Microbial biofilms and gastrointestinal diseases

Pathogens and Disease

Volumn 67, Issue 1, 2013, Pages 25-38

  von Rosenvinge, Erik C ^a,b   O'May, Graeme A ^c   Macfarlane, Sandra ^d   Macfarlane, George T ^d   Shirtliff, Mark E ^c  

^a UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^b VETERANS AFFAIRS MEDICAL CENTER   (United States)

^c UNIVERSITY OF MARYLAND DENTAL SCHOOL   (United States)

^d UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

Biofilm; Gastrointestinal disease; Gastrointestinal tract; Microbiota

Indexed keywords

ANTIBIOTIC AGENT; PLACEBO;

ANTIBIOTIC THERAPY; BACTERIAL GROWTH; BACTERIUM ADHERENCE; BARRETT ESOPHAGUS; BIOFILM; CHRONIC DISEASE; CROHN DISEASE; ENTERIC FEEDING; ENTERITIS; FUNGUS GROWTH; GASTROINTESTINAL DISEASE; HELICOBACTER INFECTION; HOST PATHOGEN INTERACTION; INTESTINE FLORA; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SHORT SURVEY; ULCERATIVE COLITIS;

ANIMALS; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BIOFILMS; BIOTA; GASTROINTESTINAL DISEASES; HUMANS;

EID: 84878128639     PISSN: None     EISSN: 2049632X     Source Type: Journal    
DOI: 10.1111/2049-632X.12020     Document Type: Short Survey

References (129)

