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

Mangesh V Suryavanshi,Shrikant S Bhute,Rahul P Gune,Yogesh S Shouche

doi:10.1038/s41598-018-33773-5

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.

Highlights

Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases
We focused on assessment of species-level differences between the compositions of the intestinal flora in individuals with recurrent kidney stone to that of healthy individuals based on 16S rRNA gene traditional clone libraries for the eubacteria, 18S rRNA gene for microeukaryotes and ITS region for the fungal species diversity analysis
The Oxalobacter formigenes and Lactobacillus plantarum abundance was decreased in the kidney stone disease subjects (KSD) group

Summary

Introduction

Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. 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. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, and to other domains like archaea and eukaryotes. Trans-domain gut inhabitants include eubacteria, archaea, eukaryotes and their diversity are the key players in gut ecology. Trans-domain diversity inside the human gut is not yet fully explored in healthy state as well as in impaired health condition. Using high throughput sequencing methods, the variations in healthy gut flora were observed and disease associated bacteria were traced universally. The persistent colonization of unique gut microflora involved in non-intestinal metabolic disorders has been correlated with host health conditions. Defining the role of species of the gut inhabitant, along with qPCR-based species-specific detection of Oxalobacter formigenes have been indispensable in kidney stone endurers[8] and only the metagenomic sequencing approach has been found productive[9,10]

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Results

Conclusion