Association of the gut microbiome with kidney function and damage in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

References

• Chapter 1: cKD in the general population. Am J Kidney Dis. 2019;73(3):S1–18. doi:10.1053/j.ajkd.2018.12.001.
   PubMedGoogle Scholar
• Chapter 3: morbidity and mortality in patients with CKD. Am J Kidney Dis. 2019;73(3):S45–78. doi:10.1053/j.ajkd.2018.12.003.
   Google Scholar
• Chapter 4: cardiovascular Disease in Patients with CKD. Am J Kidney Dis. 2019;73(3):S79–98. doi:10.1053/j.ajkd.2018.12.004.
   Google Scholar
• Wyld MLR, Chadban SJ, Morton RL. Improving our understanding of quality of life in CKD. Am J Kidney Dis. 2016;67(6):820–821. doi:10.1053/j.ajkd.2016.03.412.
   PubMed Web of Science ®Google Scholar
• Levey AS, Coresh J, Balk E, Kausz AT, Levin A, Steffes MW, Hogg RJ, Perrone RD, Lau J, Eknoyan G. National kidney foundation practice guidelines for chronic kidney disease: evaluation, classification, and stratification. Ann Intern Med. 2003;139(2):137–147. doi:10.7326/0003-4819-139-2-200307150-00013.
   PubMed Web of Science ®Google Scholar
• Zhao J, Ning X, Liu B, Dong R, Bai M, Sun S. Specific alterations in gut microbiota in patients with chronic kidney disease: an updated systematic review. Ren Fail. 2021;43(1):102–112. doi:10.1080/0886022X.2020.1864404.
   PubMed Web of Science ®Google Scholar
• Cosola C, Rocchetti MT, Sabatino A, Fiaccadori E, Di Iorio BR, Gesualdo L. Microbiota issue in CKD: how promising are gut-targeted approaches? J Nephrol. 2019;32(1):27–37. doi:10.1007/s40620-018-0516-0.
   PubMed Web of Science ®Google Scholar
• Ramezani A, Raj DS. The gut microbiome, kidney disease, and targeted interventions. J Am Soc Nephrol. 2014;25(4):657–670. doi:10.1681/ASN.2013080905.
   PubMed Web of Science ®Google Scholar
• Hobby GP, Karaduta O, Dusio GF, Singh M, Zybailov BL, Arthur JM. Chronic kidney disease and the gut microbiome. Am J Physiol Renal Physiol. 2019;316(6):F1211–7. doi:10.1152/ajprenal.00298.2018.
   PubMed Web of Science ®Google Scholar
• Kikuchi K, Saigusa D, Kanemitsu Y, Matsumoto Y, Thanai P, Suzuki N, Mise K, Yamaguchi H, Nakamura T, Asaji K, et al. Gut microbiome-derived phenyl sulfate contributes to albuminuria in diabetic kidney disease. Nat Commun. 2019;10(1):1835. doi:10.1038/s41467-019-09735-4.
   PubMedGoogle Scholar
• Wong J, Piceno YM, DeSantis TZ, Pahl M, Andersen GL, Vaziri ND. 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. doi:10.1159/000360010.
   PubMed Web of Science ®Google Scholar
• Meijers B, Evenepoel P, Anders HJ. Intestinal microbiome and fitness in kidney disease. Nat Rev Nephrol. 2019;15(9):531–545. doi:10.1038/s41581-019-0172-1.
   PubMed Web of Science ®Google Scholar
• Heaney LM, Davies OG, Selby NM. Gut microbial metabolites as mediators of renal disease: do short-chain fatty acids offer some hope? Future Sci OA. 2019;5(4):FSO384–FSO. doi:10.4155/fsoa-2019-0013.
   PubMed Web of Science ®Google Scholar
• Caggiano G, Cosola C, Di Leo V, Gesualdo M, Gesualdo L. Microbiome modulation to correct uremic toxins and to preserve kidney functions. Curr Opin Nephrol Hypertens. 2020;29(1):49–56. doi:10.1097/MNH.0000000000000565.
   PubMed Web of Science ®Google Scholar
• Anders H-J, Huber TB, Isermann B, Schiffer M. CKD in diabetes: diabetic kidney disease versus nondiabetic kidney disease. Nat Rev Nephrol. 2018;14(6):361–377. doi:10.1038/s41581-018-0001-y.
   PubMed Web of Science ®Google Scholar
• Gryp T, Huys GRB, Joossens M, Van Biesen W, Glorieux G, Vaneechoutte M. Isolation and quantification of uremic toxin precursor-generating gut bacteria in chronic kidney disease patients. Int J Mol Sci. 2020;21(6):21. doi:10.3390/ijms21061986.
