Microbiome modulation as a novel therapeutic approach in chronic kidney disease

Abstract

Purpose of review

Gut dysbiosis has been implicated in the pathogenesis of chronic kidney disease (CKD). Interventions aimed at restoring gut microbiota have emerged as a potential therapeutic option in CKD. This review summarizes the current evidence on gut microbiota-targeted strategies in patients with CKD.

Recent findings

A growing number of studies have shown that plant-based diets, low-protein diets, prebiotic, probiotic, and synbiotic supplementation, and constipation treatment may lead to favorable alterations in the gut microbiota. Current evidence suggests that the implementation of both plant-based and low-protein diets has potential benefits for the primary prevention of CKD, and for slowing CKD progression, with minimal risk of hyperkalemia and/or cachexia. The use of prebiotics, probiotics, and synbiotics and laxatives may have beneficial effects on uremic toxin generation, but their evidence is limited for the prevention and treatment of CKD. Recent advances in diagnostic technologies (e.g., high-throughput sequencing and nanotechnology) could enhance rapid diagnosis, monitoring, and design of effective therapeutic strategies for mitigating gut dysbiosis in CKD.

Summary

Plant-based and low-protein diets, prebiotic, probiotic, and synbiotic supplementation, and constipation treatment represent novel gut microbiota-targeted strategies in the conservative management of CKD, which could improve clinical outcomes in CKD.

INTRODUCTION

The recent explosion of scientific interest in the gut microbiota has dramatically advanced our understanding of its complex pathophysiologic interactions with multiple organs in health and disease. Emerging evidence has revealed that the gut microbiota is significantly altered in patients with chronic kidney disease (CKD) [1], contributing to the pathogenesis of progression of CKD and its complications [e.g., cardiovascular disease (CVD)], often referred to as the ‘gut–kidney’ or ‘gut–kidney–heart’ axes [2,3]. Uncovering these multidirectional interactions have in turn led to a growing interest in the clinical utility of gut microbiota-targeted interventions for the prevention and treatment of CKD [4]. Herein, we provide a narrative review of potential therapeutic strategies targeting gut microbiota modulation in CKD.

SYMBIOTIC INTERACTIONS BETWEEN HOST AND GUT MICROBIOTA

For millions of years, the gut microbiota has coevolved with the human host and their symbiotic interactions provide the host with various benefits [1]. The human gastrointestinal tract harbors more than 100 trillion individual microbes including 2000–4000 species [5–7]. The commensal or symbiotic gut microbiota contains three major domains of microorganisms including bacteria, archaea, and eukarya [7], encoding at least 150-fold more genes than the human genome [8]. In healthy individuals, the gut microbiota is generally dominated by two anaerobic bacterial phyla, Firmicutes and Bacteroidetes, out of over 50 bacterial phyla that also include Actinobacteria, Proteobacteria, Cyanobacteria, and Fusobacteria [9,10].

Under physiologic conditions, the gut microbiota participates in a variety of metabolic activities and thus can be considered as a metabolically active endogenous organ in itself [4]. These complementary metabolic activities include production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate [11], synthesis of certain vitamins (e.g., vitamin K6 and vitamin B group) [12], degradation of undigestible plant polysaccharides and oxalates [13], and biotransformation of conjugated bile acids [14]. In addition, the gut microbiota protects against pathogens by inhibiting their colonization via the production of antibiotics and bacteriocins [15,16], and is also involved in the development, maturation, and maintenance of gastrointestinal motility and in shaping the mucosal immune system and intestinal barrier [16,17]. Changes in the composition and function of the gut microbiota, have been associated with a variety of medical problems and illnesses including obesity [18], hypertension [19], cancers [20], CVD [21], and CKD [2].

