Multi-site microbiota alteration is a hallmark of kidney stone formation

The Role of the Gut Microbiome in Kidney Stone Disease

Microbiome dysbiosis is closely related to the etiology of kidney stone disease (KSD) and influences a multitude of pathways. Due to our knowledge gaps on this topic, it is still unclear if microbiome interventions can be translated to demonstrate clinical efficacy. Current evidence suggests that the enhancement of butyrate-producing pathways should be the next step for KSD research. While we are not yet at a point where we can make clinical recommendations for KSD, there are many simple dietary or supplement-based approaches that could be applied in the future for prophylaxis or treatment of KSD.

Unraveling the association of bacteria and urinary stones in patients with urolithiasis: an update review article

Urinary stone disease (USD) is a prevalent urological condition, ranking as one of the most common urinary tract disorders globally. Various risk factors influence the formation of kidney stones, and recent research indicates a rising prevalence of urolithiasis worldwide, particularly in developing countries. While the morbidity associated with urinary stones has decreased in recent years, long-term complications such as stone recurrence, kidney failure, and uremia continue to burden patients. Understanding the etiologies of urolithiasis, including the role of bacteria, is crucial as they can contribute to stone recurrence. The incidence of urinary tract infection (UTI) stones can be attributed to specific infectious risk factors, socio-demographic factors, and comorbid metabolic disorders. This review article explores the emerging evidence suggesting the involvement of bacteria in USD. It discusses the potential role of microorganisms in non-infection stones and highlights the association between UTIs and urolithiasis. Furthermore, it surveys the relationship between kidney stones and recurrent UTIs and the formation of bacterial biofilms in UTIs. Considering various risk factors, including biochemical stone analysis and the presence of bacteria, is essential for treating patients with infectious stones optimally. This review aims to provide an updated understanding of the association between bacteria and urinary stones in patients with urolithiasis, shedding light on the pathophysiology of urinary stone formation, urinary stone characteristics, and the urinary microbiome in urinary stones.

Species-level characterization of gut microbiota and their metabolic role in kidney stone formation using full-length 16S rRNA sequencing

The critical role of the human gut microbiota in kidney stone formation remains largely unknown, due to the low taxonomic resolution of previous sequencing technologies. Therefore, this study aimed to explore the gut microbiota using high-throughput sequencing to provide valuable insights and identify potential bacterial species and metabolite roles involved in kidney stone formation. The overall gut bacterial community and its potential functions in healthy participants and patients were examined using PacBio sequencing targeting the full-length 16S rRNA gene, coupled with stone and statistical analyses. Most kidney stones comprised calcium oxalate and calcium phosphate (75%), pure calcium oxalate (20%), and calcium phosphate and magnesium phosphate (5%), with higher content of Ca (130,510.5 ± 108,362.7 ppm) followed by P (18,746.4 ± 23,341.2 ppm). The microbial community structure was found to be weaker in patients' kidney stone samples, followed by patients' stool samples, than in healthy participants' stool samples. The most abundant bacterial species in kidney stone samples was uncultured Morganella, whereas that in patient and healthy participant stool samples was Bacteroides vulgatus. Similarly, Akkermansia muciniphila was significantly enriched in patient stool samples at the species level, whereas Bacteroides plebeius was significantly enriched in kidney stone samples than that in healthy participant stool samples. Three microbial metabolic pathways, TCA cycle, fatty acid oxidation, and urea cycle, were significantly enriched in kidney stone patients compared to healthy participants. Inferring bacteria at the species level revealed key players in kidney stone formation, enhancing the clinical relevance of gut microbiota.

Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease

Intestinal microbiome dysbiosis is a known risk factor for recurrent kidney stone disease (KSD) with prior data suggesting a role for dysfunctional metabolic pathways other than those directly utilizing oxalate. To identify alternative mechanisms, the current study analyzed differences in the metabolic potential of intestinal microbiomes of patients (n = 17) and live-in controls (n = 17) and determined their relevance to increased risk for KSD using shotgun metagenomic sequencing. We found no differences in the abundance of genes associated with known oxalate degradation pathways, supporting the notion that dysfunction in other metabolic pathways plays a role in KSD. Further analysis showed decreased abundance of key enzymes involved in butyrate biosynthesis in patient intestinal microbiomes. Furthermore, de novo construction of microbial genomes showed that the majority of genes significantly enriched in non-stone formers are affiliated with Faecalibacterium prausnitzii, a major butyrate producer. Specifically pertaining to butyrate metabolism, the majority of abundant genes mapped back to F. prausnitzii, Alistipes spp., and Akkermansia muciniphila. No differences were observed in ascorbate or glyoxylate metabolic pathways. Collectively, these data suggest that impaired bacterial-associated butyrate metabolism may be an oxalate-independent mechanism that contributes to an increased risk for recurrent KSD. This indicates that the role of the intestinal microbiome in recurrent KSD is multi-factorial, which is representative of the highly intertwined metabolic nature of this complex environment. Future bacteria-based treatments must not be restricted to targeting only oxalate metabolism.