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Health and environmental applications of gut microbiome: a review Cover

Health and environmental applications of gut microbiome: a review

Open Access
|Oct 2017

References

  1. [1] Kendall AI. Some observations on the study of the intestinal bacteria. J Biol Chem. 1909;6:499-507. http://www.jbc.org/content/6/6/499.full.pdf.10.1016/S0021-9258(18)91596-6
  2. [2] Helander HF, Fändriks L. Surface area of the digestive tract - revisited. Scand J Gastroenterol. 2014;49:681-689.10.3109/00365521.2014.898326
  3. [3] Bengmark S. Ecological control of the gastrointestinal tract. The role of probiotic flora. Gut. 1998;42:2-7. DOI: 10.1136/gut.42.1.2.10.1136/gut.42.1.2
  4. [4] Shanahan F. The host-microbe interface within the gut. Best Pract Res Clin Gastroenterol. 2002;16:915-931. DOI: 10.1053/bega.2002.0342.10.1053/bega.2002.0342
  5. [5] Cummings JH, MacFarlane GT. Role of intestinal bacteria in nutrient metabolism. JPEN J Parent Enter Nutr. 1997;21:357-365. DOI: 10.1177/0148607197021006357.10.1177/0148607197021006357
  6. [6] Willyard C. Gut reaction. Nature. 2011;479:S5-S7. DOI: 10.1038/479S5a.10.1038/479S5a
  7. [7] van Deventer SJ, ten Cate JW, Tytgat GN. Intestinal endotoxemia: Clinicalsignificance. Gastroenterology. 1988;94:825-831. http://www.gastrojournal.org/article/0016-5085(88)90261-2/pdf.10.1016/0016-5085(88)90261-2
  8. [8] MacFarlane MP, Fraker DL, Alexander HR, Norton JA, Lubensky I, Jensen RT. Prospective study of surgical resection of duodenal and pancreatic gastrinomas in multiple endocrine neoplasia type 1. Surgery. 1995;118:973-979. DOI: 10.1016/S0039-6060(05)80102-3.10.1016/S0039-6060(05)80102-3
  9. [9] Bocci V. The neglected organ: bacterial flora has a crucial immunostimulatory role. Perspect Biol Med. 1992;35:251-260. DOI: 10.1353/pbm.1992.0004.10.1353/pbm.1992.00041557302
  10. [10] O’Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Reports. 2006;7:688-693. DOI: 10.1038/sj.embor.7400731.10.1038/sj.embor.7400731150083216819463
  11. [11] Lederberg J, McCray AT. 'Ome sweet 'omics: -- A genealogical treasury of words. Scientist. 2001;15:8. http://www.the-scientist.com/?articles.view/articleNo/13313/title/-Ome-Sweet--Omics---A-Genealogical-Treasury-of-Words/.
  12. [12] Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008;6:776-788. DOI: 10.1038/nrmicro1978.10.1038/nrmicro1978
  13. [13] Guarner F, Malagelada J. Gut flora in health and disease. Lancet. 2003;361:512-519. DOI: 10.1016/S0140-6736(03)12489-0.10.1016/S0140-6736(03)12489-0
  14. [14] Canny GO, McCormick BA. Bacteria in the intestine, helpful residents or enemies from within. Infect Immunit. 2008;76:3360-3373. DOI: 10.1128/IAI.00187-08.10.1128/IAI.00187-08
  15. [15] Stephen AM, Cummings JH. The microbial contribution to human faecal mass. J Med Microbiol. 1980;13:45-56. DOI: 10.1099/00222615-13-1-45.10.1099/00222615-13-1-45
  16. [16] Haynes M, Rohwer F. The human virome. In: Nelson KE, editor. Metagenomics of the Human Body. Springer; 2011; 63-77.10.1007/978-1-4419-7089-3_4
  17. [17] Nardi JB, Mackie RI, Dawson JO. Could microbial symbionts of arthropod guts contribute significantly to nitrogen fixation in terrestrial ecosystems? J Ins Physiol. 2002;48:751-763. DOI: 10.1016/S0022-1910(02)00105-1.10.1016/S0022-1910(02)00105-1
  18. [18] Reeson AF, Jankovic T, Kasper ML, Rogers S, Austin AD. Application of 16S rDNA-DGGE to examine the microbial ecology associated with a social wasp Vespulagermanica. Insect Mol Biol. 2003;12:85-91. https://link.springer.com/article/10.1007/s00284-008-9243-4.10.1046/j.1365-2583.2003.00390.x12542639
