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Brief Report

Assessment of urinary 3-indoxyl sulfate as a marker for gut microbiota diversity and abundance of Clostridiales

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Pages 133-141 | Received 15 Feb 2018, Accepted 09 Jul 2018, Published online: 17 Aug 2018

References

  • Tetel MJ, De Vries GJ, Melcangi RC, Panzica G, O’Mahony SM. J Neuroendocrinol. 2017;30(2):e12548.
  • Quigley EMM. Microbiota-brain-gut axis and neurodegenerative diseases. Curr Neurol Neurosci Rep. 2017;17(12):94.
  • He Y, Wen Q, Yao F, Xu D, Huang Y, Wang J. Gut-lung axis: the microbial contributions and clinical implications. Crit Rev Microbiol. 2017;43(1):81–95.
  • Adamczyk-Sowa M, Medrek A, Madej P, Michlicka W, Dobrakowski P. Does the Gut Microbiota Influence Immunity and Inflammation in Multiple Sclerosis Pathophysiology? J Immunol Res. 2017;2017:7904821.
  • Taur Y, Jenq RR, Perales MA, Littmann ER, Morjaria S, Ling L, No D, Gobourne A, Viale A, Dahi PB, et al. The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood. 2014;124(7):1174–1182.
  • Weber D, Oefner PJ, Hiergeist A, Koestler J, Gessner A, Weber M, Hahn J, Wolff D, Stammler F, Spang R, et al. Low urinary indoxyl sulfate levels early after transplantation reflect a disrupted microbiome and are associated with poor outcome. Blood. 2015;126(14):1723–1728.
  • Jenq RR, Taur Y, Devlin SM, Ponce DM, Goldberg JD, Ahr KF, Littmann ER, Ling L, Gobourne AC, Miller LC, et al. Intestinal blautia is associated with reduced death from graft-versus-host disease. Biol Blood Marrow Transplant. 2015;21(8):1373–1383.
  • Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2015;517(7533):205–208.
  • Monaghan TM, Cockayne A, Mahida YR. Pathogenesis of Clostridium difficile infection and its potential role in inflammatory bowel disease. Inflamm Bowel Dis. 2015;21(8):1957–1966.
  • Cornely OA, Vehreschild MJ. Editorial commentary: where to place the new treatments for Clostridium difficile infection? Clin Infect Dis. 2016;63(6):735–736.
  • Miller MA, Louie T, Mullane K, Weiss K, Lentnek A, Golan Y, Kean Y, Sears P. Derivation and validation of a simple clinical bedside score (ATLAS) for Clostridium difficile infection which predicts response to therapy. BMC Infect Dis. 2013;13:148.
  • Figh ML, Zoog ESL, Moore RA, Dart BWT, Heath G, Butler RM, Gao C, Kong JC, Stanley JD. External validation of velazquez-gomez severity score index and ATLAS scores and the identification of risk factors associated with mortality in Clostridium difficile infections. Am Surg. 2017;83(12):1347–1351.
  • Cobo J, Merino E, Martinez C, Cozar-Llisto A, Shaw E, Marrodan T, Calbo E, Bereciartua E, Sanchez-Munoz LA, Salavert M, et al. Int J Antimicrob Agents. 2017;51(3):393–398.
  • Tariq R, Singh S, Gupta A, Pardi DS, Khanna S. Association of gastric acid suppression with recurrent Clostridium difficile infection: a systematic review and meta-analysis. JAMA Intern Med. 2017;177(6):784–791.
  • Watson T, Hickok J, Fraker S, Korwek K, Poland RE, Septimus E. Evaluating the risk factors for hospitalonset Clostridium difficile infections in a large healthcare system. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;64(2):111–115.
  • Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. 2018;555:623.
  • Pallister T, Jackson MA, Martin TC, Zierer J, Jennings A, Mohney RP, MacGregor A, Steves CJ, Cassidy A, Spector TD, et al. Hippurate as a metabolomic marker of gut microbiome diversity: modulation by diet and relationship to metabolic syndrome. Sci Rep. 2017;7(1):13670.
  • Farowski F, Bücker V, Vehreschild JJ, Biehl L, Cruz-Aguilar R, Scheid C, Holtick U, Jazmati N, Wisplinghoff H, Cornely OA, et al. Impact of choice, timing, sequence and combination of broad-spectrum antibiotics on the outcome of allogeneic haematopoietic stem cell transplantation. Bone Marrow Transplant. 2018;53(1):52–57.
