Intestinal microbiota in human health and disease: The impact of probiotics

Genes and Nutrition

Volumn 6, Issue 3, 2011, Pages 209-240

  Gerritsen, Jacoline ^a,b   Smidt, Hauke ^a   Rijkers, Ger T ^c,d   De Vos, Willem M ^a,e  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b WINCLOVE PROBIOTICS   (Netherlands)

^c ST ANTONIUS HOSPITAL   (Netherlands)

^d RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^e UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Diversity; Dysbiosis; Host microbe interactions; Intestinal microbiota; Probiotics

Indexed keywords

PROBIOTIC AGENT; RIBOSOME RNA;

BACTERIAL COLONIZATION; BACTERIAL GENETICS; BACTEROIDETES; BIFIDOBACTERIUM; CLOSTRIDIUM; DISEASE ASSOCIATION; DISEASE CLASSIFICATION; DRUG RESEARCH; ENTERITIS; ENTEROBACTERIACEAE; EUBACTERIUM; FIRMICUTES; GENE EXPRESSION; GENETIC DIFFERENCE; HIGH THROUGHPUT SCREENING; HUMAN; INTESTINE FLORA; METAGENOMICS; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; OBESITY; PHYLOGENY; REVIEW; RUMINOCOCCUS;

EID: 80955180995     PISSN: 15558932     EISSN: 18653499     Source Type: Journal    
DOI: 10.1007/s12263-011-0229-7     Document Type: Review

References (258)

1. Adlerberth I, Wold AE (2009) Establishment of the gut microbiota in Western infants. Acta Paediatr 98(2):229-238
2. Ahmed S, Macfarlane GT, Fite A, McBain AJ, Gilbert P, Macfarlane S (2007) Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples. Appl Environ Microbiol 73(22):7435-7442 (Pubitemid 350196697)
3. Andoh A, Sakata S, Koizumi Y, Mitsuyama K, Fujiyama Y, Benno Y (2007) Terminal restriction fragment length polymorphism analysis of the diversity of fecal microbiota in patients with ulcerative colitis. Inflamm Bowel Dis 13(8):955-962. (Pubitemid 47309966)
4. Andoh A, Tsujikawa T, Sasaki M, Mitsuyama K, Suzuki Y, Matsui T, Matsumoto T, Benno Y, Fujiyama Y (2008) Fecal microbiota profile of Crohn's disease determined by terminal restriction fragment length polymorphism (t-rflp) analysis. Aliment Pharmacol Ther 29:75-82.
5. Armougom F, Henry M, Vialettes B, Raccah D, Raoult D (2009) Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients. PLoS One 4(9):e7125.
6. Atuma C, Strugala V, Allen A, Holm L (2001) The adherent gastrointestinal mucus gel layer: thickness and physical state in vivo. Am J Physiol Gastrointest Liver Physiol 280(5):G922-G929.
7. Audia JP, Webb CC, Foster JW (2001) Breaking through the acid barrier: an orchestrated response to proton stress by enteric bacteria. Int J Med Microbiol 291(2):97-106. (Pubitemid 32532732)
8. Aura AM, Mattila I, Hyötyläinen T, Gopalacharyulu P, Bounsaythip C, Orešič M, Oksman-Caldentey KM (2011) Drug metabolome of the Simvastatin formed by human intestinal microbiota in vitro. Mol Biosyst 7(2):437-446.
9. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 101(44):15718-15723. (Pubitemid 39473554)
10. Bäckhed F, Manchester JK, Semenkovich CF, Gordon JI (2007) Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci USA 104(3):979-984. (Pubitemid 46154722)
11. Balamurugan R, George G, Kabeerdoss J, Hepsiba J, Chandragunasekaran AM, Ramakrishna BS (2010) Quantitative differences in intestinal Faecalibacterium prausnitzii in obese Indian children. Br J Nutr 103(3):335-338.
12. Barbara G, Stanghellini V, Brandi G, Cremon C, Di Nardo G, De Giorgio R, Corinaldesi R (2005) Interactions between commensal bacteria and gut sensorimotor function in health and disease. Am J Gastroenterol 100(11):2560-2568.
13. Bartosch S, Fite A, Macfarlane GT, McMurdo ME (2004) Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota. Appl Environ Microbiol 70(6):3575-3581. (Pubitemid 38745906)
14. Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, Yantiss R, Orsi RH, Wiedmann M, McDonough P, Kim SG, Berg D, Schukken Y, Scherl E, Simpson KW (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(5):403-418. (Pubitemid 47373247)
15. Biagi E, Nylund L, Candela M, Ostan R, Bucci L, Pini E, Nikkïla J, Monti D, Satokari R, Franceschi C, Brigidi P, De Vos W (2010) Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS One 5(5):e10667.
16. Bibiloni R, Mangold M, Madsen KL, Fedorak RN, Tannock GW (2006) The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients. J Med Microbiol 55(Pt 8):1141-1149. (Pubitemid 44215574)
17. Björkstén B, Naaber P, Sepp E, Mikelsaar M (1999) The intestinal microflora in allergic Estonian and Swedish 2-year-old children. Clin Exp Allergy 29(3):342-346. (Pubitemid 29145134)
18. Björkstén B, Sepp E, Julge K, Voor T, Mikelsaar M (2001) Allergy development and the intestinal microflora during the first year of life. J Allergy Clin Immunol 108(4):516-520. (Pubitemid 32978019)
19. Boesten RJ, De Vos WM (2008) Interactomics in the human intestine: Lactobacilli and Bifidobacteria make a difference. J Clin Gastroenterol 42(Suppl 3, Pt 2):S163-S167.
20. Booijink CC, Zoetendal EG, Kleerebezem M, De Vos WM (2007) Microbial communities in the human small intestine: coupling diversity to metagenomics. Future Microbiol 2(3):285-295. (Pubitemid 47180925)
21. Booijink CC, El-Aidy S, Rajilić-Stojanović M, Heilig HG, Troost FJ, Smidt H, Kleerebezem M, De Vos WM, Zoetendal EG (2010) High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 12(12):3213-3227.
22. Buddington RK, Sangild PT (2011) Development of the mammalian gastrointestinal tract, the resident microbiota, and the role of diet in early life. J Anim Sci 89:1506-1519.
23. Cabana MD, McKean M, Wong AR, Chao C, Caughey AB (2007) Examining the hygiene hypothesis: the Trial of Infant Probiotic Supplementation. Paediatr Perinat Epidemiol 21(Suppl 3):23-28. (Pubitemid 47568805)
24. Cani PD, Delzenne NM (2009) The role of the gut microbiota in energy metabolism and metabolic disease. Curr Pharm Des 15(13):1546-1558.
25. Carroll IM, Chang YH, Park J, Sartor RB, Ringel Y (2010) Luminal and mucosal-associated intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Gut Pathog 2(1):19.
26. Cerf-Bensussan N, Gaboriau-Routhiau V (2010) The immune system and the gut microbiota: friends or foes? Nat Rev Immunol 10(10):735-744.