  19. [19] Mrázek J, Strosová L, Fliegerová K, Kott T, Kopecný J. Diversity of insect intestinal microflora. Folia Microbiol Praha. 2008;53:229-233. DOI: 10.1007/s12223-008-0032-z.10.1007/s12223-008-0032-z18661298
  20. [20] Hernández N, Escudero JA, Millán AS, González-Zorn B, Lobo JM, Verdú JR et al. Culturable aerobic and facultative bacteria from the gut of the polyphagic dung beetle Thorecteslusitanicus Jeckel. Insect Sci. 2013;22:178-190. DOI: 10.1111/1744-7917.12094.10.1111/1744-7917.1209424339348
  21. [21] Wang Y, Gilbreath TM III, Kukutla P, Kukutla P, Yan G, Xu J. Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya. PLoS One. 2011;6:e24767. DOI: 10.1371/journal.pone.0024767.10.1371/journal.pone.0024767317782521957459
  22. [22] Dillon RJ, Dillon VM. The gut bacteria of insects: Nonpathogenic interactions. Ann Rev Entomol. 2004;49:71-92. DOI: 10.1146/annurev.ento.49.061802.123416.10.1146/annurev.ento.49.061802.12341614651457
  23. [23] Anderson KE, Sheehan TH, Mott BM, Maes P, Snyder L, Schwan MR, et al. Microbial ecology of the hive and pollination landscape: Bacterial associates from floral nectar, the alimentary tract and stored food of honey bees Apismellifera. PloS One. 2013;8:e83125. DOI: 10.1371/journal.pone.0083125.10.1371/journal.pone.0083125386626924358254
  24. [24] Engel P, Moran NA. Functional and evolutionary insights into the simple yet specific gut microbiota of the honey bee from metagenomic analysis. Gut Microbes. 2013;4:60-65. DOI: 10.4161/gmic.22517.10.4161/gmic.22517355588823060052
  25. [25] Kuraishi T, Hori A, Kurata S. Host-microbe interactions in the gut of Drosophila melanogaster. Front Physiol. 2013;4:1-8. DOI: 10.3389/fphys.2013.00375.10.3389/fphys.2013.00375386537124381562
  26. [26] Zug R, Hammerstein P. Still a host of hosts for Wolbachia: analysis of recent data suggests that 40% of terrestrial arthropod species are infected. PloS One. 2012;7:e38544. DOI: 10.1371/journal.pone.0038544.10.1371/journal.pone.0038544336983522685581
  27. [27] Friberg U, Miller PM, Stewart AD, Rice WR. Mechanisms promoting the long-term persistence of a Wolbachia infection in a laboratory-adapted population of Drosophila melanogaster. PloS One. 2011;6:e16448. DOI: 10.1371/journal.pone.0016448.10.1371/journal.pone.0016448302598421283625
  28. [28] Moreira LA, Iturbe-Ormaetxe I, Jeffery JA, Lu G, Pyke AT, Hedges LM, et al. A Wolbachia symbiont in Aedesaegypti limits infection with dengue: Chikungunya: and Plasmodium. Cell. 2009;139:1268-1278. DOI: 10.1016/j.cell.2009.11.042.10.1016/j.cell.2009.11.04220064373
  29. [29] Bian G, Xu Y, Lu P, Xie Y, Xi Z. The endosymbiotic bacterium Wolbachiainduces resistance to dengue virus in Aedesaegypti. PLoSPathog. 2010;6:e1000833. DOI: 10.1371/journal.ppat.1000833.10.1371/journal.ppat.1000833284855620368968
  30. [30] Ye YH, Woolfit M, Rancès E, O'Neill SL, McGraw EA. Wolbachia-associated bacterial protection in the mosquito Aedes aegypti. PloS Negl Trop Dis. 2013;7:e2362. DOI: 10.1371/journal.pntd.0002362.10.1371/journal.pntd.0002362373847423951381
  31. [31] Kambris Z, Blagborough AM, Pinto SB, Blagrove MS, Godfray HC, Sinden RE, et al. Wolbachia stimulates immune gene expression and inhibits plasmodium development in Anopheles gambiae. PLoS Pathog. 2010;6:e1001143. DOI: 10.1371/journal.ppat.1001143.10.1371/journal.ppat.1001143295138120949079
  32. [32] 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;486:222-227. DOI: 10.1038/nature11053.10.1038/11053
  33. [33] Berg RD. The indigenous gastrointestinal microflora. Trends Microbiol. 1996;4:430-435. http://ac.els-cdn.com/0966842X96100573/1-s2.0-0966842X96100573-main.pdf?_tid=7bcf9bf8-95fb-11e7-9065-00000aab0f27&acdnat=1505029480_08527aa67692825c2b0e52f4ee4a394f.
