Intestinal Microbiota in Experimental Acute Kidney Injury Free

Acute kidney injury (AKI) is a complex process with many key pathophysiologic processes including inflammation, cell death pathways, reactive oxygen damage, epigenetic changes, and various other mechanisms [1]. In addition, considerable advances have been made in demonstrating the important role of crosstalk between the kidney and distant organs during AKI [2]. While earlier studies demonstrated important communication between the kidney with the lung, heart, and brain, more recent data have revealed novel, unexpected relationships between the gut microbiome and kidney during AKI. This paper briefly summarizes the data on this topic.

Trillions of bacterial microbes reside in the human gut and constitute the gut bacterial microbiota, predominantly compromised by phyla Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. A healthy gut microbiota composition plays a vital role in maintaining intestinal homeostasis and immune system function. An imbalance in the gut microbiota (gut dysbiosis) has been associated with disruption in the intestinal mucosal barrier and activation of immune system-mediated inflammation in various diseases including kidney diseases. Various experimental studies that influence the gut microbiota in ischemic or cisplatin (CP)-induced AKI are detailed below and summarized in Table 1.

The kidney has abundant immune cells. To determine the role of bacteria in generating and maintaining kidney immune cells, experiments were conducted in germ-free (GF) mice by inducing AKI with renal pedicle clamping resulting in ischemic-reperfusion injury (IRI). These studies led to the unexpected findings that GF mice also had abundant immune cells, more NKT cells, and lower IL-4 levels than control mice. Ischemic AKI led to worse tubular injury and functional decline in GF mice compared to ischemia in controls, and the increased susceptibility to injury was normalized after conventionalizing GF mice with feces from normal mice bacteria [3]. Gut microbiota-mediated effects during AKI could be due to properties of SCFAs such as acetate and butyrate that are produced by fermentation end products of certain intestinal microbiota. Acetate supplementation as well as acetate-producing microbiota such as Bifidobacterium adolescentis or Bifidobacterium longum were shown to reduce CD11b⁺ and F4/80⁺ immune cells and improve renal dysfunction and tubular injury after IRI [4]. Possible mechanisms of SCFA actions include activation of G-protein receptors (such as GPR41, GPR43, Olfr78, and GPR109a), histone deacetylase inhibition that alters chromatin remodeling, and preventing decrease in methylation.

In another study on GF mice, renal tubular injury and renal function were worse with lower recovery rates compared with normal mice. Fecal transplant from normal mice attenuated the injury, suggesting renoprotective role of microbiota against ischemic damage. 16S rRNA gene sequencing of mouse feces on days 0, 2, and 10 demonstrated higher microbial diversity with increased abundance of Lactobacillus, Clostridium, and Ruminococcus and decreased abundance of Bifidobacterium and TM7 microbiota at genus level in the IRI group compared to sham surgery [5]. D-serine was increased in feces, plasma as well as kidneys of IRI mice. D-serine administration reduced tubular injury and was hypothesized to work by attenuating F4/80⁺ cells and promoting hypoxia-mediated proliferation of tubular epithelial cells [5].

Antibiotics are a clinically translatable approach to modifying gut bacteria during AKI. An AKI prevention antibiotic cocktail of neomycin, metronidazole, ampicillin, and vancomycin decreased injury after IRI [6]. Fecal transplantation of normal mice gut bacteria into GF mice was previously shown to reduce renal injury. However, a study examining GF mice colonized by gut microbiota obtained from standard mice post-AKI led to more severe renal injury [7]. Depletion of gut microbiota with antibiotic combination (neomycin, metronidazole, ampicillin, and vancomycin) conferred renal protection which was associated with reduction in Th17 and Th1 responses along with expansion of regulatory T cells and M2 macrophages. This study provided additional evidence for a bidirectional relationship between AKI and gut dysbiosis mediated via T cells. 16S sequencing of gut microbiota showed a relative increase in Escherichia and Enterobacter and decrease in Lactobacillus, Ruminococcaceae, Faecalibacterium, and Lachnospiraceae in the IRI compared to control group. This was associated with lower SCFA and higher endotoxins levels in the IRI group.

