Gut microbiota refer to those normal microorganisms in the human gastrointestinal (GI) tract, such as Bifidobacteria and Lactobacillus, which can synthesize a variety of vitamins necessary for human growth and development. Totally, there are more than 100 trillion bacterial cells from about 500 distinct species existing in the human GI tract (Arumugam et al., 2011). According to the cell numbers, gut microbiota can be classified as predominant and subdominant microbiota. The dominant microbiota include Firmicutes, Bacteroidetes, Ruminococcus and Bifidobacterium, which usually belong to the original flora, determining the physiological and pathophysiological significance of the host (Sabatino et al., 2015). Although gut microbiota will consume host energy and lead to diseases under certain conditions, gut microbiota do have beneficial effects on the host, which are listed below.

In the pathophysiological state, CKD and CVD patients are prone to gastrointestinal dysfunction and intestinal microecology disorder. In CKD patients, the gut microbial diversity is significantly reduced, and the microbial community is significantly different from healthy people (Nallu et al., 2017; Ren et al., 2020). A significant reduction of Lactobacillus, Bifidobacterium , Bacteroides, Akkermansia, Ruminococcaceae and Prevotella and proliferation of Escherichia coli (E. coli) and Enterococcus were detected in CKD patients, showing the reduction of probiotics and the proliferation of pathogenic bacteria (Table 1).

Lactobacillus is significantly reduced in CKD rats, whose intestinal barrier is impaired (Yoshifuji et al., 2016). Studies have shown that Lactobacillus supplementation ameliorated renal damage and intestinal injury through activation of a Toll-like receptor 2 (TLR2), a putative Lactobacillus receptor in the colon of CKD rats (Yoshifuji et al., 2016). In addition, Lactobacillus exerts a protective effect on CVD, which can alleviate myocardial dysfunction in obese mice with intermittent hypoxia by activating the nuclear factor E2-related factor 2 (Nrf2) pathway (Xu et al., 2019).

Bifidobacterium is a bacterial group that has been found to promote colon health, but its number is also reduced in CKD patients. Recent studies have reported that Bifidobacterium could slow the progression of CKD by increasing the production of microbial metabolites, such as SCFA (Ranganathan et al., 2009; Vaziri et al., 2013a). Another study showed that the probiotic Bifidobacterium animalis decreased the abundance of these species, reduced the levels of toxins and the severity of the disease in rats (Wang et al., 2020a).

The level of Bacteroides is reduced in CKD patients and rats (Yang et al., 2018), and its role in CKD needs further elaboration. However, studies have shown that Bacteroides can prevent CVD by reducing the levels of fecal lipopolysaccharide (LPS) and suppressing the immune response (Yoshida et al., 2020). Studies have revealed that the level of Prevotella is significantly reduced in CKD patients and mice with renal failure, and the restoration of Prevotella in the intestine helps to improve the intestinal environment, thereby inhibiting the progression of CKD and the accumulation of uremic toxins (Mishima et al., 2015; Jiang et al., 2017).

The level of Ruminococcaceae is reduced in CKD as well (Jiang et al., 2017). In fact, it has been found that Ruminococcaceae is negatively related to inflammatory bowel disease, and Ruminococcaceae is considered as the producer of butyrate, which is the preferred source of energy for colonic epithelial cells and plays an important role in maintaining colon health (Nallu et al., 2017). It can also retard CKD and CVD by improving lipids and blood pressure (Ahrens et al., 2021).

On the contrary, the level of Enterococcus is elevated in CKD patients (Jiang et al., 2017), and studies have demonstrated a positive correlation between the level of Enterococcus and the concentration of Trimethylamine N-Oxide (TMAO), which can serve as a potential biomarker of renal or cardiac dysfunction (Tang et al., 2015; Xu et al., 2017; Zeisel and Warrier, 2017; Liu et al., 2019). It has been reported that chronic dietary choline or TMAO directly contributed to progressive renal fibrosis and dysfunction in C57BL/6J mice (Tang et al., 2015). TMAO in the drinking water also aggravated renal inflammation and fibrosis in the high-fat diet/low-dose streptozotocin-induced diabetes rats (Fang et al., 2021). Besides, inhibition of TMAO production by using iodomethylcholine, an inhibitor of gut microbial trimethylamine, significantly attenuated the development of CKD and cardiac hypertrophy in mice (Zhang et al., 2021). These data revealed direct harmful effects of TMAO on both the kidney and heart, although no relationship was observed between serum TMAO concentrations and all-cause mortality or cardiovascular outcomes in ESRD patients requiring hemodialysis or peritoneal dialysis (Zeisel and Warrier, 2017).