  34. [34] Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet Jean-P, et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol. 2009;11:2574-2584. DOI: 10.1111/j.1462-2920.2009.01982.x.10.1111/j.1462-2920.2009.01982.x19601958
  35. [35] Vedantam G, Hecht DW. Antibiotics and anaerobes of gut origin. Cur Opin Microbiol. 2003;6:457-461. DOI: 10.1016/j.mib.2003.09.006.10.1016/j.mib.2003.09.00614572537
  36. [36] Newton IL, Bordenstein SR. Correlations between bacterial ecology and mobile DNA. Curr Microbiol. 2011;62:198-208. DOI: 10.1007/s00284-010-9693-3.10.1007/s00284-010-9693-3300664720577742
  37. [37] Swidsinski A, Ladhoff A, Pernthaler A, Swidsinski S, Loening-Baucke V, Ortner M, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology. 2002;122:44-54. http://www.gastrojournal.org/article/S0016-5085(02)29245-8/fulltext.10.1053/gast.2002.3029411781279
  38. [38] Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Bäckhed HK, et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell. 2012;150:470-480. DOI: 10.1016/j.cell.2012.07.008.10.1016/j.cell.2012.07.008350585722863002
  39. [39] Arumugam M, Raes J, Pelletier E, Le-Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature. 2011;473:174-180. DOI: 10.1038/nature09944.10.1038/09944
  40. [40] Marchesi JR. Human distal gut microbiome. Environ Microbiol. 2011;13:3088-3102. DOI: 10.1111/j.1462-2920.2011.02574.x.10.1111/j.1462-2920.2011.02574.x21906225
  41. [41] Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE. A core gut microbiome in obese and lean twins. Nature. 2009;457:480-484. DOI: 10.1038/nature07540.10.1038/07540
  42. [42] Ursell LK, Metcalf JL, Parfrey LW, Knight R. Defining the human microbiome. Nutr Rev. 2012;70:S38-S44. DOI: 10.1111/j.1753-4887.2012.00493.x.10.1111/j.1753-4887.2012.00493.x342629322861806
  43. [43] Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA. 2010;107:11971-11975. DOI: 10.1073/pnas.1002601107.10.1073/pnas.1002601107290069320566857
  44. [44] 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;108:4578-4585. DOI: 10.1073/pnas.1000081107.10.1073/pnas.1000081107306359220668239
  45. [45] Reyes A, Haynes M, Hanson N Angly FE, Heath AC, Rohwer F, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 2010;466:334-338. DOI: 10.1038/nature09199.10.1038/09199
  46. [46] Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 2011;21:1616-1625. DOI: 10.1101/gr.122705.111.10.1101/gr.122705.111320227921880779
  47. [47] 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;444:1027-1031. DOI: 10.1038/nature05414.10.1038/05414
  48. [48] Vijay-Kumar M, Aitken JD, Carvalho FA, Fifadara NH, Gewirtz AT. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science. 2010;328:228-231. DOI: 10.1126/science.1179721.10.1126/.1179721
  49. [49] Gophna U. Microbiology. The guts of dietary habits. Science. 2011;334:45-46. DOI: 10.1126/science.1213799.10.1126/.1213799
  50. [50] Hehemann J, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature. 2010;464:908-912. DOI: 10.1038/nature08937.10.1038/08937
  51. [51] Macdonald TT, Monteleone G. Immunity, inflammation, and allergy in the gut. Science. 2005;307:1920-1925. DOI: 10.1126/science.1106442.10.1126/.1106442
  52. [52] Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA. 2011;108:4554-4561. DOI: 10.1073/pnas.1000087107.10.1073/pnas.1000087107306358220847294
  53. [53] Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915-1920. DOI: 10.1126/science.1104816.10.1126/.1104816
