Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease

Abstract

Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p < 0.001 & FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.

Calcium Oxalate Nephrolithiasis and Gut Microbiota: Not just a Gut-Kidney Axis. A Nutritional Perspective

“…Two studies also investigated urinary microbiota composition comparing it with the microbiota of stones [50,51]. All these studies support the concept that gut microbiota dysbiosis, i.e., reduction of overall biodiversity with alteration of physiologic composition, is present in stone formers [44][45][46][47][48][49][50]. In recurrent stone formers with hyperoxaluria, Suryavanshi and colleagues found an increased representation of pathobionts and species with oxalate-degrading capacity, including Oxalobacter, compared with the controls [44].…”

“…To date, the fecal microbiota composition of calcium stone formers has been investigated with next-generation sequencing techniques in seven different studies [44][45][46][47][48][49][50], summarized in Table 3. Two studies also investigated urinary microbiota composition comparing it with the microbiota of stones [50,51].…”

“…Further studies have shown that, in healthy controls, Oxalobacter presence is associated with a complex network of bacteria, that may exhibit oxalate-degrading capacity themselves or exert a permissive role on the metabolic activity of Oxalobacter [48,49]. These networks are someway less represented in calcium stone formers [47,49] and, most of all, in stone formers not harboring Oxalobacter in their fecal microbiota [48]. Therefore, the oxalate degrading capacity of the intestinal microbiota relies on a complex ecosystem and not solely on Oxalobacter, as believed before the emergence of high throughput sequencing techniques of the microbiota [7].…”

Abundance, Functional, and Evolutionary Analysis of Oxalyl-Coenzyme A Decarboxylase in Human Microbiota

“…A multi-species bacterial network could keep healthy oxalate homeostasis to inhibit urinary stone disease (Miller et al, 2019). Microbial dysbiosis of eubacterial, archaeal and eukaryotic components occurred in the patients with recurrent oxalate kidney stones (Suryavanshi et al, 2018). Several studies showed that the abundance of Firmicutes increased while the abundance of Bacteroidetes decreased in the gut of humans (Stern et al, 2016;Suryavanshi et al, 2018;Tang et al, 2018).…”

“…Microbial dysbiosis of eubacterial, archaeal and eukaryotic components occurred in the patients with recurrent oxalate kidney stones (Suryavanshi et al, 2018). Several studies showed that the abundance of Firmicutes increased while the abundance of Bacteroidetes decreased in the gut of humans (Stern et al, 2016;Suryavanshi et al, 2018;Tang et al, 2018). In addition, both oxalate metabolizing enzymes and oxalate metabolizing bacterial species were found augmented in the gut of patients with hyperoxaluria, however, along with well-studied bacterium, Oxalobacter formigenes, other genera had significant difference in the symptomatic hyperoxaluria conditions (Suryavanshi et al, 2016), suggesting that there may be other commensal bacteria possessing the ability to utilize oxalate.…”