  • Vehreschild MJGT, Weitershagen D, Biehl LM, Tacke D, Waldschmidt D, Tox U, Wisplinghoff H, Von Bergwelt-Baildon M, Cornely OA, Vehreschild JJ. Clostridium difficile infection in patients with acute myelogenous leukemia and in patients undergoing allogeneic stem cell transplantation: epidemiology and risk factor analysis. Biology of Blood and Marrow Transplantation: Journal of the American Society for Blood and Marrow Transplantation. 2014;20(6):823–828.
  • Trifilio SM, Pi J, Mehta J. Changing epidemiology of Clostridium difficile-associated disease during stem cell transplantation. Biology of Blood and Marrow Transplantation: Journal of the American Society for Blood and Marrow Transplantation. 2013;19(3):405–409.
  • Dubberke ER, Reske KA, Srivastava A, Sadhu J, Gatti R, Young RM, Rakes LC, Dieckgraefe B, DiPersio J, Fraser VJ. Clostridium difficile-associated disease in allogeneic hematopoietic stem-cell transplant recipients: risk associations, protective associations, and outcomes. Clin Transplant. 2010;24(2):192–198.
  • Chakrabarti S, Lees A, Jones SG, Milligan DW. Clostridium difficile infection in allogeneic stem cell transplant recipients is associated with severe graft-versus-host disease and non-relapse mortality. Bone Marrow Transplant. 2000;26(8):871–876.
  • Alonso CD, Treadway SB, Hanna DB, Huff CA, Neofytos D, Carroll KC, Marr KA. Epidemiology and outcomes of Clostridium difficile infections in hematopoietic stem cell transplant recipients. Clinical Infectious Diseases: an Official Publication of the Infectious Diseases Society of America. 2012;54(8):1053–1063.
  • Seekatz AM, Theriot CM, Rao K, Chang Y-M, Freeman AE, Kao JY, Young VB. Anaerobe. 2018;S1075-9964(18)30058-1.
  • Bajaj JS, Kassam Z, Fagan A, Gavis EA, Liu E, Cox IJ, Kheradman R, Heuman D, Wang J, Gurry T, et al. Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: A randomized clinical trial. Hepatology. 2017;66(6):1727–1738.
  • Chaput N, Lepage P, Coutzac C, Soularue E, Le Roux K, Monot C, Boselli L, Routier E, Cassard L, Collins M, et al. Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab. Ann Oncol. 2017;28(6):1368–1379.
  • Miyake S, Kim S, Suda W, Oshima K, Nakamura M, Matsuoka T, Chihara N, Tomita A, Sato W, Kim S-W, et al. Dysbiosis in the gut microbiota of patients with multiple sclerosis, with a striking depletion of species belonging to clostridia XIVa and IV clusters. PLoS One. 2015;10(9):e0137429.
  • Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP, Koh AY. Metagenomic shotgun sequencing and unbiased metabolomic profiling identify specific human gut microbiota and metabolites associated with immune checkpoint therapy efficacy in melanoma patients. Neoplasia. 2017;19(10):848–855.
  • Colpitts SL, Kasper EJ, Keever A, Liljenberg C, Kirby T, Magori K, Kasper LH, Ochoa-Repáraz J. A bidirectional association between the gut microbiota and CNS disease in a biphasic murine model of multiple sclerosis. Gut Microbes. 2017;8(6):561–573.
  • Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glockner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1.
  • Illumina, 16S sample preparation guide, 2016. http://www.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf. (Accessed 2016 09 27).
  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–336.
  • Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581.
  • Pedregosa F, Varoquaux L, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, et al. Scikit-learn: Machine Learning in Python. J Mach Learn Res. 2011;12:2825–2830.
  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–6.
  • R Core Team. R: a language and environment for statistical computing. Vienna, Austria. R Foundation for Statistical Computing 2017. Available from http://www.r-project.org.
  • McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.
  • Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics. 2005;21(20):3940–3941.
  • Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, et al. vegan: community ecology package. R Package Version 2.4–5. Available from https://CRAN.Rproject.org/package=vegan
  • Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics. 2012;28(16):2106–2113.

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