   Web of Science ®Google Scholar
• Hu Q, Wu K, Pan W, Zeng Y, Hu K, Chen D, Huang X, Zhang Q. Intestinal flora alterations in patients with early chronic kidney disease: a case-control study among the Han population in southwestern China. J Int Med Res. 2020;48(6):300060520926033. doi:10.1177/0300060520926033.
   PubMed Web of Science ®Google Scholar
• Jiang S, Xie S, Lv D, Wang P, He H, Zhang T, Zhou Y, Lin Q, Zhou H, Jiang J, et al. Alteration of the gut microbiota in Chinese population with chronic kidney disease. Sci Rep. 2017;7(1):2870. doi:10.1038/s41598-017-02989-2.
   PubMed Web of Science ®Google Scholar
• Jiang S, Xie S, Lv D, Zhang Y, Deng J, Zeng L, Chen Y. 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. doi:10.1007/s10482-016-0737-y.
   PubMed Web of Science ®Google Scholar
• Lun H, Yang W, Zhao S, Jiang M, Xu M, Liu F, Wang Y. Altered gut microbiota and microbial biomarkers associated with chronic kidney disease. Microbiologyopen. 2019;8(4):e00678. doi:10.1002/mbo3.678.
   PubMed Web of Science ®Google Scholar
• Ren Z, Fan Y, Li A, Shen Q, Wu J, Ren L, et al.Alterations of the human gut microbiome in chronic kidney disease.Advanced science (Weinheim.Baden-Wurttemberg, Germany).2020;Vol. 7:p. 2001936.
   Google Scholar
• Sato N, Kakuta M, Hasegawa T, Yamaguchi R, Uchino E, Murashita K, Nakaji S, Imoto S, Yanagita M, Okuno Y. Metagenomic profiling of gut microbiome in early chronic kidney disease. Nephrol Dial Transplant. 2021;36(9):1675–1684. doi:10.1093/ndt/gfaa122.
   PubMed Web of Science ®Google Scholar
• Wang X, Yang S, Li S, Zhao L, Hao Y, Qin J, Zhang L, Zhang C, Bian W, Zuo L, et al. Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents. Gut. 2020;69(12):2131–2142. doi:10.1136/gutjnl-2019-319766.
   PubMed Web of Science ®Google Scholar
• Wu IW, Gao SS, Chou HC, Yang HY, Chang LC, Kuo YL, Dinh MCV, Chung W-H, Yang C-W, Lai H-C, et al. Integrative metagenomic and metabolomic analyses reveal severity-specific signatures of gut microbiota in chronic kidney disease. Theranostics. 2020;10(12):5398–5411. doi:10.7150/thno.41725.
   PubMed Web of Science ®Google Scholar
• K-Y X, Xia G-H, J-Q L, Chen M-X, Zhen X, Wang S, You C, Nie J, Zhou H-W, Yin J. 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. doi:10.1038/s41598-017-01387-y.
   PubMedGoogle Scholar
• Li Y, Su X, Zhang L, Liu Y, Shi M, Lv C, Gao Y, Xu D, Wang Z. Dysbiosis of the gut microbiome is associated with CKD5 and correlated with clinical indices of the disease: a case–controlled study. J Transl Med. 2019;17(1):228. doi:10.1186/s12967-019-1969-1.
   PubMedGoogle Scholar
• Wang S, Lv D, Jiang S, Jiang J, Liang M, Hou F, Chen Y. Quantitative reduction in short-chain fatty acids, especially butyrate, contributes to the progression of chronic kidney disease. Clin Sci (Lond). 2019;133(17):1857–1870. doi:10.1042/CS20190171.
   PubMed Web of Science ®Google Scholar
• Andrade-Oliveira V, Amano MT, Correa-Costa M, Castoldi A, Felizardo RJ, de Almeida DC, Bassi EJ, Moraes-Vieira PM, Hiyane MI, Rodas ACD, et al. Gut bacteria products prevent AKI induced by ischemia-reperfusion. J Am Soc Nephrol. 2015;26(8):1877–1888. doi:10.1681/ASN.2014030288.
   PubMed Web of Science ®Google Scholar
• Gai Z, Wang T, Visentin M, Kullak-Ublick GA, Fu X, Wang Z. Lipid accumulation and chronic kidney disease. Nutrients. 2019;11(4):11. doi:10.3390/nu11040722.
   Web of Science ®Google Scholar
• Shi D, Caldovic L, Tuchman M. Sources and fates of carbamyl phosphate: a labile energy-rich molecule with multiple facets. Biology. 2018;7(2):34. doi:10.3390/biology7020034.
   PubMedGoogle Scholar
• Cai Q, Dekker LH, Vinke PC, Corpeleijn E, Bakker SJL, de Borst MH, Navis GJ. Diet quality and incident chronic kidney disease in the general population: the lifelines cohort study. Clin Nutr. 2021;40(9):5099–5105. doi:10.1016/j.clnu.2021.07.033.
