Anwar, H, Dasgupta, MK & Costerton, JW (1990) Testing the susceptibility of bacteria in biofilms to antibacterial agents. Antimicrob Agents Chemother 34, 2043–2046.
Balish, E & Warner, T (2002) Enterococcus faecalis induces inflammatory bowel disease in interleukin-10 knockout mice. Am J Pathol 160, 2253–2257.
Bamba, T, Matsuda, H, Endo, M & Fujiyama, Y (1995) The pathogenic role of Bacteroides vulgatus in patients with ulcerative colitis. J Gastroenterol 30 Suppl. 8, 45–47.
Borruel, N, Carol, M, Casallas, F, Antolin, M, de Lara, F, Espin, E, Naval, J, Guarner, F & Malagelada, JR (2002) Increased mucosal tumour necrosis factor α production in Crohn's disease can be down regulated ex vivo by probiotic bacteria. Gut 51, 659–664.
Burke, D & Axon, A (1988) Adhesive E. coli in inflammatory bowel disease and infective diarrhoea. Br Med J 297, 102–104.
Butcher, EC (1991) Leukocyte-endothelial cell recognition: three (or more) steps to specificity and diversity. Cell 67, 1033–1036.
Campieri, M & Gionchetti, P (2001) Bacteria as the cause of ulcerative colitis. Gut 48, 132–135.
Chadwick, VS (1991) Etiology of chronic ulcerative colitis and Crohn's disease. In The Large Intestine: Physiology, Pathophysiology and Disease, pp. 445–463 [Phillips, SF, Pemberton, JH and Shorter, RG, editors]. New York: Raven Press.
Cummings, JH, Macfarlane, GT & Macfarlane, S (2003) Intestinal bacteria and ulcerative colitis. Curr Issues Intest Microbiol 4, 9–20.
Daig, R, Rogler, G, Aschenbrenner, E, Vogl, D, Falk, W, Gross, V, Scholmerich, J & Andus, T (2000) Human intestinal epithelial cells secrete interleukin-1 receptor antagonist and interleukin-8 but not interleukin-1 or interleukin-6. Gut 46, 350–358.
Duchman, R, Kaiser, I, Hermann, E, Mayet, W, Ewe, K, Meyer Zum, KH (1995) Tolerance exists towards resident intestinal flora but is broken down in active inflammatory bowel disease (IBD). Clin Exp Immunol 102, 448–455.
Fabia, R, Ar'Rajab, A, Johansson, ML, Willen, R, Molin, G & Bengmark, S (1993a) The effect of exogenous administration of Lactobacillus reuteri R2LC and oat fiber on acetic acid-induced colitis in the rat. Scand J Gastroenterol 28, 155–162.
Fabia, R, Ar'Rajab, A, Johansson, ML, Andersson, R, Willen, R, Jeppsson, B, Molin, G & Bengmark, S (1993b) Impairment of bacterial flora in human ulcerative colitis and experimental colitis in the rat. Digestion 54, 248–255.
Farina, C, Arosio, M, Mangia, M & Moioli, F (2001) Lactobacillus casei subsp. rhamnosus sepsis in a patient with ulcerative colitis. J Clin Gastroenterol 33, 251–252.
Fellerman, K, Wehkamp, J, Herrlinger, KR & Stange, EF (2003) Crohn's disease: a defensin deficiency syndrome?. Eur J Gastroenterol Hepatol 15, 627–634.
Furrie, E, Macfarlane, S, Cummings, JH & Macfarlane, GT (2004) Systemic antibodies towards mucosal bacteria in ulcerative colitis and Crohn's disease differentially activate the innate immune response. Gut 53, 92–99.
Furrie, E, Macfarlane, S, Kennedy, A, Cummings, JH, Walsh, SV, O'Neil, DA & Macfarlane, GT (2005) Synbiotic therapy ( Bifidobacterium longum /Synergy 1 TM ) initiates resolution of inflammation in patients with active ulcerative colitis: a randomised controlled pilot trial. Gut 54, 242–249.
Gibson, GR & Roberfroid, MB (1995) Dietary modulation of the human colonic microbiota introducing the concept of prebiotics. J Nutr 125, 1401–1412.
Gionchetti, P, Rizzello, F, Venturi, A, Brigidi, P, Matteuzzi, D, Bazzocchi, G, Poggioli, G, Miglioli, M & Campieri, M (2000) Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: a double-blind, placebo-controlled trial. Gastroenterology 119, 305–309.
Guslandi, M, Mezzi, G, Sorghi, M & Testoni, PA (2000) Saccharomyces boulardii in maintenance treatment of Crohn's disease. Dig Dis Sci 45, 1462–1464.
Hartley, MG, Hudson, MJ, Swarbrick, ET, Gent, AE, Hellier, MD & Grace, RH (1993) Adhesive and hydrophobic properties of Escherichia coli from the rectal mucosa of patients with ulcerative colitis. Gut 34, 63–67.
