D. Savage, Microbial Ecology of the Gastrointestinal Tract, Annual Review of Microbiology, vol.31, issue.1, pp.107-133, 1977.
DOI : 10.1146/annurev.mi.31.100177.000543

A. Suau, R. Bonnet, M. Sutren, J. Godon, G. Gibson et al., Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut, Appl Environ Microbiol, vol.65, pp.4799-4807, 1999.

A. Neish, Microbes in Gastrointestinal Health and Disease, Gastroenterology, vol.136, issue.1, pp.65-80, 2009.
DOI : 10.1053/j.gastro.2008.10.080

G. Goncharova, V. Dorofe?chuk, A. Smolianskaia, and S. Kia, [Microbial ecology of the intestines in health and in pathology], Antibiot Khimioter, vol.34, pp.462-466, 1989.

M. Dominguez-bello, M. Blaser, R. Ley, and R. Knight, Development of the Human Gastrointestinal Microbiota and Insights From High-Throughput Sequencing, Gastroenterology, vol.140, issue.6, pp.1713-1719, 2011.
DOI : 10.1053/j.gastro.2011.02.011

I. Mulder, B. Schmidt, M. Lewis, M. Delday, C. Stokes et al., Restricting Microbial Exposure in Early Life Negates the Immune Benefits Associated with Gut Colonization in Environments of High Microbial Diversity, PLoS ONE, vol.6, issue.12, p.28279, 2011.
DOI : 10.1371/journal.pone.0028279.s003

L. Dethlefsen, P. Eckburg, E. Bik, and D. Relman, Assembly of the human intestinal microbiota, Trends in Ecology & Evolution, vol.21, issue.9, pp.517-523, 2006.
DOI : 10.1016/j.tree.2006.06.013

V. Stanghellini, G. Barbara, C. Cremon, R. Cogliandro, A. Antonucci et al., RETRACTED ARTICLE: Gut microbiota and related diseases: clinical features, Internal and Emergency Medicine, vol.27, issue.Suppl 1, pp.57-63, 2010.
DOI : 10.1007/s11739-010-0451-0

M. Claesson, S. Cusack, O. Sullivan, O. Greene-diniz, R. De-weerd et al., Composition, variability, and temporal stability of the intestinal microbiota of the elderly, Proceedings of the National Academy of Sciences, vol.108, issue.Supplement_1, pp.4586-4591, 2011.
DOI : 10.1073/pnas.1000097107

M. 10-rajili?-stojanovi?, H. Heilig, D. Molenaar, K. Kajander, A. Surakka et al., Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults, Environmental Microbiology, vol.57, issue.7, pp.1736-1751, 2009.
DOI : 10.1111/j.1462-2920.2009.01900.x

P. Turnbaugh, F. Bäckhed, L. Fulton, and J. Gordon, Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome, Cell Host & Microbe, vol.3, issue.4, pp.213-223, 2008.
DOI : 10.1016/j.chom.2008.02.015

J. Zwielehner, K. Liszt, M. Handschur, C. Lassl, A. Lapin et al., 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, Experimental Gerontology, vol.44, issue.6-7, pp.440-446, 2009.
DOI : 10.1016/j.exger.2009.04.002

I. Ivanov, F. Rde, L. Manel, N. Yoshinaga, K. Rifkin et al., Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine, Cell Host & Microbe, vol.4, issue.4, pp.337-349, 2008.
DOI : 10.1016/j.chom.2008.09.009

J. Marchesi, Human distal gut microbiome, Environmental Microbiology, vol.68, issue.1, pp.3088-3102, 2011.
DOI : 10.1111/j.1462-2920.2011.02574.x

A. Hakansson and G. Molin, Gut Microbiota and Inflammation, Nutrients, vol.3, issue.12, pp.637-682, 2011.
DOI : 10.3390/nu3060637

I. Sekirov, S. Russell, L. Antunes, and B. Finlay, Gut Microbiota in Health and Disease, Physiological Reviews, vol.90, issue.3, pp.859-904, 2009.
DOI : 10.1152/physrev.00045.2009

D. Kelly and I. Mulder, Microbiome and immunological interactions, Nutrition Reviews, vol.70, pp.18-30, 2012.
DOI : 10.1111/j.1753-4887.2012.00498.x

W. Chen, F. Liu, Z. Ling, X. Tong, and C. Xiang, Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer, PLoS ONE, vol.682, issue.6, p.39743, 2012.
DOI : 10.1371/journal.pone.0039743.s004

J. Arthur and C. Jobin, The struggle within: Microbial influences on colorectal cancer, Inflammatory Bowel Diseases, vol.17, issue.1, pp.396-409, 2011.
DOI : 10.1002/ibd.21354

R. Ley, F. Bäckhed, P. Turnbaugh, C. Lozupone, R. Knight et al., Obesity alters gut microbial ecology, Proceedings of the National Academy of Sciences, vol.102, issue.31, pp.11070-11075, 2005.
DOI : 10.1073/pnas.0504978102

V. Mai, Dietary Modification of the Intestinal Microbiota, Nutrition Reviews, vol.62, issue.6, pp.235-242, 2004.
DOI : 10.1111/j.1753-4887.2004.tb00045.x

R. Rastall, Bacteria in the gut: friends and foes and how to alter the balance, J Nutr, vol.134, pp.2022-2026, 2004.

M. Hopkins, R. Sharp, and G. Macfarlane, Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles, Gut, vol.48, issue.2, pp.198-205, 2001.
DOI : 10.1136/gut.48.2.198

E. Zoetendal, A. Akkermans, W. Akkermans-van-vilet, J. De-visser, H. De-vos-wmhogenová et al., The host genotype affects the bacterial community in the human gastrointestinal tract Commensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseases, Microb Ecol Health Dis Immunol Lett, vol.13, issue.93, pp.129-134, 2001.