   PubMed Web of Science ®Google Scholar
• Hu EA, Coresh J, Anderson CAM, Appel LJ, Grams ME, Crews DC, Mills KT, He J, Scialla J, Rahman M, et al. Adherence to healthy dietary patterns and risk of CKD progression and all-cause mortality: findings from the CRIC (Chronic Renal Insufficiency Cohort) study. Am J Kidney Dis. 2021;77(2):235–244. doi:10.1053/j.ajkd.2020.04.019.
   PubMed Web of Science ®Google Scholar
• Qi Q, Li J, Yu B, Moon JY, Chai JC, Merino J, Hu J, Ruiz-Canela M, Rebholz C, Wang Z, et al. Host and gut microbial tryptophan metabolism and type 2 diabetes: an integrative analysis of host genetics, diet, gut microbiome and circulating metabolites in cohort studies. Gut. 2022;71(6):1095–1105. doi:10.1136/gutjnl-2021-324053.
   PubMed Web of Science ®Google Scholar
• Sun CY, Lin CJ, Pan HC, Lee CC, Lu SC, Hsieh YT, Huang S-Y, Huang H-Y. Clinical association between the metabolite of healthy gut microbiota, 3-indolepropionic acid and chronic kidney disease. Clin Nutr. 2019;38(6):2945–2948. doi:10.1016/j.clnu.2018.11.029.
   PubMed Web of Science ®Google Scholar
• Koh A, Molinaro A, Ståhlman M, Khan MT, Schmidt C, Mannerås-Holm L, Wu H, Carreras A, Jeong H, Olofsson LE, et al. Microbially produced imidazole propionate impairs insulin signaling through mTORC1. Cell. 2018;175(4):947–61.e17. doi:10.1016/j.cell.2018.09.055.
   PubMed Web of Science ®Google Scholar
• Frazier R, Cai X, Lee J, Bundy JD, Jovanovich A, Chen J, Deo R, Lash JP, Anderson AH, Go AS, et al. Deoxycholic acid and risks of cardiovascular events, ESKD, and mortality in CKD: the CRIC study. Kidney Medicine. 2022;4(1):100387. doi:10.1016/j.xkme.2021.09.004.
   PubMedGoogle Scholar
• Jovanovich A, Isakova T, Block G, Stubbs J, Smits G, Chonchol M, Miyazaki M. Deoxycholic acid, a metabolite of circulating bile acids, and coronary artery vascular calcification in CKD. Am J Kidney Dis. 2018;71(1):27–34. doi:10.1053/j.ajkd.2017.06.017.
   PubMed Web of Science ®Google Scholar
• Devlin AS, Fischbach MA. A biosynthetic pathway for a prominent class of microbiota-derived bile acids. Nat Chem Biol. 2015;11(9):685–690. doi:10.1038/nchembio.1864.
   PubMed Web of Science ®Google Scholar
• Graboski AL, Redinbo MR. Gut-derived protein-bound uremic toxins. toxins (Basel). 2020;12(9):590. doi:10.3390/toxins12090590.
   PubMed Web of Science ®Google Scholar
• ramezani a, massy za, meijers b, evenepoel p, vanholder r, raj ds. role of the gut microbiome in uremia: a potential therapeutic target. Am J Kidney Dis. 2016;67(3):483–498. doi:10.1053/j.ajkd.2015.09.027.
   PubMed Web of Science ®Google Scholar
• Gryp T, De Paepe K, Vanholder R, Kerckhof FM, Van Biesen W, Van de Wiele T, Verbeke F, Speeckaert M, Joossens M, Couttenye MM, et al. Gut microbiota generation of protein-bound uremic toxins and related metabolites is not altered at different stages of chronic kidney disease. Kidney Int. 2020;97(6):1230–1242. doi:10.1016/j.kint.2020.01.028.
   PubMed Web of Science ®Google Scholar
• Wang Y, Zhao J, Qin Y, Yu Z, Zhang Y, Ning X, Sun S. The specific alteration of gut microbiota in diabetic kidney diseases—a systematic review and meta-analysis. Front Immunol. 2022;13:908219. doi:10.3389/fimmu.2022.908219.
   PubMed Web of Science ®Google Scholar
• Rothman KJ. Causes. Am J Epidemiol. 1976;104(6):587–592. doi:10.1093/oxfordjournals.aje.a112335.
   PubMed Web of Science ®Google Scholar
• Lavange LM, Kalsbeek WD, Sorlie PD, Avilés-Santa LM, Kaplan RC, Barnhart J, Liu K, Giachello A, Lee DJ, Ryan J, et al. Sample design and cohort selection in the Hispanic community health study/study of latinos. Ann Epidemiol. 2010;20(8):642–649. doi:10.1016/j.annepidem.2010.05.006.
