614
Views
58
CrossRef citations to date
0
Altmetric
Clinical focus: Clinical Immunology & Infectious diseases - Original Research

Characterizing the gut microbiota in patients with chronic kidney disease

ORCID Icon, ORCID Icon, , ORCID Icon &
Pages 495-505 | Received 14 Feb 2020, Accepted 16 Mar 2020, Published online: 02 Apr 2020

References

  • Lozano R, Naghavi M, Foreman K, et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the global burden of disease study 2010. Lancet. 2012;380(9859):2095–2128.
  • Webster AC, Nagler EV, Morton RL, et al. Chronic kidney disease. Lancet. 2017;389(10075):1238–1252.
  • Liu ZH. Nephrology in china. Nat Rev Nephrol. 2013;9(9):523–528.
  • Zhang L, Wang F, Wang L, et al. Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet. 2012;379(9818):815–822.
  • Dai L, Golembiewska E, Lindholm B, et al. End-stage renal disease, inflammation and cardiovascular outcomes. Contrib Nephrol. 2017;191:32–43.
  • Iwagami M, Yasunaga H, Matsui H, et al. Impact of end-stage renal disease on hospital outcomes among patients admitted to intensive care units: A retrospective matched-pair cohort study. Nephrology (Carlton). 2017;22(8):617–623.
  • AO K, SK Y, DS Y, et al. The symptoms prevalence, medical interventions, and health care service needs for patients with end-stage renal disease in a renal palliative care program. Am J Hosp Palliat Care. 2016;33(10):952–958.
  • Zoccali C, Vanholder R, Massy ZA, et al. The systemic nature of CKD. Nat Rev Nephrol. 2017;13(6):344–358.
  • Cosola C, Rocchetti MT, Cupisti A, et al. Microbiota metabolites: pivotal players of cardiovascular damage in chronic kidney disease. Pharmacol Res. 2018;130:132–142.
  • Evenepoel P, Poesen R, Meijers B. The gut-kidney axis. Pediatr Nephrol. 2017;32(11):2005–2014.
  • Dunne C. Adaptation of bacteria to the intestinal niche: probiotics and gut disorder. Inflamm Bowel Dis. 2001;7(2):136–145.
  • Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science. 2001;292(5519):1115–1118.
  • Umesaki Y, Setoyama H. Structure of the intestinal flora responsible for development of the gut immune system in a rodent model. Microbes Infect. 2000;2(11):1343–1351.
  • Kanbay M, Onal EM, Afsar B, et al. The crosstalk of gut microbiota and chronic kidney disease: role of inflammation, proteinuria, hypertension, and diabetes mellitus. Int Urol Nephrol. 2018;50(8):1453–1466.
  • Meijers B, Jouret F, Evenepoel P. Linking gut microbiota to cardiovascular disease and hypertension: lessons from chronic kidney disease. Pharmacol Res. 2018;133:101–107.
  • Vaziri ND. CKD impairs barrier function and alters microbial flora of the intestine: a major link to inflammation and uremic toxicity. Curr Opin Nephrol Hypertens. 2012;21(6):587–592.
  • Wen L, Duffy A. Factors influencing the gut microbiota, inflammation, and type 2 diabetes. J Nutr. 2017;147(7):1468S–1475S.
  • Yoshifuji A, Wakino S, Irie J, et al. Gut Lactobacillus protects against the progression of renal damage by modulating the gut environment in rats. Nephrol Dial Transplant. 2016;31(3):401–412.
  • Wang Z, Klipfell E, Bennett BJ, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature. 2011;472(7341):57–63.
  • Yang T, Santisteban MM, Rodriguez V, et al. Gut dysbiosis is linked to hypertension. Hypertension. 2015;65(6):1331–1340.
  • Vaziri ND, Wong J, Pahl M, et al. Chronic kidney disease alters intestinal microbial flora. Kidney Int. 2013;83(2):308–315.
  • Kieffer DA, Piccolo BD, Vaziri ND, et al. Resistant starch alters gut microbiome and metabolomic profiles concurrent with amelioration of chronic kidney disease in rats. Am J Physiol Renal Physiol. 2016;310(9):F857–871.
  • Vaziri ND, Liu SM, Lau WL, et al. High amylose resistant starch diet ameliorates oxidative stress, inflammation, and progression of chronic kidney disease. PLoS One. 2014;9(12):e114881.