1. Adams RJ, Heazlewood SP, Gilshenan KS, O'Brien M, McGuckin MA & Florin TH (2008) IgG antibodies against common gut bacteria are more diagnostic for Crohn's disease than IgG against mannan or flagellin. Am J Gastroenterol 103: 386-396.
2. Apostolakis LW, Funk GF, Urdaneta LF, McCulloch TM & Jeyapalan MM (2001) The nasogastric tube syndrome: two case reports and review of the literature. Head Neck 23: 59-63.
3. Baik SC, Kim KM, Song SM et al. (2004) Proteomic analysis of the sarcosine-insoluble outer membrane fraction of Helicobacter pylori strain 26695. J Bacteriol 186: 949-955.
4. Bauer TT, Torres A, Ferrer R, Heyer CM, Schultze-Werninghaus G & Rasche K (2002) Biofilm formation in endotracheal tubes. Association between pneumonia and the persistence of pathogens. Monaldi Arch Chest Dis 57: 84-87.
5. Baumgart M, Dogan B, Rishniw M et al. (2007) Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum. ISME J 1: 403-418.
6. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ & Relman DA (2006) Molecular analysis of the bacterial microbiota in the human stomach. P Natl Acad Sci USA 103: 732-737.
7. Bimczok D, Clements RH, Waites KB, Novak L, Eckhoff DE, Mannon PJ, Smith PD & Smythies LE (2010) Human primary gastric dendritic cells induce a Th1 response to H. pylori. Mucosal Immunol 3: 260-269.
8. Björkholm B, Falk P, Engstrand L & Nyrén O (2003) Helicobacter pylori: resurrection of the cancer link. J Intern Med 253: 102-119.
9. Blomberg J, Lagergren J, Martin L, Mattsson F & Lagergren P (2012) Complications after percutaneous endoscopic gastrostomy in a prospective study. Scand J Gastroenterol 47: 737-742.
10. Bullock TK, Waltrip TJ, Price SA & Galandiuk S (2004) A retrospective study of nosocomial pneumonia in postoperative patients shows a higher mortality rate in patients receiving nasogastric tube feeding. Am Surg 70: 822-826.
11. Cabré E & Gassull MA (1993) Complications of enteral feeding. Nutrition 9: 1-9.
12. Cammarota G, Branca G, Ardito F et al. (2010) Biofilm demolition and antibiotic treatment to eradicate resistant Helicobacter pylori: a clinical trial. Clin Gastroenterol Hepatol 8: 817-820.e813.
13. Carron MA, Tran VR, Sugawa C & Coticchia JM (2006) Identification of Helicobacter pylori biofilms in human gastric mucosa. J Gastrointest Surg. 10: 712-717.
14. Castanie-Cornet MP, Penfound TA, Smith D, Elliott JF & Foster JW (1999) Control of acid resistance in Escherichia coli. J Bacteriol 181: 3525-3535.
15. Celli JP, Turner BS, Afdhal NH, Keates S, Ghiran I, Kelly CP, Ewoldt RH, McKinley GH, So P, Erramilli S & Bansil R (2009) Helicobacter pylori moves through mucus by reducing mucin viscoelasticity. P Natl Acad Sci USA 106: 14321-14326.
16. Cellini L, Grande R, Di Campli E, Traini T, Giulio MD, Lannutti SN & Lattanzio R (2008) Dynamic colonization of Helicobacter pylori in human gastric mucosa. Scand J Gastroenterol 43: 178-185.
17. Claesson MJ, Jeffery IB, Conde S et al. (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488: 178-184.
18. Cole SP, Harwood J, Lee R, She R & Guiney DG (2004) Characterization of monospecies biofilm formation by Helicobacter pylori. J Bacteriol 186: 3124-3132.
19. Corfield AP, Carroll D, Myerscough N & Probert CS (2001) Mucins in the gastrointestinal tract in health and disease. Front Biosci 6: D1321-D1357.
20. Coticchia JM, Sugawa C, Tran VR, Gurrola J, Kowalski E & Carron MA (2006) Presence and density of Helicobacter pylori biofilms in human gastric mucosa in patients with peptic ulcer disease. J Gastrointest Surg 10: 883-889.
21. Croucher SC, Houston AP, Bayliss CE & Turner RJ (1983) Bacterial populations associated with different regions of the human colon wall. Appl Environ Microbiol 45: 1025-1033.
22. Darfeuille-Michaud A (2002) Adherent-invasive Escherichia coli: a putative new E. coli pathotype associated with Crohn's disease. Int J Med Microbiol 292: 185-193.
23. Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser AL, Barnich N, Bringer MA, Swidsinski A, Beaugerie L & Colombel JF (2004) High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127: 412-421.
24. Dautle MP, Wilkinson TR & Gauderer MW (2003) Isolation and identification of biofilm microorganisms from silicone gastrostomy devices. J Pediatr Surg 38: 216-220.
25. Dickinson RJ, Varian SA, Axon AT & Cooke EM (1980) Increased incidence of faecal coliforms with in vitro adhesive and invasive properties in patients with ulcerative colitis. Gut 21: 787-792.
26. Eaves-Pyles T, Allen CA, Taormina J, Swidsinski A, Tutt CB, Jezek GE, Islas-Islas M & Torres AG (2008) Escherichia coli isolated from a Crohn's disease patient adheres, invades, and induces inflammatory responses in polarized intestinal epithelial cells. Int J Med Microbiol 298: 397-409.
27. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N & Pace NR (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. P Natl Acad Sci USA 104: 13780-13785.
28. Furrie E, Macfarlane S, Kennedy A, Cummings JH, Walsh SV, O'neil DA & Macfarlane GT (2005) Synbiotic therapy (Bifidobacterium longum/Synergy 1) initiates resolution of inflammation in patients with active ulcerative colitis: a randomised controlled pilot trial. Gut 54: 242-249.
29. Gisbert JP (2008) "Rescue" regimens after Helicobacter pylori treatment failure. World J Gastroenterol 14: 5385-5402.
30. Gobert AP, Mersey BD, Cheng Y, Blumberg DR, Newton JC & Wilson KT (2002) Cutting edge: urease release by Helicobacter pylori stimulates macrophage inducible nitric oxide synthase. J Immunol 168: 6002-6006.
31. Goldenberg SP, Wain SL & Marignani P (1990) Acute necrotizing esophagitis. Gastroenterology 98: 493-496.
32. Göõz M, Hammond CE, Larsen K, Mukhin YV & Smolka AJ (2000) Inhibition of human gastric H(+)-K(+)-ATPase alpha-subunit gene expression by Helicobacter pylori. Am J Physiol Gastrointest Liver Physiol 278: G981-G991.
33. Gottlieb K, DeMeo M, Borton P & Mobarhan S (1992) Gastrostomy tube deterioration and fungal colonization. Am J Gastroenterol 87: 1683.
34. Graham DY, Alpert LC, Smith JL & Yoshimura HH (1988) Iatrogenic Campylobacter pylori infection is a cause of epidemic achlorhydria. Am J Gastroenterol 83: 974-980.
35. Greenberg GR (2004) Antibiotics should be used as first-line therapy for Crohn's disease. Inflamm Bowel Dis 10: 318-320.
36. Harford WV, Barnett C, Lee E, Perez-Perez G, Blaser MJ & Peterson WL (2000) Acute gastritis with hypochlorhydria: report of 35 cases with long term follow up. Gut 47: 467-472.
37. Hill MJ, Drasar BS, Hawksworth G, Aries V, Crowther JS & Williams RE (1971) Bacteria and aetiology of cancer of large bowel. Lancet 1: 95-100.
38. Hopkins MJ, Sharp R & Macfarlane GT (2002) Variation in human intestinal microbiota with age. Dig Liver Dis 34(suppl 2): S12-S18.
39. Horie H, Kanazawa K, Okada M, Narushima S, Itoh K & Terada A (1999a) Effects of intestinal bacteria on the development of colonic neoplasm: an experimental study. Eur J Cancer Prev 8: 237-245.
40. Horie H, Kanazawa K, Kobayashi E, Okada M, Fujimura A, Yamagiwa S & Abo T (1999b) Effects of intestinal bacteria on the development of colonic neoplasm II. Changes in the immunological environment. Eur J Cancer Prev 8: 533-537.
41. Hurrell E, Kucerova E, Loughlin M, Caubilla-Barron J, Hilton A, Armstrong R, Smith C, Grant J, Shoo S & Forsythe S (2009) Neonatal enteral feeding tubes as loci for colonisation by members of the Enterobacteriaceae. BMC Infect Dis 9: 146.
42. Iijima K, Henry E, Moriya A, Wirz A, Kelman AW & McColl KE (2002) Dietary nitrate generates potentially mutagenic concentrations of nitric oxide at the gastroesophageal junction. Gastroenterology 122: 1248-1257.
43. Jain R, Maple JT, Anderson MA et al. (2011) The role of endoscopy in enteral feeding. Gastrointest Endosc 74: 7-12.