27. Chang JY, Talley NJ (2011) An update on irritable bowel syndrome: from diagnosis to emerging therapies. Curr Opin Gastroenterol 27(1):72-78.
28. Chapman CM, Gibson GR, Rowland I (2011) Health benefits of probiotics: are mixtures more effective than single strains? Eur J Nutr 50(1):1-17.
29. Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, Marchesi JR, Falush D, Dinan T, Fitzgerald G, Stanton C, van Sinderen D, O'Connor M, Harnedy N, O'Connor K, Henry C, O'Mahony D, Fitzgerald AP, Shanahan F, Twomey C, Hill C, Ross RP, O'Toole PW (2010) Microbes and Health Sackler Colloquium: Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci USA. Epub
30. Codling C, O'Mahony L, Shanahan F, Quigley EM, Marchesi JR (2010) A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome. Dig Dis Sci 55(2):392-397.
31. Collado MC, Calabuig M, Sanz Y (2007) Differences between the fecal microbiota of coeliac infants and healthy controls. Curr Issues Intest Microbiol 8(1):9-14. (Pubitemid 46604951)
32. Collado MC, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y (2008a) Imbalances in faecal and duodenal Bifidobacterium species composition in active and non-active coeliac disease. BMC Microbiol 8:232.
33. Collado MC, Isolauri E, Laitinen K, Salminen S (2008b) Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr 88(4):894-899.
34. Collado MC, Isolauri E, Laitinen K, Salminen S (2010) Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy. Am J Clin Nutr 92(5):1023-1030.
35. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez- Garayzabal J, Garcia P, Cai J, Hippe H, Farrow JA (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44(4):812-826. (Pubitemid 24315163)
36. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2009) Bacterial community variation in human body habitats across space and time. Science 326(5960):1694-1697.
37. Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P (2005) Metagenomic gene discovery: past, present and future. Trends Biotechnol 23(6):321-329. (Pubitemid 40726274)
38. Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch SV (2010) Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS One 5(1):e8745.
39. Darfeuille-Michaud A (2002) Adherent-invasive Escherichia coli: a putative new E. coli pathotype associated with Crohn's disease. Int J Med Microbiol 292(3-4):185-193.
40. 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(2):412-421. (Pubitemid 39091889)
41. De Palma G, Nadal I, Medina M, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y (2010) Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol 10:63.
42. De Preter V, Hamer HM, Windey K, Verbeke K (2010) The impact of pre- and/or probiotics on human colonic metabolism: does it affect human health? Mol Nutr Food Res 55(1):46-57.
43. Dethlefsen L, Eckburg PB, Bik EM, Relman DA (2006) Assembly of the human intestinal microbiota. Trends Ecol Evol 21(9):517-523. (Pubitemid 44233957)
44. 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(11):e280.
45. Dicksved J, Halfvarson J, Rosenquist M, Järnerot G, Tysk C, Apajalahti J, Engstrand L, Jansson JK (2008) Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J 2(7):716-727. (Pubitemid 351951567)
46. Dridi B, Henry M, El Khéchine A, Raoult D, Drancourt M (2009) High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4(9):e7063.
47. Dumas ME, Wilder SP, Bihoreau MT, Barton RH, Fearnside JF, Argoud K, D'Amato L, Wallis RH, Blancher C, Keun HC, Baunsgaard D, Scott J, Sidelmann UG, Nicholson JK, Gauguier D (2007) Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models. Nat Genet 39(5):666-672. (Pubitemid 46676110)
48. Duncan SH, Belenguer A, Holtrop G, Johnstone AM, Flint HJ, Lobley GE (2007) Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol 73(4):1073-1078.
49. Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P, Flint HJ (2008) Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 32(11):1720-1724.
50. 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(5728):1635-1638. (Pubitemid 40807514)
51. Engelbrektson A, Korzenik JR, Pittler A, Sanders ME, Klaenhammer TR, Leyer G, Kitts CL (2009) Probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy. J Med Microbiol 58(Pt 5):663-670.
52. FAO/WHO (2002) Working group report on drafting guidelines for the evaluation of probiotics in food. London, Ontario, Canada
53. Fava F, Danese S (2011) Intestinal microbiota in inflammatory bowel disease: Friend of foe? World J Gastroenterol 17(5):557-566.
54. Favier CF, Vaughan EE, De Vos WM, Akkermans AD (2002) Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 68(1):219-226. (Pubitemid 34031183)
55. Ferguson RM, Merrifield DL, Harper GM, Rawling MD, Mustafa S, Picchietti S, Balćazar JL, Davies SJ (2010) The effect of Pediococcus acidilactici on the gut microbiota and immune status of on-growing red tilapia (Oreochromis niloticus). J Appl Microbiol 109(3):851-862.
56. Finegold SM, Molitoris D, Song Y, Liu C, Vaisanen ML, Bolte E, McTeague M, Sandler R, Wexler H, Marlowe EM, Collins MD, Lawson PA, Summanen P, Baysallar M, Tomzynski TJ, Read E, Johnson E, Rolfe R, Nasir P, Shah H, Haake DA, Manning P, Kaul A (2002) Gastrointestinal microflora studies in late-onset autism. Clin Infect Dis 35(Suppl 1):S6-S16.
57. Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, Liu M, Molitoris DR, Green JA III (2010) Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 16(4):444-453.
58. Firmesse O, Mogenet A, Bresson JL, Corthier G, Furet JP (2008) Lactobacillus rhamnosus R11 consumed in a food supplement survived human digestive transit without modifying microbiota equilibrium as assessed by real-time polymerase chain reaction. J Mol Microbiol Biotechnol 14(1-3):90-99. (Pubitemid 350022337)
59. Fooks LJ, Gibson GR (2002) Probiotics as modulators of the gut flora. Br J Nutr 88(Suppl 1):S39-S49. (Pubitemid 35251942)
60. 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. Proc Natl Acad Sci USA 104(34):13780-13785. (Pubitemid 350003397)
61. Franks AH, Harmsen HJ, Raangs GC, Jansen GJ, Schut F, Welling GW (1998) Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 64(9):3336-3345. (Pubitemid 28411456)
62. Fuentes S, Egert M, Jiménez-Valera M, Ramos-Cormenzana A, Ruiz-Bravo A, Smidt H, Monteoliva-Sanchez M (2008) Administration of Lactobacillus casei and Lactobacillus plantarum affects the diversity of murine intestinal lactobacilli, but not the overall bacterial community structure. Res Microbiol 159(4):237-243.
63. García-Albiach R, Pozuelo de Felipe MJ, Angulo S, Morosini MI, Bravo D, Baquero F, del Campo R (2008) Molecular analysis of yogurt containing Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus in human intestinal microbiota. Am J Clin Nutr 87(1):91-96.
64. Gareau MG, Sherman PM, Walker WA (2010) Probiotics and the gut microbiota in intestinal health and disease. Nat Rev Gastroenterol Hepatol 7(9):503-514.
