The gut microbiota, environment and diseases of modern society

Gut Microbes

Volumn 3, Issue 4, 2012, Pages

  Kelsen, Judith R ^a   Wu, Gary D ^b  

^a CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; BACTERIAL RNA; RNA 16S;

ANTIBIOTIC THERAPY; ATHEROSCLEROSIS; BACTERIAL GENE; DIABETES MELLITUS; DNA SEQUENCE; ENVIRONMENTAL IMPACT; FOOD INTAKE; GENOTYPE; HOST SUSCEPTIBILITY; HUMAN; INNATE IMMUNITY; INTESTINE FLORA; MORBIDITY; NONHUMAN; OBESITY; PATHOGENESIS; REVIEW;

EID: 84863877508     PISSN: 19490976     EISSN: 19490984     Source Type: Journal    
DOI: 10.4161/gmic.21333     Document Type: Review

References (83)

1. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464:59-65; PMID: 20203603; DOI: 10.1038/nature08821.
2. Lozupone CA, Knight R. Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev 2008; 32:557-78; PMID: 18435746; DOI: 10.1111/j.1574-6976.2008.00111.x.
3. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science 2009; 326:1694-7; PMID: 19892944; DOI: 10.1126/science.1177486.
4. Reid G, Younes JA, Van der Mei HC, Gloor GB, Knight R, Busscher HJ. Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat Rev Microbiol 2011; 9:27-38; PMID: 21113182; DOI: 10.1038/nrmicro2473.
5. Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science 2001; 292:1115-8; PMID: 11352068; DOI: 10.1126/science.1058709.
6. Marchesi JR. Prokaryotic and eukaryotic diversity of the human gut. Adv Appl Microbiol 2010; 72:43-62; PMID: 20602987; DOI: 10.1016/S0065-2164(10)72002-5.
7. Hamady M, Knight R. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res 2009; 19:1141-52; PMID: 19383763; DOI: 10.1101/gr.085464.108.
8. Anderson IC, Cairney JW. Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 2004; 6:769-79; PMID: 15250879; DOI: 10.1111/j.1462-2920.2004.00675.x.
9. Fisher MM, Triplett EW. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 1999; 65:4630-6; PMID: 10508099.
10. Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 2007; 73:1576-85; PMID: 17220268; DOI: 10.1128/AEM.01996-06.
11. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol 2007; 5:e177; PMID: 17594176; DOI: 10.1371/journal.pbio.0050177.
12. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA 2011; 108:4578-85; PMID: 20668239; DOI: 10.1073/pnas.1000081107.
13. Schwartz S, Friedberg I, Ivanov IV, Davidson LA, Goldsby JS, Dahl DB, et al. A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response. Genome Biol 2012; 13:r32; PMID: 22546241; DOI: 10.1186/gb-2012-13-4-r32.
14. Roger LC, McCartney AL. Longitudinal investigation of the faecal microbiota of healthy full-term infants using fluorescence in situ hybridization and denaturing gradient gel electrophoresis. Microbiology 2010; 156:3317-28; PMID: 20829292; DOI: 10.1099/mic.0.041913-0.
15. Fallani M, Amarri S, Uusijarvi A, Adam R, Khanna S, Aguilera M, et al. INFABIO team. Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres. Microbiology 2011; 157:1385-92; PMID: 21330436; DOI: 10.1099/mic.0.042143-0.
16. Fallani M, Young D, Scott J, Norin E, Amarri S, Adam R, et al. Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics. J Pediatr Gastroenterol Nutr 2010; 51:77-84; PMID: 20479681; DOI: 10.1097/MPG.0b013e3181d1b11e.
17. Fanaro S, Chierici R, Guerrini P, Vigi V. Intestinal microflora in early infancy: composition and development. Acta Paediatr Suppl 2003; 91:48-55; PMID: 14599042.
18. Grönlund MM, Lehtonen OP, Eerola E, Kero P. Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery. J Pediatr Gastroenterol Nutr 1999; 28:19-25; PMID: 9890463; DOI: 10.1097/00005176-199901000-00007.
19. Huurre A, Kalliomäki M, Rautava S, Rinne M, Salminen S, Isolauri E. Mode of delivery-effects on gut microbiota and humoral immunity. Neonatology 2008; 93:236-40; PMID: 18025796; DOI: 10.1159/000111102.
20. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature 2009; 457:480-4; PMID: 19043404; DOI: 10.1038/nature07540.
21. Spor A, Koren O, Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 2011; 9:279-90; PMID: 21407244; DOI: 10.1038/nrmicro2540.
22. Diamond J. Evolution, consequences and future of plant and animal domestication. Nature 2002; 418:700-7; PMID: 12167878; DOI: 10.1038/nature01019.
23. Walter J, Ley R. The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol 2011; 65:411-29; PMID: 21682646; DOI: 10.1146/annurev-micro-090110-102830.
24. Pflughoeft KJ, Versalovic J. Human Microbiome in Health and Disease. Annu Rev Pathol 2011;; PMID: 21910623.
25. Sonnenburg JL, Xu J, Leip DD, Chen CH, Westover BP, Weatherford J, et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 2005; 307:1955-9; PMID: 15790854; DOI: 10.1126/science.1109051.
26. Sonnenburg ED, Zheng H, Joglekar P, Higginbottom SK, Firbank SJ, Bolam DN, et al. Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 2010; 141:1241-52; PMID: 20603004; DOI: 10.1016/j.cell.2010.05.005.
27. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science 2008; 320:1647-51; PMID: 18497261; DOI: 10.1126/science.1155725.
28. Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 2011; 332:970-4; PMID: 21596990; DOI: 10.1126/science.1198719.
29. Faith JJ, McNulty NP, Rey FE, Gordon JI. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 2011; 333:101-4; PMID: 21596954; DOI: 10.1126/science.1206025.
30. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011; 334:105-8; PMID: 21885731; DOI: 10.1126/science.1208344.
31. Crawford PA, Crowley JR, Sambandam N, Muegge BD, Costello EK, Hamady M, et al. Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc Natl Acad Sci USA 2009; 106:11276-81; PMID: 19549860; DOI: 10.1073/pnas.0902366106.
32. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009; 1:ra14; PMID: 20368178; DOI: 10.1126/scitranslmed.3000322.
33. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. MetaHIT Consortium. Enterotypes of the human gut microbiome. Nature 2011; 473:174-80; PMID: 21508958; DOI: 10.1038/nature09944.
34. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 2010; 107:14691-6; PMID: 20679230; DOI: 10.1073/pnas.1005963107.
35. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature 2012; 486:222-7; PMID: 22699611.
36. Baker M. Genomics: The search for association. Nature 2010; 467:1135-8; PMID: 20981103; DOI: 10.1038/4671135a.
37. Badman MK, Flier JS. The adipocyte as an active participant in energy balance and metabolism. Gastroenterology 2007; 132:2103-15; PMID: 17498506; DOI: 10.1053/j.gastro.2007.03.058.
38. Bonora E. The metabolic syndrome and cardiovascular disease. Ann Med 2006; 38:64-80; PMID: 16448990; DOI: 10.1080/07853890500401234.
39. Khor B, Gardet A, Xavier RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature 2011; 474:307-17; PMID: 21677747; DOI: 10.1038/nature10209.
40. Samuel BS, Gordon JI. A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci USA 2006; 103:10011-6; PMID: 16782812; DOI: 10.1073/pnas.0602187103.
41. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006; 444:1027-31; PMID: 17183312; DOI: 10.1038/nature05414.
42. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 2004; 101:15718-23; PMID: 15505215; DOI: 10.1073/pnas.0407076101.
43. Bäckhed F, Manchester JK, Semenkovich CF, Gordon JI. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci USA 2007; 104:979-84; PMID: 17210919; DOI: 10.1073/pnas.0605374104.
44. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307:1915-20; PMID: 15790844; DOI: 10.1126/science.1104816.
45. Samuel BS, Shaito A, Motoike T, Rey FE, Backhed F, Manchester JK, et al. Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc Natl Acad Sci USA 2008; 105:16767-72; PMID: 18931303; DOI: 10.1073/pnas.0808567105.
46. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006; 444:1022-3; PMID: 17183309; DOI: 10.1038/4441022a.
47. Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P, et al. Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 2008; 32:1720-4; PMID: 18779823; DOI: 10.1038/ijo.2008.155.
48. Bajzer M, Seeley RJ. Physiology: obesity and gut flora. Nature 2006; 444:1009-10; PMID: 17183300; DOI: 10.1038/4441009a.
49. Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, et al. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 2009; 137:1716-24, e1-2; PMID: 19706296; DOI: 10.1053/j.gastro.2009.08.042.
50. Murphy EF, Cotter PD, Healy S, Marques TM, O'Sullivan O, Fouhy F, et al. Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut 2010; 59:1635-42; PMID: 20926643; DOI: 10.1136/gut.2010.215665.
51. de La Serre CB, Ellis CL, Lee J, Hartman AL, Rutledge JC, Raybould HE. Propensity to high-fat diet-induced obesity in rats is associated with changes in the gut microbiota and gut inflammation. Am J Physiol Gastrointest Liver Physiol 2010; 299:G440-8; PMID: 20508158; DOI: 10.1152/ajpgi.00098.2010.
52. Virgin HW, Todd JA. Metagenomics and personalized medicine. Cell 2011; 147:44-56; PMID: 21962506; DOI: 10.1016/j.cell.2011.09.009.
53. Yeung WC, Rawlinson WD, Craig ME. Enterovirus infection and type 1 diabetes mellitus: systematic review and meta-analysis of observational molecular studies. BMJ 2011; 342:d35; PMID: 21292721; DOI: 10.1136/bmj.d35.
54. Craig ME, Howard NJ, Silink M, Rawlinson WD. Reduced frequency of HLA DRB1*03-DQB1*02 in children with type 1 diabetes associated with enterovirus RNA. J Infect Dis 2003; 187:1562-70; PMID: 12721936; DOI: 10.1086/374742.
55. Lönnrot M, Korpela K, Knip M, Ilonen J, Simell O, Korhonen S, et al. Enterovirus infection as a risk factor for beta-cell autoimmunity in a prospectively observed birth cohort: the Finnish Diabetes Prediction and Prevention Study. Diabetes 2000; 49:1314-8; PMID: 10923631; DOI: 10.2337/diabetes.49.8.1314.
56. Salminen K, Sadeharju K, Lönnrot M, Vähäsalo P, Kupila A, Korhonen S, et al. Enterovirus infections are associated with the induction of beta-cell autoimmunity in a prospective birth cohort study. J Med Virol 2003; 69:91-8; PMID: 12436483; DOI: 10.1002/jmv.10260.
57. McCartney SA, Vermi W, Lonardi S, Rossini C, Otero K, Calderon B, et al. RNA sensor-induced type I IFN prevents diabetes caused by a β cell-tropic virus in mice. J Clin Invest 2011; 121:1497-507; PMID: 21403398; DOI: 10.1172/JCI44005.
58. Pozzilli P, Signore A, Williams AJ, Beales PE. NOD mouse colonies around the world--recent facts and figures. Immunol Today 1993; 14:193-6; PMID: 8517916; DOI: 10.1016/0167-5699(93)90160-M.
59. Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 2008; 455:1109-13; PMID: 18806780; DOI: 10.1038/nature07336.
60. Wellen KE, Hotamisligil GS. Inflammation, stress, and diabetes. J Clin Invest 2005; 115:1111-9; PMID: 15864338.
61. Medzhitov R. Toll-like receptors and innate immunity. Nat Rev Immunol 2001; 1:135-45; PMID: 11905821; DOI: 10.1038/35100529.
62. Poltorak A, He X, Smirnova I, Liu MY, Van Huffel C, Du X, et al. Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science 1998; 282:2085-8; PMID: 9851930; DOI: 10.1126/science.282.5396.2085.
63. Lee JY, Ye J, Gao Z, Youn HS, Lee WH, Zhao L, et al. Reciprocal modulation of Toll-like receptor-4 signaling pathways involving MyD88 and phosphatidylinositol 3-kinase/AKT by saturated and polyunsaturated fatty acids. J Biol Chem 2003; 278:37041-51; PMID: 12865424; DOI: 10.1074/jbc.M305213200.
64. Zuany-Amorim C, Hastewell J, Walker C. Toll-like receptors as potential therapeutic targets for multiple diseases. Nat Rev Drug Discov 2002; 1:797-807; PMID: 12360257; DOI: 10.1038/nrd914.