44. Le Moal G, Lemerre D, Grollier G, Desmont C, Klossek JM & Robert R (1999) Nosocomial sinusitis with isolation of anaerobic bacteria in ICU patients. Intensive Care Med 25: 1066-1071.
45. Ledder RG, Gilbert P, Huws SA, Aarons L, Ashley MP, Hull PS & McBain AJ (2007) Molecular analysis of the subgingival microbiota in health and disease. Appl Environ Microbiol 73: 516-523.
46. Lehours P & Yilmaz O (2007) Epidemiology of Helicobacter pylori infection. Helicobacter 12(suppl 1): 1-3.
47. Leibovitz A, Dan M, Zinger J, Carmeli Y, Habot B & Segal R (2003) Pseudomonas aeruginosa and the oropharyngeal ecosystem of tube-fed patients. Emerg Infect Dis 9: 956-959.
48. Leibovitz A, Baumoehl Y, Steinberg D & Segal R (2005) Biodynamics of biofilm formation on nasogastric tubes in elderly patients. Isr Med Assoc J 7: 428-430.
49. Levdikov VM, Blagova E, Joseph P, Sonenshein AL & Wilkinson AJ (2006) The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in Gram-positive bacteria. J Biol Chem 281: 11366-11373.
50. Lin CC, Lin CD, Cheng YK, Tsai MH & Chang CS (2006) Middle ear effusion in intensive care unit patients with prolonged endotracheal intubation. Am J Otolaryngol 27: 109-111.
51. Lin CS, He PJ, Hsu WT, Wu MS, Wu CJ, Shen HW, Hwang CH, Lai YK, Tsai NM & Liao KW (2010) Helicobacter pylori-derived Heat shock protein 60 enhances angiogenesis via a CXCR2-mediated signaling pathway. Biochem Biophys Res Commun 397: 283-289.
52. Liu L, Xu-Welliver M, Kanugula S & Pegg AE (2002) Inactivation and degradation of O(6)-alkylguanine-DNA alkyltransferase after reaction with nitric oxide. Cancer Res 62: 3037-3043.
53. Lodes MJ, Cong Y, Elson CO, Mohamath R, Landers CJ, Targan SR, Fort M & Hershberg RM (2004) Bacterial flagellin is a dominant antigen in Crohn's disease. J Clin Invest 113: 1296-1306.
54. Macfarlane S & Dillon JF (2007) Microbial biofilms in the human gastrointestinal tract. J Appl Microbiol 102: 1187-1196.
55. Macfarlane GT & Gibson GR (1991) Formation of glycoprotein degrading enzymes by Bacteroides fragilis. FEMS Microbiol Lett 61: 289-293.
56. Macfarlane S & Macfarlane GT (2004) Bacterial diversity in the human gut. Adv Appl Microbiol 54: 261-289.
57. Macfarlane GT, Cummings JH, Macfarlane S & Gibson GR (1989) Influence of retention time on degradation of pancreatic enzymes by human colonic bacteria grown in a 3-stage continuous culture system. J Appl Bacteriol 67: 520-527.
58. Macfarlane GT, Hay S, Macfarlane S & Gibson GR (1990) Effect of different carbohydrates on growth, polysaccharidase and glycosidase production by Bacteroides ovatus, in batch and continuous culture. J Appl Bacteriol 68: 179-187.
59. Macfarlane GT, Gibson GR & Cummings JH (1992) Comparison of fermentation reactions in different regions of the human colon. J Appl Bacteriol 72: 57-64.
60. Macfarlane S, McBain AJ & Macfarlane GT (1997) Consequences of biofilm and sessile growth in the large intestine. Adv Dent Res 11: 59-68.
61. Macfarlane S, Cummings JH, & Macfarlane G (1999) Bacterial colonisation of surfaces in the large intestine. Colonic Microflora, Nutrition and Health (Gibson G & Roberfroid M, eds), pp. 71-87. Chapman & Hall, London.
62. Macfarlane S, Furrie E, Cummings JH & Macfarlane GT (2004) Chemotaxonomic analysis of bacterial populations colonizing the rectal mucosa in patients with ulcerative colitis. Clin Infect Dis 38: 1690-1699.
63. Macfarlane S, Woodmansey EJ & Macfarlane GT (2005) Colonization of mucin by human intestinal bacteria and establishment of biofilm communities in a two-stage continuous culture system. Appl Environ Microbiol 71: 7483-7492.
64. Macfarlane S, Macfarlane GT & Cummings JH (2006) Review article: prebiotics in the gastrointestinal tract. Aliment Pharmacol Ther 24: 701-714.
65. Macfarlane S, Furrie E, Macfarlane GT & Dillon JF (2007) Microbial colonization of the upper gastrointestinal tract in patients with Barrett's esophagus. Clin Infect Dis 45: 29-38.
