Gastrointestinal Microbial Ecology with Perspectives on Health and Disease

Physiology of the Gastrointestinal Tract

Volumn 1, Issue , 2012, Pages 1119-1134

  Gillilland, Merritt G ^a   Young, Vincent B ^b   Huffnagle, Gary B ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882468857     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-382026-6.00040-3     Document Type: Chapter

References (140)

1. Savage DC Microbial ecology of the gastrointestinal-tract. Annu Rev Microbiol 1977, 31:107-133.
2. Whitman WB, Coleman DC, Wiebe WJ Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 1998, 95:6578-6583.
3. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 2006, 103:12115-12120.
4. Young VB, Schmidt TM Overview of the gastrointestinal microbiota. Gi Microbiota and Regulation of the Immune System 2008, Vol. 635. Springer-Verlag, Berlin, Berlin, pp. 29-40.
5. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, et al. The NIH human microbiome project. Genome Res 2009, 19:2317-2323.
6. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science 2005, 308:1635-1638.
7. Peterson DA, Frank DN, Pace NR, Gordon JI Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host & Microbe 2008, 3:417-427.
8. Lederberg J, McCray AT 'Ome sweet' omics -A genealogical treasury of words. Scientist 2001, 15. 8-8.
9. Ley RE, Turnbaugh PJ, Klein S, Gordon JI Microbial ecology -Human gut microbes associated with obesity. Nature 2006, 444:1022-1023.
10. Frank DN, Amand ALS, Feldman RA, Boedeker EC, Harpaz N, Pace NR Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 2007, 104:13780-13785.
11. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 2006, 55:205-211.
12. Cummings JH, Pomare EW, Branch WJ, Naylor CPE, Macfarlane GT Short chain fatty-acids in human large-intestine, protal, hepatic and venous-blood. Gut 1987, 28:1221-1227.
13. Sartor RB Therapeutic manipulation of the enteric microflora in inflammatory bowel diseases: antibiotics, probiotics, and prebiotics. Gastroenterology 2004, 126:1620-1633.
14. Collado MC, Calabulg M, Sanz Y Differences between the fecal microbiota of coeliac infants and healthy controls. Curr Iss Intest Microbiol 2007, 8:9-14.
15. Sogin SJ, Sogin ML, Woese CR Phylogenetic measurement in procaryotes by primary structural characterization. J Mol Evol 1971, 1:173-184.
16. Woese CR, Fox GE Phylogentic structure of prokaryotic domain -primary kingdoms. Proc Natl Acad Sci USA 1977, 74:5088-5090.
17. Woese CR, Sogin ML, Sutton LA Procaryotic phylogeny. 1. Concerning relatedness of aerobacter-aerogenes to Escherichia-coli. J Mol Evol 1974, 3:293-299.
18. Pace NR, Stahl DA, Lane DJ, Olsen GJ Analyzing natural microbial populations by rRNA sequences. ASM News 1985, 51:4-12.
19. Pace NR A molecular view of microbial diversity and the biosphere. Science 1997, 276:734-740.
20. Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, et al. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 2006, 72:3685-3695.
21. Committe on Metagenomics The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet 2007, The National Academic Press, Washington, D.C.
22. Hamady M, Knight R Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 2009, 19:1141-1152.
23. Zoetendal EG, Collier CT, Koike S, Mackie RI, Gaskins HR Molecular ecological analysis of the gastrointestinal microbiota: a review. J Nutr 2004, 134:465-472.
24. Blackwood CB, Marsh T, Kim SH, Paul EA Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl Environ Microbiol 2003, 69:926-932.
25. Kitts CL Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curr Issues Intest Microbiol 2001, 2:17-25.
26. Schutte UME, Abdo Z, Bent SJ, Shyu C, Williams CJ, Pierson JD, et al. Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl Microbiol Biotechnol 2008, 80:365-380.
27. Muyzer G, Ramsing NB Molecular methods to study the organization of microbial communities. Water Sci Technol 1995, 32:1-9.