He, F, Tuomola, E, Arvilommi, H & Seppo, S (2000) Modulation of humoral immune response through probiotic intake. FEMS Immunol Med Microbiol 29, 47–52.
Hill, MJ (1986) The possible role of bacteria in inflammatory bowel disease. Curr Concepts Gastroenterol 3, 10–14.
Ibnou-Zekri, N, Blum, S, Schiffrin, EJ, von der Weid, T (2003) Divergent patterns of colonization and immune response elicited from two intestinal Lactobacillus strains that display similar properties in vitro. Infect Immun 71, 428–436.
Kruis, W, Schutz, Fric P, Fixa, B, Judmaier, G, Stolte, M (1997) Double-blind comparison of an oral Escherichia coli preparation and mesalazine in maintaining remission in ulcerative colitis. Aliment Pharmacol Ther 11, 853–858.
Maassen, CB, van Holten-Neelen, C, Balk, F, den Bak-Glashouwer, MJ, Leer, RJ, Lamen, JD, Boersma, WJ & Claassen, E (2000) Strain-dependent induction of cytokine profiles in the gut by orally administered Lactobacillus strains. Vaccine 18, 2613–2623.
Macdonald, TT, Monteleone, G & Pender, SLF (2000) Recent developments in the immunology of inflammatory bowel disease. Scand J Immunol 51, 2–9.
Macfarlane, GT & Cummings, JH (2002) Probiotics, infection and immunity. Curr Opin Infect Dis 15, 501–506.
Macfarlane, S, Cummings, JH & Macfarlane, GT (1999) Bacterial colonisation of surfaces in the large intestine. In Colonic Microflora, Nutrition and Health, pp. 71–87 [Gibson, GR and Roberfroid, M, editors] London: Chapman & Hall.
Macfarlane, S, Hopkins, MJ & Macfarlane, GT (2000) Bacterial growth and metabolism on surfaces in the large intestine. Microb Ecol Health Dis 2, 64–72.
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.
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.
Madsen, KL, Doyle, JS, Jewell, LD, Tavernini, MM & Fedorak, RN (1999) Lactobacillus species prevent colitis in interleukin 10 gene-deficient mice. Gastroenterology 116, 1107–1114.
Mao, Y, Nobaek, S, Kasravi, B, Adawi, D, Stenram, U, Molin, G & Jeppsson, B (1996) The effects of Lactobacillus strains and oat fiber on methotrexate-induced enterocolitis in rats. Gastroenterology 111, 334–344.
Matsuda, H, Fujiyama, Y, Andoh, A, Ushijima, T, Kajinami, T & Bamba, T (2000) Characterization of antibody responses against rectal mucosa-associated bacterial flora in patients with ulcerative colitis. J Gastroenterol Hepatol 15, 61–68.
Monteiro, E, Fossey, J, Shiner, M, Draser, BS & Allison, AC (1971) Antibacterial antibodies in rectal and colonic mucosa in ulcerative colitis. Lancet 1, 249–251.
Navarro, F & Hanauer, SB (2003) Treatment of inflammatory bowel disease: safety and tolerability issues. Am J Gastroenterol 98, S18–S23.
Niness, KR (1999) Inulin and oligofructose: what are they?. British J Nutr 129, Suppl. 7, 1402S–1406S.
Onderdonk, AB (1983) Role of the intestinal microflora in ulcerative colitis. in Human Intestinal Microflora in Health and Disease, 481–493 [Hentges, DJ, editors]. New York: Academic Press.
Onderdonk, AB & Bartlett, MD (1979) Bacteriological studies of experimental ulcerative colitis. Am J Clin Nutr 32, 258–265.
O'Neil, DA (2003) Regulation of expression of beta-defensins: endogenous enteric peptide antibiotics. Mol Immunol 40, 445–450.
O'Neil, DA, Porter, EM, Elewaut, D, Anderson, GM, Eckmann, L, Ganz, T & Kagnoff, MF (1999) Expression and regulation of the human beta-defensins hBD-1 and hBD-2 in intestinal epithelium. J Immunol 163, 6718–6724.
Ott, SJ, Musfeldt, M, Wendererorh, DF, Hampe, J, Brant, O, Folsch, UR, Timmis, KN & Schrieiber, S (2004) Reduction in diversity of the colonic mucosa associated microflora in patients with active inflammatory bowel disease. Gut 53, 685–693.
Pathmakanthan, S, Thornley, JP & Hawkey, CJ (1999) Mucosally associated bacterial flora of the human colon: quantitative and species specific differences between normal and inflammed colonic biopsies. Microb Ecol Health Dis 11, 169–174.
Poxton, IR, Brown, R, Sawyerr, A & Ferguson, A (1997) Mucosa-associated bacterial flora of the human colon. J Med Microbiol 46, 85–91.
Rembacken, BJ, Snelling, AM, Hawkey, PM, Chalmers, DM & Axon, ATR (1999) Non-pathogenic Escherichia coli versus mesalazine for the treatment of ulcerative colitis: a randomised trial. Lancet 354, 636–639.