65. Garrett WS, Gallini CA, Yatsunenko T, Michaud M, DuBois A, Delaney ML, Punit S, Karlsson M, Bry L, Glickman JN, Gordon JI, Onderdonk AB, Glimcher LH (2010) Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8(3):292-300.
66. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312(5778):1355-1359. (Pubitemid 43839542)
67. Gophna U, Sommerfeld K, Gophna S, Doolittle WF, Veldhuyzen van Zanten SJ (2006) Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis. J Clin Microbiol 44(11):4136-4141. (Pubitemid 44737260)
68. Gore C, Munro K, Lay C, Bibiloni R, Morris J, Woodcock A, Custovic A, Tannock GW (2008) Bifidobacterium pseudocatenulatum is associated with atopic eczema: a nested case-control study investigating the fecal microbiota of infants. J Allergy Clin Immunol 121(1):135-140.
69. Gosalbes MJ, Durbán A, Pignatelli M, Abellan JJ, Jiménez-Hernández N, Pérez-Cobas AE, Latorre A, Moya A (2011) Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One 6(3):e17447.
70. 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(2):104-119. (Pubitemid 350256609)
71. Hansen J, Gulati A, Sartor RB (2010) The role of mucosal immunity and host genetics in defining intestinal commensal bacteria. Curr Opin Gastroenterol 26(6):564-571.
72. Harmsen HJ, Wildeboer-Veloo AC, Raangs GC, Wagendorp AA, Klijn N, Bindels JG, Welling GW (2000) Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J Pediatr Gastroenterol Nutr 30(1):61-67. (Pubitemid 30349947)
73. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA (2009) Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci USA 106(40):17187-17192.
74. Hayashi H, Takahashi R, Nishi T, Sakamoto M, Benno Y (2005) Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. J Med Microbiol 54(Pt 11):1093-1101. (Pubitemid 41566781)
75. Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, Wu GD (2009) High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137(5):1716-1724.
76. Holmes E, Loo RL, Stamler J, Bictash M, Yap IK, Chan Q, Ebbels T, De Iorio M, Brown IJ, Veselkov KA, Daviglus ML, Kesteloot H, Ueshima H, Zhao L, Nicholson JK, Elliott P (2008) Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 453(7193):396-400. (Pubitemid 351693125)
77. Holzapfel WH, Haberer P, Snel J, Schillinger U, Huis in't Veld JH (1998) Overview of gut flora and probiotics. Int J Food Microbiol 41(2):85-101. (Pubitemid 28369424)
78. Iannitti T, Palmieri B (2010) Therapeutical use of probiotic formulations in clinical practice. Clin Nutr 29(6):701-725.
79. Iwaya A, Iiai T, Okamoto H, Ajioka Y, Yamamoto T, Asahara T, Nomoto K, Hatakeyama K (2006) Change in the bacterial flora of pouchitis. Hepatogastroenterology 53(67):55-59.
80. Jernberg C, Löfmark S, Edlund C, Jansson JK (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1(1):56-66. (Pubitemid 46717132)
81. Jernberg C, Löfmark S, Edlund C, Jansson JK (2010) Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 156(Pt 11):3216-3223.
82. Jiménez E, Fernández L, Marín ML, Martín R, Odriozola JM, Nueno-Palop C, Narbad A, Olivares M, Xaus J, Rodríguez JM (2005) Isolation of commensal bacteria from umbilical cord blood of healthy neonates born by cesarean section. Curr Microbiol 51(4):270-274. (Pubitemid 41426207)
83. Jiménez E, Marín ML, Martín R, Odriozola JM, Olivares M, Xaus J, Fernández L, Rodríguez JM (2008) Is meconium from healthy newborns actually sterile? Res Microbiol 159(3):187-193.
84. Johansson ME, Phillipson M, Petersson J, Velcich A, Holm L, Hansson GC (2008) The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci USA 105(39):15064-15069.
85. Johansson ME, Holmén Larsson JM, Hansson GC (2010) Microbes and Health Sackler Colloquium: The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc Natl Acad Sci USA. Epub
86. Joossens M, Huys G, Cnockaert M, De Preter V, Verbeke K, Rutgeerts P, Vandamme P, Vermeire S (2011) Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 60(5):631-637.
87. Kajander K, Myllyluoma E, Rajilić-Stojanović M, Kyrönpalo S, Rasmussen M, Järvenpää S, Zoetendal EG, De Vos WM, Vapaatalo H, Korpela R (2008) Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota. Aliment Pharmacol Ther 27(1):48-57. (Pubitemid 350212625)
88. Kalliomäki M, Kirjavainen P, Eerola E, Kero P, Salminen S, Isolauri E (2001) Distinct patterns of neonatal gut microflora in infants in whom atopy was and was not developing. J Allergy Clin Immunol 107(1):129-134. (Pubitemid 32105256)
89. Kalliomäki M, Collado MC, Salminen S, Isolauri E (2008) Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr 87(3):534-538. (Pubitemid 351364532)
90. Kanazawa K, Konishi F, Mitsuoka T, Terada A, Itoh K, Narushima S, Kumemura M, Kimura H (1996) Factors influencing the development of sigmoid colon cancer. Bacteriologic and biochemical studies. Cancer 77(8 Suppl):1701-1706. (Pubitemid 26111855)
91. Kang S, Denman SE, Morrison M, Yu Z, Doré J, Leclerc M, McSweeney CS (2010) Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis 16(12):2034-2042.
92. Kankainen M, Paulin L, Tynkkynen S, von Ossowski I, Reunanen J, Partanen P, Satokari R, Vesterlund S, Hendrickx AP, Lebeer S, De Keersmaecker SC, Vanderleyden J, Hämäläinen T, Laukkanen S, Salovuori N, Ritari J, Alatalo E, Korpela R, Mattila-Sandholm T, Lassig A, Hatakka K, Kinnunen KT, Karjalainen H, Saxelin M, Laakso K, Surakka A, Palva A, Salusjärvi T, Auvinen P, De Vos WM (2009) Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a humanmucus binding protein. Proc Natl Acad Sci USA 106(40): 17193-17198.
93. Karantanos T, Markoutsaki T, Gazouli M, Anagnou NP, Karamanolis DG (2010) Current insights into the pathophysiology of Irritable Bowel Syndrome. Gut Pathog 2(1):3.
94. Kassinen A, Krogius-Kurikka L, Mäkivuokko H, Rinttilä T, Paulin L, Corander J, Malinen E, Apajalahti J, Palva A (2007) The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133(1):24-33. (Pubitemid 47031125)
95. Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K, Akkermans LM (2009) Lower bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients. World J Gastroenterol 15(23):2887-2892.
96. Kerckhoffs AP, Ben-Amor K, Samsom M, van der Rest ME, de Vogel J, Knol J, Akkermans LM (2010) Molecular analysis of faecal and duodenal samples reveals significantly higher prevalence and numbers of Pseudomonas aeruginosa in IBS. J Med Microbiol 60:236-245.
