Abstract
The human gastrointestinal (GI) tract represents a vast microbial ecosystem with a high degree of complexity and inter-individual diversity. The large intestine contains an estimated 1011–1012 bacteria per gram of contents and it is thought that total bacterial cells outnumber human cells by at least an order of magnitude (O’Sullivan 2005; O’Hara and Shanahan 2006). These bacteria comprise between 1,000 and 1,150 different species including 160 species which are common between individuals and may provide core functions that are essential for the health of the host (Qin et al. 2010). In this context the human individual has been proposed as a ‘superorganism’ in which the individual co-exists with their unique microbiota (Wilson and Sober 1989; Zilber-Rosenberg and Rosenberg 2008). The gut microbiota therefore comprise a ‘virtual organ’ that carries out significant metabolic, digestive and immunoregulatory roles that benefit the host (O’Sullivan 2005; O’Hara and Shanahan 2006).
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Allen SJ, Okoko B, Martinez E, Gregorio G, Dans LF (2004) Probiotics for treating infectious diarrhoea. Cochrane Database Syst Rev. doi:10.1002/14651858 (CD003048)
Altenhoefer A, Oswald S, Sonnenborn U, Enders C, Schulze J, Hacker J, Oelschlaeger TA (2004) The probiotic Escherichia coli strain Nissle 1917 interferes with invasion of human intestinal epithelial cells by different enteroinvasive bacterial pathogens. FEMS Immunol Med Microbiol 40:223–229
Asahara T, Shimizu K, Nomoto K, Hamabata T, Ozawa A, Takeda Y (2004) Probiotic bifidobacteria protect mice from lethal infection with Shiga toxin-producing Escherichia coli O157:H7. Infect Immun 72:2240–2247
Barc MC, Bourlioux F, Rigottier-Gois L, Charrin-Sarnel C, Janoir C, Boureau H, Dore J, Collignon A (2004) Effect of amoxicillin-clavulanic acid on human faecal flora in a gnotobiotic mouse model assessed with fluorescence hybridization using group-specific 16S rRNA probes in combination with flow cytometry. Antimicrob Agents Chemother 48:1365–1368
Brandl K, Plitas G, Mihu CN, Ubeda C, Jia T, Fleisher M, Schnabl B, DeMatteo RP, Pamer EG (2008) Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits. Nature 455:804–807
Carey CM, Kostrzynska M, Ojha S, Thompson S (2008) The effect of probiotics and organic acids on Shiga-toxin 2 gene expression in enterohemorrhagic Escherichia coli O157:H7. J Microbiol Methods 73:125–132
Claesson MJ, Li Y, Leahy S et al. (2006) Multireplicon genome architecture of Lactobacillus salivarius. Proc Natl Acad Sci U S A 103:6718–6723
Collado MC, Isolauri E, Salminen S (2008) Specific probiotic strains and their combinations counteract adhesion of Enterobacter sakazakii to intestinal mucus. FEMS Microbiol Lett 285:58–64
Cook SI, Sellin JH (1998) Review article: short chain fatty acids in health and disease. Aliment Pharmacol Ther 12:499–507
Corr SC, Gahan CG, Hill C (2007a) Impact of selected Lactobacillus and Bifidobacterium species on Listeria monocytogenes infection and the mucosal immune response. FEMS Immunol Med Microbiol 50:380–388
Corr SC, Li Y, Riedel CU, O’Toole PW, Hill C, Gahan CG (2007b) Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118. Proc Natl Acad Sci U S A 104:7617–7621
Corr SC, Hill C, Gahan CG (2009) Understanding the mechanisms by which probiotics inhibit gastrointestinal pathogens (Chap. 1). Adv Food Nutr Res 56:1–15
Cotter PD, Hill C, Ross RP (2005) Bacteriocins: developing innate immunity for food. Nat Rev Microbiol 3:777–788
Deshpande A, Pant C, Jain A, Fraser TG, Rolston DD (2008) Do fluoroquinolones predispose patients to Clostridium difficile associated disease? A review of the evidence. Curr Med Res Opin 24:329–333
Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6:e280
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638
Ewaschuk JB, Diaz H, Meddings L, Diederichs B, Dmytrash A, Backer J, Looijer-van Langen M, Madsen KL (2008) Secreted bioactive factors from Bifidobacterium infantis enhance epithelial cell barrier function. Am J Physiol Gastrointest Liver Physiol 295:G1025–G1034
Farnworth ER (2008) The evidence to support health claims for probiotics. J Nutr 138:1250S–1254S
Filho-Lima JV, Vieira EC, Nicoli JR (2000) Antagonistic effect of Lactobacillus acidophilus, Saccharomyces boulardii and Escherichia coli combinations against experimental infections with Shigella flexneri and Salmonella enteritidis subsp. typhimurium in gnotobiotic mice. J Appl Microbiol 88:365–370
Flynn S, van Sinderen D, Thornton GM, Holo H, Nes IF, Collins JK (2002) Characterization of the genetic locus responsible for the production of ABP-118, a novel bacteriocin produced by the probiotic bacterium Lactobacillus salivarius subsp. salivarius UCC118. Microbiology 148:973–984
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
Gopal PK, Prasad J, Smart J, Gill HS (2001) In vitro adherence properties of Lactobacillus rhamnosus DR20 and Bifidobacterium lactis DR10 strains and their antagonistic activity against an enterotoxigenic Escherichia coli. Int J Food Microbiol 67:207–216
Gotteland M, Poliak L, Cruchet S, Brunser O (2005) Effect of regular ingestion of Saccharomyces boulardii plus inulin or Lactobacillus acidophilus LB in children colonized by Helicobacter pylori. Acta Paediatr 94:1747–1751
Gotteland M, Brunser O, Cruchet S (2006) Systematic review: are probiotics useful in controlling gastric colonization by Helicobacter pylori? Aliment Pharmacol Ther 23:1077–1086
Guandalini S, Pensabene L, Zikri MA et al. (2000) Lactobacillus GG administered in oral rehydration solution to children with acute diarrhoea: a multicenter European trial. J Pediatr Gastroenterol Nutr 30:54–60
Hedin C, Whelan K, Lindsay JO (2007) Evidence for the use of probiotics and prebiotics in inflammatory bowel disease: a review of clinical trials. Proc Nutr Soc 66:307–315
Heimesaat MM, Fischer A, Siegmund B et al. (2007) Shift towards pro-inflammatory intestinal bacteria aggravates acute murine colitis via toll-like receptors 2 and 4. PLoS One 2:e662
Hickson M, D’Souza AL, Muthu N, Rogers TR, Want S, Rajkumar C, Bulpitt CJ (2007) Use of probiotic Lactobacillus preparation to prevent diarrhoea associated with antibiotics: randomised double blind placebo controlled trial. BMJ 335:80
Hudault S, Liévin V, Bernet-Camard MF, Servin AL (1997) Antagonistic activity exerted in vitro and in vivo by Lactobacillus casei (strain GG) against Salmonella typhimurium C5 infection. Appl Environ Microbiol 63:513–518
Hugo AA, Kakisu E, De Antoni GL, Perez PF (2008) Lactobacilli antagonize biological effects of enterohaemorrhagic Escherichia coli in vitro. Lett Appl Microbiol 46:613–619
Inagaki H, Suzuki T, Nomoto K, Yoshikai Y (1996) Increased susceptibility to primary infection with Listeria monocytogenes in germfree mice may be due to lack of accumulation of L-selectin+ CD44+ T cells in sites of inflammation. Infect Immun 64:3280–3287
Johnson-Henry KC, Mitchell DJ, Avitzur Y, Galindo-Mata E, Jones NL, Sherman PM (2004) Probiotics reduce bacterial colonization and gastric inflammation in H. pylori-infected mice. Dig Dis Sci 49:1095–1102
Kabir AM, Aiba Y, Takagi A, Kamiya S, Miwa T, Koga Y (1997) Prevention of Helicobacter pylori infection by lactobacilli in a gnotobiotic murine model. Gut 41:49–55
Kankainen M, Paulin L, Tynkkynen S et al. (2009) Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proc Natl Acad Sci U S A 106:17193–17198
