Gentile CL, Weir TL. The gut microbiota at the intersection of diet and human health. Science. 2018;362(6416):776–80.
Article
CAS
PubMed
Google Scholar
Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature. 2019;570(7762):462–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Separating host and microbiome contributions to drug pharmacokinetics and toxicity. Science. 2019;363(6427).
Wu WK, Hsu CC, Sheen LY, Wu MS. Measurement of gut microbial metabolites in cardiometabolic health and translational research. Rapid Commun Mass Spectrom. 2019.
Tang WH, Wang Z, Levison BS, Koeth RA, Britt EB, Fu X, Wu Y, Hazen SL. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med. 2013;368(17):1575–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med. 2013;19(5):576–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu W, Gregory JC, Org E, Buffa JA, Gupta N, Wang Z, Li L, Fu X, Wu Y, Mehrabian M, et al. Gut microbial metabolite TMAO enhances platelet hyperreactivity and thrombosis risk. Cell. 2016;165(1):111–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tang WHW, Backhed F, Landmesser U, Hazen SL. Intestinal microbiota in cardiovascular health and disease: JACC State-of-the-Art Review. J Am Coll Cardiol. 2019;73(16):2089–2105.
Schiattarella GG, Sannino A, Toscano E, Giugliano G, Gargiulo G, Franzone A, Trimarco B, Esposito G, Perrino C. Gut microbe-generated metabolite trimethylamine-N-oxide as cardiovascular risk biomarker: a systematic review and dose-response meta-analysis. Eur Heart J. 2017;38(39):2948–56.
Article
CAS
PubMed
Google Scholar
Roberts AB, Gu X, Buffa JA, Hurd AG, Wang Z, Zhu W, Gupta N, Skye SM, Cody DB, Levison BS, et al. Development of a gut microbe-targeted nonlethal therapeutic to inhibit thrombosis potential. Nat Med. 2018;24(9):1407–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu WK, Chen CC, Liu PY, Panyod S, Liao BY, Chen PC, Kao HL, Kuo HC, Kuo CH, Chiu THT, et al. Identification of TMAO-producer phenotype and host-diet-gut dysbiosis by carnitine challenge test in human and germ-free mice. Gut. 2019;68(8):1439–49.
Article
CAS
PubMed
Google Scholar
Guasch-Ferre M, Satija A, Blondin SA, Janiszewski M, Emlen E, O'Connor LE, Campbell WW, Hu FB, Willett WC, Stampfer MJ. Meta-analysis of randomized controlled trials of red meat consumption in comparison with various comparison diets on cardiovascular risk Factors. circulation. 2019;139(15):1828–45.
Article
PubMed
Google Scholar
Zeraatkar D, Johnston BC, Bartoszko J, Cheung K, Bala MM, Valli C, Rabassa M, Sit D, Milio K, Sadeghirad B, et al. Effect of lower versus higher red meat intake on cardiometabolic and cancer outcomes: a systematic review of randomized trials. Ann Intern Med. 2019.
DiNicolantonio JJ, Lavie CJ, Fares H, Menezes AR, O'Keefe JH. L-carnitine in the secondary prevention of cardiovascular disease: systematic review and meta-analysis. Mayo Clin Proc. 2013;88(6):544–51.
Article
CAS
PubMed
Google Scholar
Shang R, Sun Z, Li H. Effective dosing of L-carnitine in the secondary prevention of cardiovascular disease: a systematic review and meta-analysis. BMC Cardiovasc Disord. 2014;14:88.
Article
PubMed
PubMed Central
CAS
Google Scholar
Craciun S, Balskus EP. Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. Proc Natl Acad Sci U S A. 2012;109(52):21307–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Romano KA, Vivas EI, Amador-Noguez D, Rey FE. Intestinal microbiota composition modulates choline bioavailability from diet and accumulation of the proatherogenic metabolite trimethylamine-N-oxide. MBio. 2015;6(2):e02481.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang Z, Roberts AB, Buffa JA, Levison BS, Zhu W, Org E, Gu X, Huang Y, Zamanian-Daryoush M, Culley MK, et al. Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis. Cell. 2015;163(7):1585–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Skye SM, Zhu W, Romano KA, Guo CJ, Wang Z, Jia X, Kirsop J, Haag B, Lang JM, DiDonato JA, et al. Microbial transplantation with human gut commensals containing CutC is sufficient to transmit enhanced platelet reactivity and thrombosis potential. Circ Res. 2018;123(10):1164–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu Y, Jameson E, Crosatti M, Schafer H, Rajakumar K, Bugg TD, Chen Y. Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota. Proc Natl Acad Sci U S A. 2014;111(11):4268–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koeth RA, Lam-Galvez BR, Kirsop J, Wang Z, Levison BS, Gu X, Copeland MF, Bartlett D, Cody DB, Dai HJ, et al. l-Carnitine in omnivorous diets induces an atherogenic gut microbial pathway in humans. J Clin Invest. 2019;129(1):373–87.