97. Kim YS, Ho SB (2010) Intestinal goblet cells and mucins in health and disease: recent insights and progress. Curr Gastroenterol Rep 12(5):319-330.
98. Kinross JM, Darzi AW, Nicholson JK (2011) Gut microbiome-host interactions in health and disease. Genome Med 3(3):14.
99. Kirjavainen PV, Apostolou E, Arvola T, Salminen SJ, Gibson GR, Isolauri E (2001) Characterizing the composition of intestinal microflora as a prospective treatment target in infant allergic disease. FEMS Immunol Med Microbiol 32(1):1-7. (Pubitemid 34025068)
100. Klaassens ES, De Vos WM, Vaughan EE (2007) Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl Environ Microbiol 73(4):1388-1392.
101. Klaassens ES, Boesten RJ, Haarman M, Knol J, Schuren FH, Vaughan EE, De Vos WM (2009) Mixed-species genomic microarray analysis of fecal samples reveals differential transcriptional responses of bifidobacteria in breast-and formula-fed infants. Appl Environ Microbiol 75(9):2668-2676.
102. Kleerebezem M, Vaughan EE (2009) Probiotic and gut lactobacilli and bifidobacteria: molecular approaches to study diversity and activity. Annu Rev Microbiol 63:269-290.
103. Kleessen B, Kroesen AJ, Buhr HJ, Blaut M (2002) Mucosal and invading bacteria in patients with inflammatory bowel disease compared with controls. Scand J Gastroenterol 37(9):1034-1041.
104. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE (2010) Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA Epub
105. Koide A, Yamaguchi T, Odaka T, Koyama H, Tsuyuguchi T, Kitahara H, Ohto M, Saisho H (2000) Quantitative analysis of bowel gas using plain abdominal radiograph in patients with irritable bowel syndrome. Am J Gastroenterol 95(7):1735-1741. (Pubitemid 30485011)
106. Komanduri S, Gillevet PM, Sikaroodi M, Mutlu E, Keshavarzian A (2007) Dysbiosis in pouchitis: evidence of unique microfloral patterns in pouch inflammation. Clin Gastroenterol Hepatol 5(3):352-360. (Pubitemid 46401536)
107. Koning CJ, Jonkers D, Smidt H, Rombouts F, Pennings HJ, Wouters E, Stobberingh E, Stockbrügger R (2010) The effect of a multispecies probiotic on the composition of the faecal microbiota and bowel habits in chronic obstructive pulmonary disease patients treated with antibiotics. Br J Nutr 103(10):1452-1460.
108. Kotlowski R, Bernstein CN, Sepehri S, Krause DO (2007) High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease. Gut 56(5):669-675. (Pubitemid 46662933)
109. Kovatcheva-Datchary P, Egert M, Maathuis A, Rajilić- Stojanović M, De Graaf AA, Smidt H, De Vos WM, Venema K (2009) Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ Microbiol 11(4):914-926.
110. Krogius-Kurikka L, Lyra A, Malinen E, Aarnikunnas J, Tuimala J, Paulin L, Mäkivuokko H, Kajander K, Palva A (2009) Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers. BMC Gastroenterol 9:95.
111. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14(4):169-181.
112. Lahtinen SJ, Tammela L, Korpela J, Parhiala R, Ahokoski H, Mykkänen H, Salminen SJ (2009) Probiotics modulate the Bifidobacterium microbiota of elderly nursing home residents. Age (Dordr) 31(1):59-66.
113. Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sørensen SJ, Hansen LH, Jakobsen M (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 5(2):e9085.
114. Lepage P, Seksik P, Sutren M, de la Cochetière MF, Jian R, Marteau P, Doré J (2005) Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD. Inflamm Bowel Dis 11(5):473-480. (Pubitemid 40704082)
115. Ley RE (2010) Obesity and the human microbiome. Curr Opin Gastroenterol 26(1):5-11.
116. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102(31):11070-11075. (Pubitemid 41105994)
117. Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444(7122):1022-1023. (Pubitemid 46018512)
118. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6(10):776-788.
119. Lim M, Adams JD, Wilcox M, Finan P, Sagar P, Burke D (2009) An assessment of bacterial dysbiosis in pouchitis using terminal restriction fragment length polymorphisms of 16S ribosomal DNA from pouch effluent microbiota. Dis Colon Rectum 52(8):1492-1500.
120. Longstreth GF, Thompson WG, Chey WD, Houghton LA, Mearin F, Spiller RC (2006) Functional bowel disorders. Gastroenterology 130(5):1480-1491.
121. López P, Gueimonde M, Margolles A, Suárez A (2010) Distinct Bifidobacterium strains drive different immune responses in vitro. Int J Food Microbiol 138(1-2):157-165.
122. Lyra A, Rinttilä T, Nikkïla J, Krogius-Kurikka L, Kajander K, Malinen E, Mättö J, Mäkelä L, Palva A (2009) Diarrhoeapredominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantification. World J Gastroenterol 15(47):5936-5945.
123. Mackie RI, Sghir A, Gaskins HR (1999) Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr 69(5):1035S-1045S (Pubitemid 29205082)
124. Mai V, Greenwald B, Morris JG Jr, Raufman JP, Stine OC (2006) Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition. Gut 55(12):1822-1823. (Pubitemid 44893588)
125. Malinen E, Rinttilä T, Kajander K, Mättö J, Kassinen A, Krogius L, Saarela M, Korpela R, Palva A (2005) Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol 100(2):373-382. (Pubitemid 40314522)
126. Malinen E, Krogius-Kurikka L, Lyra A, Nikkïla J, Jääskeläinen A, Rinttilä T, Vilpponen-Salmela T, von Wright AJ, Palva A (2010) Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome.World JGastroenterol 16(36):4532-4540.
127. Mangin I, Bonnet R, Seksik P, Rigottier-Gois L, Sutren M, Bouhnik Y, Neut C, Collins MD, Colombel JF, Marteau P, Doré J (2004) Molecular inventory of faecal microflora in patients with Crohn's disease. FEMS Microbiol Ecol 50(1):25-36. (Pubitemid 39265393)
128. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Doré J (2006) Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55(2):205-211. (Pubitemid 43117279)
129. Mariat D, Firmesse O, Levenez F, Guimarǎes V, Sokol H, Doré J, Corthier G, Furet JP (2009) The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9:123.
130. Martin FP, Sprenger N, Montoliu I, Rezzi S, Kochhar S, Nicholson JK (2010) Dietary modulation of gut functional ecology studied by fecal metabonomics. J Proteome Res 9(10):5284-5295.