  54. [54] Khan KJ, Ullman TA, Ford AC, Abreu MT, Abadir A, Marshall JK, et al. Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis. Am J Gastroenterol. 2011;106:661-673. DOI: 10.1038/ajg.2011.72.10.1038/ajg.2011.7221407187
  55. [55] Willing BP, Russell SL, Finlay BB. Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol. 2011;9:233-243. DOI: 10.1038/nrmicro2536.10.1038/nrmicro253621358670
  56. [56] Silverman MS, Davis I, Pillai DR. Success of self-administered home fecal transplantation for chronic Clostridium difficile infection. Clin Gastroenterol Hepatol. 2010;8:471-473. DOI: 10.1016/j.cgh.2010.01.007.10.1016/j.cgh.2010.01.00720117243
  57. [57] Scaldaferri F, Pizzoferrato M, Pecere S, Forte F, Gasbarrini A. Bacterial flora as a cause or treatment of chronic diarrhea. Gastroenterol Clin North Amer. 2012;41:581-602. DOI: 10.1016/j.gtc.2012.06.002.10.1016/j.gtc.2012.06.00222917165
  58. [58] Ringel Y, Quigley E, Lin H. Probiotics and gastrointestinal disorders. Amer J Gastroenterol Suppl. 2012;1:34-40. DOI: 10.1038/ajgsup.2012.7.10.1038/ajgsup.2012.7
  59. [59] McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, et al. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med. 2011;3:106ra106. DOI: 10.1126/scitranslmed.3002701.10.1126/scitranslmed.3002701330360922030749
  60. [60] Backhed F, Fraser CM, Ringel Y, Backhed, F, Fraser CM, Ringel Y, et al. Defining a healthy human gut microbiome: Current concepts, future directions, and clinical applications. Cell Host Microbe. 2012;12:611-622. DOI: 10.1016/j.chom.2012.10.012.10.1016/j.chom.2012.10.01223159051
  61. [61] Gibson GR, Probert HM, Loo JV, Rastall RA, Roberfroid MB. Dietary modulation of the human colonic microbiota: updating the concept of prebiotics. Nutr Res Rev. 2004;17:259-275. DOI: 10.1079/NRR200479.10.1079/NRR20047919079930
  62. [62] Brownawell AM, Caers W, Gibson GR, Kendall CW, Lewis KD, Ringel Y, et al. Prebiotics and the health benefits of fiber: current regulatory status, future research, and goals. J Nutr. 2012;142:962-974. DOI: 10.3945/jn.112.158147.10.3945/jn.112.15814722457389
  63. [63] Sharon G, Segal D, Ringo JM, Hefetz A, Zilber-Rosenberg I, Rosenberg E. Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proc Natl Acad Sci USA. 2010;107:20051-20056. DOI: 10.1073/pnas.1009906107.10.1073/pnas.1009906107299336121041648
  64. [64] Morimoto J, Simpson SJ, Ponton F. Direct and trans-generational effects of male and female gut microbiota in Drosophila melanogaster. Biol Lett. 2017;13(7). pii: 20160966. DOI: 10.1098/rsbl.2016.0966.10.1098/rsbl.2016.0966554301628724687
  65. [65] Coyne JA. Genetics of sexual isolation in females of the Drosophila-Simulans species complex. Genet Res. 1992;60:25-31. DOI: 10.1017/S0016672300030639.10.1017/S00166723000306391452013
  66. [66] Smadja C, Butlin RK. On the scent of speciation: the chemosensory system and its role in premating isolation. Heredity. 2009;102:77-97. DOI: 10.1038/hdy.2008.55.10.1038/hdy.2008.5518685572
  67. [67] de Oliveira AK, Cordeiro AR. Adaptation of Drosophila-Willistoni experimental populations to extreme pH medium. I. Changes in viability and developmental rate. Heredity. 1980;44:111-122. DOI: 10.1038/hdy.1980.10.10.1038/hdy.1980.10
  68. [68] Dodd DMB. Reproductive isolation as a consequence of adaptive divergence in Drosophila-pseudoobscura. Evolution. 1989;43:1308-1311. http://www.jstor.org/stable/2409365.10.1111/j.1558-5646.1989.tb02577.x28564510
