Microbial biofilms in the human gastrointestinal tract

Journal of Applied Microbiology

Volumn 102, Issue 5, 2007, Pages 1187-1196

  Macfarlane, S ^a   Dillon, J F ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

Gastrointestinal tract; Microbial biofilms; Oesophageal mucosa; Prebiotics; Probiotics; Ulcerative colitis

Indexed keywords

BACTERIA; METABOLISM; PROBIOTICS;

BACTERIAL COMMUNITY; ESOPHAGEAL MUCOSA; GASTROINTESTINAL TRACT; MICROBIAL BIOFILM; MICROBIOTAS; MICROHABITATS; MUCUS LAYER; PREBIOTICS; PROBIOTICS; ULCERATIVE COLITIS;

BIOFILMS;

MESALAZINE; PREBIOTIC AGENT; PROBIOTIC AGENT;

BACTERIUM; BIOFILM; DIGESTIVE SYSTEM DISORDER; GROWTH RATE; METABOLISM; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; PROBIOTICS;

BACTERIAL COLONIZATION; BACTERIAL OVERGROWTH; BACTERIAL STRAIN; BACTERIUM CULTURE; BARRETT ESOPHAGUS; BIOFILM; CANCER RISK; CONFERENCE PAPER; DIET SUPPLEMENTATION; DNA DAMAGE; DYSPHAGIA; ENTERIC FEEDING; ESCHERICHIA COLI; ESOPHAGEAL ADENOCARCINOMA; ESOPHAGUS MUCOSA; GASTROINTESTINAL TRACT; HELICOBACTER PYLORI; HUMAN; INTESTINE FLORA; LOWER ESOPHAGUS SPHINCTER; MALIGNANT TRANSFORMATION; NONHUMAN; PERCUTANEOUS ENDOSCOPIC GASTROSTOMY; SPECIES COMPOSITION; SPECIES DIVERSITY; SQUAMOUS EPITHELIUM; THERAPY EFFECT; TREATMENT OUTCOME; TREATMENT RESPONSE; ULCERATIVE COLITIS;

BACTERIA (MICROORGANISMS);

EID: 34247354093     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2007.03287.x     Document Type: Conference Paper

References (56)

