Roux-en-Y gastric bypass and sleeve gastrectomy induce substantial and persistent changes in microbial communities and metabolic pathways

References

• Buchwald H, Oien DM. Metabolic/Bariatric surgery worldwide 2011. Obesity Surgery. 2013;23(4):427–15. doi:10.1007/s11695-012-0864-0.
   PubMed Web of Science ®Google Scholar
• Sjöström L, Lindroos A-K, Peltonen M, Torgerson J, Bouchard C, Carlsson B, Dahlgren S, Larsson B, Narbro K, Sjöström CD, et al. Lifestyle, diabetes, and cardiovascular risk factors 10 years after bariatric surgery. N Engl J Med. 2004;351:2683–2693.
   PubMed Web of Science ®Google Scholar
• Le Roux CW, Bloom SR. Editorial: why do patients lose weight after Roux-en-Y gastric bypass? J Clin Endocrinol Metab. 2005;90:591–592.
   PubMed Web of Science ®Google Scholar
• Miras AD, le Roux CW. Mechanisms underlying weight loss after bariatric surgery. Nat Rev Gastroenterol Hepatol [Internet]. 2013;10:575–584. Available from. doi:10.1038/nrgastro.2013.119.
   PubMed Web of Science ®Google Scholar
• Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell MD, Wing R, Rittmann BE, et al. Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci U S A. 2009;106:2365–2370. .
   PubMed Web of Science ®Google Scholar
• Palleja A, Kashani A, Allin KH, Nielsen T, Zhang C, Li Y, Brach T, Liang S, Feng Q, Jørgensen NB, et al. Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota. Genome Med [Internet] [cited 2017 Nov 23]; 8:67. Available from. 2016;(1): http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0312-1.
   PubMed Web of Science ®Google Scholar
• Sanmiguel CP, Jacobs J, Gupta A, Ju T, Stains J, Coveleskie K, Lagishetty V, Balioukova A, Chen Y, Dutson E, et al. Surgically induced changes in gut microbiome and hedonic eating as related to weight loss. Psychosom Med [Internet] 2017 [[cited 2017 Nov 23]]. 79:880–887. Available from http://www.ncbi.nlm.nih.gov/pubmed/28570438
   PubMed Web of Science ®Google Scholar
• Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, Shi J, Zhao S, Liu W, Wang X, et al. Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. Nat Med [Internet] 2017 [[cited 2017 Nov 23]]. 23:859–868. Available from http://www.nature.com/doifinder/10.1038/nm.4358
   PubMed Web of Science ®Google Scholar
• Damms-Machado A, Mitra S, Schollenberger AE, Kramer KM, Meile T, Königsrainer A, Huson DH, Bischoff SC. Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption. Biomed Res Int [Internet]. 2015 [cited 2017 Nov 23];2015:1–12. Available from http://www.hindawi.com/journals/bmri/2015/806248/.
   Web of Science ®Google Scholar
• Patil DP, Dhotre DP, Chavan SG, Sultan A, Jain DS, Lanjekar VB, Gangawani J, Shah PS, Todkar JS, Shah S, et al. Molecular analysis of gut microbiota in obesity among Indian individuals. J Biosci [Internet] 2012 [[cited 2017 Nov 23]]. 37:647–657. Available from http://link.springer.com/10.1007/s12038-012-9244-0
   PubMed Web of Science ®Google Scholar
• Kong LC, Tap J, Aron-Wisnewsky J, Pelloux V, Basdevant A, Bouillot JL, Zucker JD, Doré J, Clément K, Kong Judith Aron-Wisnewsky L-C, et al. 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 [cited 2017 Nov 23]. 98:16–24. Available from http://www.ncbi.nlm.nih.gov/pubmed/23719559
   PubMed Web of Science ®Google Scholar
• Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong M-LM, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, et al. Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters. Pharmacogenomics J. 2013;13:514–522.
   PubMed Web of Science ®Google Scholar
• Ward EK, Schuster DP, Stowers KH, Royse AK, Ir D, Robertson CE, Frank DN, Austin GL. The effect of PPI use on human gut microbiota and weight loss in patients undergoing laparoscopic Roux-en-Y gastric bypass. Obes Surg [Internet]. 2014 [cited 2017 Nov 23];24:1567–1571. Available from http://link.springer.com/10.1007/s11695-014-1275-1.
   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. 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. 2015;22(2):228–238. doi:10.1016/j.cmet.2015.07.009.
