Gut microbiota in nonalcoholic fatty liver disease: a PREDIMED-Plus trial sub analysis

References

• Younossi ZM, Koenig AB, Abdelatif D, Fazel Y, Henry L, Wymer M. Global epidemiology of nonalcoholic fatty liver disease—Meta-analytic assessment of prevalence, incidence, and outcomes. Hepatology. 2016;64(1):73–17. doi:10.1002/hep.28431.
   PubMed Web of Science ®Google Scholar
• Martínez-Montoro JI, Cornejo-Pareja I, Gómez-Pérez AM, Tinahones FJ. Impact of genetic polymorphism on response to therapy in non-alcoholic fatty liver disease. Nutrients. 2021;13(11):4077. doi:10.3390/nu13114077.
   PubMed Web of Science ®Google Scholar
• Eslam M, Newsome PN, Sarin SK, Anstee QM, Targher G, Romero-Gomez M, Zelber-Sagi S, Wai-Sun Wong V, Dufour J-F, Schattenberg JM, et al. A new definition for metabolic dysfunction-associated fatty liver disease: an international expert consensus statement. J Hepatol. 2020;73(1):202–209. doi:10.1016/j.jhep.2020.03.039.
   PubMed Web of Science ®Google Scholar
• Zhou J, Tripathi M, Sinha RA, Singh BK, Yen PM. Gut microbiota and their metabolites in the progression of non-alcoholic fatty liver disease. Hepatoma Res. 2021;7:11. doi:10.20517/2394-5079.2020.134.
   PubMedGoogle Scholar
• Hoyles L, Fernández-Real J-M, Federici M, Serino M, Abbott J, Charpentier J, Heymes C, Luque JL, Anthony E, Barton RH, et al. Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women. Nat Med. 2018;24(7):1070–1080. doi:10.1038/s41591-018-0061-3.
   PubMed Web of Science ®Google Scholar
• Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, et al. Gut microbiome-based metagenomic signature for non-invasive detection of advanced fibrosis in human nonalcoholic fatty liver disease. Cell Metab. 2017;25(5):1054–1062.e5. doi:10.1016/j.cmet.2017.04.001.
   PubMed Web of Science ®Google Scholar
• Zhu L, Baker SS, Gill C, Liu W, Alkhouri R, Baker RD, Gill SR. Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH. Hepatology. 2013;57(2):601–609. doi:10.1002/hep.26093.
   PubMed Web of Science ®Google Scholar
• Younossi Z, Anstee QM, Marietti M, Hardy T, Henry L, Eslam M, George J, Bugianesi E. Global burden of NAFLD and NASH: trends, predictions, risk factors and prevention. Nat Rev Gastroenterol Hepatol. 2018;15(1):11–20. doi:10.1038/nrgastro.2017.109.
   PubMed Web of Science ®Google Scholar
• Marchesini G, Brizi M, Bianchi G, Tomassetti S, Bugianesi E, Lenzi M, McCullough AJ, Natale S, Forlani G, Melchionda N. Nonalcoholic fatty liver disease: a feature of the metabolic syndrome. Diabetes. 2001;50(8):1844–1850. doi:10.2337/diabetes.50.8.1844.
   PubMed Web of Science ®Google Scholar
• Albillos A, de Gottardi A, Rescigno M. The gut-liver axis in liver disease: pathophysiological basis for therapy. J Hepatol. 2020;72(3):558–577. doi:10.1016/j.jhep.2019.10.003.
   PubMed Web of Science ®Google Scholar
• Hrncir T, Hrncirova L, Kverka M, Hromadka R, Machova V, Trckova E, Kostovcikova K, Kralickova P, Krejsek J, Tlaskalova-Hogenova H. Gut microbiota and NAFLD: pathogenetic mechanisms, microbiota signatures, and therapeutic interventions. Microorganisms. 2021;9(5):957. doi:10.3390/microorganisms9050957.
   PubMed Web of Science ®Google Scholar
• Martínez-Urbistondo D, San Cristóbal R, Villares P, Martínez-González MÁ, Babio N, Corella D, Del Val JL, Ordovás JM, Alonso-Gómez ÁM, Wärnberg J, et al. Role of NAFLD on the health related QoL response to lifestyle in patients with metabolic syndrome: the PREDIMED plus cohort. Front Endocrinol (Lausanne). 2022;13:868795. doi:10.3389/fendo.2022.868795.
   PubMed Web of Science ®Google Scholar
• Adams LA, Wang Z, Liddle C, Melton PE, Ariff A, Chandraratna H, Tan J, Ching H, Coulter S, de Boer B, et al. Bile acids associate with specific gut microbiota, low-level alcohol consumption and liver fibrosis in patients with non-alcoholic fatty liver disease. Liver Int. 2020;40(6):1356–1365. doi:10.1111/liv.14453.