A study simultaneously correlating plasma metabolites with gut microbiota and renal function 48 h after IRI found an increase in 31 acetylcarnitines and decrease in 3 amino acids (tyrosine, tryptophan, and proline) [8]. Gut microbiota Rothia and Staphylococcus species were positively correlated with rise in serum creatinine, while Prevotella copri, Faecalibacterium prausnitzii, and Coprococcus eutactus were inversely correlated. This suggests that certain gut microbiota may aggravate, while others may ameliorate AKI. In another study, antibiotic-induced gut microbiota depletion using a cocktail of ampicillin, vancomycin, and levofloxacin was associated with reduced concentration of SCFA, renal glucose, and pyruvate levels with more severe tubular injury after IRI [9]. Gut microbiota depletion was hypothesized to increase the vulnerability of kidneys to IRI by possible renal gluconeogenesis-mediated pyruvate depletion. The effect of oral Lactobacillus casei administration prior to IRI was also recently studied. Treated mice had less renal damage and better renal function when compared with control mice [10]. A higher proportion of phylum Bacteroidetes and SCFA-producing bacteria such as genera Alloprevotella and NK3B31 from family Prevotellaceae were observed in L. casei-administered mice. Simultaneous decrease in macrophage stimulation such as F4/80+ and chemokines CCR2 and CX3CR1 in L. casei-administered mice suggested it may have been protected by immune regulation of macrophages.

Similar beneficial effects of SCFA-producing bacteria have been observed in CP-induced AKI in two separate studies. One study supplemented Lactobacillus salivarius BP121 in CP-induced AKI in rats and noted prevention of AKI associated with decrease in inflammation, oxidative stress, and uremic toxins such as indoxyl sulfate and p-cresol sulfate [11]. There was an increase in Lactobacillus species and SCFA concentration in feces associated with reduction in tight junction protein damage suggesting that the anti-inflammatory effect of this bacteria was mediated by reducing intestinal permeability. Another study supplemented Lactobacillus reuteri and Clostridium butyricum in CP-treated rats and observed a significant decrease in blood endotoxin and uremic toxin indoxyl sulfate levels which was also associated with decrease in renal inflammation and injury [12]. Gut microbiota changes at genus level were significant for increase in Bifidobacterium, Ruminococcaceae, Ruminiclostridium_9, and Oscillibacter and decrease in Escherichia Shigella genera. The findings from these studies indicated that inflammation and renal injury in CP-induced AKI are mediated by gut dysbiosis which is alleviated by butyrate (SCFA)-producing bacteria such as L. Salivarius, L. reuteri, and C. butyricum.

A key component in studies modifying the gut microbiome during AKI is to accurately measure the bacteria in the gut. Given that ischemic AKI could have different effects on the stool microbiome from nephrotoxic AKI, this was evaluated in a mouse model (Fig. 1) [13]. Ischemic AKI at 72 h led to significant changes in families Erysipelotrichaceae, Lachnospiraceae, Porphyromonadaceae, and Ruminococcaceae. At the genus level, significant changes were observed in Oscillibacter, Eisenbergiella, and Barnesiella genera. In contrast, CP-induced AKI led to significant changes in families Lachnospiraceae, Lactobacillaceae, Porphyromonadaceae, and Ruminococcaceae and genera Oscillibacter, Lactobacillus, Clostridium, and Barnesiella. On further analysis, a significant increase in the proportion of Erysipelotrichaceae incertae sedis was observed in both IRI (p = 0.03) and CP (p = 0.007) groups at 72 h post renal injury when compared to baseline. Conversely, the proportion of Lactobacillus decreased significantly (p = 0.02) in the CP treatment group at 72 h post renal injury when compared to baseline.

In summary, gut microbiota play an important role in mediating experimental AKI. Current evidence supports a beneficial effect of certain SCFA- and D-serine-producing bacteria in reducing kidney damage and enhancing recovery after ischemic AKI. Given the novelty of this field of research with limited studies and variations in methodology of testing, future studies using consistent testing methods are needed. Measuring precise changes in individual gut microbiota with specific antibiotic and probiotic interventions and mechanistic studies on SCFA and inflammatory cells/molecules is required.

The studies summarized above demonstrate a direct pathophysiologic role of gut microbiota in AKI. The different courses of AKI found in GF mice studies corrected by fecal transplants, as well as interventions modifying AKI in conventional rodents have demonstrated a key role of microbiome in AKI using complementary approaches. A key question in the field of microbiome and AKI is which antibiotic combination is optimal for prevention and which can accelerate the repair of AKI. Other approaches such as probiotics, prebiotics, modified SCFAs and other creative solutions could be used. In addition, there are other microbiome sources besides the gut, such as skin, nares, and even blood and urine that have not been studied in AKI. Finally, human studies on microbiome and AKI are needed to evaluate if similar changes are going on as in experimental models, and the best ways to intervene to improve AKI outcomes.

Review article, not applicable.

The authors have no conflicts of interest to declare.

None.

Neal Shah performed literature review and drafted the manuscript. Hamid Rabb edited and finalized the manuscript.

All data generated or analyzed during this study are included in this article. Further inquiries can be directed to the corresponding author.