   PubMed Web of Science ®Google Scholar
• Palleja A, Kashani A, Allin KH, Nielsen T, Zhang C, Li Y, Brach T, Liang S, Feng Q, Jørgensen NB, et al. Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota. Genome Med [Internet] 2016 [[cited 2017 Nov 23]]. 8:67. Available from http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0312-1
   PubMed Web of Science ®Google Scholar
• Murphy R, Tsai P, Jüllig M, Liu A, Plank L, Booth M. Differential changes in gut microbiota after gastric bypass and sleeve gastrectomy bariatric surgery vary according to diabetes remission. Obes Surg [Internet]. 2017 [cited 2017 Nov 23];27:917–925. Available from http://link.springer.com/10.1007/s11695-016-2399-2.
   PubMed Web of Science ®Google Scholar
• Ilhan ZE, DiBaise JK, Isern NG, Hoyt DW, Marcus AK, Kang D-W, Crowell MD, Rittmann BE, Krajmalnik-Brown R. Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding. ISME J Internet] 2017 [cited 2017 Nov 23]; 11:2047–2058. Available from. http://www.ncbi.nlm.nih.gov/pubmed/28548658.
   PubMed Web of Science ®Google Scholar
• Vester-Andersen MK, Mirsepasi-Lauridsen HC, Prosberg MV, Mortensen CO, Träger C, Skovsen K, Thorkilgaard T, Nøjgaard C, Vind I, Krogfelt KA, et al. Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis. Sci Rep. 2019;9:1–10.
   PubMed Web of Science ®Google Scholar
• Shao Y, Ding R, Xu B, Hua R, Shen Q, He K, Yao Q. Alterations of gut microbiota after Roux-en-Y gastric bypass and sleeve gastrectomy in Sprague-Dawley rats. Obes Surg. 2017;27:295–302.
   PubMed Web of Science ®Google Scholar
• Celiker H. A new proposed mechanism of action for gastric bypass surgery: air hypothesis. Med Hypotheses [Internet]. 2017;107:81–89. Available from. doi:10.1016/j.mehy.2017.08.012.
   PubMed Web of Science ®Google Scholar
• Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, Grunberg S, Baldassano RN, Lewis JD, Li H, et al. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology [Internet]. 2014;147:1055–1063.e8. Available from. doi:10.1053/j.gastro.2014.07.020.
   PubMed Web of Science ®Google Scholar
• Ferrara PJ, Rong X, Maschek JA, Verkerke ARP, Siripoksup P, Song H, Green TD, Krishnan KC, Johnson JM, Turk J, et al. Lysophospholipid acylation modulates plasma membrane lipid organization and insulin sensitivity in skeletal muscle. J Clin Invest 2021; 131.
   Google Scholar
• Zeng Q, Li D, He Y, Li Y, Yang Z, Zhao X, Liu Y, Wang Y, Sun J, Feng X, et al. Discrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities. Sci Rep [Internet]. 2019;9:1–10. Available from. doi:10.1038/s41598-019-49462-w.
   PubMed Web of Science ®Google Scholar
• Vazquez-Moreno M, Perez-Herrera A, Locia-Morales D, Dizzel S, Meyre D, Stearns JC, Cruz M. Association of gut microbiome with fasting triglycerides, fasting insulin and obesity status in Mexican children. Pediatr Obes. 2021;16:1–8.
   Web of Science ®Google Scholar
• Cui H, Li Y, Wang Y, Jin L, Yang L, Wang L, Liao J, Wang H, Peng Y, Zhang Z, et al. Da-Chai-Hu decoction ameliorates high fat diet-induced nonalcoholic fatty liver disease through remodeling the gut microbiota and modulating the serum metabolism. Front Pharmacol. 2020;11:1–17.
   PubMed Web of Science ®Google Scholar
• Kasai C, Sugimoto K, Moritani I, Tanaka J, Oya Y, Inoue H, Tameda M, Shiraki K, Ito M, Takei Y, et al. Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing. BMC Gastroenterol [Internet]. 2015;15:1–10. Available from. doi:10.1186/s12876-015-0330-2.
   PubMed Web of Science ®Google Scholar
• Tims S, Derom C, Jonkers DM, Vlietinck R, Saris WH, Kleerebezem M, De Vos WM, Zoetendal EG. Microbiota conservation and BMI signatures in adult monozygotic twins. ISME J. 2013;7:707–717.
   PubMed Web of Science ®Google Scholar
• Sheppard K, Yuan J, Hohn MJ, Jester B, Devine KM, Söll D. From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucleic Acids Res. 2008;36:1813–1825.
   PubMed Web of Science ®Google Scholar
• Abbott JA, Francklyn CS, Robey-Bond SM. Transfer RNA and human disease. Front Genet. 2014;5:1–18.