E. coli is also significantly elevated in CKD (Devlin et al., 2016), which can convert tryptophan to indole with the catalysis of tryptophanase, and then to indoxyl sulfate, aggravating CKD, CVD and intestinal barrier injury (Jin et al., 2019; Huang et al., 2020b). It was also reported that ESRD patients showed an increase of the number of E. coli, leading to a significant increase of urease, uricase, indole and p-cresol forming enzymes, resulting in increased metabolites (Wong et al., 2014). In addition, Eggerthella lenta and Fusobacterium nucleatum increased the production of uremic toxins and promoted the development of renal disease in a CKD rat model (Wang et al., 2020a). Similarly, metagenomic and metabolomic studies showed a significant difference in the bacterial composition between patients with chronic heart failure and control subjects. The pathophysiological mechanisms of gut microbiota dysbiosis in CKD and CVD patients include reduced intake of dietary fibers, prolonged colonic transit time and increased amounts of protein available for proteolytic bacterial species (Nallu et al., 2017). Similarly, Karlsson et al. (2012) demonstrated that the genus Collinsella was enriched in patients with symptomatic atherosclerosis, while Roseburia and Eubacterium were enriched in healthy controls. Further analysis of the metagenomes revealed that the patients’ gut metagenomes were enriched in genes encoding peptidoglycan synthesis, an inflammatory component in the bacterial cell wall, and depleted in phytoene dehydrogenase, a rate-limiting enzyme involved in the metabolism of lipid-soluble anti-oxidants (Schertzer et al., 2011; Karlsson et al., 2012). These studies clearly showed that the altered microbial metabolism contributes to the pathogenesis of CKD and CVD.

Colon microbes are responsible for the protein fermentation. Ammonia and urea are the products of protein catabolism, which can be converted to urea by ornithine-urea cycle (Ren et al., 2020). In colon, urea is cleaved by bacteria urease into ammonia, which in turn can alter the pH of surrounding environment and induce epithelial cell injury. Although urea is generally considered as a nontoxic retained metabolite, experiments revealed that urea caused a concentration-dependent disruption of intestinal tight junction and barrier function (Vaziri et al., 2013b).

The alpha-NH3 nitrogen (amino acids and intermediates) can be converted into phenols and indoles, which are subsequently metabolized to p-cresyl sulfate (PCS) and indoxyl sulfate (IS) or indole acetic acid (IAA). Under normal conditions, these metabolites are excreted through the kidney, but are accumulated in case of renal insufficiency (Vanholder et al., 2014). PCS and IS are prototype protein-bound uremic toxins, to which many biological and biochemical effects have been attributed (Vanholder et al., 2014). The concentrations of PCS and IS increase concomitantly with the progression of CKD because of their decreased excretion from urine (Vanholder et al., 2014).Besides, the gut microbiota dysbiosis can also result in increased production of PCS and IS. These protein binding toxins are difficult to be removed by ordinary maintenance hemodialysis (Huang et al., 2020b). Recently, a study revealed more than 30 uremic solutes in CKD patients by using high-resolution mass spectrometry, besides PCS and IS (Aronov et al., 2011). These findings suggest that uremic toxins generated from protein fermentation by gut microbiota are much complicated.

A large number of clinical and basic observations, including ours, have confirmed that PCS and IS can damage the cardiovascular system, accelerate the progression of CKD and increase the incidence of cardiovascular events in CKD patients (Vanholder et al., 2014; Yang et al., 2017; Huang et al., 2020b). Experimental studies reveal that PCS and IS can negatively affect endothelial function and repair through several mechanisms including inducing oxidative stress and inflammation.

