Amann RI, Krumholz L, Stahl DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172:762–770
CAS
PubMed
Google Scholar
Andoh A, Benno Y, Kanauchi O, Fujiyama Y (2009) Recent advances in molecular approaches to gut microbiota in inflammatory bowel disease. Curr Pharm Des 15:2066–2073
CAS
Article
PubMed
Google Scholar
Bäckhed F, Normark S, Schweda EK, Oscarson S, Richter-Dahlfors A (2003) Structural requirements for TLR4-mediated LPS signalling: a biological role for LPS modifications. Microbes Infect 12:1057–1063
Article
Google Scholar
Berg RD (1996) The indigenous gastrointestinal microflora. Trends Microbiol 4:430–435
CAS
Article
PubMed
Google Scholar
Camp JG, Kanther M, Semova I, Rawls JF (2009) Patterns and scales in gastrointestinal microbial ecology. Gastroenterology 136:1989–2002
Article
PubMed
Google Scholar
Cario E (2005) Bacterial interactions with cells of the intestinal mucosa: toll-like receptors and NOD2. Gut 54:1182–1193
CAS
Article
PubMed
Google Scholar
Collado MC, Isolauri E, Salminen S, Sanz Y (2009) The impact of probiotic on gut health. Curr Drug Metab 10:68–78
CAS
Article
PubMed
Google Scholar
Collins SM, Bercik P (2009) The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease. Gastroenterology 136:2003–2014
Article
PubMed
Google Scholar
Dinoto A, Suksomcheep A, Ishizuka S, Kimura H, Hanada S, Kamagata Y, Asano K, Tomita F, Yokota A (2006) Modulation of rat cecal microbiota by administration of raffinose and encapsulated Bifidobacterium breve. Appl Environ Microbiol 72:784–792
CAS
Article
PubMed
Google Scholar
Duncan SH, Scott KP, Ramsay AG, Harmsen HJ, Welling GW, Stewart CS, Flint HJ (2003) Effects of alternative dietary substrates on competition between human colonic bacteria in an anaerobic fermentor system. Appl Environ Microbiol 69:1136–1142
CAS
Article
PubMed
Google Scholar
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 5728:1635–1638
Article
Google Scholar
Fujisawa M, Kiyosue M, Hori M, Ozaki H (2006) Identification of Card15/Nod2 mRNA in intestinal tissue of experimentally induced colitis in rats. J Vet Med Sci 68:701–708
CAS
Article
PubMed
Google Scholar
Galdeano CM, Perdigon G (2006) The probiotic bacterium Lactobacillus casei induces activation of the gut mucosal immune system through innate immunity. Clin Vaccine Immunol 13:219–226
CAS
Article
PubMed
Google Scholar
Garcia-Lafuente A, Antolin M, Guarner F, Crespo E, Salas A, Forcada P, Laguarda M, Gavalda J, Baena JA, Vilaseca J, Malagelada JR (1997) Incrimination of anaerobic bacteria in the induction of experimental colitis. Am J Physiol 272:G10–G15
CAS
PubMed
Google Scholar
Guarner F, Bourdet-Sicard R, Brandtzaeg P, Gill HS, McGuirk P, Van EW, Versalovic J, Weinstock JV, Rook GA (2006) Mechanisms of disease: the hygiene hypothesis revisited. Nat Clin Pract Gastroenterol Hepatol 3:275–284
CAS
Article
PubMed
Google Scholar
Heine H, Delude RL, Monks BG, Espevik T, Golenbock DT (1999) Bacterial lipopolysaccharide induces expression of the stress response genes hop and H411. J Biol Chem 30:21049–21055
Article
Google Scholar
Hoentjen F, Welling GW, Harmsen HJ, Zhang X, Snart J, Tannock GW, Lien K, Churchill TA, Lupicki M, Dieleman LA (2005) Reduction of colitis by prebiotics in HLA-B27 transgenic rats is associated with microflora changes and immunomodulation. Inflamm Bowel Dis 11:977–985
Article
PubMed
Google Scholar
Hojberg O, Canibe N, Poulsen HD, Hedemann MS, Jensen BB (2005) Influence of dietary zinc oxide and copper sulfate on the gastrointestinal ecosystem in newly weaned piglets. Appl Environ Microbiol 71:2267–2277
CAS
Article
PubMed
Google Scholar
Karlsson H, Hessle AR (2002) Innate immune responses of human neonatal cells to bacteria from the normal gastrointestinal flora. Infect Immun 70:6688–6696
CAS
Article
PubMed
Google Scholar
Kim SC, Tonkonogy SL, Karrasch T, Jobin C, Sartor RB (2007) Dual-association of gnotobiotic IL-10−/− mice with 2 nonpathogenic commensal bacteria induces aggressive pancolitis. Inflamm Bowel Dis 13:1457–1466
Article
PubMed
Google Scholar
Kitts CL (2001) Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curr Issues Intest Microbiol 2:17–25
CAS
PubMed
Google Scholar
Looijer-van Langen MA, Dieleman LA (2009) Prebiotics in chronic intestinal inflammation. Inflamm Bowel Dis 15:454–462
Article
PubMed
Google Scholar
Mai V, Katki HA, Harmsen H, Gallaher D, Schatzkin A, Baer DJ, Clevidence B (2004) Effects of a controlled diet and black tea drinking on the fecal microflora composition and the fecal bile acid profile of human volunteers in a double-blinded randomized feeding study. J Nutr 134:473–478
CAS
PubMed
Google Scholar
Marteau PR (2002) Probiotics in clinical conditions. Clin Rev Allergy Immunol 22:255–273
Article
PubMed
Google Scholar
Montesi A, Garcia-Albiach R, Pozuelo MJ, Pintado C, Goni 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 98:281–289