28. Gueimonde M, Reyes-Gavilan C Detection and enumeration of gastrointestinal microorganism. Handbook of Probiotics and Prebiotics 2009, Vol. 2:25-43. Wiley & Sons, Inc., New Jersey.
29. Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, Young VB Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun 2009, 77:2367-2375.
30. Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science 2006, 312:1355-1359.
31. 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.
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.
33. Stackebrandt E, Goebel BM A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994, 44:846-849.
34. Hugenholtz P, Goebel BM, Pace NR Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 1998, 180:4765-4774.
35. Schloss PD, Handelsman J Status of the microbial census. Microbiol Mol Biol Rev 2004, 68:686.
36. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009, 75:7537-7541.
37. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 2001, 67:4399-4406.
38. Chao A Nonparametric estimation of the number of classes in a population. Scand J Stat 1984, 11:265-270.
39. Ley RE, Peterson DA, Gordon JI Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006, 124:837-848.
40. Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI Host-bacterial mutualism in the human intestine. Science 2005, 307:1915-1920.
41. Rieu-Lesme F, Delbes C, Sollelis L Recovery of partial 16S rDNA sequences suggests the presence of Crenarchaeota in the human digestive ecosystem. Curr Microbiol 2005, 51:317-321.
42. O'Hara AM, Shanahan F The gut flora as a forgotten organ. EMBO Rep 2006, 7:688-693.
43. Wilson M Microbial Inhabitants of Humans: Their Ecology and Role in Health and Disease 2005, Cambridge University Press.
44. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, et al. Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA 2006, 103:732-737.
45. Dethlefsen L, Eckburg PB, Bik EM, Relman DA Assembly of the human intestinal microbiota. Trends Ecol Evol 2006, 21:517-523.
46. Collignon A, Butel.M-J Establishment and composition of the gut microflora. Gut Microflora: Digestive Physiology and Pathology 2006, 19-35. John Libbey Eurotext. J. Rambaud, J. Buts, G. Corthier, B. Flourie (Eds.).
47. Hayashi H, Takahashi R, Nishi T, Sakamoto M, Benno Y Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. J Med Microbiol 2005, 54:1093-1101.
48. Marteau P, Pochart P, Dore J, Bera-Maillet C, Bernalier A, Corthier G Comparative study of bacterial groups within the human cecal and fecal microbiota. Appl Environ Microbiol 2001, 67:4939-4942.
49. Noverr MC, Huffnagel GB Does the microbiota regulate immune responses outside the gut?. Trends Microbiol 2004, 12:562-568.
50. Backhed 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, 101:15718-15723.
51. Cuff MA, Shirazi-Beechey SP The importance of butyrate transport to the regulation of gene expression in the colonic epithelium. Biochem Soc Trans 2004, 32:1100-1102.
52. Dominguez-Bello MG, Blaser MJ Do you have a probiotic in your future?. Microbes Infect 2008, 10:1072-1076.
53. Schwiertz A, Taras D, Schafer K, Beijer S, Bos NA, Donus C, et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity 2010, 18:190-195.
54. He F The intestinal microbiota of the elderly. Gastrointestinal Microbiology 2006, 75-91. Taylor and Francis Group, New York. A.C. Ouwehand, E.E. Vaughan (Eds.).
55. Chow WL, Lee Y Mucosal interactions and gastrointestinal microbiota. Gastrointestinal Microbiology 2006, 123-136. Taylor and Francis Group, New York. A.C. Ouwehand, E.E. Vaughan (Eds.).
56. McCracken VJ, Lorenz RG The gastrointestinal ecosystem: a precarious alliance among epithelium, immunity and microbiota. Cell Microbiol 2001, 3:1-11.
57. Tannock GW, Fuller R, Smith SL, Hall MA Plasmid profiling of members of the family Enterobacteriaceae, Lactobacilli, and Bifidobacteria to study the transmission of bacteria from mother to infant. J Clin Microbiol 1990, 28:1225-1228.