GUT DYSBIOSIS IN CHRONIC KIDNEY DISEASE

Emerging evidence has revealed that patients with CKD show significant alterations of the gut microbiota (a.k.a. gut dysbiosis) in specific microbial taxa of both aerobic and anaerobic bacteria [22]. In a study comparing the composition of the gut microbiota between CKD and control rats, Vaziri et al. [1] demonstrated a significant difference in the abundance of 175 bacterial operational taxonomic units (OTUs), which are microbial genomic sequences clustered by sequence similarity, with a notable decrease in Lactobacillaceae and Prevotellaceae families in the CKD animals. Further, they showed a significant difference in the abundance of 190 bacterial OTUs between patients with end-stage renal disease (ESRD) and healthy individuals [1]. Other groups have reported that the number of Enterobacteriaceae (especially Enterobacter, Klebsiella, and Escherichia), Enterococci and Clostridium perfringens were significantly higher in patients with ESRD than in healthy controls [23,24].

One of the contributing factors to the gut dysbiosis in CKD is changes in the biochemical environment due to accumulation of retained metabolic waste products (such as urea) which diffuse into the gut. Bacterial urease of the gut microbiota hydrolyzes urea and produces large quantities of ammonia and ammonium hydroxide, which raises luminal pH and alters gut microbial subpopulations [15,25]. Restricted intake of high-fiber products to avoid hyperkalemia [26] also impacts the gut microbiota. The CKD milieu combined with low-fiber diet shifts the microbiome from a saccharolytic (carbohydrate-fermenting) to a more proteolytic phenotype which generates gut-derived uremic toxins from amino acid catabolism [e.g., indoxyl sulfate, p-cresyl sulfate and trimethylamine-N-oxide (TMAO)] [27]. Other pathways that contribute to gut dysbiosis in CKD include medication use (e.g., phosphate binders, iron, and antibiotics) [28–30], metabolic acidosis [31], and slow intestinal transit time [32]. It is important to note that all of these factors have been suggested to account for the intestinal barrier dysfunction in patients with CKD [33–35], allowing translocation of gut-derived products, such as gut-derived uremic toxins (e.g., indoxyl sulfate, TMAO, etc.), bacterial endotoxins (i.e., lipopolysaccharide) and DNA fragments, and intact bacteria, into the systemic circulation. The translocation of these gut-derived products can contribute to the activation of host inflammatory responses, which have been associated with excess morbidity and mortality in patients with CKD [17,36–38] (Figs. 1 and 2).

FIGURE 1.

Interaction between environment, agent, and host in chronic kidney disease.

FIGURE 2.

Potential pathways linking gut dysbiosis to protein-energy wasting, cardiovascular disease, and chronic kidney disease.

STRATEGIES TARGETING GUT DYSBIOSIS IN CHRONIC KIDNEY DISEASE

Improved understanding of the pathologic roles of gut dysbiosis has triggered enormous interest and vigorous efforts to the development of several therapeutic strategies aimed at re-establishing symbiotic status of the gut microbiota [4]. These include dietary modifications [e.g., plant-based diet and low-protein diet (LPD)] [39■■,40,41], dietary supplementation of prebiotics (i.e., nondigestible food ingredients that induce specific modifications in the composition and/or activity of the gut microbiota) [42], probiotics (i.e., live microorganisms which confer health beneficial effects when administered in adequate amounts to the host) [43], and synbiotics (i.e., both probiotics and prebiotics) [44], and constipation treatment [45■] (Table 1).

Table 1.

Potential clinical benefits from gut microbiota-targeted strategies in chronic kidney disease

Therapeutic strategies	Potential benefits
Plant-based diet	Reductions in inflammatory markers blood urea nitrogen uremic toxins proteinuria
	Improved controls of metabolic acidosis lipid metabolism mineral bone disorders body weight blood pressure bowel habits
	Slowing CKD progression
Low-protein diet	Reductions in inflammatory markers blood urea nitrogen uremic toxins proteinuria
	Improved controls of metabolic acidosis mineral bone disorders blood pressure
	Slowing CKD progression
	Improvement of physical function
Probiotic, prebiotic, and synbiotic supplements	Reductions in inflammatory markers blood urea nitrogen uremic toxins
	Normalization of bowel habits
Constipation treatment	Reduction in uremic toxin X Improvement of gut motility Lowering incidence of hyperkalemia Slowing CKD progression

CKD, chronic kidney disease.