66. Macfarlane GT, Steed H & Macfarlane S (2008) Bacterial metabolism and health-related effects of galacto-oligosaccharides and other prebiotics. J Appl Microbiol 104: 305-344.
67. Macfarlane GT, Blackett KL, Nakayama T, Steed H & Macfarlane S (2009) The gut microbiota in inflammatory bowel disease. Curr Pharm Des 15: 1528-1536.
68. Macpherson A, Khoo UY, Forgacs I, Philpott-Howard J & Bjarnason I (1996) Mucosal antibodies in inflammatory bowel disease are directed against intestinal bacteria. Gut 38: 365-375.
69. Majerczyk CD, Dunman PM, Luong TT, Lee CY, Sadykov MR, Somerville GA, Bodi K & Sonenshein AL (2010) Direct targets of CodY in Staphylococcus aureus. J Bacteriol 192: 2861-2877.
70. Marrie TJ, Sung JY & Costerton JW (1990) Bacterial biofilm formation on nasogastric tubes. J Gastroenterol Hepatol 5: 503-506.
71. Martin HM, Campbell BJ, Hart CA, Mpofu C, Nayar M, Singh R, Englyst H, Williams HF & Rhodes JM (2004) Enhanced Escherichia coli adherence and invasion in Crohn's disease and colon cancer. Gastroenterology 127: 80-93.
72. Martinez-Medina M, Aldeguer X, Lopez-Siles M, González-Huix F, López-Oliu C, Dahbi G, Blanco JE, Blanco J, Garcia-Gil LJ & Darfeuille-Michaud A (2009a) Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn's disease. Inflamm Bowel Dis 15: 872-882.
73. Martinez-Medina M, Naves P, Blanco J, Aldeguer X, Blanco JE, Blanco M, Ponte C, Soriano F, Darfeuille-Michaud A & Garcia-Gil LJ (2009b) Biofilm formation as a novel phenotypic feature of adherent-invasive Escherichia coli (AIEC). BMC Microbiol 9: 202.
74. Mathus-Vliegen EM, Bredius MW & Binnekade JM (2006) Analysis of sites of bacterial contamination in an enteral feeding system. JPEN J Parenter Enteral Nutr 30: 519-525.
75. McCormick BA, Stocker BA, Laux DC & Cohen PS (1988) Roles of motility, chemotaxis, and penetration through and growth in intestinal mucus in the ability of an avirulent strain of Salmonella typhimurium to colonize the large intestine of streptomycin-treated mice. Infect Immun 56: 2209-2217.
76. McKenzie H, Main J, Pennington CR & Parratt D (1990) Antibody to selected strains of Saccharomyces cerevisiae (baker's and brewer's yeast) and Candida albicans in Crohn's disease. Gut 31: 536-538.
77. Megraud F, Trimoulet P, Lamouliatte H & Boyanova L (1991) Bactericidal effect of amoxicillin on Helicobacter pylori in an in vitro model using epithelial cells. Antimicrob Agents Chemother 35: 869-872.
78. Mobley HL, Cortesia MJ, Rosenthal LE & Jones BD (1988) Characterization of urease from Campylobacter pylori. J Clin Microbiol 26: 831-836.
79. Mpofu CM, Campbell BJ, Subramanian S, Marshall-Clarke S, Hart CA, Cross A, Roberts CL, McGoldrick A, Edwards SW & Rhodes JM (2007) Microbial mannan inhibits bacterial killing by macrophages: a possible pathogenic mechanism for Crohn's disease. Gastroenterology 133: 1487-1498.
80. Nagy KN, Sonkodi I, Szöke I, Nagy E & Newman HN (1998) The microflora associated with human oral carcinomas. Oral Oncol 34: 304-308.
81. Ohlsen K & Lorenz U (2010) Immunotherapeutic strategies to combat staphylococcal infections. Int J Med Microbiol 300: 402-410.
82. O'May GA, Reynolds N & Macfarlane GT (2005a) Effect of pH on an in vitro model of gastric microbiota in enteral nutrition patients. Appl Environ Microbiol 71: 4777-4783.
83. O'May GA, Reynolds N, Smith AR, Kennedy A & Macfarlane GT (2005b) Effect of pH and antibiotics on microbial overgrowth in the stomachs and duodena of patients undergoing percutaneous endoscopic gastrostomy feeding. J Clin Microbiol 43: 3059-3065.
84. Onderdonk AB & Bartlett JG (1979) Bacteriological studies of experimental ulcerative colitis. Am J Clin Nutr 32: 258-265.
85. Onderdonk AB, Cisneros RL & Bronson RT (1983) Enhancement of experimental ulcerative colitis by immunization with Bacteroides vulgatus. Infect Immun 42: 783-788.
86. Osias GL, Bromer MQ, Thomas RM, Friedel D, Miller LS, Suh B, Lorber B, Parkman HP & Fisher RS (2004) Esophageal bacteria and Barrett's esophagus: a preliminary report. Dig Dis Sci 49: 228-236.