58. Gronlund 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.
59. Mandar R, Mikelsaar M Transmission of mother's microflora to the newborn at birth. Biol Neonate 1996, 69:30-35.
60. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO Development of the human infant intestinal microbiota. PLoS Biol 2007, 5:1556-1573.
61. Collins MD, Gibson GR Probiotics, prebiotics, and synbiotics: approaches for modulating the microbial ecology of the gut. Am J Clin Nutr 1999, 69:1052S-1057S.
62. Allison SD, Martiny JBH Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA 2008, 105:11512-11519.
63. Elton CS The Ecology of Invasions by Animals and Plants 1958, Methuen & Co. Ltd., London.
64. Levine JM Species diversity and biological invasions: relating local process to community pattern. Science 2000, 288:852-854.
65. Zachar Z, Savage DC Microbial interference and colonization of the murine gastrointestinal tract by Listeria monocytogenes. Infect Immun 1979, 23:168-174.
66. Bernalier-Donadille A Main metabolic functions of the human intestinal microflora. Gut Microflora: Digestive Physiology and Pathology 2006, 61-80. John Libbey Eurotext. J. Rambaud, J. Buts, G. Corthier, B. Flourie (Eds.).
67. Dethlefsen L, Huse S, Sogin ML, Relman DA The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 2008, 6:2383-2400.
68. Sullivan A, Edlund.C, Nord.NE Effect of antimicrobial agents on the ecological balance of human microflora. Lancet Infect Dis 2001, 1:101-114.
69. Kalliomaki M, Salminen S, Isolauri E Positive interactions with the microbiota: probiotics. GI Microbiota and Regulation of the Immune System 2008, Vol. 635. Landes Bioscience/Springer Science + Business Media, LLC.
70. Mason KL, Huffnagle GB, Noverr MC, Kao JY Overview of gut immunology. In:. GI Microbiota and Regulation of the Immune System 2008, Vol. 635. Landes Bioscience/Springer Science + Business Media, LLC.
71. Apostolou E, Pelto L, Kirjavainen PV, Isolauri E, Salminen SJ, Gibson GR Differences in the gut bacterial flora of healthy and milk-hypersensitive adults, as measured by fluorescence in situ hybridization. FEMS Immunol Med Microbiol 2001, 30:217-221.
72. Bjorksten B, Naaber P, Sepp E, Mikelsaar M The intestinal microflora in allergic Estonian and Swedish 2-year-old children. Clin Exp Allergy 1999, 29:342-346.
73. Duchmann R, Kaiser I, Hermann E, Mayet W, Ewe K, ZumBuschenfelde KHM Tolerance exists towards resident intestinal flora but is broken in active inflammatory bowel disease (IBD). Clin Exp Immunol 1995, 102:448-455.
74. Kuhbacher T, Schreiber S, Runkel N Pouchitis: pathophysiology and treatment. Int J Colorectal Dis 1998, 13:196-207.
75. O'Brien R Bacterial vaginosis: many questions-any answers?. Curr Opin Pediatr 2005, 17:473-479.
76. Penders J, Stobberingh EE, Thijs C, Adams H, Vink C, van Ree R, et al. Molecular fingerprinting of the intestinal microbiota of infants in whom atopic eczema was or was not developing. Clin Exp Allergy 2006, 36:1602-1608.
77. Sepp E, Julge K, Mikelsaar M, Bjorksten B Intestinal microbiota and immunoglobulin E responses in 5-year-old Estonian children. Clin Exp Allergy 2005, 35:1141-1146.
78. De La Cochetiere MF, Durand T, Lalande V, Petit JC, Potel G, Beaugerie L Effect of antibiotic therapy on human fecal microbiota and the relation to the development of Clostridium difficile. Microb Ecol 2008, 56:395-402.
79. Black F, Einarsson K, Lidbeck A, Orrhage K, Nord CE Effect of lactic acid producing bacteria on the human intestinal microflora during ampicillin treatment. Scand J Infect Dis 1991, 23:247-254.