   PubMed Web of Science ®Google Scholar
• Sorlie PD, Avilés-Santa LM, Wassertheil-Smoller S, Kaplan RC, Daviglus ML, Giachello AL, Schneiderman N, Raij L, Talavera G, Allison M, et al. Design and implementation of the Hispanic community health study/study of latinos. Ann Epidemiol. 2010;20(8):629–641. doi:10.1016/j.annepidem.2010.03.015.
   PubMed Web of Science ®Google Scholar
• Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon J-Y, et al. Gut microbiome composition in the Hispanic community health study/study of latinos is shaped by geographic relocation, environmental factors, and obesity. Genome Biol. 2019;20(1):219. doi:10.1186/s13059-019-1831-z.
   PubMed Web of Science ®Google Scholar
• Inker LA, Eneanya ND, Coresh J, Tighiouart H, Wang D, Sang Y, Crews DC, Doria A, Estrella MM, Froissart M, et al. New creatinine- and cystatin c–based equations to estimate GFR without race. 2021;385(19):1737–1749. doi:10.1056/NEJMoa2102953.
   Google Scholar
• Delgado C, Baweja M, Crews DC, Eneanya ND, Gadegbeku CA, Inker LA, Mendu ML, Miller WG, Moxey-Mims MM, Roberts GV, et al. A unifying approach for GFR estimation: recommendations of the NKF-ASN task force on reassessing the inclusion of race in diagnosing kidney disease. Am J Kidney Dis. 2022;79(2):268–88.e1. doi:10.1053/j.ajkd.2021.08.003.
   PubMed Web of Science ®Google Scholar
• Sorlie PD, Allison MA, Aviles-Santa ML, Cai J, Daviglus ML, Howard AG, Kaplan R, LaVange LM, Raij L, Schneiderman N, et al. Prevalence of hypertension, awareness, treatment, and control in the Hispanic community health study/study of latinos. Am J Hypertens. 2014;27(6):793–800. doi:10.1093/ajh/hpu003.
   PubMed Web of Science ®Google Scholar
• Qi Q, Strizich G, Merchant G, Sotres-Alvarez D, Buelna C, Castaneda SF, Gallo LC, Cai J, Gellman MD, Isasi CR, et al. Objectively measured sedentary time and cardiometabolic biomarkers in US Hispanic/Latino adults: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Circulation. 2015;132(16):1560–1569. doi:10.1161/CIRCULATIONAHA.115.016938.
   PubMed Web of Science ®Google Scholar
• Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D. Evaluating the information content of shallow shotgun metagenomics. mSystems. 2018;3(6):e00069–18. doi:10.1128/mSystems.00069-18.
   PubMed Web of Science ®Google Scholar
• Peters BA, Lin J, Qi Q, Usyk M, Isasi CR, Mossavar-Rahmani Y, Derby CA, Santoro N, Perreira KM, Daviglus ML, et al.Menopause is associated with an altered gut microbiome and estrobolome with implications for adverse cardiometabolic risk in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).mSystems 2022.73:10.1128/msystems.00273-22.
   Google Scholar
• Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551(7681):457–463. doi:10.1038/nature24621.
   PubMed Web of Science ®Google Scholar
• Glenn TC, Nilsen RA, Kieran TJ, Sanders JG, Bayona-Vasquez NJ, Finger JW, Pierson TW, Bentley KE, Hoffberg SL, Louha S, et al. Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext). PeerJ, 2019;7:e7755. doi:10.7717/peerj.7755.
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–359. doi:10.1038/nmeth.1923.
   PubMed Web of Science ®Google Scholar
• Pj M, Holmes S, Watson M. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217. doi:10.1371/journal.pone.0061217.
   PubMed Web of Science ®Google Scholar
• Oksanen J, Blanchet F, Kindt R, Legendre P, O’hara R, Simpson G, et al. Multivariate analysis of ecological communities in R: vegan tutorial. R Package Version 2.6-4. 2013. https://CRAN.R-project.org/package=vegan
   Google Scholar
• Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, et al.Associating microbiome composition with environmental covariates using generalized UniFrac distances.Bioinformatics (Oxford.England).2012;Vol. 28:pp. 2106–2113.
   Google Scholar
• Chen G-C, Chai JC, Yu B, Michelotti GA, Grove ML, Fretts AM, Daviglus ML, Garcia-Bedoya OL, Thyagarajan B, Schneiderman N, et al. Serum sphingolipids and incident diabetes in a US population with high diabetes burden: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Am J Clin Nutr. 2020;112(1):57–65. doi:10.1093/ajcn/nqaa114.
   PubMed Web of Science ®Google Scholar
• Mandal S, Van Treuren W, White RA, Eggesbo M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015;26(0):27663. doi:10.3402/mehd.v26.27663.
   PubMedGoogle Scholar