Article
PubMed
Google Scholar
Wang Z, Bergeron N, Levison BS, Li XS, Chiu S, Jia X, Koeth RA, Li L, Wu Y, Tang WHW, et al. Impact of chronic dietary red meat, white meat, or non-meat protein on trimethylamine N-oxide metabolism and renal excretion in healthy men and women. Eur Heart J. 2019;40(7):583–94.
Article
CAS
PubMed
Google Scholar
Ndongo S, Lagier JC, Fournier PE, Raoult D, Khelaifia S. “Ihubacter massiliensis”: a new bacterium isolated from the human gut. New Microbes New Infect. 2016;13:104–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Romano KA, Dill-McFarland KA, Kasahara K, Kerby RL, Vivas EI, Amador-Noguez D, Herd P, Rey FE. Fecal aliquot straw technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation. Microbiome. 2018;6(1):91.
Article
PubMed
PubMed Central
Google Scholar
Rebouche CJ, Chenard CA. Metabolic fate of dietary carnitine in human adults: identification and quantification of urinary and fecal metabolites. J Nutr. 1991;121(4):539–46.
Article
CAS
PubMed
Google Scholar
Evans AM, Fornasini G. Pharmacokinetics of L-carnitine. Clin Pharmacokinet. 2003;42(11):941–67.
Article
CAS
PubMed
Google Scholar
Rebouche CJ. Kinetics, pharmacokinetics, and regulation of L-carnitine and acetyl-L-carnitine metabolism. Ann N Y Acad Sci. 2004;1033:30–41.
Article
CAS
PubMed
Google Scholar
Koeth RA, Levison BS, Culley MK, Buffa JA, Wang Z, Gregory JC, Org E, Wu Y, Smith JD LL, et al. gamma-Butyrobetaine is a proatherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO. Cell Metab. 2014;20(5):799–812.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fuhrman JA. Microbial community structure and its functional implications. Nature. 2009;459(7244):193–9.
Article
CAS
PubMed
Google Scholar
Wu WK, Chen CC, Panyod S, Chen RA, Wu MS, Sheen LY, Chang SC. Optimization of fecal sample processing for microbiome study—the journey from bathroom to bench. J Formos Med Assoc. 2019;118(2):545–55.
Article
PubMed
Google Scholar
Comeau AM, Douglas GM, Langille MG. Microbiome helper: a custom and streamlined workflow for microbiome research. mSystems. 2017;2(1).
Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina paired-end reAd mergeR. Bioinformatics. 2014;30(5):614–20.
Article
CAS
PubMed
Google Scholar
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):335–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kuczynski J, Stombaugh J, Walters WA, Gonzalez A, Caporaso JG, Knight R. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics. 2011;Chapter 10:Unit 10 17.
Google Scholar
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.
CAS
PubMed
Google Scholar
Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glockner FO. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res. 2014;42(D1):D643–8.
Article
CAS
PubMed
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460–1.
Article
CAS
PubMed
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
Article
PubMed
PubMed Central
CAS
Google Scholar
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H. vegan: community ecology package. R package version 2.3-1. In: Oulu, Finland; 2015.
Google Scholar
R Core Team. R: A language and environment for statistical computing. In: R Foundation for Statistical Computing, Vienna, Austria; 2015.
Google Scholar
Vavrek MJ. fossil: palaeoecological and palaeogeographical analysis tools. Palaeontol Electron. 2011;14(1):16.
Google Scholar
Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26(1):32–46.
Google Scholar
Kolde R. pheatmap: Pretty heatmaps. R package version 1.0.8. In; 2015.
Google Scholar
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008;36(Web Server):W465–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dereeper A, Audic S, Claverie JM, Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol. 2010;10:8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Edgar RCMUSCLE. a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113.
Article
PubMed
PubMed Central
CAS
Google Scholar
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17(4):540–52.
Article
CAS
PubMed
Google Scholar
Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52(5):696–704.
Article
PubMed
Google Scholar
Rambaut A. FigTree version 1.4.3. In.; 2009.
Google Scholar
Liaw A, Wiener M. Classification and Regression by randomForest. R News. 2002;2(3):18–22.
Google Scholar
Kuhn M. Building Predictive Models inRUsing thecaretPackage. J Stat Softw. 2008;28(5).
Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics. 2005;21(20):3940–1.
Article
CAS
PubMed
Google Scholar