87. Ott SJ, Kühbacher T, Musfeldt M, Rosenstiel P, Hellmig S, Rehman A, Drews O, Weichert W, Timmis KN & Schreiber S (2008) Fungi and inflammatory bowel diseases: alterations of composition and diversity. Scand J Gastroenterol 43: 831-841.
88. Papp M, Altorjay I, Dotan N et al. (2008) New serological markers for inflammatory bowel disease are associated with earlier age at onset, complicated disease behavior, risk for surgery, and NOD2/CARD15 genotype in a Hungarian IBD cohort. Am J Gastroenterol 103: 665-681.
89. Parsek MR & Singh PK (2005) Bacterial biofilms: an emerging link to disease pathogenesis. Annu Rev Microbiol 57: 677-701.
90. Peek RM & Blaser MJ (2002) Helicobacter pylori and gastrointestinal tract adenocarcinomas. Nat Rev Cancer 2: 28-37.
91. Pei Z, Yang L, Peek RM Jr, Levine SM, Pride DT & Blaser MJ (2005) Bacterial biota in reflux esophagitis and Barrett's esophagus. World J Gastroenterol 11: 7277-7283.
92. Peters BM, Jabra-Rizk MA, Scheper MA, Leid JG, Costerton JW & Shirtliff ME (2010) Microbial interactions and differential protein expression in Staphylococcus aureus -Candida albicans dual-species biofilms. FEMS Immunol Med Microbiol 59: 493-503.
93. Poxton IR, Brown R, Sawyerr A & Ferguson A (1997) Mucosa-associated bacterial flora of the human colon. J Med Microbiol 46: 85-91.
94. Qin J, Li R, Raes J et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
95. Quigley M & Kelly S (1995) Structure, Function and Metabolism of Host Mucus Glycoproteins. CRC Press, Boca Raton, FL, pp. 175-199.
96. Reiff C & Kelly D (2010) Inflammatory bowel disease, gut bacteria and probiotic therapy. Int J Med Microbiol 300: 25-33.
97. Rex DK, Cummings OW, Shaw M, Cumings MD, Wong RK, Vasudeva RS, Dunne D, Rahmani EY & Helper DJ (2003) Screening for Barrett's esophagus in colonoscopy patients with and without heartburn. Gastroenterology 125: 1670-1677.
98. Richardson AR, Libby SJ & Fang FC (2008) A nitric oxide-inducible lactate dehydrogenase enables Staphylococcus aureus to resist innate immunity. Science 319: 1672-1676.
99. Ronkainen J, Aro P, Storskrubb T, Johansson SE, Lind T, Bolling-Sternevald E, Vieth M, Stolte M, Talley NJ & Agréus L (2005) Prevalence of Barrett's esophagus in the general population: an endoscopic study. Gastroenterology 129: 1825-1831.
100. Sadlack B, Merz H, Schorle H, Schimpl A, Feller AC & Horak I (1993) Ulcerative colitis-like disease in mice with a disrupted interleukin-2 gene. Cell 75: 253-261.
101. Saha A, Hammond CE, Gooz M & Smolka AJ (2007) IL-1beta modulation of H, K-ATPase alpha-subunit gene transcription in Helicobacter pylori infection. Am J Physiol Gastrointest Liver Physiol 292: G1055-G1061.
102. Scanlan PD, Shanahan F, O'Mahony C & Marchesi JR (2006) Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. J Clin Microbiol 44: 3980-3988.
103. Scanlan PD, Shanahan F & Marchesi JR (2008) Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol 8: 79.
104. Schrager J & Oates MD (1978) Relation of human gastrointestinal mucus to disease states. Br Med Bull 34: 79-82.
105. Segal R, Pogoreliuk I, Dan M, Baumoehl Y & Leibovitz A (2006) Gastric microbiota in elderly patients fed via nasogastric tubes for prolonged periods. J Hosp Infect 63: 79-83.
106. Simon PM, Goode PL, Mobasseri A & Zopf D (1997) Inhibition of Helicobacter pylori binding to gastrointestinal epithelial cells by sialic acid-containing oligosaccharides. Infect Immun 65: 750-757.
107. Smith AC & Podolsky DK (1986) Colonic mucin glycoproteins in health and disease. Clin Gastroenterol 15: 815-837.
108. Smith AR, Macfarlane S, Furrie E, Ahmed S, Bahrami B, Reynolds N & Macfarlane GT (2011) Microbiological and immunological effects of enteral feeding on the upper gastrointestinal tract. J Med Microbiol 60: 359-365.
