252. Published 2021 Mar 31. doi:10.3390/toxins13040252

Ramezani A, Raj DS. The gut microbiome, kidney disease, and targeted interventions. J Am Soc Nephrol. 2014;25(4):657-670. doi:10.1681/ASN.2013080905

Sumida K, Yamagata K, Kovesdy CP. Constipation in CKD. Kidney Int Rep. 2019;5(2):121-134. Published 2019 Nov 13. doi:10.1016/j.ekir.2019.11.002

Di Iorio BR, Rocchetti MT, De Angelis M, et al. Nutritional Therapy Modulates Intestinal Microbiota and Reduces Serum Levels of Total and Free Indoxyl Sulfate and P-Cresyl Sulfate in Chronic Kidney Disease (Medika Study). J Clin Med. 2019;8(9):1424. Published 2019 Sep 10. doi:10.3390/jcm8091424

Einheber A, Carter D. The role of the microbial flora in uremia. I. Survival times of germfree, limited-flora, and conventionalized rats after bilateral nephrectomy and fasting. J Exp Med. 1966;123(2):239-250. doi:10.1084/jem.123.2.239

Davenport A. More frequent hemodialysis does not effectively clear protein-bound azotemic solutes derived from gut microbiome metabolism. Kidney Int. 2017;91(5):1008-1010. doi:10.1016/j.kint.2016.12.036

Lai S, Molfino A, Testorio M, et al. Effect of Low-Protein Diet and Inulin on Microbiota and Clinical Parameters in Patients with Chronic Kidney Disease. Nutrients. 2019;11(12):3006. Published 2019 Dec 9. doi:10.3390/nu11123006

Perna AF, Luciano MG, Ingrosso D, et al. Hydrogen sulphide-generating pathways in haemodialysis patients: a study on relevant metabolites and transcriptional regulation of genes encoding for key enzymes. Nephrol Dial Transplant. 2009;24(12):3756-3763. doi:10.1093/ndt/gfp378

Perna AF, Lanza D, Sepe I, et al. Hydrogen sulfide, a toxic gas with cardiovascular properties in uremia: how harmful is it?. Blood Purif. 2011;31(1-3):102-106. doi:10.1159/000321838

Perna AF, Anishchenko E, Vigorito C, et al. Zebrafish, a Novel Model System to Study Uremic Toxins: The Case for the Sulfur Amino Acid Lanthionine. Int J Mol Sci. 2018;19(5):1323. Published 2018 Apr 29. doi:10.3390/ijms19051323