TMAO is an end-product of choline and carnitine metabolism (Shan et al., 2018). Carnitine is a conditionally essential metabolite that plays a critical role in cell physiology. Of note, carnitine supplementation may be associated with some clinical benefits. Choline and carnitine can be converted to TMA by gut microbiota, and then oxidized in host liver (Bennett et al., 2013; Shan et al., 2018). Like other toxins, TMAO in the circulation is excreted by the kidney, and increases in case of renal insufficiency (Bennett et al., 2013; Aron-Wisnewsky and Clément, 2016). One of the target organs is cardiovascular system, with pathophysiological effects including increasing platelet hyperreactivity and thrombosis potential, enhancing the accumulation of macrophage cholesterol and the development of atherosclerosis (Aron-Wisnewsky and Clément, 2016). In addition, dietary choline or TMAO directly contributed to renal fibrosis and dysfunction (Tang et al., 2015; Fang et al., 2021), while inhibition of TMAO production attenuated CKD development and cardiac hypertrophy in mice (Zeisel and Warrier, 2017; Zhang et al., 2021). Therefore, TMAO is recognized as a biomarker of CVD or renal dysfunction (Zeisel and Warrier, 2017).

Colon is the place where dietary carbohydrates (CHO) are fermented to SCFAs by gut microbes (Lau and Vaziri, 2019). The metabolites of SCFAs mainly include butyrate, propanoate and acetate, and their molar ratio is about 20:20:60. There are two predominant microbes in the colon, Faecalibacterium prausnitzii and Eubacterium rectale, which are responsible for producing SCFAs (Segain et al., 2000; Yang et al., 2018; Lau and Vaziri, 2019). Actually, SCFAs play an important role in maintaining energy homeostasis and gut epithelial integrity (Segain et al., 2000; Yang et al., 2018; Lau and Vaziri, 2019). One of the SCFAs is butyrate, which is a key energy substrate for the colonic epithelial cells (Zhu et al., 2021). Besides, butyrate is also known as an inhibitor of histone deacetylases, which possesses an epigenetic regulation of many genes (Segain et al., 2000; Yang et al., 2018; Lau and Vaziri, 2019). For example, inflammatory pathway was activated in colonic biopsies from patients with Crohn’s disease, but was inhibited by applying butyrate to the specimen, which was evidenced by the reduction of several pro-inflammatory cytokines (Segain et al., 2000). In addition, SCFAs can exert the anti-inflammatory effects through activating certain G protein-coupled receptors (GPRs) (Maslowski et al., 2009; Li et al., 2020). It was reported that SCFAs could increase the protein expression of GPR43, the receptor of SCFAs, in glomerular mesangial cells (GMCs) treated by high glucose and LPS, suggesting that SCFAs-induced signaling pathway might act as a therapeutic target of diabetic nephropathy (DN) (Maslowski et al., 2009; Huang et al., 2017; Li et al., 2020).

The indigestible CHO in the diet is the primary source of substrates for microbes’ fermentation. In CKD patients, CHO availability is reduced due to the dietary restrictions of potassium intake. Consistently, ESRD patients exhibited significant contraction of bacterial families possessing butyrate-forming enzymes compared with healthy subjects (Wong et al., 2014).

Advanced glycation end products (AGEs) are a group of proteins, lipids or nucleic acids that are glycated and oxidized after contact with reducing sugars or short-chain aldehydes (Deluyker et al., 2017). AGEs can be ingested with high temperature processed foods, but also endogenously formed as a consequence of a high dietary sugar intake (Aragno and Mastrocola, 2017; Snelson and Coughlan, 2019; Zhang et al., 2020). It has been reported that excessive sugar consumption, particularly fructose, contributes to endogenous AGEs formation, which are associated with carotid thickening, ischemic heart disease, CKD and uremic cardiomyopathy (Inagi, 2014; Aragno and Mastrocola, 2017; Gill et al., 2019). Following gastrointestinal digestion, the absorption of dietary AGEs is primarily in the forms of free-AGEs and peptide-bound AGEs (Zhang et al., 2020). Free AGEs can be absorbed by simple diffusion, while peptide-bound AGEs may be transported into intestinal cells through an intestinal peptide transporter (PEPT), PEPT1, followed by a proteolytic process into their free counterparts (Snelson and Coughlan, 2019; Zhang et al., 2020). Of note, many dietary AGEs with high molecular weight are neither absorbed in the intestine nor excreted in the feces or urine, instead, they pass through to the colon, where they may be degraded and metabolized by the colonic microbiome, although the precise mechanism remains elusive (Alamir et al., 2013; Snelson and Coughlan, 2019; Zhang et al., 2020). Recent studies observed a contraction in Lactobacilli both in humans and rats following a high-AGEs diet (Seiquer et al., 2014; Zhang et al., 2020). Besides, a high-AGEs diet is associated with increased intestinal permeability, decreased microbial diversity and reduced SCFAs (Snelson and Coughlan, 2019). Emerging researches have demonstrated that AGEs contribute to the development of cardiac dysfunction and renal failure mainly through cross-linking of proteins or binding to their cell surface receptor, the receptor for advanced glycation end products (RAGE), independent of diabetes (Willemsen et al., 2012; Deluyker et al., 2017). Further studies are required to elucidate the complicated network of the absorption, distribution, biotransformation and excretion of AGEs.