   PubMed Web of Science ®Google Scholar
• Caussy C, Hsu C, Lo MT, Liu A, Bettencourt R, Ajmera VH, Bassirian S, Hooker J, Sy E, Richards L, et al. Link between gut-microbiome derived metabolite and shared gene-effects with hepatic steatosis and fibrosis in NAFLD. Hepatology (Baltimore, Md) [Internet]. 2018;68:918–932. [accessed 2022 Jun 7]. https://pubmed.ncbi.nlm.nih.gov/29572891/.
   PubMed Web of Science ®Google Scholar
• Vallianou N, Christodoulatos GS, Karampela I, Tsilingiris D, Magkos F, Stratigou T, Kounatidis D, Dalamaga M. Understanding the role of the gut microbiome and microbial metabolites in non-alcoholic fatty liver disease: current evidence and perspectives. Biomolecules [Internet]. 2021;12:56. [accessed 2022 Jun 7]. https://pubmed.ncbi.nlm.nih.gov/35053205/.
   PubMed Web of Science ®Google Scholar
• Maillard F, Vazeille E, Sauvanet P, Sirvent P, Bonnet R, Combaret L, Chausse P, Chevarin C, Otero YF, Delcros G, et al. Preventive effect of spontaneous physical activity on the gut-adipose tissue in a mouse model that mimics crohn’s disease susceptibility. Cells. 2019;8(1):E33. doi:10.3390/cells8010033.
   PubMed Web of Science ®Google Scholar
• Haro C, Montes-Borrego M, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Tinahones FJ, Landa BB, et al. Two healthy diets modulate gut microbial community improving insulin sensitivity in a human obese population. J Clin Endocrinol Metab. 2016;101(1):233–242. doi:10.1210/jc.2015-3351.
   PubMed Web of Science ®Google Scholar
• Oscillospira - a candidate for the next-generation probiotics - PubMed [Internet]. [accessed 2022 Jul 6]. https://pubmed.ncbi.nlm.nih.gov/34693878/
   Google Scholar
• Liu X, Mao B, Gu J, Wu J, Cui S, Wang G, Zhao J, Zhang H, Chen W. Blautia-a new functional genus with potential probiotic properties? Gut Microbes. 2021;13:1–21. doi:10.1080/19490976.2021.1875796.
   Web of Science ®Google Scholar
• Vaughn BP, Kaiser T, Staley C, Hamilton MJ, Reich J, Graiziger C, Singroy S, Kabage AJ, Sadowsky MJ, Khoruts A. A pilot study of fecal bile acid and microbiota profiles in inflammatory bowel disease and primary sclerosing cholangitis. Clin Exp Gastroenterol. 2019;12:9–19. doi:10.2147/CEG.S186097.
   PubMed Web of Science ®Google Scholar
• Vallianou N, Dalamaga M, Stratigou T, Karampela I, Tsigalou C. Do antibiotics cause obesity through long-term alterations in the gut microbiome? A review of current evidence. Curr Obes Rep. 2021;10(3):244–262. doi:10.1007/s13679-021-00438-w.
   PubMed Web of Science ®Google Scholar
• Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA, Holscher HD, Woods JA. Exercise alters gut microbiota composition and function in lean and obese humans. Med Sci Sports Exerc. 2018;50:747–757. doi:10.1249/MSS.0000000000001495.
   PubMed Web of Science ®Google Scholar
• Tremaroli V, Karlsson F, Werling M, Ståhlman M, Kovatcheva-Datchary P, Olbers T, Fändriks L, le Roux CW, Nielsen J, Bäckhed F, et al. Roux-en-Y gastric bypass and vertical banded gastroplasty induce long-term changes on the human gut Microbiome Contributing to Fat Mass Regulation. Cell Metab [Internet]. 2015;22:228–238. [accessed 2022 Jun 17]. https://www.cell.com/cell-metabolism/abstract/S1550-4131(15)00338-1.
   PubMed Web of Science ®Google Scholar
• Kong L-C, Tap J, Aron-Wisnewsky J, Pelloux V, Basdevant A, Bouillot J-L, Zucker J-D, Doré J, Clément K. Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes. Am J Clin Nutr [Internet]. 2013;98(1):16–24. [accessed 2022 Jun 17]. doi:10.3945/ajcn.113.058743.
   PubMed Web of Science ®Google Scholar
• Celiker H. A new proposed mechanism of action for gastric bypass surgery: air hypothesis. Med Hypotheses. 2017;107:81–89. doi:10.1016/j.mehy.2017.08.012.
   PubMed Web of Science ®Google Scholar
• Steinert RE, Rehman A, Lima EJS, Agamennone V, Schuren FHJ, Gero D, Schreiner P, Vonlanthen R, Ismaeil A, Tzafos S, et al. Roux-en-Y gastric bypass surgery changes fungal and bacterial microbiota in morbidly obese patients—A pilot study. PLos One. 2020;15(7):e0236936. doi:10.1371/journal.pone.0236936.
   PubMed Web of Science ®Google Scholar
• Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome: Cell Host & Microbe [Internet]. [accessed 2022 Jun 17]. https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(08)00089-9?returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1931312808000899%3Fshowall%3Dtrue.