109. Spechler SJ, Lee E, Ahnen D et al. (2001) Long-term outcome of medical and surgical therapies for gastroesophageal reflux disease: follow-up of a randomized controlled trial. JAMA 285: 2331-2338.
110. Stark RM, Gerwig GJ, Pitman RS et al. (1999) Biofilm formation by Helicobacter pylori. Lett Appl Microbiol 28: 121-126.
111. Steed H, Macfarlane GT & Macfarlane S (2008) Prebiotics, synbiotics and inflammatory bowel disease. Mol Nutr Food Res 52: 898-905.
112. Suzuki H, Iijima K, Scobie G, Fyfe V & McColl KE (2005) Nitrate and nitrosative chemistry within Barrett's oesophagus during acid reflux. Gut 54: 1527-1535.
113. Swidsinski A, Weber J, Loening-Baucke V, Hale LP & Lochs H (2005) Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol 43: 3380-3389.
114. Swidsinski A, Loening-Baucke V, Vaneechoutte M & Doerffel Y (2008a) Active Crohn's disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora. Inflamm Bowel Dis 14: 147-161.
115. Swidsinski A, Loening-Baucke V, Bengmark S, Scholze J & Doerffel Y (2008b) Bacterial biofilm suppression with antibiotics for ulcerative and indeterminate colitis: consequences of aggressive treatment. Arch Med Res 39: 198-204.
116. Swidsinski A, Loening-Baucke V & Herber A (2009) Mucosal flora in Crohn's disease and ulcerative colitis - an overview. J Physiol Pharmacol 60(suppl 6): 61-71.
117. Thompson-Chagoyán OC, Maldonado J & Gil A (2005) Aetiology of inflammatory bowel disease (IBD): role of intestinal microbiota and gut-associated lymphoid tissue immune response. Clin Nutr 24: 339-352.
118. Vasquez N, Mangin I, Lepage P et al. (2007) Patchy distribution of mucosal lesions in ileal Crohn's disease is not linked to differences in the dominant mucosa-associated bacteria: a study using fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis. Inflamm Bowel Dis 13: 684-692.
119. Walters MC, Roe F, Bugnicourt A, Franklin MJ & Stewart PS (2003) Contributions of antibiotic penetration, oxygen limitation, and low metabolic activity to tolerance of Pseudomonas aeruginosa biofilms to ciprofloxacin and tobramycin. Antimicrob Agents Chemother 47: 317-323.
120. Wang F, Xia P, Wu F et al. (2008) Helicobacter pylori VacA disrupts apical membrane-cytoskeletal interactions in gastric parietal cells. J Biol Chem 283: 26714-26725.
121. Wang SL, Wang ZR & Yang CQ (2012) Meta-analysis of broad-spectrum antibiotic therapy in patients with active inflammatory bowel disease. Exp Ther Med 4: 1051-1056.
122. Weeks DL, Eskandari S, Scott DR & Sachs G (2000) A H+-gated urea channel: the link between Helicobacter pylori urease and gastric colonization. Science 287: 482-485.
123. Williams C & McColl KE (2006) Review article: proton pump inhibitors and bacterial overgrowth. Aliment Pharmacol Ther 23: 3-10.
124. Williams JC, McInnis KA & Testerman TL (2008) Adherence of Helicobacter pylori to abiotic surfaces is influenced by serum. Appl Environ Microbiol 74: 1255-1258.
125. Winters C, Spurling TJ, Chobanian SJ et al. (1987) Barrett's esophagus. A prevalent, occult complication of gastroesophageal reflux disease. Gastroenterology 92: 118-124.
126. Ye W, Held M, Lagergren J, Engstrand L, Blot WJ, McLaughlin JK & Nyrén O (2004) Helicobacter pylori infection and gastric atrophy: risk of adenocarcinoma and squamous-cell carcinoma of the esophagus and adenocarcinoma of the gastric cardia. J Natl Cancer Inst 96: 388-396.
127. Yonezawa H, Osaki T, Kurata S, Fukuda M, Kawakami H, Ochiai K, Hanawa T & Kamiya S (2009) Outer membrane vesicles of Helicobacter pylori TK1402 are involved in biofilm formation. BMC Microbiol 9: 197.
128. Yonezawa H, Osaki T, Kurata S, Zaman C, Hanawa T & Kamiya S (2010) Assessment of in vitro biofilm formation by Helicobacter pylori. J Gastroenterol Hepatol 25(suppl 1): S90-S94.
129. Zavros Y, Eaton KA, Kang W, Rathinavelu S, Katukuri V, Kao JY, Samuelson LC & Merchant JL (2005) Chronic gastritis in the hypochlorhydric gastrin-deficient mouse progresses to adenocarcinoma. Oncogene 24: 2354-2366.