65. Davis JE, Gabler NK, Walker-Daniels J, Spurlock ME. Tlr-4 deficiency selectively protects against obesity induced by diets high in saturated fat. Obesity (Silver Spring) 2008; 16:1248-55; PMID: 18421279; DOI: 10.1038/oby.2008.210.
66. Kim JK. Fat uses a TOLL-road to connect inflammation and diabetes. Cell Metab 2006; 4:417-9; PMID: 17141623; DOI: 10.1016/j.cmet.2006.11.008.
67. Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, Delzenne NM, et al. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes 2008; 57:1470-81; PMID: 18305141; DOI: 10.2337/db07-1403.
68. Tsukumo DM, Carvalho-Filho MA, Carvalheira JB, Prada PO, Hirabara SM, Schenka AA, et al. Loss-of-function mutation in Toll-like receptor 4 prevents diet-induced obesity and insulin resistance. Diabetes 2007; 56:1986-98; PMID: 17519423; DOI: 10.2337/db06-1595.
69. Shi H, Kokoeva MV, Inouye K, Tzameli I, Yin H, Flier JS. TLR4 links innate immunity and fatty acid-induced insulin resistance. J Clin Invest 2006; 116:3015-25; PMID: 17053832; DOI: 10.1172/JCI28898.
70. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 2007; 56:1761-72; PMID: 17456850; DOI: 10.2337/db06-1491.
71. Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 2010; 328:228-31; PMID: 20203013; DOI: 10.1126/science.1179721.
72. Koren O, Spor A, Felin J, Fåk F, Stombaugh J, Tremaroli V, et al. Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci USA 2011; 108:4592-8; PMID: 20937873; DOI: 10.1073/pnas.1011383107.
73. Epstein SE, Speir E, Zhou YF, Guetta E, Leon M, Finkel T. The role of infection in restenosis and atherosclerosis: focus on cytomegalovirus. Lancet 1996; 348:s13-7; PMID: 8918522; DOI: 10.1016/S0140-6736(96)98005-8.
74. Patel P, Mendall MA, Carrington D, Strachan DP, Leatham E, Molineaux N, et al. Association of Helicobacter pylori and Chlamydia pneumoniae infections with coronary heart disease and cardiovascular risk factors. BMJ 1995; 311:711-4; PMID: 7549683; DOI: 10.1136/bmj.311.7007.711.
75. Danesh J, Collins R, Peto R. Chronic infections and coronary heart disease: is there a link?. Lancet 1997; 350:430-6; PMID: 9259669; DOI: 10.1016/S0140-6736(97)03079-1.
76. Epstein SE, Zhu J, Burnett MS, Zhou YF, Vercellotti G, Hajjar D. Infection and atherosclerosis: potential roles of pathogen burden and molecular mimicry. Arterioscler Thromb Vasc Biol 2000; 20:1417-20; PMID: 10845851; DOI: 10.1161/01.ATV.20.6.1417.
77. O'Connor CM, Dunne MW, Pfeffer MA, Muhlestein JB, Yao L, Gupta S, et al. Azithromycin for the secondary prevention of coronary heart disease events: the WIZARD study: a randomized controlled trial. JAMA 2003; 290:1459-66; PMID: 13129985; DOI: 10.1001/jama.290.11.1459.
78. Cannon CP, Braunwald E, McCabe CH, Grayston JT, Muhlestein B, Giugliano RP, et al. Antibiotic treatment of Chlamydia pneumoniae after acute coronary syndrome. N Engl J Med 2005; 352:1646-54; PMID: 15843667; DOI: 10.1056/NEJMoa043528.
79. Andraws R, Berger JS, Brown DL. Effects of antibiotic therapy on outcomes of patients with coronary artery disease: a meta-analysis of randomized controlled trials. JAMA 2005; 293:2641-7; PMID: 15928286; DOI: 10.1001/jama.293.21.2641.
80. Wright SD, Burton C, Hernandez M, Hassing H, Montenegro J, Mundt S, et al. Infectious agents are not necessary for murine atherogenesis. J Exp Med 2000; 191:1437-42; PMID: 10770809; DOI: 10.1084/jem.191.8.1437.
81. Mattila KJ, Nieminen MS, Valtonen VV, Rasi VP, Kesäniemi YA, Syrjälä SL, et al. Association between dental health and acute myocardial infarction. BMJ 1989; 298:779-81; PMID: 2496855; DOI: 10.1136/bmj.298.6676.779.
82. Holmes E, Loo RL, Stamler J, Bictash M, Yap IK, Chan Q, et al. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 2008; 453:396-400; PMID: 18425110; DOI: 10.1038/nature06882.
83. Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, Dugar B, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 2011; 472:57-63; PMID: 21475195; DOI: 10.1038/nature09922.