Plant-based diet

Plant-based diets have been used with growing popularity for the treatment of a wide range of lifestyle-related diseases, including diabetes, hypertension, obesity, and CKD [46■]. This dietary pattern focuses primarily on plant products, such as whole grains, seeds, nuts, legumes, fruits, vegetables, tubers and starchy vegetables, while minimizing animal products including meat, fish, eggs and dairy [41] (Fig. 3).

FIGURE 3.

The effects of animal-based and plant-dominant low-protein diets on the gut microbiota and uremic milieu in chronic kidney disease.

Dietary fibers are one of the important sources for intestinal bacterial fermentation [47], and hence have been extensively studied with the aim of modulating gut microbiota [48,49]. Dietary fibers of edible plants comprise of insoluble and soluble carbohydrates (e.g., cellulose, lignin, and nonstarch polysaccharides) and nondigestible oligosaccharides and resistant starch [50]. The nondigestible fiber components pass intact into the large intestine, increase viscosity and bulking of the fecal matter [51], and more importantly undergo fermentation by the resident anaerobic microbiota (mainly by Bacteroidetes and Firmicutes) into intestinal gases and SCFAs that play a vital role in regulating the homeostasis of human body and progression of diseases [11,52,53■]. Specifically, SCFAs serve as important energy resources for colonic epithelial cells and maintain the integrity of the epithelial barrier function by regulating tight junction proteins such as occluding, claudin-1, and Zonula Occludens-1 [54,55]. In addition, SCFAs enhance the modulation of host immune responses and thereby protect the intestinal epithelium [56–58]. In fact, consumption of diet enriched with amylose resistant starch, a fermentable and indigestible complex carbohydrates, have been shown to improve gut microbial dysbiosis, attenuate inflammation and oxidative stress, ameliorate metabolic disorders, and retard progression of kidney disease in CKD rats [59,60].

Other than dietary fibers, fractions of unabsorbed dietary fat reach the large intestine and thus can potentially be substrates that differentially influence the microbial system [61,62]. While Western diets rich in saturated fats and low in antioxidants, phytosterols, and other phytochemicals have been shown to change gut microbiota favoring a proinflammatory state [63], linoleic acid, mainly coming from plant sources, are utilized by different gut microbial species to produce conjugated linoleic acid that has shown anti-inflammatory, antiadipogenic, antidiabetogenic, and anticarcinogenic properties [64]. Another common benefit of plant-based diets is that they could lead to less production of uremic toxins and reduced glomerular hyperfiltration associated with excess protein intake [46■].

From an epidemiological perspective, the beneficial effects of a plant-based diet in CKD have been reported in several observational studies and clinical trials [65–70]. In an observational study of 15 vegetarians and 11 individuals consuming an unrestricted diet, the production rates of p-cresol sulfate and indoxyl sulfate were markedly lower in vegetarians than in individuals consuming an unrestricted diet [71]. Using a prospective cohort of 14 686 middle-aged adults in the Atherosclerosis Risk in Communities study, Kim et al. [67] showed that higher (vs. lower) adherence to a plant-based diet was significantly associated with lower risk of incident CKD and slower estimated glomerular filtration rate decline. In the three seminal trials examining the effects of fruits and vegetables (vs. oral bicarbonate) on metabolic acidosis and kidney outcomes, Goraya et al. demonstrated a favorable effect of these diets on the treatment of metabolic acidosis in CKD, even in its advanced stages, with additional benefits of reducing urine albumin-to-creatinine ratio, weight, and SBP [72–74]. Moreover, plant-based foods have a lower phosphorus content than other food sources, and plant phosphorus which binds to phytate has a lower bioavailability than animal phosphorus [75,76]. In fact, plant-based (vs. meat-based) diets have been associated with lower levels of serum phosphorus and fibroblast growth factor-23 in CKD patients [77]. It is important to note that the concern of hyperkalemia related to a plant-based diet has not been supported by current scientific evidence [46■], presumably due to the enhancement of bowel motility and alkalization induced by plant-based dietary sources [78–81].