80. Nord CE, Bergan T, Aase S Impact of azlocillin on the colon microflora. Scand J Infect Dis 1986, 18:163-166.
81. Knothe H, Dette GA, Shah PM Impact of injectable cephalosporins on the gastrointestinal microflora -observations in healthy volunteers and hospitalized patients. Infection 1985, 13:S129-S133.
82. Garner CD, Antonopoulos DA, Wagner B, Duhamel GE, Keresztes I, Ross DA, et al. Perturbation of the small intestine microbial ecology by streptomycin alters pathology in a salmonella enterica serovar typhimurium murine model of infection. Infect Immun 2009, 77:2691-2702.
83. Garland CD, Lee A, Dickson MR Segmented filamentous bacteria in the rodent small intestine -theri colonization of growing animals and possible role in host resistance to Salmonella. Microb Ecol 1982, 8:181-190.
84. Saavedra JM Microbes to fight microbes -a not so novel approach to controlling diarrheal disease. J Pediatr Gastroenterol Nutr 1995, 21:125-129.
85. FAO/WHO. Report of a Joint FAO/WHO Expert Consultation on Evaluation of Health and Nutritional Properties of Probiotics in Food Including Powder Milk with Live Lactic Acid Bacteria Food and Agriculture Organization of the United Nations and the World Health Organization, 2001.
86. Lahtinen S, Ouwehand A Mechanisms of probiotics. Handbook of Probiotcs and Prebiotics 2009, Vol. 2:377-440. Wiley & Sons, Inc., New Jersey.
87. Johnson-Henry KC, Hagen KE, Gordonpour M, Tompkins TA, Sherman PM Surface-layer protein extracts from Lactobacillus helveticus inhibit enterohaemorrhagic Escherichia coli O157: H7 adhesion to epithelial cells. Cell Microbiol 2007, 9:356-367.
88. Kim Y, Kim SH, Whang KY, Kim YJ, Oh S Inhibition of Escherichia coli O157: H7 attachment by interactions between lactic acid bacteria and intestinal epithelial cells. J Microbiol Biotechnol 2008, 18:1278-1285.
89. Rea MC, Clayton E, O'Connor PM, Shanahan F, Kiely B, Ross RP, et al. Antimicrobial activity of lacticin 3147 against clinical Clostridium difficile strains. J Med Microbiol 2007, 56:940-946.
90. Han KS, Kim Y, Kim SH, Oh S Characterization and purification of acidocin 1B, a bacteriocin produced by Lactobacillus acidophilus GP1B. J Microbiol Biotechnol 2007, 17:774-783.
91. Kabir AMA, Aiba Y, Takagi A, Kamiya S, Miwa T, Koga Y Prevention of Helicobacter pylori infection by lactobacilli in a gnotobiotic murine model. Gut 1997, 41:49-55.
92. Aiba Y, Suzuki N, Kabir AMA, Takagi A, Koga Y Lactic acid-mediated suppression of Helicobacter pylori by the oral administration of Lactobacillus salivarius as a probiotic in a gnotobiotic murine model. Am J Gastroenterol 1998, 93:2097-2101.
93. Gorbach SL, Chang TW, Goldin B Successful treatment of relapsing Clostridium difficile colitis with Lactobacillus GG. Lancet 1987, 2. 1519-1519.
94. Black FT, Anderson PL, Orskov J, Lauland S Prophylactic efficacy of lactobacilli on traveller's diarrhea. J Travel Med 1989, 7:333-335.
95. Khedkar CD, Ouwehand AC Modifying the gastrointestinal microbiota with probiotics. Gastrointestinal Microbiology 2006, 315-333. Taylor & Francis Group, New York. A.C.A. Ouwehand (Ed.).
96. Gibson GR, Roberfroid MB Dietary modulation of the human colonic microbiota -introducing the concept of prebiotics. J Nutr 1995, 125:1401-1412.
97. Crittenden R, Playne MJ Prebiotics. Handbook of Probiotics and Prebiotics 2009, Vol. 2:535-581. John Wiley & Sons, Inc, New Jersey.
