Studying the host-microbiota interaction in the human gastrointestinal tract: Basic concepts and in vitro approaches

Annals of Microbiology

Volumn 61, Issue 4, 2011, Pages 709-715

  Marzorati, Massimo ^a   Van Den Abbeele, Pieter ^a   Possemiers, Sam ^a   Benner, Jessica ^a   Verstraete, Willy ^a   Van De Wiele, Tom ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

Biofilm; Gut microbiota; Microaerophilic conditions; Shear forces; Signal exchange

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 84863511086     PISSN: 15904261     EISSN: 18692044     Source Type: Journal    
DOI: 10.1007/s13213-011-0242-5     Document Type: Review

References (51)

1. Blaser MJ, Kirschner D (2007) The equilibria that allow bacterial persistence in human hosts. Nature 449:843-849
2. Cheesman SE, Guillemin K (2007) We know you are in there: conversing with the indigenous gut microbiota. Res Microbiol 158:2-9
3. Cinquin C, Le Blay G, Fliss I, Lacroix C (2004) Immobilization of infant fecal microbiota and utilization in an in vitro colonic fermentation model. Microb Ecol 48:128-138
4. Cinquin C, Le Blay G, Fliss I, Lacroix C (2006) New three-stage in vitro model for infant colonic fermentation with immobilized fecal microbiota. FEMS Microbiol Ecol 57:324-336
5. Corthésy B, Gaskins HR, Mercenier A (2007) Cross-talk between probiotic bacteria and the host immune system. J Nutr 137:781S-790S
6. Cummings JH, Macfarlane GT (1991) The control and consequences of bacterial fermentation in the human colon. J Appl Bacteriol 70:443-459
7. 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
8. Fooks LJ, Gibson GR (2002) Probiotics as modulators of the gut flora. Br J Nutr 88:S39-S49
9. Gibson SA, Macfarlane C, Hay S, Macfarlane GT (1989) Significance of microflora in proteolysis in the colon. Appl Environ Microbiol 55:679-683
10. Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer RJ (2008) Review article: the role of butyrate on colonic function. Aliment Pharmacol Ther 27:104-119
11. Höner zu Bentrup K, Ramamurthy R, Ott CM, Emami K, Nelman-Gonzalez M, Wilson JW, Richter EG, Goodwin TJ, Alexander JS, Pierson DL, Pellis N, Buchanan KL, Nickerson CA (2006) Three-dimensional organotypic models of human colonic epithelium to study the early stages of enteric salmonellosis. Microbes Infect 8:1813-1825
12. Hooper LV (2009) Do symbiotic bacteria subvert host immunity? Nat Rev Microbiol 7:367-374
13. Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, Gordon JI (2001) Molecular analysis of commensal host-microbial relationships in the intestine. Science 291:881-884
14. Hughes DT, Sperandio V (2008) Inter-kingdom signalling: communication between bacteria and their hosts. Nat Rev Microbiol 6:111-120
15. 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
16. Kolenbrander PE (2000) Oral microbial communities: biofilms, interactions, and genetic systems. Annu Rev Microbiol 54:413-437
17. Konstantinov SR, Smidt H, de Vos WM, Bruijns SC, Singh SK, Valence F, Molle D, Lortal S, Altermann E, Klaenhammer TR, van Kooyk Y (2009) S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. Proc Natl Acad Sci USA 105:19474-19479
18. Laube B, Winkler S, Ladstetter B, Scheller T, Schwarz LR (2000) Establishment of a novel in vitro system for studying the interaction of xenobiotic metabolism of liver and intestinal microflora. Arch Toxicol 74:379-387
19. Lebeer S, Verhoeven TL, Perea Vélez M, Vanderleyden J, De Keersmaecker SC (2007) Impact of environmental and genetic factors on biofilm formation by the probiotic strain Lactobacillus rhamnosus GG. Appl Environ Microbiol 73:6768-6775
20. Lebeer S, Vanderleyden J, De Keersmaecker SC (2008) Genes and molecules of lactobacilli supporting probiotic action. Microbiol Mol Biol Rev 72:728-764
21. Li XJ, Yue LY, Guan XF, Qiao SY (2008) The adhesion of putative probiotic lactobacilli to cultured epithelial cells and porcine intestinal mucus. J Appl Microbiol 104:1082-1091
22. Macfarlane S (2008) Microbial biofilm communities in the gastrointestinal tract. J Clin Gastroenterol 42(Suppl 3):S142-S143
23. Macfarlane S, Dillon JF (2007) Microbial biofilms in the human gastrointestinal tract. J Appl Microbiol 102:1187-1196
24. Macfarlane GT, Macfarlane S (2007) Models for intestinal fermentation: association between food components, delivery systems, bioavailability and functional interactions in the gut. Curr Opin Biotechnol 18:156-162