Kelly D, Campbell JI, King TP, Grant G, Jansson EA, Coutts AG, Pettersson S, Conway S (2004) Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-gamma and RelA. Nat Immunol 5:104–112
Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ (2009) Changes in the composition of the human faecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhoea. J Clin Gastroenterol 44(5):354–360
Kida Y, Shimizu T, Kuwano K (2006) Sodium butyrate up-regulates cathelicidin gene expression via activator protein-1 and histone acetylation at the promoter region in a human lung epithelial cell line, EBC-1. Mol Immunol 43:1972–1981
Klostermann K, Crispie F, Flynn J, Meaney WJ, Paul Ross R, Hill C (2009) Efficacy of a teat dip containing the bacteriocin lacticin 3147 to eliminate Gram-positive pathogens associated with bovine mastitis. J Dairy Res 77(2):231–238
Kotowska M, Albrecht P, Szajewska H (2005) Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea in children: a randomized double-blind placebo-controlled trial. Aliment Pharmacol Ther 21:583–590
Lavermicocca P, Valerio F, Lonigro SL, Di Leo A, Visconti A (2008) Antagonistic activity of potential probiotic Lactobacilli against the ureolytic pathogen Yersinia enterocolitica. Curr Microbiol 56:175–181
Lawley TD, Bouley DM, Hoy YE, Gerke C, Relman DA, Monack DM (2008) Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota. Infect Immun 76:403–416
Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC, Finlay BB (2007) Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2:204
Mack DR, Michail S, Wei S, McDougall L, Hollingsworth MA (1999) Probiotics inhibit enteropathogenic E. coli adherence in vitro by inducing intestinal mucin gene expression. Am J Physiol 276:G941–G950
Mack DR, Ahrne S, Hyde L, Wei S, Hollingsworth MA (2003) Extracellular MUC3 mucin secretion follows adherence of Lactobacillus strains to intestinal epithelial cells in vitro. Gut 52:827–833
Macpherson AJ, Harris NL (2004) Interactions between commensal intestinal bacteria and the immune system. Nat Rev Immunol 4:478–485
Madsen K, Cornish A, Soper P, McKaigney C, Jijon H, Yachimec C, Doyle J, Jewell L, De Simone C (2001) Probiotic bacteria enhance murine and human intestinal epithelial barrier function. Gastroenterology 121:580–591
Mastretta E, Longo P, Laccisaglia A, Balbo L, Russo R, Mazzaccara A, Gianino P (2002) Effect of Lactobacillus GG and breast-feeding in the prevention of rotavirus nosocomial infection. J Pediatr Gastroenterol Nutr 35:527–531
Mattar AF, Drongowski RA, Coran AG, Harmon CM (2001) Effect of probiotics on enterocyte bacterial translocation in vitro. Pediatr Surg Int 17:265–268
Mattar AF, Teitelbaum DH, Drongowski RA, Yongyi F, Harmon CM, Coran AG (2002) Probiotics up-regulate MUC-2 mucin gene expression in a Caco-2 cell-culture model. Pediatr Surg Int 18:586–590
McFarland LV (2006) Meta-analysis of probiotics for the prevention of antibiotic associated diarrhoea and the treatment of Clostridium difficile disease. Am J Gastroenterol 101:812–822
McFarland LV (2007) Meta-analysis of probiotics for the prevention of traveler’s diarrhoea. Travel Med Infect Dis 5:97–105
McFarland LV (2009) Evidence-based review of probiotics for antibiotic-associated diarrhoea and Clostridium difficile infections. Anaerobe 15:274–280
McFarland LV, Surawicz CM, Greenberg RN et al. (1994) A randomized placebo-controlled trial of Saccharomyces boulardii in combination with standard antibiotics for Clostridium difficile disease. JAMA 271:1913–1918
Medellin-Pena MJ, Griffiths MW (2009) Effect of molecules secreted by Lactobacillus acidophilus strain La-5 on Escherichia coli O157:H7 colonization. Appl Environ Microbiol 75:1165–1172