1. Allen, A. (1981) Structure and function of gastrointestinal mucus. In Physiology of the Gastrointestinal Tract ed. Johnson, L.R. pp. 617 639. New York: Raven Press.
2. Aminov, R.I., Walker, A.W., Duncan, S.H., Harmsen, H.J.M., Welling, G.W. Flint, H.J. (2006) Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale. Appl Environ Microbiol 72, 6371 6376.
3. Anwar, H., Dasgupta, M.K. Costerton, J.W. (1990) Testing the susceptibility of bacteria in biofilms to antibacterial agents. Antimicrob Agents Chemother 34, 2043 2046.
4. Araya-Kojima, A., Yaeshima, T., Ishibashi, N., Shimamur, S. Hayasawa, H. (1995) Inhibitory effects of Bifidobacterium longum BB536 on harmful intestinal bacteria. Bifidobact Microflora 14, 59 66.
5. Cabre, E. Gassull, M.A. (1993) Complications of enteral feeding. Nutrition 9, 1 9.
6. Chadwick, V.S. (1991) Etiology of chronic ulcerative colitis and Crohn's disease. In The Large Intestine: Physiology, Pathophysiology and Disease ed. Phillips, S.F., Pemberton, J.H. Shorter, R.G. pp. 445 463. New York: Raven Press Ltd.
7. Cohen, M.B. Giannella, R.A. (1991) Bacterial infections: pathophysiology, clinical features and treatment. In The Large Intestine: Physiology, Pathophysiology and Disease ed. Phillips, S.F., Pemberton, J.H. Shorter, R.G. pp. 395 428. New York: Raven Press Ltd.
8. Croucher, S.C., Houston, A.P., Bayliss, C.E. Turner, R.J. (1983) Bacterial populations associated with different regions of the human colon wall. Appl Environ Microbiol 45, 1025 1033.
9. Cummings, J.H., Macfarlane, G.T. Macfarlane, S. (2003) Intestinal bacteria and ulcerative colitis. Curr Issues Intest Microbiol 4, 9 20.
10. De Simone, C., Ciardi, A., Grassi, A., Lambert Gardini, S., Tzantzoglou, S., Trinchieri, V., Moretti, S. Jirillo, E. (1992) Effect of Bifidobacterium bifidum and Lactobacillus acidophilus on gut mucosa and peripheral blood B lymphocytes. Immunopharmacol Immunotoxicol 14, 331 340.
11. Edmiston, C.E. Jr., Avant, G.R. Wilson, F.A. (1982) Anaerobic bacterial populations on normal and diseased human biopsy tissue obtained at colonoscopy. Appl Environ Microbiol 43, 1173 1181.
12. Famularo, G., Moretti, S., Marcellini, S. De Simone, C. (1997) Stimulation of immunity by probiotics. In Probiotics: Therapeutic and Other Beneficial Effects ed. Fuller, R. pp. 133 161. London: Chapman & Hall.
13. Faure, J.C., Schellenberg, D.A., Bexter, A. Wuerzuer, H.P. (1984) Barrier effect of Bifidobacterium longum on a pathogenic Escherichia coli strain by gut colonization in the germ-free rat. Z Ernahrungswiss 23, 41 44.
14. Fite, A., Macfarlane, G.T., Cummings, J.H., Hopkins, M.J., Kong, S.C., Furrie, E. Macfarlane, S. (2004) Identification and quantitation of mucosal and faecal desulfovibrios using real-time PCR. Gut 53, 523 529.
15. Florey, H. (1955) Mucin and the protection of the body. Proc R Soc Lon B Biol Sci 143, 144 158.
16. Furrie, E., Macfarlane, S., Kennedy, A., Cummings, J.H., Walsh, S.V., O'Neil, D.A. Macfarlane, G.T. (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.
17. Gianella, R.A., Broitman, S.A. Zamcheck, N. (1972) Gastric acid barrier to ingested microorganisms in man: studies in vivo and in vitro. Gut 13, 251 256.
18. Gibson, G.R., Cummings, J.H. Macfarlane, G.T. (1991) Growth and activities of sulphate-reducing bacteria in gut contents from healthy subjects and patients with ulcerative colitis. FEMS Microbiol Ecol 86, 103 112.
19. Gill, H.S., Rutherfurd, K.J., Cross, M.L. Gopal, P.K. (2001) Enhancement of immunity in the elderly by dietary supplementation with the probiotic Bifidobacterium lactis HN019. Am J Clin Nutr 74, 833 839.
20. Gottlieb, K., Leya, J., Kruss, D.M., Mobarhan, S. Iber, F.L. (1993) Intraluminal fungal colonization of gastrostomy tubes. Gastrointest Endosc 39, 413 415.
21. Hold, G.L., Pryde, S.E., Russell, V.J., Furrie, E. Flint, H.J. (2002) Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol 39, 33 39.
22. Hoshino, T., Noda, N., Tsuneda, S., Hirata, A. Inamori, Y. (2001) Direct detection by in situ PCR of the amoA gene in biofilm resulting from a nitrogen removal process. Appl Environ Microbiol 67, 5261 6266.
23. Kruis, W., Schutz, E., Fric, P., Fixa, B., Judmaier, G. Stolte, M. (1997) Double-blind comparison of an oral Escherichia coli preparation and mesalazine in maintaining remission of ulcerative colitis. Aliment Pharmacol Ther 11, 853 858.
24. Langlands, S.J., Hopkins, M.J., Coleman, N. Cummings, J.H. (2004) Prebiotic carbohydrates modify the mucosa-associated microflora of the human large bowel. Gut 53, 1610 1616.
25. Lee, A. (1980) Normal flora of animal intestinal surfaces. In Adsorption of Microorganisms to Surfaces ed. Bitton, G. Marshall, K.C. pp. 145 174. New York: John Wiley.
26. Lee, F.D., Kraszewski, A., Gordon, J., Howie, J.G.R., McSeveney, D. Harland, W.A. (1971) Intestinal spirochaetosis. Gut 12, 126 133.
27. Lin, J., Lee, I.S., Frey, J., Slonczewski, J.L. Foster, J.W. (1995) Comparative analysis of extreme acid survival in Salmonella typhimurium, Shigella flexneri, and Escherichia coli. J Bacteriol 177, 4097 4104.
28. van Loosdrecht, M.C.M., Lyklema, J., Norde, W. Zehnder, A.J.B. (1990) Influence of interfaces on microbial activity. Microbiol Rev 54, 75 87.