131. Martinez C, Antolin M, Santos J, Torrejon A, Casellas F, Borruel N, Guarner F, Malagelada JR (2008) Unstable composition of the fecal microbiota in ulcerative colitis during clinical remission. Am J Gastroenterol 103(3):643-648. (Pubitemid 351405965)
132. Martinez-Medina M, Aldeguer X, Gonzalez-Huix F, Acero D, Garcia-Gil LJ (2006) Abnormal microbiota composition in the ileocolonic mucosa of Crohn's disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. Inflamm Bowel Dis 12(12):1136-1145. (Pubitemid 44847471)
133. Marzotto M, Maffeis C, Paternoster T, Ferrario R, Rizzotti L, Pellegrino M, Dellaglio F, Torriani S (2006) Lactobacillus paracasei A survives gastrointestinal passage and affects the fecalmicrobiota of healthy infants. Res Microbiol 157(9):857-866. (Pubitemid 44528975)
134. Matsuki T, Watanabe K, Fujimoto J, Kado Y, Takada T, Matsumoto K, Tanaka R (2004) Quantitative PCR with 16S rRNA-genetargeted species-specific primers for analysis of human intestinal bifidobacteria. Appl Environ Microbiol 70(1):167-173. (Pubitemid 38090201)
135. Mättö J, Maunuksela L, Kajander K, Palva A, Korpela R, Kassinen A, Saarela M (2005) Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome-a longitudinal study in IBS and control subjects. FEMS Immunol Med Microbiol 43(2):213-222. (Pubitemid 40170291)
136. Maukonen J, Satokari R, Mättö J, Söderlund H, Mattila-Sandholm T, Saarela M (2006) Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. J Med Microbiol 55(Pt 5):625-633.
137. McFarland LV (1998) Epidemiology, risk factors and treatments for antibiotic-associated diarrhea. Dig Dis 16(5):292-307. (Pubitemid 128527395)
138. Medina M, Izquierdo E, Ennahar S, Sanz Y (2007) Differential immunomodulatory properties of Bifidobacterium longum strains: relevance to probiotic selection and clinical applications. Clin Exp Immunol 150(3):531-538. (Pubitemid 350098744)
139. Meijerink M, van Hemert S, Taverne N, Wels M, De Vos P, Bron PA, Savelkoul HF, van Bilsen J, Kleerebezem M, Wells JM (2010) Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization. PLoS One 5(5):e10632.
140. Merritt ME, Donaldson JR (2009) Effect of bile salts on the DNA and membrane integrity of enteric bacteria. J Med Microbiol 58(Pt 12):1533-1541.
141. Mihajlovski A, Alric M, Brugère JF (2008) A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene. Res Microbiol 159(7-8): 516-521.
142. Mohan R, Koebnick C, Schildt J, Schmidt S, Mueller M, Possner M, Radke M, Blaut M (2006) Effects of Bifidobacterium lactis Bb12 supplementation on intestinal microbiota of preterm infants: a double-blind, placebo-controlled, randomized study. J Clin Microbiol 44(11):4025-4031. (Pubitemid 44737246)
143. Mondot S, Kang S, Furet JP, Aguirre de Carcer D, McSweeney C, Morrison M, Marteau P, Doré J, Leclerc M (2011) Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm Bowel Dis 17(1):185-192.
144. Montesi A, García-Albiach R, Pozuelo MJ, Pintado C, Goñi I, Rotger R (2005) Molecular and microbiological analysis of caecal microbiota in rats fed with diets supplemented either with prebiotics or probiotics. Int J Food Microbiol 98(3):281-289. (Pubitemid 40215386)
145. Moore WE, Moore LH (1995) Intestinal floras of populations that have a high risk of colon cancer. Appl Environ Microbiol 61(9):3202-3207.
146. Mortensen PB, Andersen JR, Arffmann S, Krag E (1987) Short-chain fatty acids and the irritable bowel syndrome: the effect of wheat bran. Scand J Gastroenterol 22(2):185-192. (Pubitemid 17024403)
147. Mshvildadze M, Neu J, Shuster J, Theriaque D, Li N, Mai V (2010) Intestinal microbial ecology in premature infants assessed with non-culture-based techniques. J Pediatr 156(1):20-25.
148. Mueller S, Saunier K, Hanisch C, Norin E, Alm L, Midtvedt T, Cresci A, Silvi S, Orpianesi C, Verdenelli MC, Clavel T, Koebnick C, Zunft HJ, Doré J, Blaut M (2006) Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl Environ Microbiol 72(2):1027-1033. (Pubitemid 43271206)
149. Murphy EF, Cotter PD, Healy S, Marques TM, O'Sullivan O, Fouhy F, Clarke SF, O'Toole PW, Quigley EM, Stanton C, Ross PR, O'Doherty RM, Shanahan F (2010) Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut 59(12):1635-1642.
150. Musso G, Gambino R, Cassader M (2010) Obesity, diabetes, and gut microbiota: the hygiene hypothesis expanded? Diabetes Care 33(10):2277-2284.
151. Mylonaki M, Rayment NB, Rampton DS, Hudspith BN, Brostoff J (2005) Molecular characterization of rectal mucosa-associated bacterial flora in inflammatory bowel disease. Inflamm Bowel Dis 11(5):481-487. (Pubitemid 40704083)
152. Nadal I, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y (2007) Imbalance in the composition of the duodenal microbiota of children with coeliac disease. J Med Microbiol 56(Pt 12): 1669-1674. (Pubitemid 350276518)
153. Nadal I, Santacruz A, Marcos A, Warnberg J, Garagorri M, Moreno LA, Martin-Matillas M, Campoy C, Martí A, Moleres A, Delgado M, Veiga OL, García-Fuentes M, Redondo CG, Sanz Y (2009) Shifts in clostridia, bacteroides and immunoglobulincoating fecal bacteria associated with weight loss in obese adolescents. Int J Obes (Lond) 33(7):758-767.
154. Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D (2010) A catalog of reference genomes from the human microbiome. Science 328(5981):994-999.
155. Ng SC, Hart AL, Kamm MA, Stagg AJ, Knight SC (2009) Mechanisms of action of probiotics: recent advances. Inflamm Bowel Dis 15(2):300-310.
156. Nicholson JK, Lindon JC (2008) Systems biology: metabonomics. Nature 455(7216):1054-1056.
157. Nishikawa J, Kudo T, Sakata S, Benno Y, Sugiyama T (2009) Diversity of mucosa-associated microbiota in active and inactive ulcerative colitis. Scand J Gastroenterol 44(2):180-186.
158. O'Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7(7):688-693. (Pubitemid 43986264)
159. Ohge H, Furne JK, Springfield J, Rothenberger DA, Madoff RD, Levitt MD (2005) Association between fecal hydrogen sulfide production and pouchitis. Dis Colon Rectum 48(3):469-475. (Pubitemid 40767867)
160. Onderdonk AB, Dvorak AM, Cisneros RL, McLeod RS, Antionoli D, Silen W, Blair JE, Monahan-Earley RA, Cullen J, Cohen Z (1992) Microbiologic assessment of tissue biopsy samples from ileal pouch patients. J Clin Microbiol 30(2):312-317.
161. Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, Fölsch UR, Timmis KN, Schreiber S (2004) Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53(5):685-693. (Pubitemid 38561447)
162. 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(7):831-841. (Pubitemid 351918525)
163. Ouwehand AC, Bergsma N, Parhiala R, Lahtinen S, Gueimonde M, Finne-Soveri H, Strandberg T, Pitkälä K, Salminen S (2008) Bifidobacterium microbiota and parameters of immune function in elderly subjects. FEMS Immunol Med Microbiol 53(1):18-25. (Pubitemid 351659703)
164. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5(7):e177.
165. Parracho HM, Bingham MO, Gibson GR, McCartney AL (2005) Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J Med Microbiol 54(Pt 10):987-991. (Pubitemid 41395858)
166. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, van den Brandt PA, Stobberingh EE (2006) Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118(2):511-521. (Pubitemid 46085405)
167. Penders J, Thijs C, van den Brandt PA, Kummeling I, Snijders B, Stelma F, Adams H, van Ree R, Stobberingh EE (2007) Gut microbiota composition and development of atopic manifestations in infancy: the KOALA birth cohort study. Gut 56(5): 661-667. (Pubitemid 46662932)
168. Pettker CM, Buhimschi IA, Magloire LK, Sfakianaki AK, Hamar BD, Buhimschi CS (2007) Value of placental microbial evaluation in diagnosing intra-amniotic infection. Obstet Gynecol 109(3):739-749. (Pubitemid 46339416)
169. Pham M, Lemberg DA, Day AS (2008) Probiotics: sorting the evidence from the myths. Med J Aust 188(5):304-308.
170. Preidis GA, Versalovic J (2009) Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology 136(6):2015-2031.
171. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285):59-65.
172. Rajilić-Stojanović M, Smidt H, De Vos WM (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9(9):2125-2136. (Pubitemid 47222128)
173. Rijkers GT, Bengmark S, Enck P, Haller D, Herz U, Kalliomäki M, Kudo S, Lenoir-Wijnkoop I, Mercenier A, Myllyluoma E, Rabot S, Rafter J, Szajewska H, Watzl B, Wells J, Wolvers D, Antoine JM (2010) Guidance for substantiating the evidence for beneficial effects of probiotics: current status and recommendations for future research. J Nutr 140(3):671S-676S
174. Roberfroid M, Gibson GR, Hoyles L, McCartney AL, Rastall R, Rowland I, Wolvers D, Watzl B, Szajewska H, Stahl B, Guarner F, Respondek F, Whelan K, Coxam V, Davicco MJ, Léotoing L, Wittrant Y, Delzenne NM, Cani PD, Neyrinck AM, Meheust A (2010) Prebiotic effects: metabolic and health benefits. Br J Nutr 104(Suppl 2):S1-S63.
175. Rochet V, Rigottier-Gois L, Ledaire A, Andrieux C, Sutren M, Rabot S, Mogenet A, Bresson JL, Cools S, Picard C, Goupil-Feuillerat N, Doré J (2008) Survival of Bifidobacterium animalis DN-173 010 in the faecal microbiota after administration in lyophilised form or in fermented product-a randomised study in healthy adults. J Mol Microbiol Biotechnol 14(1-3):128-136. (Pubitemid 350022342)
176. Roger LC, McCartney AL (2010) Longitudinal investigation of the faecal microbiota of healthy full-term infants using fluorescence in situ hybridization and denaturing gradient gel electrophoresis. Microbiology 156(Pt 11):3317-3328.
177. Roger LC, Costabile A, Holland DT, Hoyles L, McCartney AL (2010) Examination of faecal Bifidobacterium populations in breast-and formula-fed infants during the first 18 months of life. Microbiology 156(Pt 11):3329-3341.
178. Rooijers K, Kolmeder C, Juste C, Doré J, de Been M, Boeren S, Galan P, Beauvallet C, De Vos WM, Schaap PJ (2011) An iterative workflow for mining the human intestinal metaproteome. BMC Genomics 12(1):6.
179. Rosenfeld G, Bressler B (2010) Mycobacterium avium paratuberculosis and the etiology of Crohn's disease: a review of the controversy from the clinician's perspective. Can J Gastroenterol 24(10):619-624.
180. Ruseler-van Embden JG, Schouten WR, van Lieshout LM (1994) Pouchitis: result of microbial imbalance? Gut 35(5):658-664. (Pubitemid 24163794)
181. Salonen A, De Vos WM, Palva A (2010a) Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology 156(Pt 11):3205-3215.
182. Salonen A, Nikkïla J, Jalanka-Tuovinen J, Immonen O, Rajilić-Stojanović M, Kekkonen RA, Palva A, De Vos WM (2010b) Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods 81(2):127-134.
183. Santacruz A, Marcos A, Wärnberg J, Martí A, Martin-Matillas M, Campoy C, Moreno LA, Veiga O, Redondo-Figuero C, Garagorri JM, Azcona C, Delgado M, García-Fuentes M, Collado MC, Sanz Y (2009) Interplay between weight loss and gut microbiota composition in overweight adolescents. Obesity (Silver Spring) 17(10):1906-1915.
184. Santacruz A, Collado MC, García-Valdés L, Segura MT, Martín-Lagos JA, Anjos T, Martí-Romero M, Lopez RM, Florido J, Campoy C, Sanz Y (2010) Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. Br J Nutr 104(1):83-92.
185. Sanz Y, Sánchez E, Marzotto M, Calabuig M, Torriani S, Dellaglio F (2007) Differences in faecal bacterial communities in coeliac and healthy children as detected by PCR and denaturing gradient gel electrophoresis. FEMS Immunol Med Microbiol 51(3):562-568. (Pubitemid 350076169)
186. Sanz Y, Santacruz A, Gauffin P (2010) Gut microbiota in obesity and metabolic disorders. Proc Nutr Soc 69(3):434-441.
187. Sartor RB (2008) Microbial influences in inflammatory bowel diseases. Gastroenterology 134(2):577-594. (Pubitemid 351173057)
188. Satokari RM, Vaughan EE, Akkermans AD, Saarela M, De Vos WM (2001) Polymerase chain reaction and denaturing gradient gel electrophoresis monitoring of fecal bifidobacterium populations in a prebiotic and probiotic feeding trial. Syst Appl Microbiol 24(2):227-231. (Pubitemid 32705672)
189. Satokari R, Grönroos T, Laitinen K, Salminen S, Isolauri E (2009) Bifidobacterium and lactobacillus DNA in the human placenta. Lett Appl Microbiol 48(1):8-12.
190. Savage DC (1977) Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 31:107-133.
191. Scanlan PD, Marchesi JR (2008) Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J 2(12):1183-1193.
192. Scanlan PD, Shanahan F, O'Mahony C, Marchesi JR (2006) Cultureindependent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. J Clin Microbiol 44(11):3980-3988. (Pubitemid 44737239)
193. Scanlan PD, Shanahan F, Clune Y, Collins JK, O'Sullivan GC, O'Riordan M, Holmes E, Wang Y, Marchesi JR (2008) Cultureindependent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol 10(3):789-798. (Pubitemid 351160918)
194. Schiffrin EJ, Morley JE, Donnet-Hughes A, Guigoz Y (2010) The inflammatory status of the elderly: the intestinal contribution. Mutat Res 690(1-2):50-56.