As renal function gradually decreases, CKD frequently damages multiple systems, including intestinal, cardiovascular and endocrine systems, among which CVD is the most common complication and the leading cause of death (over 50%), while intestinal dysfunction is also a common complication and initial symptom of CKD in many cases (Mishima et al., 2015; Schefold et al., 2016; Tuegel and Bansal, 2017; Webster et al., 2017; Huang et al., 2020a). Although we and others have confirmed the important role of the gut-kidney axis and the heart-kidney axis, few researchers have studied the gut, kidney, and heart as a whole (Huang et al., 2020a; Huang et al., 2020b). In fact, the renal, intestinal and cardiovascular systems in CKD are closely related: renal dysfunction will lead to the accumulation of numerous uremic toxins in the body, resulting in intestinal and cardiac damage; in return, intestinal dysfunction can lead to intestinal barrier destruction and microbial imbalance, promoting the production of uremic toxins and further aggravating systemic inflammation, which is also a significant inducer of renal and cardiovascular injury (Huang et al., 2020a; Huang et al., 2020b). These findings suggest that the gut, kidney and heart could interact with each other as a whole. Thus we proposed the concept of the “gut-kidney-heart” axis, whose dysfunction would lead to a vicious circle, contributing to the progression of CKD and its complications (Figure 1). However, the relevant pathogenic mechanism remains unclear, and the intervention methods need to be explored urgently.

Traditional risk factors of CVD and intestinal dysfunction also exist in CKD patients, which can hardly explain such high prevalence of the complicated diseases (Huang et al., 2020a; Huang et al., 2020b). Therefore, we focus on the effect of the gut and kidney-specific risk factors, uremic toxins and their intestinal microbiota (discussed in the part of Pathophysiological Effects of Gut Microbiota listed in Table 1 and Table 3).

Dietary intervention serves as the first-line treatment for CKD, due to its role in improving CKD outcomes and preventing or delaying dialysis initiation (Kalantar-Zadeh et al., 2020; Lobel et al., 2020). Modifying dietary protein intake has been identified as a clinical strategy in the management of CKD patients for decades (Lobel et al., 2020). Many diet-microbiome studies have focused on the effects of dietary fiber, protein and phosphates (Conlon and Bird, 2014; Kalantar-Zadeh et al., 2020; Lobel et al., 2020).

Probiotics are defined as “living microorganisms” composed of live bacteria, such as Bifidobacteria, Lactobacillus and Streptococci (Rastall et al., 2005). In CKD patients, oral treatment with Streptococcus thermophilus, Lactobacillus acidophilus and Bifidobacterium longum can slow the progression of kidney disease (Ranganathan et al., 2009; Ranganathan et al., 2010). Oral Lactobacillus acidophilus for hemodialysis patients significantly reduced serum dimethylamine, a potential uremic toxin (Yoshifuji et al., 2016). In another study, treatment with Lactobacillus acidophilus ATCC-4356 reduced the burden of atherosclerosis in apolipoprotein e (ApoE)^−/− mice (Chen et al., 2013). In uremic patients undergoing hemodialysis, oral antibiotic-resistant lactic acid bacteria preparations, Lebenin, can normalize the composition of the intestinal microbiota and inhibit the accumulation of uremic toxins, including phenol, p-cresol and indicant (Sabatino et al., 2015). The beneficial effect of Lactobacillus may be the result of the influence of this bacterium on the permeability and immune status of the intestinal epithelium.

A recent study demonstrated that oral probiotic Lactobacillus casei (L. casei Zhang) corrected intestinal microbial imbalance, alleviated kidney damage, and delayed the progression to CKD through increasing the levels of SCFA and nicotinamide in mice (Zhu et al., 2021). In patients with stage 3–5 CKD, oral administration of L. casei Zhang also slowed down the decline of renal function (Zhu et al., 2021). Various approaches based on the use of probiotics, prebiotics and synbiotics can adjust the intestinal microbiota and intestinal barrier structure/function, thereby alleviating CKD and its complications: CVD and intestinal dysfunction (Sabatino et al., 2015; Cuevas et al., 2017).