  • Laffin MR, Tayebi Khosroshahi H, Park H, et al. Amylose resistant starch (HAM-RS2) supplementation increases the proportion of Faecalibacterium bacteria in end-stage renal disease patients: microbial analysis from a randomized placebo-controlled trial. Hemodial Int. 2019;23(3):343–347.
  • Tayebi Khosroshahi H, Vaziri ND, Abedi B, et al. Effect of high amylose resistant starch (HAM-RS2) supplementation on biomarkers of inflammation and oxidative stress in hemodialysis patients: a randomized clinical trial. Hemodial Int. 2018;22(4):492–500.
  • Levey AS, Eckardt KU, Tsukamoto Y, et al. Definition and classification of chronic kidney disease: a position statement from kidney disease: improving global outcomes (KDIGO). Kidney Int. 2005;67(6):2089–2100.
  • Kong X, Ma Y, Chen J, et al. Evaluation of the chronic kidney disease epidemiology collaboration equation for estimating glomerular filtration rate in the Chinese population. Nephrol Dial Transplant. 2013;28(3):641–651.
  • Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261–5267.
  • Aßhauer KP, Wemheuer B, Daniel R, et al. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics. 2015;31(17):2882–2884.
  • Chung S, Barnes JL, Astroth KS. Gastrointestinal microbiota in patients with chronic kidney disease: a systematic review. Adv Nutr. 2019;10(5):888–901.
  • Sampaio-Maia B, Simões-Silva L, Pestana M, et al. The role of the gut microbiome on chronic kidney disease. Adv Appl Microbiol. 2016;96:65–94.
  • Jiang S, Xie S, Lv D, et al. A reduction in the butyrate producing species Roseburia spp. and Faecalibacterium prausnitzii is associated with chronic kidney disease progression. Antonie Van Leeuwenhoek. 2016;109(10):1389–1396.
  • Li F, Wang M, Wang J, et al. Alterations to the gut microbiota and their correlation with inflammatory factors in chronic kidney disease. Front Cell Infect Microbiol. 2019;9:206.
  • Barrios C, Beaumont M, Pallister T, et al. Gut-microbiota-metabolite axis in early renal function decline. PLoS One. 2015;10(8):e0134311.
  • Claesson MJ, Jeffery IB, Conde S, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature. 2012;488(7410):178–184.
  • Jiang S, Xie S, Lv D, et al. Alteration of the gut microbiota in Chinese population with chronic kidney disease. Sci Rep. 2017;7(1):2870.
  • Mahmoodpoor F, Rahbar Saadat Y, Barzegari A, et al. The impact of gut microbiota on kidney function and pathogenesis. Biomed Pharmacother. 2017;93:412–419.
  • Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015;33(9):496–503.
  • Lupp C, Robertson ML, Wickham ME, et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe. 2007;2(3):204.
  • Xu KY, Xia GH, Lu JQ, et al. Impaired renal function and dysbiosis of gut microbiota contribute to increased trimethylamine-N-oxide in chronic kidney disease patients. Sci Rep. 2017;7(1):1445.
  • Wang F, Jiang H, Shi K, et al. Gut bacterial translocation is associated with microinflammation in end-stage renal disease patients. Nephrology (Carlton). 2012;17(8):733–738.
  • Strid H, Simrén M, Stotzer PO, et al. Patients with chronic renal failure have abnormal small intestinal motility and a high prevalence of small intestinal bacterial overgrowth. Digestion. 2003;67(3):129–137.
  • Chassaing B, Koren O, Carvalho FA, et al. AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition. Gut. 2014;63(7):1069–1080.
  • Pan W, Kang Y. Gut microbiota and chronic kidney disease: implications for novel mechanistic insights and therapeutic strategies. Int Urol Nephrol. 2018;50(2):289–299.
  • Flannigan KL, Taylor MR, Pereira SK, et al. An intact microbiota is required for the gastrointestinal toxicity of the immunosuppressant mycophenolate mofetil. J Heart Lung Transplant. 2018;37(9):1047–1059.
  • Tesh VL, O’Brien AD. The pathogenic mechanisms of Shiga toxin and the Shiga-like toxins. Mol Microbiol. 1991;5(8):1817–1822.