Ruseler, van, Embden, JGH, Schouten, WR, Van Lieshout, LMC (1994) Pouchitis: result of microbial imbalance?. Gut 35, 658–664.
Sadlack, B, Merz, H & Schorle, H (1993) Ulcerative colitis-like disease in mice with a disrupted interleukin-2 gene. Cell 175, 253–261.
Sartor, RB, Rath, HC & Sellon, HK (1996) Microbial factors in chronic intestinal inflammation. Curr Opin Gastroenterol 12, 327–333.
Schultsz, C, Moussa, M, van Ketel, R, Tytgat, GN & Dankert, J (1997) Frequency of pathogenic and enteroadherent Escherichia coli in patients with inflammatory bowel disease and controls. J Clin Pathol 50, 573–579.
Schultsz, C, Van der Berg, FM, ten Kate, FW, Tytgat, GN & Dankert, J (1999) The intestinal mucous layer from patients with inflammatory bowel disease harbors high numbers of bacteria compared with controls. Gastroenterology 117, 1089–1097.
Schultz, M, Veltkamp, C & Dieleman, LA (2002) Lactobacillus plantarum 299V in the treatment and prevention of spontaneous colitis in interleukin-10-deficient mice. Inflamm Bowel Dis 8, 71–80.
Seksik, P, Rigottier-Gois, L, Gramet, G, Sutren, M, Pochart, P, Marteau, P, Jian, R & Dore, J (2003) Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut 52, 237–242.
Shanahan, F & McCarthy, J (2000) Functional foods and prebiotics – time for gastroenterologists to embrace the concepts. Curr Gastroenterol Rep 2, 345–346.
Steidler, L, Hans, W, Schotte, L, Neirynck, S, Obermeier, F, Falk, W, Fiers, W & Remaut, E (2000) Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science 289, 1352–1355.
Swidsinski, A, Ladhoff, A & Pernthaler, A (2002) Mucosal flora in inflammatory bowel disease. Gastroenterology 122, 44–54.
Taurog, JD, Richardson, JA, Croft, JT, Simmons, WA, Zhou, M, Fernandez-Sueiro, JL, Balish, E & Hammer, RE (1994) The germ free state prevents development of gut and joint inflammatory disease in HLA-B27 transgenic rats. J Exp Med 180, 2359–2364.
Tvede, M, Bondesen, S, Nielsen, OH & Rasmussen, SN (1983) Serum antibodies to Bacteroides species in chronic inflammatory bowel disease. Scand J Gastroenterol 18, 783–789.
Van der Waaij, D, Cohen, BJ & Anver, MR (1974) Mitigation of experimental inflammatory bowel disease in guinea pigs by selective elimination of the aerobic gram-negative intestinal microflora. Gastroenterology 67, 460–472.
Van der Wiel-Korstanje, J & Winkler, K (1975) The faecal flora in ulcerative colitis. J Med Microbiol 8, 491–501.
Venturi, A, Gionchetti, P, Rizzello, F, Johansson, R, Zucconi, E, Brigidi, P, Matteuzzi, D & Campiere, 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.
Von Wulffen, H, Russmann, H, Karch, H, Meyer, T, Bitzan, M, Kohrt, TC & Aleksic, S (1989) Verocytotoxin-producing Escherichia coli O2:H5 isolated from patients with ulcerative colitis. Lancet 1, 1449–1450.
Walmsey, RS, Anthony, A, Sim, R, Pounder, RE & Wakefield, AJ (1998) Absence of Escherichia coli, Listeria monocytogenes, and Klebsiella pneumoniae antigens within inflammatory bowel disease tissues. J Clin Patholol 51, 657–661.
Wehkamp, J, Harder, J, Weichenthal, M, Mueller, O, Herrlinger, KR, Fellermann, K, Schroeder, JM & Stange, EF (2003) Inducible and constitutive beta-defensins are differentially expressed in Crohn's disease and ulcerative colitis. Inflamm Bowel Dis 9, 215–223.
Woywodt, A, Ludwig, D, Neustock, P, Kruse, A, Schwarting, K, Jantschek, G, Kirchner, H & Stange, EF (1999) Mucosal cytokine expression, cellular markers and adhesion molecules in inflammatory bowel disease. Eur J Gastroenterol Hepatol 11, 267–276.
Yamaguchi, Y, Nagase, T, Makita, R, Fukuhara, S, Tomita, T, Tominaga, T, Kurihara, H & Ouchi, Y (2002) Identification of multiple novel epididymis-specific beta-defensin isoforms in humans and mice. J Immunol 169, 2516–2523.
Zhao, C, Wang, I & Lehrer, RI (1996) Widespread expression of beta defensin hBD-1 in human secretory glands and epithelial cells. FEBS Lett 396, 319–325.
Zoetendal, EG, von Wright, A, Vilpponen-Salmela, T, Ben-Amor, K, Akkermans, AD, de Vos, WM (2002) Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distrubuted along the colon and differ from the community recovered from feces. Appl Environ Microbiol 68, 3401–3407.