Low-protein diet

Low-protein diet, defined as dietary protein intake 0.6–0.8 g/kg/day, has long been considered as an option of conservative management for patients with nondialysis-dependent CKD (NDD-CKD) who wish to avoid or defer dialysis initiation and to retard the progression of CKD [82,83]. While several mechanisms have been suggested for the potential renoprotective benefits of LPD, including lower intraglomerular pressure, alleviation of metabolic acidosis, and lower phosphorus burden [83], the major benefits of LPD potentially attributable to gut microbiota modulation may be through reduced production of uremic toxins, such as p-cresyl sulfate, indoxyl sulfate, and TMAO [27]. p-Cresyl sulfate, for example, is a 188-Da protein-bound solute that originates from sulfation of the intestinally generated p-cresol, which is a colonic fermentation product of the amino acid tyrosine and phenylalanine via deaminase enzymes produced by Bacteroides, Bifidobacterium, Lactobacillus, Enterobacter, and Clostridium genera [84,85]. Indoxyl sulfate, on the other hand, is a protein-bound uremic toxin generated from bacterial tryptophanase, which is expressed by Clostridiaceae, Enterobacteriaceae, and Verrucomicrobiaceae [27,84]. TMAO is a circulating organic compound derived from bacterial metabolism of dietary L-carnitine and choline [86,87]. Importantly, all of these gut-derived uremic toxins have been associated with higher risk of CKD progression, CVD, and mortality [88–91], suggesting that the modulation of gut microbiota towards reduced production of uremic toxins could be a novel therapeutic option for adverse outcomes in CKD.

There are a few studies that support utilizing LPDs as possible gut microbiota-targeted interventions. In an observational study of 30 NDD-CKD patients undergoing LPD for 6 months, Black et al. [92] demonstrated that those who adhere (vs. did not adhere) to the LPD had significantly lower levels of serum p-cresyl sulfate, along with the change in the gut microbiome profile. Similarly, a recent prepost study of 16 CKD patients found that a 6-month intervention with a LPD significantly modified gut microbiota and modulated inflammatory and metabolic parameters [93■]. The study also showed a significant improvement of physical function scores after the LPD intervention [93■]. Other beneficial effects, such as higher serum bicarbonate levels, lower phosphorus levels, lower azotemia, and lower risk of CKD progression associated with the intervention with LPDs, have also been reported in several clinical trials [82].

Since a plant (vs. animal) protein intake has been associated with lower risk of incident CKD [66], the source of protein, as well as its amount, may need to be considered for the implementation of a LPD in patients with CKD. In this context, a plant-dominant LPD (a.k.a. PLADO, defined as a type of LPD with dietary protein intake of 0.6–0.8 g/kg/day with at least 50% plant-based sources) recently proposed by Kalantar-Zadeh et al. [39■■] may be of high biologic value (Fig. 3). In addition, given that coronavirus disease 2019 (COVID-19) susceptibility and severity may be related to gut microbiome [94] and since COVID-19 can cause acute kidney injury including through direct kidney involvement [95] modulating microbiome including by PLADO may have additional favorable impact on both infection control and kidney health. Future studies should examine the effects of PLADO regimens on gut microbiota and on clinical outcomes in CKD.