   PubMed Web of Science ®Google Scholar
• Wei F, Suzuki T, Tomizawa K, Wei F, Suzuki T, Watanabe S, Kimura S, Kaitsuka T. Deficit of tRNA Lys modification by Cdkal1 causes the development of type 2 diabetes in mice Find the latest version : deficit of tRNA Lys modification by Cdkal1 causes the development of type 2 diabetes in mice. J Clin Invest. 2011;121:3598–3608.
   PubMed Web of Science ®Google Scholar
• Wei FY, Tomizawa K. Functional loss of Cdkal1, a novel tRNA modification enzyme, causes the development of type 2 diabetes. Endocr J. 2011;58:819–825.
   PubMed Web of Science ®Google Scholar
• Palmer CJ, Bruckner RJ, Paulo JA, Kazak L, Long JZ, Mina AI, Deng Z, LeClair KB, Hall JA, Hong S, et al. Cdkal1, a type 2 diabetes susceptibility gene, regulates mitochondrial function in adipose tissue. Mol Metab [Internet]. 2017;6:1212–1225. Available from. doi:10.1016/j.molmet.2017.07.013.
   PubMed Web of Science ®Google Scholar
• Wang M, Liu H, Zheng J, Chen B, Zhou M, Fan W, Wang H, Liang X, Zhou X, Eriani G, et al. A deafness-and diabetes-associated tRNA Mutation causes deficient pseudouridinylation at position 55 in tRNAGlu and mitochondrial dysfunction. J Biol Chem. 2016;291:21029–21041.
   PubMed Web of Science ®Google Scholar
• Igoillo-Esteve M, Genin A, Lambert N, Désir J, Pirson I, Abdulkarim B, Simonis N, Drielsma A, Marselli L, Marchetti P, et al. tRNA methyltransferase homolog gene TRMT10A mutation in young onset diabetes and primary microcephaly in humans. PLoS Genet. 2013;9:1–5.
   Web of Science ®Google Scholar
• Yu YC, Han JM, Kim S Jan . Aminoacy-tRNA Synthetases and amino acid signaling. Biochim Biophys Acta (BBA)-Molecular Cell Res. 2021;1868(1):118889.
   PubMed Web of Science ®Google Scholar
• Guo Y, Liu CQ, Liu GP, Huang ZP, Zou DJ. Roux-en-Y gastric bypass decreases endotoxemia and inflammatory stress in association with improvements in gut permeability in obese diabetic rats. J Diabetes. 2019;11:786–793.
   PubMed Web of Science ®Google Scholar
• Sui J, He M, Wang Y, Zhao X, He Y, Shi B. Sphingolipid metabolism in type 2 diabetes and associated cardiovascular complications. Exp Ther Med. 2019;18(5):3603–3614.
   PubMed Web of Science ®Google Scholar
• Khan SR, Manialawy Y, Obersterescu A, Cox BJ, Gunderson EP, Wheeler MB. Diminished Sphingolipid Metabolism, a Hallmark of Future Type 2 Diabetes Pathogenesis, Is Linked to Pancreatic β Cell Dysfunction. iScience. 2020;23(10):101566.
   PubMed Web of Science ®Google Scholar
• Sun L, Xie C, Wang G, Wu Y, Wu Q, Wang X, Liu J, Deng Y, Xia J, Chen B, et al. Gut microbiota and intestinal FXR mediate the clinical benefits of metformin. Nat Med [Internet]. 2018;24:1919–1929. Available from. doi:10.1038/s41591-018-0222-4.
   PubMed Web of Science ®Google Scholar
• Willing BP, Russell SL, Finlay BB. Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol [Internet]. 2011;9:233–243. Available from. doi:10.1038/nrmicro2536.
   PubMed Web of Science ®Google Scholar
• University of Oxford. HOMA2 Calculator [Internet]. Accessed 27 May 2020. Available from: https://www.dtu.ox.ac.uk/homacalculator/
   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;13:581–583.
   PubMed Web of Science ®Google Scholar
• McMurdie PJ, Holmes S. Phyloseq: an R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS One. 2013;8(4):e61217.
   PubMed Web of Science ®Google Scholar
• Ni Y, Yu G, Chen H, Deng Y, Wells PM, Steves CJ, Ju F, Fu J. M2IA: a web server for microbiome and metabolome integrative analysis. Bioinformatics. 2020;36:3493–3498.
   PubMed Web of Science ®Google Scholar
• Wemheuer F, Taylor JA, Daniel R, Johnston E, Meinicke P, Thomas T, Wemheuer B. Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environ Microbiomes. 2020;15:1–12.
   PubMedGoogle Scholar