  • Song YF, Pei LX, Chen L, et al. Electroacupuncture relieves irritable bowel syndrome by regulating IL-18 and gut microbial dysbiosis in a trinitrobenzene sulfonic acid-induced post-inflammatory animal model. Am J Chin Med. 2020;48(1):77–90.
  • Dong Y, Cheng H, Liu Y, et al. Red yeast rice ameliorates high-fat diet-induced atherosclerosis in Apoe-/- mice in association with improved inflammation and altered gut microbiota composition. Food Funct. 2019;10(7):3880–3889.
  • Huang S, Mao J, Zhou L, et al. The imbalance of gut microbiota and its correlation with plasma inflammatory cytokines in pemphigus vulgaris patients. Scand J Immunol. 2019;90(3):e12799.
  • He Z, Shao T, Li H, et al. Alterations of the gut microbiome in Chinese patients with systemic lupus erythematosus. Gut Pathog. 2016;8:64.
  • Caspi R, Billington R, Ferrer L, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2016;44(D1):D471–480.
  • Pan X, Xue F, Nan X, et al. Illumina sequencing approach to characterize thiamine metabolism related bacteria and the impacts of thiamine supplementation on ruminal microbiota in dairy cows fed high-grain diets. Front Microbiol. 2017;8:1818.
  • Kunisawa J. Metabolic changes during B cell differentiation for the production of intestinal IgA antibody. Cell Mol Life Sci. 2017;74(8):1503–1509.
  • Kunisawa J, Sugiura Y, Wake T, et al. Mode of bioenergetic metabolism during B cell differentiation in the intestine determines the distinct requirement for vitamin B1. Cell Rep. 2015;13(1):122–131.
  • Hung SC, Hung SH, Tarng DC, et al. Thiamine deficiency and unexplained encephalopathy in hemodialysis and peritoneal dialysis patients. Am J Kidney Dis. 2001;38(5):941–947.
  • Saka Y, Naruse T, Kato A, et al. Thiamine status in end-stage chronic kidney disease patients: a single-center study. Int Urol Nephrol. 2018;50(10):1913–1918.
  • Tang WH, Wang Z, Kennedy DJ, et al. Gut microbiota-dependent trimethylamine N-oxide (TMAO) pathway contributes to both development of renal insufficiency and mortality risk in chronic kidney disease. Circ Res. 2015;116(3):448–455.
  • Schulthess J, Pandey S, Capitani M, et al. The short chain fatty acid butyrate imprints an antimicrobial program in macrophages. Immunity. 2019;50(2):432–445.e7.
  • Genoni A, Christophersen CT, Lo J, et al. Long-term Paleolithic diet is associated with lower resistant starch intake, different gut microbiota composition and increased serum TMAO concentrations. Eur J Nutr. 2019:1–14.
  • Chen L, Chen DQ, Liu JR, et al. Unilateral ureteral obstruction causes gut microbial dysbiosis and metabolome disorders contributing to tubulointerstitial fibrosis. Exp Mol Med. 2019;51(3):1–18.
  • Oliphant K, Allen-Vercoe E. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome. 2019;7(1):91.
  • Wong J, Piceno YM, DeSantis TZ, et al. Expansion of urease- and uricase-containing, indole- and p-cresol-forming and contraction of short-chain fatty acid-producing intestinal microbiota in ESRD. Am J Nephrol. 2014;39(3):230–237.
  • Lun H, Yang W, Zhao S, et al. Altered gut microbiota and microbial biomarkers associated with chronic kidney disease. Microbiologyopen. 2019;8(4):e00678.
  • Qin J, Li Y, Cai Z, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55–60.
  • Ren Z, Li A, Jiang J, et al. Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma. Gut. 2019;68(6):1014–1023.
  • Zhou D, Liu Y. Renal fibrosis in 2015: understanding the mechanisms of kidney fibrosis. Nat Rev Nephrol. 2016;12(2):68–70.
  • Bagnasco S, Balaban R, Fales HM, et al. Predominant osmotically active organic solutes in rat and rabbit renal medullas. J Biol Chem. 1986;261(13):5872–5877.
  • Burg MB. Renal osmoregulatory transport of compatible organic osmolytes. Curr Opin Nephrol Hypertens. 1997;6(5):430–433.
  • Gentile CL, Weir TL. The gut microbiota at the intersection of diet and human health. Science. 2018;362(6416):776–780.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.