Prebiotics are non-digestible food ingredients that have beneficial effects by selectively stimulating the growth or activity of bacteria in the colon. Common prebiotics contains inulin, fructooligosaccharides, galactooligosaccharides, soybean oligosaccharides, xylo-oligosaccharides and pyrodextrins (Sabatino et al., 2015). Evidence showed that prebiotic oligofructose-enriched inulin (p-inulin) could promote the growth of bifidobacteria species, inhibit inflammation and improve metabolic function (Cani et al., 2007). Another report found that oral intake of p-inulin reduced the serum concentrations of PCS and IS in hemodialysis patients (Meijers et al., 2010). A number of clinical trials and experimental studies on CKD have also shown that taking prebiotics, probiotics and synbiotics can reduce uremic toxins and inflammatory mediators, as well as improving colonic epithelial tight junctions (Vaziri et al., 2014; Ramezani et al., 2016).

A diet with high levels of resistant starch, a prebiotic, is beneficial to change the characteristics of the gut microbiota and cecum, serum and urine metabolites, such as IS, in adenine-induced CKD rats (Kieffer et al., 2016). In addition, high dietary fiber intake is associated with a low risk of inflammation and mortality in CKD patients (Krishnamurthy et al., 2012).

It was reported that S-sulfhydration or mutation of E. coli TnaA reduced its activity as measured by indole production from tryptophan both in vitro and in bacterial cultures, thus alleviating serum indoxyl sulfate levels and kidney injury (Lobel et al., 2020). In addition, another study identified a widely distributed family of TnaA in the gut commensal Bacteroides and found that deleting TnaA eliminates the production of indole in vitro (Devlin et al., 2016). Further altering the status or abundance of the Bacteroides TnaA also modulated IS levels in vivo (Devlin et al., 2016). These results suggest a new strategy for treating CKD by genetically modulating the microbiome and the downstream products.

Fecal microbiota transplantation (FMT) is an emerging therapy involving the transfer of stool from healthy donors into the GI tract of diseased recipients (Mamic et al., 2021). FMT has already been approved for administration in the treatment of recurrent Clostridium difficile infection (McDonald et al., 2018), which is the only application reported so far. It has also been highlighted that FMT could restore the dysbiosis to promote host homeostasis, including the control of intestinal inflammation through secreting IL-10 (Cammarota et al., 2017; Burrello et al., 2018).

Recently, several studies demonstrated that the implantation of fecal microbiota from CKD patients into renal injured germ-free mice or antibiotic-treated rats could induce higher production of uremic toxins, renal fibrosis and oxidative stress (Kelly, 2013; Kootte et al., 2017). Transplantation of stool samples obtained from donor AKI mice also aggravated the kidney injury in ischemia-reperfusion (I/R)-induced AKI mice (Zhu et al., 2021). Reversely, FMT treatment from healthy mice significantly improved gut microbiota disturbance and decreased PCS accumulation in CKD mice (Caggiano et al., 2020).

Further studies, especially clinical trials, are required to investigate the feces amount, the timing and the efficiency of FMT, which may serve as a therapeutic option in CKD patients. Of note, strict and comprehensive donor screening protocols remain essential to avoid adverse infectious events, since two immunocompromised FMT recipients suffered from E. coli bacteremia originating from the gut microbiota of the donor in two independent clinical trials (DeFilipp et al., 2019). Further identification of the benefits and risks of FMT across different populations are also indispensable. Despite these challenges addressed above, FMT may still be a feasible option in the future.

Recent studies suggested that removing the gut microbiota with oral antibiotics, vancomycin, can significantly decrease the plasma concentration of two gut-derived uremic solutes, IS and PCS, in ESRD patients (Nazzal et al., 2017). Antibiotic administration also improved kidney I/R injury by preventing inflammatory response (Furusawa et al., 2013).

However, the I/R-induce AKI and CKD models in germ-free mice showed more severe renal damage than in mice with commensal intestinal microbiota (Jang et al., 2009; Mishima et al., 2017), making the conclusions contradictory. Of note, the administration of large-spectrum antibiotics is not recommended as a long-term therapy because of disturbing intestinal microbiota (Knoop et al., 2016) and enriching antibiotic-resistant bacteria (Baym et al., 2016). Therefore, further studies and clinical trials are required to explore the efficacy of antibiotics in patients.