   Google Scholar
• The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level | Gut [Internet]. [accessed 2022 Jun 17]. https://gut.bmj.com/content/67/4/625.long.
   Google Scholar
• Shin J, Noh J-R, Choe D, Lee N, Song Y, Cho S, Kang E-J, Go M-J, Ha SK, Chang D-H, et al. Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing. Microbiome. 2021;9(1):240. doi:10.1186/s40168-021-01189-5.
   PubMed Web of Science ®Google Scholar
• Hong Y, Sheng L, Zhong J, Tao X, Zhu W, Ma J, Yan J, Zhao A, Zheng X, Wu G, et al. Desulfovibrio vulgaris, a potent acetic acid-producing bacterium, attenuates nonalcoholic fatty liver disease in mice. Gut Microbes. 2021;13(1):1930874. doi:10.1080/19490976.2021.1930874.
   PubMed Web of Science ®Google Scholar
• Meslier V, Laiola M, Roager HM, De Filippis F, Roume H, Quinquis B, Giacco R, Mennella I, Ferracane R, Pons N, et al. Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake. Gut. 2020;69(7):1258–1268. doi:10.1136/gutjnl-2019-320438.
   PubMed Web of Science ®Google Scholar
• Lanthier N, Rodriguez J, Nachit M, Hiel S, Trefois P, Neyrinck AM, Cani PD, Bindels LB, Thissen J-P, Delzenne NM. Microbiota analysis and transient elastography reveal new extra-hepatic components of liver steatosis and fibrosis in obese patients. Sci Rep. 2021;11(1):659. doi:10.1038/s41598-020-79718-9.
   PubMed Web of Science ®Google Scholar
• Kaakoush NO. Sutterella Species, IgA-degrading bacteria in ulcerative colitis. Trends Microbiol. 2020;28(7):519–522. doi:10.1016/j.tim.2020.02.018.
   PubMed Web of Science ®Google Scholar
• Sayón-Orea C, Razquin C, Bulló M, Corella D, Fitó M, Romaguera D, Vioque J, Alonso-Gómez ÁM, Wärnberg J, Martínez JA, et al. Effect of a nutritional and behavioral intervention on energy-reduced Mediterranean diet adherence among patients with metabolic syndrome: interim analysis of the PREDIMED-Plus randomized clinical trial. JAMA. 2019;322(15):1486–1499. doi:10.1001/jama.2019.14630.
   PubMed Web of Science ®Google Scholar
• Lee J-H, Kim D, Kim HJ, Lee C-H, Yang JI, Kim W, Kim YJ, Yoon J-H, Cho S-H, Sung M-W, et al. Hepatic steatosis index: a simple screening tool reflecting nonalcoholic fatty liver disease. Dig Liver Dis. 2010;42(7):503–508. doi:10.1016/j.dld.2009.08.002.
   PubMedGoogle Scholar
• Development of a simple noninvasive index to predict significant fibrosis in patients with HIV/HCV coinfection - Sterling - 2006 - Hepatology - Wiley Online Library [Internet]. [accessed 2022 Mar 8]. https://aasldpubs.onlinelibrary.wiley.com/doi/full/10.1002/hep.21178.
   Google Scholar
• Martínez-González MA, Buil-Cosiales P, Corella D, Bulló M, Fitó M, Vioque J, Romaguera D, Martínez JA, Wärnberg J, López-Miranda J, et al. Cohort profile: design and methods of the PREDIMED-Plus randomized trial. Int J Epidemiol. 2019;48(2):387–388o. doi:10.1093/ije/dyy225.
   PubMed Web of Science ®Google Scholar
• Bairaktari ET, Seferiadis KI, Elisaf MS. Evaluation of methods for the measurement of low-density lipoprotein cholesterol [Internet]. 2005 [accessed 2022 Sep 21]. https://journals.sagepub.com/doi/10.1177/107424840501000106.
   Google Scholar
• Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–857. doi:10.1038/s41587-019-0209-9.
   PubMed Web of Science ®Google Scholar
• 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(7):581–583. doi:10.1038/nmeth.3869.
   PubMed Web of Science ®Google Scholar
• Dhariwal A, Chong J, Habib S, King IL, Agellon LB, Xia J. MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res. 2017;45(W1):W180–8. doi:10.1093/nar/gkx295.
   PubMed Web of Science ®Google Scholar
• McMurdie PJ, Holmes S, McHardy AC. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014;10(4):e1003531. doi:10.1371/journal.pcbi.1003531.
   PubMed Web of Science ®Google Scholar
• Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI. Picrust2 for prediction of metagenome functions. Nat Biotechnol. 2020;38(6):685–688. doi:10.1038/s41587-020-0548-6.
   PubMed Web of Science ®Google Scholar
• Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD. The MetaCyc database of metabolic pathways and enzymes - a 2019 update. Nucleic Acids Res. 2020;48(D1):D445–53. doi:10.1093/nar/gkz862.
   PubMed Web of Science ®Google Scholar
• Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30(21):3123–3124. doi:10.1093/bioinformatics/btu494.
   PubMed Web of Science ®Google Scholar