Happy gut, happy kidneys? Restoration of gut microbiome ameliorates acute and chronic kidney disease

Abstract

In a new study, Zhu et al. (2021) show that mitigating dysbiosis by the probiotic L. casei Zhang reduces kidney inflammation via restoring short-chain fatty acid-producing gut microbiome and nicotinamide metabolism. These findings shed light on the underlying mechanisms of probiotics in treating human kidney diseases.

Dysregulation of the gut microbiota, also known as dysbiosis, has been increasingly recognized as an important pathophysiology in different organs, including the kidneys. The abundance of resident immune cells in the gut provides a logical and physiological link between the socalled gut-and-kidney axis, supported by evidence such as IgA nephropathy. Emerging data in murine models further suggest the aberrancy of gut microbiota-derived metabolites could affect the outcomes of acute kidney injury (AKI) and, in part, explain the presence of circulating uremic toxins in chronic kidney disease (CKD) (Knauf et al., 2019). These findings have led to several clinical trials using probiotics in patients with CKD with promising results, conceptualized by their potential benefits of correcting dysbiosis (Koppe et al., 2015). Yet exactly how probiotics restore kidney health remains poorly understood, and in particular, how the gut-and-kidney axis potentially facilitates the AKI-to-CKD transition is unclear. In this issue of Cell Metabolism, Zhu et al. (2021) demonstrate renoprotective effects of the probiotic Lactobacillus casei Zhang (L. casei Zhang) in AKI and CKD progression and revealed an important metabolic switch to prevent overt inflammation after kidney injury (Figure 1).

Figure 1.

Schematic of the kidney-and-gut axis mediating maladaptive kidney repair to kidney fibrosis

Based on its known anti-inflammatory properties, Zhu et al. focused on L. casei Zhang (Lac.z) and the commonly used probiotic supplement L. acidophilus (Lact) and their effects on AKI and kidney fibrosis outcomes. First, the authors used both surgical and chemical-induced AKI and CKD to avoid possible variances of the renal outcome among different models. Based on histology and function, they showed that Lac.z treatment resulted in a consistently better renoprotective profile compared to Lact or to no treatment across the models. Then, in order to prove the link between gut microbiota and kidney outcomes, they analyzed the stool samples collected from mice treated by Lac.z and demonstrated improved intestinal homeostasis with a higher percentage of Bacteroidetes population closer to the sham animals and greater abundance of short-chain fatty acid (SCFA)-producing bacteria after ischemia-reperfusion (IR) injury. They used occludin expression level by immunofluorescence and RT-PCR as a surrogate to prove that Lac.z treatment preserved intestinal physical barrier, another essential player to maintain gut microbiota integrity. Intriguingly, similar effects of Lac.z were reproduced after depleting the original intestinal microbiome by broad-spectrum antibiotics administration followed by probiotics treatment or fecal microbiota transplants prior to IR injury. The authors then concluded that renoprotection by Lac.z treatment might not be limited to modulation of gut microbiome but also have direct effects on kidney resident cells.

Mechanistically, these data were somewhat consistent with the prior findings and the general concept in the field that the presence of SCFA-producing bacteria is crucial in maintaining kidney homeostasis and can be restored by Lac.z treatment after kidney injury (Gong et al., 2019). Zhu et al. took a further step using UHPLC-MRM-MS/MS technique to analyze the kidney metabolites and found that mice treated with Lac.z after IR injury at day 5 had higher nicotinamide metabolism. Nicotinamide adenine dinucleotide (NAD⁺) is an essential molecule in mitochondrial fatty acid b-oxidation and ATP production, which proximal renal tubules heavily depend on. Augmentation of NAD⁺ metabolism by supplementing the mice with the NAD precursor niacinamide was shown to ameliorate AKI in murine models (Tran et al., 2016), although the subsequent clinical trial (NCT03176628) did not demonstrate significant clinical improvement (Simic et al., 2020). Nevertheless, exactly how Lac.z affects nicotinamide metabolism in the kidneys (presumably mediated by kidney tubules) and whether this was independent of the gut microbiome remains unclear based on these data.

Next, Zhu et al. performed a single-cell analysis to decipher the intrarenal responses to Lac.z treatment. They demonstrated that in Lac.z-treated mice, most subclusters of macrophages were diminished at day 5 of IR injury, suggesting the renoprotective effects of Lac.z might be mediated by the reduction of the macrophage infiltrate. In addition, expression of profibrotic and proinflammatory genes was reduced in Lac.z-treated mice in each cell subtype, and the differences remained significant depending on the expression of either an SCFA receptor (GPR43) or two SCFA-related transporters (Slc5a8 and Slc18a1) at the RNA level. Lastly, Zhu et al. conducted a placebo-controlled study of oral Lac.z use in patients with stage 3–5 CKD. After 3 months of treatment, the authors noted a diminished decline of kidney function based on serum cystatin C and creatinine level at 3- and 12-month follow-ups, respectively, suggesting potential therapeutic effects on CKD progression.

These data indeed shed more light on how probiotics can improve outcomes of AKI and CKD, supported by functional readouts and histological analysis in murine models and clinical parameters of a human clinical trial. However, several questions remain to be answered. First, T cells, such as regulatory T cells and CD4⁺ T cells, are pivotal to regulate local immunological responses in the gut and subsequent phenotypic changes of macrophage (Gong et al., 2019), so was the reduced kidney inflammation mediated by T cells after Lac.z treatment? Second, the degree of macrophage infiltrate is known to correlate with tubular damage in AKI (Zuk and Bonventre, 2016), and the authors noted that there were fewer of most of the macrophage subclusters (excepted for Mø 3, the smallest population among the four) in the Lac.z group at IR injury day 5. Was this phenotype mostly driven by reduced tubular damage followed by less macrophage infiltration? More importantly, depletion of macrophages has been clearly shown to exacerbate maladaptive repair with increased fibrosis by liposomal clodronate and CD11b-DTR studies (Zhang et al., 2012). The authors only demonstrated the immunophenotype (determined by single-cell analysis instead of more functional studies) and the Ccr2^−/− mice data at day 5. Therefore, future studies would be warranted to demonstrate the dynamic changes, especially at the later time points, of immunophenotypes with functional studies, given that macrophage classification based purely on surface markers might conflict from study to study. As the authors rightfully pointed out, the expression of SCFA receptors is heterogeneous, and therefore using tubular or monocyte-specific knockout mice would be helpful to answer this question. Lastly, although the safety profile of Lac.z use in humans appeared to be promising in the present study, most commonly used clinical parameters such as blood urea nitrogen (BUN) and creatinine could be largely affected by probiotics use itself (Lempert, 2019). The differences in urine albumin-to-creatinine ratio and parathyroid hormone were intriguing, but they might reflect pathophysiology aside from tubular pathobiology and kidney inflammation.

The clinical application of modulating the gut-kidney axis in treating kidney diseases is supported by another recent report on the association between processed food intake and kidney inflammation (Snelson et al., 2021). Thus, probiotics remain an attractive approach and will need larger double-blinded clinical trials to pave their way to success.