CAS
Article
PubMed
Google Scholar
Okada H, Kuhn C, Feillet H, Bach JF (2010) The ‘hygiene hypothesis’ for autoimmune and allergic diseases: an update. Clin Exp Immunol 160:1–9
CAS
Article
PubMed
Google Scholar
Ootsubo M, Shimizu T, Tanaka R, Sawabe T, Tajima K, Yoshimizu M, Ezura Y, Ezaki T, Oyaizu H (2002) Oligonucleotide probe for detecting Enterobacteriaceae by in situ hybridization. J Appl Microbiol 93:60–68
CAS
Article
PubMed
Google Scholar
Porras M, Martin MT, Soler M, Vergara P (2004) Intestinal motor disorders associated with cyclical bacterial overgrowth in a rat model of enteritis. Am J Physiol Gastrointest Liver Physiol 287:G58–G64
CAS
Article
PubMed
Google Scholar
Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R (2004) Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118:229–241
CAS
Article
PubMed
Google Scholar
Rolhion N, Rfeuille-Michaud A (2007) Adherent-invasive Escherichia coli in inflammatory bowel disease. Inflamm Bowel Dis 13:1277–1283
Article
PubMed
Google Scholar
Rousseaux C, Thuru X, Gelot A, Barnich N, Neut C, Dubuquoy L, Dubuquoy C, Merour E, Geboes K, Chamaillard M, Ouwehand A, Leyer G, Carcano D, Colombel JF, Ardid D, Desreumaux P (2007) Lactobacillus acidophilus modulates intestinal pain and induces opioid and cannabinoid receptors. Nat Med 13:35–37
CAS
Article
PubMed
Google Scholar
Ruiz PA, Hoffmann M, Szcesny S, Blaut M, Haller D (2005) Innate mechanisms for Bifidobacterium lactis to activate transient pro-inflammatory host responses in intestinal epithelial cells after the colonization of germ-free rats. Immunology 115:441–450
CAS
Article
PubMed
Google Scholar
Salzman NH, de Paterson JH, Harmsen HJ, Welling GW, Bos A (2002) Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria. Microbiology 148:3651–3660
CAS
PubMed
Google Scholar
Setoyama H, Imaoka A, Ishikawa H, Umesaki Y (2003) Prevention of gut inflammation by Bifidobacterium in dextran sulfate-treated gnotobiotic mice associated with Bacteroides strains isolated from ulcerative colitis patients. Microbes Infect 5:115–122
Article
PubMed
Google Scholar
Siggers RH, Siggers J, Boye M, Thymann T, Mølbak L, Leser T, Jensen BB, Sangild PT (2008) Early administration of probiotics alters bacterial colonization and limits diet-induced gut dysfunction and severity of necrotizing enterocolitis in preterm pigs. J Nutr 138:1437–1444
CAS
PubMed
Google Scholar
Silva MA, Jury J, Porras M, Vergara P, Perdue MH (2008) Intestinal epithelial barrier dysfunction and dendritic cell redistribution during early stages of inflammation in the rat: role for TLR-2 and -4 blockage. Inflamm Bowel Dis 14:632–644
Article
PubMed
Google Scholar
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 43:3380–3389
Article
PubMed
Google Scholar
Szebeni B, Veres G, Dezsofi A, Rusai K, Vannay A, Mraz M, Majorova E, Arato A (2008) Increased expression of toll-like receptor (TLR) 2 and TLR4 in the colonic mucosa of children with inflammatory bowel disease. Clin Exp Immunol 151:34–41
CAS
Article
PubMed
Google Scholar
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 298:463–472
CAS
Article
PubMed
Google Scholar
Takeuchi O, Hoshino K, Kawai T, Sanjo H, Takada H, Ogawa T, Takeda K, Akira S (1999) Differential roles of TLR2 and TLR4 in recognition of gram-negative and gram-positive bacterial cell wall components. Immunity 11:443–451
CAS
Article
PubMed
Google Scholar
Tilg H, Moschen AR, Kaser A (2009) Obesity and the microbiota. Gastroenterology 136:1476–1483
Article
PubMed
Google Scholar
Vaahtovuo J, Korkeamaki M, Munukka E, Viljanen MK, Toivanen P (2005) Quantification of bacteria in human feces using 16S rRNA-hybridization, DNA-staining and flow cytometry. J Microbiol Methods 63:276–286
CAS
Article
PubMed
Google Scholar
Verdú EF, Bercik P, Verma-Gandhu M, Huang XX, Blennerhassett P, Jackson W, Mao Y, Wang L, Rochat F, Collins S (2006) Specific probiotic therapy attenuates antibiotic induced visceral hypersensitivity in mice. Gut 55:182–190
Article
PubMed
Google Scholar
Wirtz S, Neurath MF (2007) Mouse models of inflammatory bowel disease. Adv Drug Deliv Rev 59:1073–1083
CAS
Article
PubMed
Google Scholar
Wohlgemuth S, Haller D, Blaut M, Loh G (2009) Reduced microbial diversity and high numbers of one single Escherichia coli strain in the intestine of colitic mice. Environ Microbiol 11:1562–1571
Article
PubMed
Google Scholar
Wohlsen T, Bayliss J, Gray B, Bates J, Katouli M (2006) Evaluation of an alternative method for the enumeration and confirmation of Clostridium perfringens from treated and untreated sewages. Lett Appl Microbiol 42:438–444
CAS
Article
PubMed
Google Scholar
Xavier RJ, Podolsky DK (2007) Unravelling the pathogenesis of inflammatory bowel disease. Nature 448:427–434
CAS
Article
PubMed
Google Scholar