Supplementation of prebiotics, probiotics, and synbiotics

Prebiotics, probiotics, and synbiotics have become familiar to the public as the components of dietary supplements and bioyogurt, and the administration of these supplements is increasingly recognized as a potential gut microbiota-targeted intervention for CKD patients. In a recent systematic review and meta-analysis of 16 randomized controlled trials investigating the effects of prebiotics, probiotics, and/or synbiotic supplementation (>1 week) in patients with CKD, McFarlane et al. [96] reported that the synbiotic supplementation led to higher abundances of Bifidobacterium and Lachnospiraceae and a decrease in Ruminococcaceae, and that prebiotic supplementation led to a slight but significant reduction in serum urea concentration. Although a few trials demonstrated a favorable change in serum p-cresyl sulfate [97,98], there was a low certainty of evidence to support the overall treatment effect of prebiotic, probiotic, and synbiotic supplementation on uremic toxins, as well as on serum creatinine, blood glucose, total cholesterol, low-density cholesterol, high-density cholesterol, triglyceride, and weight [96]. Currently, there is insufficient evidence to conclude whether one type of nutrition supplementation is superior to another. Future well designed clinical trials are needed to establish the appropriate microbiota-targeted supplementation formulation and to confirm its effectiveness on patient-centered clinical outcomes.

Constipation treatment

Constipation is one of the most common gastrointestinal disorders among patients with CKD, due in part to low fiber and fluid intake, concomitant medications, and multiple comorbidities. Although constipation is usually perceived as a benign condition, recent epidemiological studies have revealed its independent associations with adverse clinical outcomes such as ESRD, CVD, and mortality [99,100]. The adequate management of constipation may therefore be more important than previously considered, and gut microbiota-targeted interventions would be a reasonable option for constipation management in CKD [45■].

The alterations of gut microbiota in patients with constipation has been characterized by a relative decrease in obligate anaerobic bacteria (e.g., Bifidobacterium and Lactobacillus genus) and a parallel increase in potentially pathogenic microorganisms (e.g., Enterobacteriaceae family) [101–103]. A recent study reported that the overall microbial composition of the colonic mucosa was associated with constipation, and constipated patients (in comparison with healthy controls) had a significantly higher abundance of phylum Bacteroidetes in the colon [104]. These alterations of microbiota have been suggested to influence gastrointestinal motility through several mechanisms, such as the release of bacterial end-products, intestinal neuroendocrine factors, and mediators in the gut immune response [105]. For example, the decrease in relative abundance of anaerobic bacteria could result in reduced production of SCFAs that stimulate ileal and colonic smooth muscle contractility and could thereby contribute to constipation [101]. The increase in relative abundance of methanogenic microbes such as archaeae can also cause constipation through increased methane production that reduces gut motility [106].

Nonpharmacological treatment is traditionally considered the first step of a comprehensive management of constipation [107–110]. Although patients with CKD are typically advised to restrict the intake of fiber-rich foods to prevent hyperkalemia, given the lack of evidence supporting this concern and the scientific premise of a plant-based diet (vide supra), the potential health and gastrointestinal benefits of dietary fiber, along with its low cost, may justify consideration of a plant-based, fiber-rich diet as a first step in the management of constipation in CKD. This is also supported by the fact that the gut plays an increasing role in intestinal potassium wasting in CKD and constipation is a likely contributor to hyperkalemia in CKD [45■]. Pharmacological interventions may often be required for secondary (e.g., drug-induced) constipation, which is predominant in CKD patients and is unlikely to respond well to nonpharmacological treatment alone. In fact, the use of laxatives has been shown to increase considerably as patients progressed to ESRD [111]. Among a wide range of pharmacological treatments currently available, a few types of laxative agents, such as lactulose, a chloride channel activator (lubiprostone), and a guanylate cyclase C agonist (linaclotide), have been shown to have unique pharmacological properties for gut microbiota modulation, along with a reduction in circulating levels of uremic toxins [112–115]. Although the issues of high drug costs and long-term safety profiles remain to be addressed, given the close links of gut dysbiosis with both CKD and constipation, the gut microbiota-targeted approach using these drugs seems particularly relevant to the constipation management in patients with CKD.