98. Moro G, Arslanoglu S, Stahl B, Jelinek J, Wahn U, Boehm G A mixture of prebiotic oligosaccharides reduces the incidence of atopic dermatitis during the first six months of age. Arch Dis Child 2006, 91:814-819.
99. Furrie E, Macfarlane S, Kennedy A, Cummings JH, Walsh SV, O'Neil DA, et al. Synbiotic therapy (Bifidobacterium longum/Synergy 1) initiates resolution of inflammation in patients with active ulcerative colitis: a randomised controlled pilot trial. Gut 2005, 54:242-249.
100. Macfarlane S, Furrie E, Kennedy A, Cummings JH, Macfarlane GT Mucosal bacteria in ulcerative colitis. Br J Nutr 2005, 93:S67-S72.
101. Welters CFM, Heineman E, Thunnissen F, van den Bogaard A, Soeters PB, Baeten C Effect of dietary inulin supplementation on inflammation of pouch mucosa in patients with an heal pouch-anal anastomosis. Dis Colon Rectum 2002, 45:621-627.
102. Tannock GW, Munro K, Bibiloni R, Simon MA, Hargreaves P, Gopal P, et al. Impact of consumption of oligosaccharide-containing biscuits on the fecal microbiota of humans. Appl Environ Microbiol 2004, 70:2129-2136.
103. Topping DL, Clifton PM Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol Rev 2001, 81:1031-1064.
104. Cherbay C, Blottiere H, Duee P Gut microflora and the colonic epithelium. Gut Microflora: Digestive Physiology and Pathology 2006, 107-130. John Libby Eurotext Limited, Paris. J. Rambaud, J. Buts, G. Corthier, B. Flourie (Eds.).
105. Rowland IR Toxicological implications of the normal microflora. Medical Importance of the Normal Microflora 1999, 295-311. Kluwer Academic Publishers. G.W. Tannock (Ed.).
106. Birkbeck J Colon cancer: the potential involvement of the normal microflora. Medical Importance of the Normal Microflora 1999, 262-294. Kluwer Academic Publishers. G.W. Tannock (Ed.).
107. Eldere JV Chemical transformations of bile salts by the intestinal microflora. Medical Importance of the Normal Microflora 1999, 312-337. Kluwer Academic Publishers. G.W. Tannock (Ed.).
108. Wilpart M, Mainguet P, Maskens A, Roberfroid M Structure activity relationship amongst biliary acids showing comutagenic activity towards 1,2-dimethylhydrazine. Carcinogenesis 1983, 4:1239-1241.
109. Reddy BS, Wynder EL Large bowel carcinogenesis -fecal constituents of populations with diverse incidence rates of colon cancer. J Natl Cancer Inst 1973, 50:1437-1442.
110. Venturi M, Hambly RJ, Glinghammar B, Rafter JJ, Rowland IR Genotoxic activity in human faecal water and the role of bile acids: a study using the alkaline comet assay. Carcinogenesis 1997, 18:2353-2359.
111. Baron SF, Hylemon PB Biotransformation of bile acids, cholesterol and steroid hormones. Gastrointestinal Microbiology, Gastrointestinal Ecosystems and Fermentations 1997, 470-510. Chapman & Hall, New York. R.I.A. Mackie (Ed.).
112. Roediger WEW, Duncan A, Kapaniris O, Millard S Reducing sulfur compounds of the colon impair colonocyte nutrition -implications for ulcerative colitis. Gastroenterology 1993, 104:802-809.
113. Roediger WEW Utilization of nutrients by isolated epithelial cells of the rat colon. Gastroenterology 1982, 83:424-429.
114. Sengupta S, Muir JG, Gibson PR Does butyrate protect from colorectal cancer?. J Gastroenterol Hepatol 2006, 21:209-218.
115. Blottiere HM, Buecher B, Galmiche JP, Cherbut C Molecular analysis of the effect of short-chain fatty acids on intestinal cell proliferation. Proc Nutr Soc 2003, 62:101-106.
116. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 2005, 102:11070-11075.
117. Podolsky DK Inflammatory bowel disease. N Engl J Med 2002, 347:417-429.
118. Cummings JH, Macfarlane GT, Macfarlane S Intestinal bacteria and ulcerative colitis. Curr Iss Intest Microbiol 2003, 4:9-20.
119. Dicksved J, Halfvarson J, Rosenquist M, Jarnerot G, Tysk C, Apajalahti J, et al. Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J 2008, 2:716-727.
120. Gophna U, Sommerfeld K, Gophna S, Doolittle WF, Veldhuyzen van Zanten SJO Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis. J Clin Microbiol 2006, 44:4136-4141.
121. Guarner F, Casellas F, Borruel N, Antolin M, Videla S, Vilaseca J, et al. Role of microecology in chronic inflammatory bowel diseases. Eur J Clin Nutr 2002, 56:S34-S38.
122. Shanahan F Therapeutic manipulation of gut flora. Science 2000, 289:1311-1312.
123. Shanahan F Probiotics and inflammatory bowel disease: is there a scientific rationale?. Inflamm Bowel Dis 2000, 6:107-115.
124. Shanahan F Crohn's disease. Lancet 2002, 359:62-69.
125. Tamboli CP, Neut C, Desreumaux P, Colombel JF Dysbiosis in inflammatory bowel disease. Gut 2004, 53:1-4.
126. Sartor RB Intestinal microflora in human and experimental inflammatory bowel disease. Curr Opin Gastroenterol 2001, 17:324-330.
127. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier L, Beaugerie L, et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 2009, 15:1183-1189.
128. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA 2008, 105:16731-16736.
129. McFarland LV Meta-analysis of probiotics for the prevention of antibiotic associated diarrhea and the treatment of Clostridium difficile disease. Am J Gastroenterol 2006, 101:812-822.
130. Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, Schmidt TM, et al. Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. J Infect Dis 2008, 197:435-438.
131. Vollaard EJ, Clasener HAL Colonization resistance. Antimicrob Agents Chemother 1994, 38:409-414.
132. Wilson KH The microecology of Clostridium difficile. Clin Infect Dis 1993, 16:S214-S218.
133. Lee YK, Salminen S Effects on human health and diseases. Handbook of Probiotics and Prebiotics 2009, 267-321. John Wiley & SOns, Inc., New Jersey. Y.K. Lee, S. Salminen (Eds.).
134. Kagnoff MF Overview and pathogenesis of celiac disease. Gastroenterology 2005, 128:S10-S18.
135. Asaka M, Kimura T, Kato M, Kudo M, Miki K, Ogoshi K, et al. Possible role of Helicobacter pylori infection in early gastric cancer development. Cancer 1994, 73:2691-2694.
136. Heavey PM, Rowland IR, Rafter JJ The gastrointestinal microbiota in cancer. Gastrointestinal Microbiology 2006, 225-236. Taylor & Francis Group, New York. A.C.A. Ouwehand (Ed.).
137. Kato T, Saito Y, Niwa M, Inoue H, Motoyama N, Ogoshi K, et al. Helicobacter pylori infection in gastric carcinoma. Eur J Gastroenterol Hepatol 1994, 6:S93-S96.
138. Kikuchi S, Wada O, Nakajima T, Nishi T, Kobayashi O, Konishi T, et al. Serum anti-Helicobacter pylori antibody and gastric carcinoma among young adults. Cancer 1995, 75:2789-2793.
139. Sykora J, Valeckova KN, Amlerova J, Siala K, Dedek P, Watkins S, et al. Effects of a specially designed fermented milk product containing probiotic Lactobacillus casei DN-114 001 and the eradication of H-pylori in children -A prospective randomized double-blind study. J Clin Gastroenterol 2005, 39:692-698.
140. Moore WEC, Moore LH Intestinal floras of populations that have a high risk of colon cancer. Appl Environ Microbiol 1995, 61:3202-3207.