Medellin-Pena MJ, Wang H, Johnson R, Anand S, Griffiths MW (2007) Probiotics affect virulence-related gene expression in Escherichia coli O157:H7. Appl Environ Microbiol 73:4259–4267
Nardi RM, Vieira EC, Crocco-Afonso LC, Silva ME, Bambirra EA, Andrade AM, Nicoli JR (1991) Bacteriological and immunological aspects of conventional and germfree mice infected with Salmonella typhimurium. Rev Latinoam Microbiol 33:239–243
Ng SC, Hart AL, Kamm MA, Stagg AJ, Knight SC (2009) Mechanisms of action of probiotics: recent advances. Inflamm Bowel Dis 15:300–310
O’Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7:688–693
O’Hara AM, O’Regan P, Fanning A, O’Mahony C, Macsharry J, Lyons A, Bienenstock J, O’Mahony L, Shanahan F (2006) Functional modulation of human intestinal epithelial cell responses by Bifidobacterium infantis and Lactobacillus salivarius. Immunology 118:202–215
O’Mahony L, McCarthy J, Kelly P et al. (2005) Lactobacillus and bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterology 128:541–551
O’Mahony C, Scully P, O’Mahony D et al. (2008) Commensal-induced regulatory T cells mediate protection against pathogen-stimulated NF-kappaB activation. PLoS Pathog 4:e1000112
O’Sullivan GC, Kelly P, O’Halloran S, Collins C, Collins JK, Dunne C, Shanahan F (2005) Probiotics: an emerging therapy. Curr Pharm Des 11:3–10
Otte JM, Podolsky DK (2004) Functional modulation of enterocytes by gram-positive and gram-negative microorganisms. Am J Physiol Gastrointest Liver Physiol 286:G613–G626
Penner R, Fedorak RN, Madsen KL (2005) Probiotics and nutraceuticals: non-medicinal treatments of gastrointestinal diseases. Curr Opin Pharmacol 5:596–603
Pridmore RD, Pittet AC, Praplan F, Cavadini C (2008) Hydrogen peroxide production by Lactobacillus johnsonii NCC 533 and its role in anti-Salmonella activity. FEMS Microbiol Lett 283:210–215
Qin HL, Shen TY, Gao ZG, Fan XB, Hang XM, Jiang YQ, Zhang HZ (2005). Effect of lactobacillus on the gut microflora and barrier function of the rats with abdominal infection. World J Gastroenterol 11:2591–2596
Qin J, Li R, Raes J et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65
Resta-Lenert S, Barrett KE (2003) Live probiotics protect intestinal epithelial cells from the effects of infection with enteroinvasive Escherichia coli (EIEC). Gut 52:988–997
Rodrigues AC, Cara DC, Fretez SH, Cunha FQ, Vieira EC, Nicoli JR, Vieira LQ (2000) Saccharomyces boulardii stimulates sIgA production and the phagocytic system of gnotobiotic mice. J Appl Microbiol 89:404–414
Ryan KA, O’Hara AM, van Pijkeren JP, Douillard FP, O’Toole PW (2009) Lactobacillus salivarius modulates cytokine induction and virulence factor gene expression in Helicobacter pylori. J Med Microbiol 58:996–1005
Schlee M, Harder J, Koten B, Stange EF, Wehkamp J, Fellermann K (2008) Probiotic lactobacilli and VSL#3 induce enterocyte beta-defensin 2. Clin Exp Immunol 151:528–535
Sekirov I, Finlay BB (2009) The role of the intestinal microbiota in enteric infection. J Physiol 587:4159–4167
Sekirov I, Tam NM, Jogova M, Robertson ML, Li Y, Lupp C, Finlay BB (2008) Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infect Immun 76:4726–4736
Shanahan F (2010) Gut microbes: from bugs to drugs. Am J Gastroenterol 105:275–279
Sherman PM, Johnson-Henry KC, Yeung HP, Ngo PS, Goulet J, Tompkins TA (2005) Probiotics reduce enterohemorrhagic Escherichia coli O157:H7- and enteropathogenic E. coli O127:H6-induced changes in polarized T84 epithelial cell monolayers by reducing bacterial adhesion and cytoskeletal rearrangements. Infect Immun 73:5183–5188