  69. [69] Rice WR, Hostert EE. Laboratory experiments on speciation: What have we learned in 40 years? Evolution. 1993;47:1637-1653. http://www.jstor.org/stable/2410209.10.1111/j.1558-5646.1993.tb01257.x28568007
  70. [70] Rosengaus RB, Zecher CN, Schultheis KF, Brucker RM, Bordenstein SR. Disruption of the termite gut microbiota and its prolonged consequences for fitness. Appl Environ Microbiol. 2011;77:4303-4312. DOI: 10.1128/AEM.01886-10.10.1128/AEM.01886-10312772821571887
  71. [71] Brucker RM, Bordenstein SR. The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science. 2013;9:667-669. DOI: 10.1126/science.1240659.10.1126/.1240659
  72. [72] Brucker RM, Bordenstein SR. The capacious hologenome. Zoology Jena. 2013;116:260-261. DOI: 10.1126/science.1240659.10.1126/.1240659
  73. [73] Teaford MF, Ungar PS. Diet and the evolution of the earliest human ancestors. Proc Natl Acad Sci USA. 2000;97:13506-13511. DOI: 10.1073/pnas.260368897.10.1073/pnas.2603688971760511095758
  74. [74] Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, et al. Diet and the evolution of human amylase gene copy number variation. Nat Genet. 2007;39:1256-1260. DOI: 10.1038/ng2123.10.1038/ng2123237701517828263
  75. [75] Woese CR. On the evolution of cells. Proc Natl Acad Sci USA. 2002;99:8742-8747. DOI: 10.1073/pnas.132266999.10.1073/pnas.13226699912436912077305
  76. [76] Beja-Pereira A, Luikart G, England PR, Bradley DG, Jann OC, Bertorelle G, et al. Gene-culture co-evolution between cattle milk protein genes and human lactase genes. Nat Genet. 2003;35:311-313. DOI: 10.1038/ng1263.10.1038/ng126314634648
  77. [77] Ungar PS, Grine FE, Teaford MF. Diet in early homo: A review of the evidence and a new model of adaptive versatility. Ann Rev Anthrop. 2006;35:209-228. DOI: 10.1146/annurev.anthro.35.081705.123153.10.1146/annurev.anthro.35.081705.123153
  78. [78] Yeakel JD, Bennett NC, Koch PL, Dominy NJ. The isotopic ecology of African mole rats informs hypotheses on the evolution of human diet. Proc Royal Soc B: Biol Sci. 2007;274:1723-1730. DOI: 10.1098/rspb.2007.0330.10.1098/rspb.2007.0330249357817472915
  79. [79] Zhu J, Wang J, Shi Z, Franklin JL, Deane NG, Coffey RJ, et al. Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis. PLoS One. 2013;15:8e79282. DOI: 10.1371/journal.pone.0079282.10.1371/journal.pone.0079282382985324260186
  80. [80] Sekirov I, Russell SL, Antunes LCM, Finlay BB. Gut microbiota in health and disease. Physiol Rev. 2010;90:859-904. DOI: 10.1152/physrev.00045.2009.10.1152/physrev.00045.200920664075
  81. [81] Mohammadi M, Czinn S, Redline R, Nedrud J. Helicobacter specific cell-mediated immune responses display a predominant Th1 phenotype and promote a delayed-type hypersensitivity response in the stomachs of mice. J Immunol. 1996;156:4729-4738. http://www.jimmunol.org/content/156/12/4729.10.4049/jimmunol.156.12.4729
  82. [82] Roth KA, Kapadia SB, Martin SM, Lorenz RG. Cellular immune responses are essential for the development of Helicobacter felis associated gastric pathology. J Immunol. 1999;163:1490-1497. http://www.jimmunol.org/content/163/3/1490.10.4049/jimmunol.163.3.1490
  83. [83] Mannick EE, Bravo LE, Zarama G, Realpe JL, Zhang XJ, Ruiz B, et al. Inducible nitric oxide synthase, nitrotyrosine, and apoptosis in Helicobacter pylori Gastritis: effect of antibiotics and antioxidants. Cancer Res. 1996;56:3238-3243. http://cancerres.aacrjournals.org/content/56/14/3238.long.