Lubiprostone is a synthetic derivative of prostaglandin activating chloride channel, frequently used in the treatment of constipation. In a rat model of CKD, oral administration of lubiprostone decreased the plasma level of microbiome-derived uremic toxins, such as IS and hippurate, and attenuated tubulointerstitial damage, renal fibrosis and inflammation probably through restoring Lactobacillaceae family and Prevotella genus (Mishima et al., 2015).

Accumulated studies demonstrated the microbiota-modulating effects of antidiabetic drugs. Metformin could increase Lactobacillus and Akkermansia in diabetic mice and patients, which can also improve atherosclerosis and gut barrier integrity (Lee and Ko, 2014; Li et al., 2016; de La Cuesta-Zuluaga et al., 2017; Caggiano et al., 2020).

The α-glucosidase inhibitors, such as acarbose, increased the relative abundances of Lactobacillus and Bifidobacterium and depleted Bacteroides, thereby regulating the relative abundance of microbial genes involved in bile acid metabolism in type 2 diabetes (T2D) patients (Gu et al., 2017).

In fact, multiple studies revealed an increased ratio of Firmicutes/Bacteroidetes (F/B) in diabetes (Caggiano et al., 2020). It has been demonstrated that sodium glucose cotransporter 2 inhibitors (SGLT2i) could reduce uremic toxins, improve vascular dysfunction and modulate the gut microbiota, including the decrease of F/B ratio and the increase of colonic SCFAs-forming bacteria, in diabetic mouse models (Lee et al., 2018; Mishima et al., 2018; Caggiano et al., 2020). Though contradicting with other studies, it cannot be ignored that Shenyan Kangfu tablet (SYKFT), a prescription of traditional Chinese medicine for treating CKD, was reported to enhance the relative abundance of Firmicutes and reduce Bacteroidetes in diabetic mice with diabetic kidney disease (Chen et al., 2021). In-depth experiments are indispensable to distinct the accompanying phenomena or causal efficacy between microbiota and conventional drugs-induced effects (Magne et al., 2020).

Very recently, increasing evidences showed the beneficial effects of traditional Chinese medicine (TCM) in CKD treatment through modulating microbiota. Jian-Pi-Yi-Shen (JPYS) decoction not only improved renal function but also restored the blood reticulocyte counting and serum calcium level possibly through modulating Corynebacterium, Coprococcus, and Clostridium_XIVb, which may serve as candidate microbiome targets for further studies on their roles in medicating the drug efficacy of TCM in 5/6 nephrectomized CKD rats (Zheng et al., 2020). Qing-Re-Xiao-Zheng formula protected the renal function via regulating gut microbiota dysbiosis, reducing the levels of gut-derived LPS and inhibiting inflammatory responses in rats with diabetic kidney disease (DKD) (Gao et al., 2021). Another report demonstrated that herbal formula granule prescription Mahuang decoction ameliorated kidney functional and structural impairment in CKD rats, which were associated with the restoration of the impaired richness and diversity of intestinal microflora and the disrupted microbial community (Ming et al., 2021). However, further mechanism studies and intervention experiments, such as FMT and germ-free mice, are still in urgent need to prove the role of gut microbiota in TCM-mediated effects.

The emergence of high-throughput bacterial DNA sequencing techniques, including 16S ribosomal DNA (rDNA) microbial profiling and shotgun metagenomics, has facilitated better understanding of human gut microbiota composition and illumination of their pathophysiological roles in human diseases (Ventura et al., 2009; Marchesi et al., 2016; Ticinesi et al., 2018). It has been demonstrated that whole genome shotgun sequencing has multiple advantages compared with the 16S amplicon method, including deeper characterization of the microbial complexity, enhanced detection of bacterial species, increased detection of diversity, identification of more taxa and increased prediction of genes (Ranjan et al., 2016; Laudadio et al., 2018; Liu Y. et al., 2020). Several studies combined 16S and metagenomic sequencing to analyze the gut microbiota composition and function of stone formers to gain a more comprehensive understanding of the changes in the gut-kidney axis in kidney stones (Ranjan et al., 2016; Ticinesi et al., 2018; Liu Y. et al., 2020). Further, the 16S rDNA sequencing or shotgun metagenomic data in combined with the profiles of transcriptome, proteomics and metabolomics of gut microbial community, may contribute to novel therapeutic targets against the diseases of the host.