195. Schippa S, Iebba V, Barbato M, Di Nardo G, Totino V, Checchi MP, Longhi C, Maiella G, Cucchiara S, Conte MP (2010) A distinctive 'microbial signature' in celiac pediatric patients. BMC Microbiol 10:175.
196. Schwiertz A, Taras D, Schäfer K, Beijer S, Bos NA, Donus C, Hardt PD (2010) Microbiota and SCFA in lean and overweight healthy subjects. Obesity (Silver Spring) 18(1):190-195.
197. Sekirov I, Russell SL, Antunes LC, Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90(3):859-904.
198. Seksik P, Rigottier-Gois L, Gramet G, Sutren M, Pochart P, Marteau P, Jian R, Doré J (2003) Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut 52(2):237-242. (Pubitemid 36115065)
199. Shen XJ, Rawls JF, Randall T, Burcal L, Mpande CN, Jenkins N, Jovov B, Abdo Z, Sandler RS, Keku TO (2010) Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes 1(3):138-147.
200. Sjögren YM, Jenmalm MC, Bottcher MF, Björkstén B, Sverremark-Ekström E (2009) Altered early infant gut microbiota in children developing allergy up to 5 years of age. Clin Exp Allergy 39(4):518-526.
201. Snel J, Vissers YM, Smit BA, Jongen JM, van der Meulen ET, Zwijsen R, Ruinemans-Koerts J, Jansen AP, Kleerebezem M, Savelkoul HF (2010) Strain-specific immunomodulatory effects of Lactobacillus plantarum strains on birch-pollen-allergic subjects out of season. Clin Exp Allergy 41(2):232-242.
202. Sokol H, Seksik P (2010) The intestinal microbiota in inflammatory bowel diseases: time to connect with the host. Curr Opin Gastroenterol 26(4):327-331.
203. Sokol H, Seksik P, Rigottier-Gois L, Lay C, Lepage P, Podglajen I, Marteau P, Doré J (2006) Specificities of the fecal microbiota in inflammatory bowel disease. Inflamm Bowel Dis 12(2):106-111.
204. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez- Humáran LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottière HM, Doré J, Marteau P, Seksik P, Langella P (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA 105(43):16731-16736.
205. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, Cosnes J, Corthier G, Marteau P, Doré J (2009) Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 15(8):1183-1189.
206. Song Y, Liu C, Finegold SM (2004) Real-time PCR quantitation of clostridia in feces of autistic children. Appl Environ Microbiol 70(11):6459-6465. (Pubitemid 39518551)
207. Stewart JA, Chadwick VS, Murray A (2005) Investigations into the influence of host genetics on the predominant eubacteria in the faecal microflora of children. J Med Microbiol 54(Pt 12):1239-1242. (Pubitemid 41783834)
208. Štšepetova J, Sepp E, Julge K, Vaughan E, Mikelsaar M, De Vos WM (2007) Molecularly assessed shifts of Bifidobacterium ssp. and less diverse microbial communities are characteristic of 5-yearold allergic children. FEMS Immunol Med Microbiol 51(2): 260-269. (Pubitemid 47547504)
209. Suzuki S, Shimojo N, Tajiri Y, Kumemura M, Kohno Y (2007) Differences in the composition of intestinal Bifidobacterium species and the development of allergic diseases in infants in rural Japan. Clin Exp Allergy 37(4):506-511. (Pubitemid 46537739)
210. Swidsinski A, Ladhoff A, Pernthaler A, Swidsinski S, Loening-Baucke V, Ortner M, Weber J, Hoffmann U, Schreiber S, Dietel M, Lochs H (2002) Mucosal flora in inflammatory bowel disease. Gastroenterology 122(1):44-54. (Pubitemid 34049193)
211. 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(7):3380-3389. (Pubitemid 40981351)
212. Takaishi H, Matsuki T, Nakazawa A, Takada T, Kado S, Asahara T, Kamada N, Sakuraba A, Yajima T, Higuchi H, Inoue N, Ogata H, Iwao Y, Nomoto K, Tanaka R, Hibi T (2008) Imbalance in intestinal microflora constitution could be involved in the pathogenesis of inflammatory bowel disease. Int J Med Microbiol 298(5-6):463-472. (Pubitemid 351734793)
213. Tana C, Umesaki Y, Imaoka A, Handa T, Kanazawa M, Fukudo S (2010) Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome. Neurogastroenterol Motil 22(5):512-519.
214. Tannock GW, Munro K, Harmsen HJ, Welling GW, Smart J, Gopal PK (2000) Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol 66(6):2578-2588. (Pubitemid 30353968)
215. Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz-Tamayo R, Paslier DL, Nalin R, Doré J, Leclerc M (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11(10):2574-2584.
216. Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 20(11):1605-1612.
217. Tiihonen K, Ouwehand AC, Rautonen N (2010) Human intestinal microbiota and healthy ageing. Ageing Res Rev 9(2):107-116.
218. Timmerman HM, Koning CJ, Mulder L, Rombouts FM, Beynen AC (2004) Monostrain, multistrain and multispecies probiotics-A comparison of functionality and efficacy. Int J Food Microbiol 96(3):219-233. (Pubitemid 39349161)
219. Treem WR, Ahsan N, Kastoff G, Hyams JS (1996) Fecal short-chain fatty acids in patients with diarrhea-predominant irritable bowel syndrome: in vitro studies of carbohydrate fermentation. J Pediatr Gastroenterol Nutr 23(3):280-286. (Pubitemid 26307732)
220. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444(7122):1027-1031. (Pubitemid 46018515)
221. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI (2009) A core gut microbiome in obese and lean twins. Nature 457(7228):480-484.
222. Vaahtovuo J, Munukka E, Korkeamäki M, Luukkainen R, Toivanen P (2008) Fecal microbiota in early rheumatoid arthritis. J Rheumatol 35(8):1500-1505.
223. Vael C, Desager K (2009) The importance of the development of the intestinal microbiota in infancy. Curr Opin Pediatr 21(6):794-800.
224. Van Baarlen P, Troost FJ, van Hemert S, van der Meer C, De Vos WM, de Groot PJ, Hooiveld GJ, Brummer RJ, Kleerebezem M (2009) Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proc Natl Acad Sci USA 106(7):2371-2376.
225. Van den Bogert B, De Vos WM, Zoetendal EG, Kleerebezem M (2011) Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol. 77(6): 2071-2080.
226. Van Hemert S, Meijerink M, Molenaar D, Bron PA, De Vos P, Kleerebezem M, Wells JM, Marco ML (2010) Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells. BMC Microbiol 10:293.