  84. [84] Bartsch H, Nair J. Chronic inflammation and oxidative stress in the genesis and perpetuation of cancer: role of lipid peroxidation, DNA damage, and repair. Langenbecks Arch Surg. 2006;391:499-510. DOI: 10.1007/s00423-006-0073-1.10.1007/s00423-006-0073-116909291
  85. [85] Hope ME, Hold GL, Kain R, El-Omar EM. Sporadic colorectal cancer-role of the commensal microbiota. FEMS Microbiol Lett. 2005;244:1-7. DOI: 10.1016/j.femsle.2005.01.029.10.1016/j.femsle.2005.01.02915727814
  86. [86] Moore WE, Moore LH. Intestinal floras of populations that have a high risk of colon cancer. Appl Environ Microbiol. 1995;61:3202-3207. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC167598/pdf/613202.pdf.10.1128/aem.61.9.3202-3207.19951675987574628
  87. [87] Scanlan PD, Shanahan F, Clune Y, Collins JK, O’Sullivan GC, O’Riordan M, et al. Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol. 2008;10:789-798. DOI: 10.1111/j.1462-2920.2007.01503.x.10.1111/j.1462-2920.2007.01503.x18237311
  88. [88] Bingham SA. Diet and colorectal cancer prevention. Biochem Soc Trans. 2000;28:12-16.10.1042/bst028001210816091
  89. [89] O’Keefe SJ. Nutrition and colonic health: the critical role of the microbiota. Curr Opin Gastroenterol. 2008;24:51-58. DOI: 10.1097/MOG.0b013e3282f323f3.10.1097/MOG.0b013e3282f323f318043233
  90. [90] Huycke MM, Abrams V, Moore DR. Enterococcus faecalis produces extracellular superoxide and hydrogen peroxide that damages colonic epithelial cell DNA. Carcinogenesis. 2002;23:529-536. https://carcin.oxfordjournals.org/content/23/3/529.full.pdf+html.10.1093/carcin/23.3.52911895869
  91. [91] Wang X, Allen TD, May RJ, Lightfoot S, Houchen CW, Huycke MM. Enterococcus faecalis induces aneuploidy and tetraploidy in colonic epithelial cells through a bystander effect. Cancer Res. 2008;68:9909-9917. DOI: 10.1158/0008-5472.CAN-08-1551.10.1158/0008-5472.CAN-08-1551259664619047172
  92. [92] Bakken JS, Borody T, Brandt LJ, Brill JV, Demarco DC, Franzos MA, et al. Fecal microbiota transplantation workgroup. Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol. 2011;9:1044-1049. DOI: 10.1016/j.cgh.2011.08.014.10.1016/j.cgh.2011.08.014322328921871249
  93. [93] Brandt LJ, Borody TJ, Campbell J. Endoscopic fecal microbiota transplantation: “first-line” treatment for severe Clostridium difficile infection? J Clin Gastroenterol. 2011;45:655-657. DOI: 10.1097/MCG.0b013e3182257d4f.10.1097/MCG.0b013e3182257d4f21716124
  94. [94] Hamilton MJ, Weingarden AR, Sadowsky MJ, Khoruts A. Standardised frozen preparation for transplantation of fecal microbiota for recurrent Clostridium difficile infection. Amer J Gastroenterol. 2012;107:761-767. DOI: 10.1038/ajg.2011.482.10.1038/ajg.2011.48222290405
  95. [95] Weinbauer MG. Ecology of prokaryotic viruses. FEMS Microbiol Rev. 2004;28:127-181. DOI: 10.1016/j.femsre.2003.08.001.10.1016/j.femsre.2003.08.00115109783
  96. [96] Stern A, Mick E, Tirosh I, Sagy O, Sorek R. CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res. 2012;22:1985-1994. DOI: 10.1101/gr.138297.112.10.1101/gr.138297.112346019322732228