25. MacFarlane GT, MacFarlane S, Gibson GR (1998) Validation of a three-stage compound continuous culture system for investigating the effect of retention time on the ecology and metabolism of bacteria in the human colon. Microb Ecol 35:180-187
26. 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
27. Manning TS, Gibson GR (2004) Microbial-gut interactions in health and disease: prebiotics. Best Pract Res Clin Gastroenterol 18:287-298
28. Marzorati M, Wittebolle L, Boon N, Daffonchio D, Verstraete W (2008) How to get more out of molecular fingerprints: practical tools for microbial ecology. Environ Microbiol 10:1571-1581
29. Marzorati M, Possemiers S, Verstraete W (2009) The use of the SHIME-related technology platform to assess the efficacy of pre-and probiotics. Agro Food Ind Hi-Tech 20:S50-S55
30. Marzorati M, Verhelst A, Luta G et al. (2010) Modulation of the human gastrointestinal microbial community by plant-derived polysaccharide-rich dietary supplements. 139:168-176
31. Mazmanian SK, Round JL, Kasper DL (2008) A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453:620-625
32. Minekus M, Smeets-Peeters MJE, Bernalier A, Marol-Bonnin S, Havenaar R, Marteau P, Alric M, Fonty G, Huis in't Veld JHJ (1999) A computer-controlled system to simulate conditions of the large intestine with peristaltic mixing, water absorption and absorption of fermentation products. Appl Microbiol Biotechnol 53:108-114
33. Molly K, Vande Woestyne M et al (1994) Validation of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) reactor using microorganism- associated activities. Microb Ecol Health Dis 7:191-200
34. Monds RD, O'Toole GA (2009) The developmental model of microbial biofilms: ten years of a paradigm up for review. Trends Microbiol 17:73-87
35. Nollevaux G, Devillé C, El Moualij B, Zorzi W, Deloyer P, Schneider YJ, Peulen O, Dandrifosse G (2006) Development of a serum-free co-culture of human intestinal epithelium cell-lines (Caco-2/HT29-5M21). BMC Cell Biol 7:20
36. O'Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7:688-693
37. O'Hara AM, Shanahan F (2007) Gut microbiota: mining for therapeutic potential. Clin Gastroenterol Hepatol 5:274-284
38. Oliveira MJ, Van Damme J, Lauwaet T et al (2003) Beta-casein-derived peptides, produced by bacteria, stimulate cancer cell invasion and motility. EMBO J 22:6161-6173
39. Parlesak A, Haller D, Brinz S, Baeuerlein A, Bode C (2004) Modulation of cytokine release by differentiated CACO-2 cells in a compartmentalized coculture model with mononuclear leucocytes and nonpathogenic bacteria. Scand J Immunol 60:477-485
40. Pedersen K, Tannock GW (1989) Colonization of the porcine gastrointestinal tract by lactobacilli. Appl Environ Microbiol 55:279-283
41. Pham H, Boon N, Marzorati M, Verstraete W (2009) Enhanced removal of 1, 2-dichloroethane by anodophilic microbial consortia. Water Res 43:2936-2946
42. Possemiers S, Grootaert C, Vermeiren J, Gross G, Marzorati M, Verstraete W, Van de Wiele T (2009) The intestinal environment in health and disease\recent insights on the potential of intestinal bacteria to influence human health. Curr Pharm Des 15:2051-2065
43. Possemiers S, Marzorati M, Verstraete W, Van de Wiele T (2010) Bacteria and chocolate: a successful combination for probiotic delivery. J Food Microbiol 141:97-103
44. Probert HM, Gibson GR (2002) Bacterial biofilms in the human gastrointestinal tract. Curr Issues Intest Microbiol 3:23-27
45. Probert HM, Gibson GR (2004) Development of a fermentation system to model sessile bacterial populations in the human colon. Biofilms 1:13-19
46. Rajilic-Stojanovic M, Smidt H, de Vos WM (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Micro-biol 9:2125-2136
47. Sanchez JI, Marzorati M, Grootaert C, Baran M et al (2009) Arabinoxylan-oligosaccharides (AXOS) affect the protein/carbohydrate fermentation balance and microbial population dynamics of the Simulator of Human Intestinal Microbial Ecosystem. Microb Biotechnol 2:101-113
48. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. Nature 449:804-810
49. Van den Abbeele P, Grootaert C, Marzorati M, Possemiers S et al (2010) Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX. Appl Environ Micro-biol 76:5237-5246
50. Vélez PM, De Keersmaecker SC, Vanderleyden J (2007) Adherence factors of Lactobacillus in the human gastrointestinal tract. FEMS Microbiol Lett 276:140-148
51. Verstraete W (2007) Microbial ecology and environmental biotechnology. ISME J 1:4-8