Shornikova AV, Casas IA, Isolauri E, Mykkanen H, Vesikari T (1997) Lactobacillus reuteri as a therapeutic agent in acute diarrhoea in young children. J Pediatr Gastroenterol Nutr 24:399–404
Silva AM, Barbosa FH, Duarte R, Vieira LQ, Arantes RM, Nicoli JR (2004) Effect of Bifidobacterium longum ingestion on experimental salmonellosis in mice. J Appl Microbiol 97:29–37
Stecher B, Hardt WD (2008) The role of microbiota in infectious disease. Trends Microbiol 16:107–114
Stecher B, Robbiani R, Walker AW et al. (2007) Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol 5:2177–2189
Stecher B, Barthel M, Schlumberger MC, Haberli L, Rabsch W, Kremer M, Hardt WD (2008) Motility allows S. typhimurium to benefit from the mucosal defence. Cell Microbiol 10:1166–1180
Szajewska H, Kotowska M, Mrukowicz JZ, Armanska M, Mikolajczyk W (2001) Efficacy of Lactobacillus GG in prevention of nosocomial diarrhoea in infants. J Pediatr 138:361–365
Tagg JR, Dierksen KP (2003) Bacterial replacement therapy: adapting ‘germ warfare’ to infection prevention. Trends Biotechnol 21:217–223
Taguchi H, Takahashi M, Yamaguchi H, Osaki T, Komatsu A, Fujioka Y, Kamiya S (2002) Experimental infection of germ-free mice with hyper-toxigenic enterohaemorrhagic Escherichia coli O157:H7, strain 6. J Med Microbiol 51:336–343
Termen S, Tollin M, Rodriguez E, Sveinsdottir SH, Johannesson B, Cederlund A, Sjovall J, Agerberth B, Gudmundsson GH (2008) PU.1 and bacterial metabolites regulate the human gene CAMP encoding antimicrobial peptide LL-37 in colon epithelial cells. Mol Immunol 45:3947–3955
Tsai CC, Hsih HY, Chiu HH, Lai YY, Liu JH, Yu B, Tsen HY (2005) Antagonistic activity against Salmonella infection in vitro and in vivo for two Lactobacillus strains from swine and poultry. Int J Food Microbiol 102:185–194
Valeur N, Engel P, Carbajal N, Connolly E, Ladefoged K (2004) Colonization and immunomodulation by Lactobacillus reuteri ATCC 55730 in the human gastrointestinal tract. Appl Environ Microbiol 70:1176–1181
Vieira LQ, dos Santos LM, Neumann E, da Silva AP, Moura LN, Nicoli JR (2008) Probiotics protect mice against experimental infections. J Clin Gastroenterol 42(3 Suppl, Pt 2):S168–S169
Wehkamp J, Harder J, Wehkamp K et al. (2004) NF-kappaB- and AP-1-mediated induction of human beta defensin-2 in intestinal epithelial cells by Escherichia coli Nissle 1917: a novel effect of a probiotic bacterium. Infect Immun 72:5750–5758
Wilcox MH (2003) Gastrointestinal disorders and the critically ill. Clostridium difficile infection and pseudomembranous colitis. Best Pract Res Clin Gastroenterol 17:475–493
Wilson DS, Sober E (1989) Reviving the superorganism. J Theor Biol 136:337–356
Wilson KH, Sheagren JN, Freter R, Weatherbee L, Lyerly D (1986) Gnotobiotic models for study of the microbial ecology of Clostridium difficile and Escherichia coli. J Infect Dis 153:547–551
Woo H, Okamoto S, Guiney D, Gunn JS, Fierer J (2008) A model of Salmonella colitis with features of diarrhoea in SLC11A1 wild-type mice. PLoS One 3:e1603
Zilber-Rosenberg I, Rosenberg E (2008) Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev 32:723–735
Zyrek AA, Cichon C, Helms S, Enders C, Sonnenborn U, Schmidt MA (2007) Molecular mechanisms underlying the probiotic effects of Escherichia coli Nissle 1917 involve ZO-2 and PKCzeta redistribution resulting in tight junction and epithelial barrier repair. Cell Microbiol 9:804–816
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Gahan, C.G.M., O’Sullivan, G.C., Collins, J.K. (2011). The Gut Microbiota, Probiotics and Infectious Disease. In: Malago, J., Koninkx, J., Marinsek-Logar, R. (eds) Probiotic Bacteria and Enteric Infections. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0386-5_5
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