  97. [97] Marinelli LJ, Fitz-Gibbon S, Hayes C, Bowman C, Inkeles M, Loncaric A, et al. Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. mBio2012;3:e00279-12. DOI: 10.1128/mBio.00279-12.10.1128/mBio.00279-12344816723015740
  98. [98] Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, Burt A, et al. Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci USA. 2004;101:4894-4899. DOI: 10.1073/pnas.0307800101.10.1073/pnas.030780010138734515044706
  99. [99] Popgeorgiev N, Temmam S, Raoult D, Desnues C. Describing the silent human virome with an emphasis on giant viruses. Intervirology. 2013;56:395-412. DOI: 10.1159/000354561.10.1159/00035456124157886
  100. [100] Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, et al. Viral diversity and dynamics in an infant gut. Res Microbiol. 2008;159:367-373. DOI: 10.1016/j.resmic.2008.04.006.10.1016/j.resmic.2008.04.00618541415
  101. [101] Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, et al. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol. 2003;185:6220-6223. DOI: 10.1128/JB.185.20.6220-6223.2003.10.1128/JB.185.20.6220-6223.200322503514526037
  102. [102] Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD. Rapid evolution of the human gut virome. Proc Natl Acad Sci USA. 2013;110:12450-12455. DOI: 10.1073/pnas.1300833110.10.1073/pnas.1300833110372507323836644
  103. [103] Kim MS, Park EJ, Roh SW, Bae JW. Diversity and abundance of single-stranded DNA viruses in human feces. Appl Environ Microbiol. 2011;77:8062-8070. DOI: 10.1128/AEM.06331-11.10.1128/AEM.06331-11320897621948823
  104. [104] Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci USA. 2013;110:10771-10776. DOI: 10.1073/pnas.1305923110.10.1073/pnas.1305923110369681023690590
  105. [105] Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, Soh SW, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 2006;4:e3. DOI: 10.1371/journal.pbio.0040003.10.1371/journal.pbio.0040003131065016336043
  106. [106] Colson P, Richet H, Desnues C, Balique F, Moal V, Grob JJ, et al. Pepper mild mottle virus, a plant virus associated with specific immune responses, fever, abdominal pains, and pruritus in humans. PLoS One. 2010;5:e10041. DOI: 10.1371/journal.pone.0010041.10.1371/journal.pone.0010041285031820386604
  107. [107] Ogilvie LA, Caplin J, Dedi C, Diston D, Cheek E, Bowler L, et al. Comparative (meta)genomicanalysis and ecological profiling of human gut-specific bacteriophage wB124-14. PLoS One. 2012;7:e35053. DOI: 10.1371/journal.pone.0035053.10.1371/journal.pone.0035053333881722558115
  108. [108] Kim BS, Jeon YS, Chun J. Current status and future promise of the human microbiome. Pediatr Gastroenterol Hepatol Nutr. 2013;16:71-79. DOI: 10.5223/pghn.2013.16.2.71.10.5223/pghn.2013.16.2.71376069724010110
DOI: https://doi.org/10.1515/eces-2017-0032 | Journal eISSN: 2084-4549 | Journal ISSN: 1898-6196
Language: English
Page range: 467 - 482
Published on: Oct 11, 2017
Published by: Society of Ecological Chemistry and Engineering
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2017 Soumya Chatterjee, Sibnarayan Datta, Sonika Sharma, Sarika Tiwari, Dharmendra K. Gupta, published by Society of Ecological Chemistry and Engineering
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.