29. Loubinoux, J., Bronowicji, J.-P., Pereira, I.A.C., Moungenel, J.-L. Faou, A.E. (2002) Sulfate-reducing bacteria in human feces and their association with inflammatory diseases. FEMS Microbiol Ecol 40, 107 112.
30. Macfarlane, G.T. Cummings, J.H. (1991) The colonic flora, fermentation and large bowel digestive function. In The Colonic Flora, Fermentation and Large Bowel Digestive Function ed. Phillips, S.F., Pemberton, J.H. Shorter, R.G. pp. 51 92. New York: Raven Press Ltd.
31. Macfarlane, G.T. McBain, A.J. (1999) The human colonic microbiota. In Colonic Microflora, Nutrition and Health ed. Gibson, G.R. Roberfroid, M. pp. 1 25. London: Chapman & Hall.
32. Macfarlane, S. Macfarlane, G.T. (2006) Composition and metabolic activities of bacterial biofilms colonizing food residues in the human gut. Appl Environ Microbiol 72, 6204 6211.
33. Macfarlane, G.T., Gibson, G.R., Drasar, B.S. Cummings, J.H. (1995) Metabolic significance of the colonic microflora. In Gastrointestinal and Oesophageal Physiology ed. Whitehead, R. pp. 249 274. Edinburgh: Churchill Livingston.
34. Macfarlane, S., McBain, A.J. Macfarlane, G.T. (1997) Consequences of biofilm and sessile growth in the large intestine. Adv Dent Res 11, 59 68.
35. Macfarlane, S., Hopkins, M.J. Macfarlane, G.T. (2000) Bacterial growth and metabolism on surfaces in the large intestine. Microb Ecol Health Dis 2, 64 72.
36. Macfarlane, S., Furrie, E., Cummings, J.H. Macfarlane, G.T. (2004) Chemotaxonomic analysis of bacterial populations colonizing the rectal mucosa in patients with ulcerative colitis. Clin Infect Dis 38, 1690 1699.
37. Mahida, Y.R., Rose, F. Chan, W.C. (1997) Antimicrobial peptides in the gastrointestinal tract. Gut 40, 161 163.
38. Monteiro, E., Fossey, J., Shiner, M., Draser, B.S. Allison, A.C. (1971) Antibacterial antibodies in rectal and colonic mucosa in ulcerative colitis. Lancet 1, 249 251.
39. Mozes, N. Rouxhet, P.G. (1992) Influence of surfaces on microbial activity. In Biofilms-Science and Technology ed. Melo, L.F., Bott, T.R. Capdeville, B. pp. 125 136. Dordrecht: Kluwer Academic Publishers.
40. Nelson, D.P. Mata, L.J. (1970) Bacterial flora associated with the human gastrointestinal mucosa. Gastroenterology 58, 56 61.
41. Onderdonk, A.B. (1983) Role of the intestinal microflora in ulcerative colitis. In Human Intestinal Microflora in Health and Disease ed. Hentges, D.J. pp. 481 493. London: Academic Press.
42. Onderdonk, A.B. Bartlett, M.D. (1979) Bacteriological studies of experimental ulcerative colitis. Am J Clin Nutr 32, 258 265.
43. O'May, G.A., Reynolds, N. Macfarlane, G.T. (2005a) Effect of pH on an in vitro model of gastric microbiota in enteral nutrition patients. Appl Environ Microbiol 71, 4777 4783.
44. O'May, G.A., Reynolds, N., Smith, A.R., Kennedy, A. Macfarlane, G.T. (2005b) Effect of pH and antibiotics on microbial overgrowth in the stomach and duodenum of patients undergoing percutaneous endoscopic gastrostomy feeding. J Clin Microbiol 43, 3059 3065.
45. Prindiville, T., Cantrell, M. Wilson, K. (2004) Ribosomal DNA sequence analysis of mucosa-associated bacteria in Crohn's disease. Inflamm Bowel Dis 10, 824 833.
46. Rembacken, B.J., Snelling, A.M., Hawkey, P.M., Chalmers, D.M. Axon, A.T.R. (1999) Non-pathogenic Escherichia coli versus mesalazine for the treatment of ulcerative colitis: a randomised trial. Lancet 354, 636 639.
47. Ruseler van Embden, J.G.H., Schouten, W.R. van Lieshout, L.M.C. (1994) Pouchitis: result of microbial imbalance Gut 35, 658 664.
48. Salmond, G.P., Bycroft, B.W., Stewart, G.S. Williams, P. (1995) The bacterial 'enigma': cracking the code of cell-cell communication. Mol Microbiol 16, 615 624.
49. Smith, H. (1995) The revival of interest in mechanisms of bacterial pathogenicity. Biol Rev 70, 277 316.
50. Suau, A., Bonnet, R., Sutren, M., Godon, J.J., Gibson, G.R., Collins, M.D. Dore, J. (1999) Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65, 4799 4807.
51. Venturi, A., Gionchetti, P., Rizzello, F., Johansson, R., Zucconi, E., Brigidi, P., Matteuzzi, D. Campieri, M. (1999) Impact on the composition of the faecal flora by a new probiotic preparation: preliminary data on maintenance treatment of patients with ulcerative colitis. Aliment Pharmacol Ther 13, 1103 1108.
52. Wallace, R.J., Cheng, K.-J., Dinsdale, D. Orskov, E.R. (1979) An independent microbial flora of the epithelium and its role in the microbiology of the rumen. Nature 279, 424 426.
53. Williams, C. (2001) Occurrence and significance of gastric colonization during acid-inhibitory therapy. Best Pract Res Clin Gastroenterol 15, 511 521.
54. Wilson, K.H. Blitchington, R.B. (1996) Human colonic biota studied by ribosomal DNA sequence analysis. Appl Environ Microbiol 62, 2273 2278.
55. Zinkevich, V. Beech, I.B. (2000) Screening of sulfate-reducing bacteria in colonoscopy samples from healthy and colitic gut mucosa. FEMS Microbiol Ecol 34, 147 155.
56. Zoetendal, E.G., von Wright, A., Vilpponen-Salmela, T., Ben-Amor, K., Akkermans, A.D. de Vos, W.M. (2002) Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 68, 3401 3407.