Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease.

Menghan Liu,Angelina Volkova,Jiyuan Hu,Huilin Li,Joseph C Devlin,Thomas W Battaglia,Martin J Blaser,Lama Nazzal,Kelly V Ruggles,Allyson Byrd,John R Asplin,Melody Ho,P'Ng Loke,Aristotelis Tsirigos

doi:10.7554/elife.63642

Abstract

Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Furthermore, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with inflammatory bowel disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn's disease (CD) patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.

Highlights

Over-accumulation of oxalate in humans leads to toxicity (Asplin et al, 1998; Beck et al, 2013)
Oxalate degradation by the human microbiota has been known since the 1940s (Allison and Cook, 1981; Allison et al, 1986; Allison et al, 1985; Allison et al, 1977; Barber and Gallimore, 1940), but the taxa involved in vivo has not been systematically described
Our finding that multiple human gut microbes encode oxalate degradation pathways (ODP) is consistent with prior studies (Abratt and Reid, 2010; Klimesova et al, 2015; Mogna et al, 2014; Stern et al, 2016; Ticinesi et al, 2018)

Summary

Introduction

Over-accumulation of oxalate in humans leads to toxicity (Asplin et al, 1998; Beck et al, 2013). The most common oxalate toxicity is calcium oxalate nephrolithiasis, which accounts for more than 70% of overall nephrolithiasis, affecting 9% of the US population with a 20% 5-year recurrence rate (Lieske et al, 2014; Rule et al, 2014; Saran et al, 2018; Scales et al, 2012; Stamatelou et al, 2003). Oxalate toxicity can induce chronic kidney disease, an illness affecting more than 30 million Americans, via multiple mechanisms including the activation of the NALP3 inflammasome pathway (Knauf et al, 2013; Mulay et al, 2017; Mulay et al, 2013; Saran et al, 2018; Waikar et al, 2019), RIPK3-MLKL-mediated necroptosis (Mulay et al, 2016a), and oxidative stress-induced cell injury (Khan et al, 2006).

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