DEVELOPMENT OF MICROBIOME DIAGNOSTICS

Analyzing the composition of the human gut microbiota has long been dependent on culturing methods, which access only a tiny subset of the broad diversity of microorganisms [116]. With the recent advances of innovative analytical technologies, culture-independent molecular identification of species in the gut microbiota has become the main diagnostics. Among various high-throughput methods, next-generation sequencing technologies have revolutionized our view of microbial communities [117]. The DNA sequencing methodology has allowed us to characterize and analyze microbiomes with greater accuracy and precision and with less bias, compared with culture-based approaches [117]. A common approach used to identify bacterial populations is based on sequencing of the bacterial 16S ribosomal RNA (rRNA) subunit [117]. Hypervariable regions within this gene contain species-specific sequences, which allow identification of the bacteria of origin by comparing with reference databases [118]. Based on the sequences of the internal transcribed spacer region lying between the fungal 18S and 5.8S rRNA genes, fungal populations can also be identified [119]. Increasing throughput and decreasing costs associated with gene sequencing, along with the development of computational tools for resultant sequence data analyses, have made these approaches more feasible to identify and characterize microbial communities in various disease states including CKD [117].

Another emerging and future frontier to influence the gut microbiota manipulation and hence CKD management is nanotechnology. Nanotechnology, or systems/device manufacture at the molecular level, is a multidisciplinary scientific field undergoing explosive development and substantially contributing to molecular diagnostics in current medicine [120]. Recent progress in nanotechnology has been directed toward understanding the microbiomes of humans, as well as animals, plants, and even the ocean and the atmosphere [121]. The great advantage of nanotechnology in studying microbiomes is that the nanoscale is the scale of function in biology, and the application of this technology enables microbial community manipulation, chemical analysis, and imaging [122], potentially leading to rapid diagnosis, monitoring, and design of effective therapeutic actions for conditions linked to gut dysbiosis, such as CKD. For example, noninvasive breath tests, with arrays of nanomaterials, can identify the presence of volatile organic compounds with the signatures of modulated microbiota (e.g., abundance of Prevotella) and hence could lead to quick diagnosis and monitoring of certain conditions in CKD [53■,122,123]. Ingestible sensors could be designed for the detection of a specific type of uremic toxins derived from gut microbiota [124]. Nanotechnology could also efficiently be implemented in designing intelligent drugs or functional foods, with the possibility of localized delivery in the gut [125–127]. Although still at an early stage, there are a few precision antimicrobials that have shown efficacy in model systems of human disease [128,129]. These precision antimicrobials, as well as genetically engineered bacteria, could help restore symbiotic bacterial populations in the gut and reduce levels of gut-derived uremic toxins in patients with CKD [122,130].

CONCLUSION

The gut microbiota is significantly altered in patients with CKD, leading to structural and functional disruption of the intestine and intestinal epithelial barrier. The reduced gastrointestinal motility and increased gut permeability allows translocation of gut-derived uremic toxins and bacterial fragments into the systemic circulation and contributes to adverse clinical outcomes in CKD through activation of inflammatory responses. Strategies aimed at restoring gut microbiota composition are a novel therapeutic option. Although evidence from clinical trials is currently limited, interventions such as plant-based diet, LPD, prebiotic, probiotic, and synbiotic supplementation, and constipation treatment have shown some benefit in terms of attenuating gut microbial alterations and reducing circulating levels of uremic toxins. With the use of emerging technologies, more in-depth clinical trials should examine the impact of gut microbiota-targeted interventions on clinical outcomes in CKD.

KEY POINTS.

• Plant-based diets, low-protein diets, prebiotic, probiotic, and synbiotic supplementation, and constipation treatment can shift the gut microbiota profile towards reduced production of uremic toxins.

• Both plant-based and low-protein diets have potential benefits for primary prevention of CKD, as well as for slowing CKD progression, with minimal risk of hyperkalemia and/or cachexia.

• Currently, limited evidence supports the use of prebiotics, probiotics, and synbiotics and laxatives in the prevention and treatment of CKD.

• New technologies could contribute to rapid diagnosis, monitoring, and design of effective therapeutic strategies targeting gut microbiota in CKD.