227. Van Tongeren SP, Slaets JP, Harmsen HJ, Welling GW (2005) Fecal microbiota composition and frailty. Appl Environ Microbiol 71(10):6438-6442. (Pubitemid 41456954)
228. Vanhoutte T, Huys G, Brandt E, Swings J (2004) Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol 48(3):437-446. (Pubitemid 38648930)
229. Vanhoutte T, De Preter V, De Brandt E, Verbeke K, Swings J, Huys G (2006) Molecular monitoring of the fecal microbiota of healthy human subjects during administration of lactulose and Saccharomyces boulardii. Appl Environ Microbiol 72(9):5990-5997. (Pubitemid 44414627)
230. Veiga P, Gallini CA, Beal C, Michaud M, Delaney ML, DuBois A, Khlebnikov A, van Hylckama Vlieg JE, Punit S, Glickman JN, Onderdonk A, Glimcher LH, Garrett WS (2010) Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes. Proc Natl Acad Sci USA 107(42):18132-18137.
231. Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK (2009) Shotgun metaproteomics of the human distal gut microbiota. ISME J 3(2):179-189.
232. Vissers YM, Snel J, Zuurendonk PF, Smit BA, Wichers HJ, Savelkoul HF (2010) Differential effects of Lactobacillus acidophilus and Lactobacillus plantarum strains on cytokine induction in human peripheral blood mononuclear cells. FEMS Immunol Med Microbiol 59(1):60-70.
233. Vissers YM, Snel J, Zuurendonk PF, Kleerebezem M, Wichers HJ, Savelkoul HF (2011) Lactobacillus strains differentially modulate cytokine production by hPBMC from pollen-allergic patients. FEMS Immunol Med Microbiol 61(1):28-40.
234. Vitali B, Ndagijimana M, Cruciani F, Carnevali P, Candela M, Guerzoni ME, Brigidi P (2010) Impact of a synbiotic food on the gut microbial ecology and metabolic profiles. BMC Microbiol 10:4.
235. Vrieze A, Holleman F, Zoetendal EG, De Vos WM, Hoekstra JB, Nieuwdorp M (2010) The environment within: how gut microbiota may influence metabolism and body composition. Diabetologia 53(4):606-613.
236. Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, Brown D, Stares MD, Scott P, Bergerat A, Louis P, McIntosh F, Johnstone AM, Lobley GE, Parkhill J, Flint HJ (2011a) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. Isme J 5(2):220-230.
237. Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G, Petrovska L (2011b) High-throughput clone library analysis of the mucosaassociated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol 11(1):7.
238. Wang X, Heazlewood SP, Krause DO, Florin TH (2003) Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis. J Appl Microbiol 95(3):508-520. (Pubitemid 37041083)
239. Wang M, Ahrné S, Jeppsson B, Molin G (2005) Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Microbiol Ecol 54(2):219-231. (Pubitemid 41317922)
240. Wang M, Karlsson C, Olsson C, Adlerberth I, Wold AE, Strachan DP, Martricardi PM, Å berg N, Perkin MR, Tripodi S, Coates AR, Hesselmar B, Saalman R, Molin G, Ahrné S (2008) Reduced diversity in the early fecal microbiota of infants with atopic eczema. J Allergy Clin Immunol 121(1):129-134.
241. Wang Y, Hoenig JD, Malin KJ, Qamar S, Petrof EO, Sun J, Antonopoulos DA, Chang EB, Claud EC (2009) 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J 3(8):944-954.
242. Wang Y, Devkota S, Musch MW, Jabri B, Nagler C, Antonopoulos DA, Chervonsky A, Chang EB (2010) Regional mucosaassociated microbiota determine physiological expression of TLR2 and TLR4 in murine colon. PLoS One 5(10):e13607.
243. Watanabe S, Narisawa Y, Arase S, Okamatsu H, Ikenaga T, Tajiri Y, Kumemura M (2003) Differences in fecal microflora between patients with atopic dermatitis and healthy control subjects. J Allergy Clin Immunol 111(3):587-591. (Pubitemid 36337881)
244. Weichselbaum E (2010) Potential benefits of probiotics-main findings of an in-depth review. Br J Community Nurs 15(3):110, 112, 114.
245. Willing B, Halfvarson J, Dicksved J, Rosenquist M, Järnerot G, Engstrand L, Tysk C, Jansson JK (2009) Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease. Inflamm Bowel Dis 15(5):653-660.
246. Wong JM, de Souza R, Kendall CW, Emam A, Jenkins DJ (2006) Colonic health: fermentation and short chain fatty acids. J Clin Gastroenterol 40(3):235-243. (Pubitemid 44309560)
247. Woodmansey EJ (2007) Intestinal bacteria and ageing. J Appl Microbiol 102(5):1178-1186. (Pubitemid 46633436)
248. Wu X, Ma C, Han L, Nawaz M, Gao F, Zhang X, Yu P, Zhao C, Li L, Zhou A, Wang J, Moore JE, Millar BC, Xu J (2010) Molecular characterisation of the faecal microbiota in patients with type II diabetes. Curr Microbiol 61(1):69-78.
249. Zella GC, Hait EJ, Glavan T, Gevers D, Ward DV, Kitts CL, Korzenik JR (2011) Distinct microbiome in pouchitis compared to healthy pouches in ulcerative colitis and familial adenomatous polyposis. Inflamm Bowel Dis 17(5):1092-1100.
250. Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, CrowellMD, Wing R, Rittmann BE, Krajmalnik-Brown R (2009) Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA 106(7):2365-2370.
251. Zivkovic AM, German JB, Lebrilla CB, Mills DA (2010) Microbes and Health Sackler Colloquium: Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc Natl Acad Sci USA. Epub
252. Zoetendal EG, Akkermans AD, De Vos WM (1998) Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 64(10):3854-3859. (Pubitemid 28462983)
253. Zoetendal EG, Akkermans ADL, Akkermans-Van Vliet WM, de Visser JAGM, De Vos WM (2001) The host genotype affects the bacterial community in the human gastrointestinal tract. Microbial Ecol Health Dis 13(3):129-134. (Pubitemid 32905860)
254. 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 distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 68(7):3401-3407. (Pubitemid 34734038)
255. Zoetendal EG, Vaughan EE, De Vos WM (2006) A microbial world within us. Mol Microbiol 59(6):1639-1650.
256. Zoetendal EG, Rajilić-Stojanović M, De Vos WM (2008) Highthroughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57(11):1605-1615.
257. Zoetendal EG, Raes J, Van den Bogert B, Arumugam M, Booijink CCGM, Troost FJ, Bork P, Wels M, De Vos WM, Kleerebezem M (2011) Metagenomic and metatranscriptomic analyses of the human small intestinal microbiota reveals a community that is driven by fast uptake and conversion of carbohydrates. Submitted for publication
258. Zwielehner J, Liszt K, Handschur M, Lassl C, Lapin A, Haslberger AG (2009) Combined PCR-DGGE fingerprinting and quantitative-PCR indicates shifts in fecal population sizes and diversity of Bacteroides, bifidobacteria and Clostridium cluster IV in institutionalized elderly. Exp Gerontol 44(6-7):440-446