Gut-Microbiota-Metabolite Axis in Early Renal Function Decline

RESEARCH ARTICLE Gut-Microbiota-Metabolite Axis in Early Renal Function Decline Clara Barrios1,2☯*, Michelle Beaumont1☯, Tess Pallister1, Judith Villar3, Julia K. Goodrich4, Andrew Clark4, Julio Pascual2, Ruth E. Ley4, Tim D. Spector1, Jordana T. Bell1, Cristina Menni1* 1 Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom, 2 Department of Nephrology, Hospital del Mar, Institut Mar d’Investigacions Mediques, Barcelona, Spain, 3 Department of Infectious Diseases, Hospital del Mar, Institut Mar d’Investigacions Mediques, Barcelona, Spain, 4 Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States of America ☯ These authors contributed equally to this work. * (CB); (CM) Abstract OPEN ACCESS Citation: Barrios C, Beaumont M, Pallister T, Villar J, Goodrich JK, Clark A, et al. (2015) Gut-MicrobiotaMetabolite Axis in Early Renal Function Decline. PLoS ONE 10(8): e0134311. doi:10.1371/journal. pone.0134311 Editor: Giuseppe Remuzzi, Mario Negri Institute for Pharmacological Research and Azienda Ospedaliera Ospedali Riuniti di Bergamo, ITALY Introduction Several circulating metabolites derived from bacterial protein fermentation have been found to be inversely associated with renal function but the timing and disease severity is unclear. The aim of this study is to explore the relationship between indoxyl-sulfate, p-cresyl-sulfate, phenylacetylglutamine and gut-microbial profiles in early renal function decline. Received: April 29, 2015 Results Accepted: July 7, 2015 Indoxyl-sulfate (Beta(SE) = -2.74(0.24); P = 8.8x10-29), p-cresyl-sulfate (-1.99(0.24), P = 4.6x10-16), and phenylacetylglutamine(-2.73 (0.25), P = 1.2x10-25) were inversely associated with eGFR in a large population base cohort (TwinsUK, n = 4439) with minimal renal function decline. In a sub-sample of 855 individuals, we analysed metabolite associations with 16S gut microbiome profiles (909 profiles, QIIME 1.7.0). Three Operational Taxonomic Units (OTUs) were significantly associated with indoxyl-sulfate and 52 with phenylacetylglutamine after multiple testing; while one OTU was nominally associated with p-cresyl sulfate. All 56 microbial members belong to the order Clostridiales and are represented by anaerobic Gram-positive families Christensenellaceae, Ruminococcaceae and Lachnospiraceae. Within these, three microbes were also associated with eGFR. Published: August 4, 2015 Copyright: © 2015 Barrios et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper. Funding: TwinsUK was funded by the Wellcome Trust; European Community’s Seventh Framework Programme (FP7/2007-2013). The study also receives support from the National Institute for Health Research (NIHR) Clinical Research Facility at Guy’s & St Thomas’ NHS Foundation Trust and NIHR Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust, the King's College London, the Cornell Centre for Comparative Population Genomics. Tim Spector is the holder of an Conclusions Our data suggest that indoxyl-sulfate, p-cresyl-sulfate and phenylacetylglutamine are early markers of renal function decline. Changes in the intestinal flora associated with these metabolites are detectable in early kidney disease. Future efforts should dissect this relationship to improve early diagnostics and therapeutics strategies. PLOS ONE | DOI:10.1371/journal.pone.0134311 August 4, 2015 1/9 Microbiota, Metabolites and Renal Function ERC Advanced Principal Investigator award. Clara Barrios is supported by a grant from the Spanish Society of Nephrology. Competing Interests: The authors have declared that no competing interests exist. Introduction It is increasingly recognized that the microbiome may affect health and disease of the host. Indeed the endogenous flora has been recently associated with type 2 diabetes, obesity, metabolic syndrome, cancer and liver cirrhosis among others [1–4] Metabolites derived from bacteria provide a readout of the metabolic state of an individual and are the product of genetic [5,6] and exogenous (diet, lifestyle, gut microbial activity) factors under a particular set of conditions [7]. Under physiological conditions, there is a balance between the intestinal bacteria and the host, due to the innate immunity that maintains equilibrium in inflammation pathways and the intestinal barrier integrity. However, in chronic kidney disease (CKD), the uremic environment affects the intestinal barrier leading to bacterial dysbiosis [8]. This activates inflammatory pathways and immune processes and leads to systemic inflammation [9]. However, the degree of renal impairment that leads into modification of the intestinal milieu or the deficit of gut-metabolites excretion remains unclear. A deeper understanding of the gut-microbe-metabolite axis is a prerequisite to improve therapeutic strategies that manipulate the gut microbiota in the onset of kidney dysfunction. Indoxyl-sulfate and p-cresyl-sulfate are end-products of bacterial protein fermentation of tryptophan and tyrosine respectively in the colon [10]. In vitro and ex vivo data show that indoxylsulfate and p-cresyl-sulfate may trigger or accelerate cardiovascular disease and progression of kidney failure [11,12]. Clinical observational studies also correlate high levels of both metabolites with overall mortality as well as cardiovascular disease and renal disease progression [13– 15]. Phenylacetylglutamine is a major nitrogenous metabolite that accumulates in uremia. Its plasma levels increase after cigarette smoke exposure, in ischemic heart failure patients, hypertension, cardiovascular risk [16] and in the progression to end stage renal disease in type2 diabetic patients [17–19]. To date studies have concentrated on changes in intestinal flora and gut-metabolite levels in advanced stages of CKD [8,9,15,20–24], but potential changes in intestinal microbiota and gut microbial metabolites in early renal function decline have not yet been fully explored. To this end, we analyzed the links between metabolites indoxyl-sulfate, p-cresyl-sulfate and phenylacetylglutamine and gut microbiota to investigate whether changes at the individual operational taxonomic units (OTUs) level are detectable in early renal function decline. Results and Discussion Association of plasma circulating metabolites derived from bacterial protein fermentation was analyzed in 4439 individuals with different eGFR from the TwinsUK cohort. The demographic characteristics of the study populations are presented in Table 1. Out of 4439 individuals only 7.4% had eGFR<60 mL/min/1.73m2. Indoxyl-sulfate (Beta(SE) = -2.74(0.24), P = 8.8x10-29), p-cresyl-sulfate (-1.99(0.24), P = 4.6x10-16), an (...truncated)