D. Peterson, D. Frank, N. Pace, and J. Gordon, Metagenomic Approaches for Defining the Pathogenesis of Inflammatory Bowel Diseases, Cell Host & Microbe, vol.3, issue.6, pp.417-427, 2008.
DOI : 10.1016/j.chom.2008.05.001

A. Boleij, H. Tjalsma, and F. Shanahan, Gut bacteria in health and disease: a survey on the interface between intestinal microbiology and colorectal cancer, Biological Reviews, vol.44, issue.Suppl. 1, pp.701-730, 2006.
DOI : 10.1111/j.1469-185X.2012.00218.x

Y. Umesaki, Y. Okada, S. Matsumoto, A. Imaoka, and H. Setoyama, Segmented Filamentous Bacteria Are Indigenous Intestinal Bacteria That Activate Intraepithelial Lymphocytes and Induce MHC Class II Molecules and Fucosyl Asialo GM1 Glycolipids on the Small Intestinal Epithelial Cells in the Ex-Germ-Free Mouse, Microbiology and Immunology, vol.3, issue.8, pp.555-562, 1995.
DOI : 10.1111/j.1348-0421.1995.tb02242.x

J. Xu and J. Gordon, Honor thy symbionts, Proceedings of the National Academy of Sciences, vol.100, issue.18, pp.10452-10459, 2003.
DOI : 10.1073/pnas.1734063100

S. Mazmanian, C. Liu, A. Tzianabos, and D. Kasper, An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune System, Cell, vol.122, issue.1, pp.107-118, 2005.
DOI : 10.1016/j.cell.2005.05.007

S. 32-rakoff-nahoum, J. Paglino, F. Eslami-varzaneh, S. Edberg, and R. Medzhitov, Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis, Cell, vol.118, issue.2, pp.229-241, 2004.
DOI : 10.1016/j.cell.2004.07.002

P. Weinstein and J. Cebra, The preference for switching to IgA expression by Peyer's patch germinal center B cells is likely due to the intrinsic influence of their microenvironment, J Immunol, vol.147, pp.4126-4135, 1991.

J. Cebra, Influences of microbiota on intestinal immune system development, Am J Clin Nutr, vol.69, pp.1046-1051, 1999.

F. Shanahan, The host???microbe interface within the gut, Best Practice & Research Clinical Gastroenterology, vol.16, issue.6, pp.915-931, 2002.
DOI : 10.1053/bega.2002.0342

Y. Li, P. Kundu, S. Seow, C. De-matos, L. Aronsson et al., Gut microbiota accelerate tumor growth via c-jun and STAT3 phosphorylation in APCMin/+ mice, Carcinogenesis, vol.33, issue.6, pp.1231-1238, 2012.
DOI : 10.1093/carcin/bgs137

F. Bäckhed, H. Ding, T. Wang, L. Hooper, G. Koh et al., The gut microbiota as an environmental factor that regulates fat storage, Proceedings of the National Academy of Sciences, vol.101, issue.44, pp.15718-15723, 2004.
DOI : 10.1073/pnas.0407076101

F. Bäckhed, R. Ley, J. Sonnenburg, D. Peterson, and J. Gordon, Host-Bacterial Mutualism in the Human Intestine, Science, vol.307, issue.5717, pp.1915-1920, 2005.
DOI : 10.1126/science.1104816

J. Laparra, Y. R. Sanz, R. Ross, F. Shanahan, O. Mahony et al., Interactions of gut microbiota with functional food components and nutraceuticals Metabolic activity of the enteric microbiota influences the fatty acid composition of murine and porcine liver and adipose tissues, Pharmacol Res Am J Clin Nutr, vol.61, issue.89, pp.219-225, 2008.

T. Manning, G. R. Gibson, H. Pforte, G. Jacobasch, and M. Blaut, Prebiotics, Best Practice & Research Clinical Gastroenterology, vol.18, issue.2, pp.287-298, 2002.
DOI : 10.1016/j.bpg.2003.10.008

B. Stecher and W. Hardt, The role of microbiota in infectious disease, Trends in Microbiology, vol.16, issue.3, pp.107-114, 2008.
DOI : 10.1016/j.tim.2007.12.008

R. Sandler, EPIDEMIOLOGY AND RISK FACTORS FOR COLORECTAL CANCER, Gastroenterology Clinics of North America, vol.25, issue.4, pp.717-735, 1996.
DOI : 10.1016/S0889-8553(05)70271-5

A. Knudson, Alfred Knudson and his two-hit hypothesis. (Interview by Ezzie Hutchinson), Lancet Oncol, vol.2, issue.01, pp.642-645, 2001.

Z. Hausen and H. , The search for infectious causes of human cancers: Where and why, Virology, vol.392, issue.1, pp.1-10, 2009.
DOI : 10.1016/j.virol.2009.06.001

D. Collins, A. Hogan, and D. Winter, Microbial and viral pathogens in colorectal cancer, The Lancet Oncology, vol.12, issue.5, pp.504-512, 2011.
DOI : 10.1016/S1470-2045(10)70186-8

O. Handa, Y. Naito, and T. Yoshikawa, Helicobacter pylori: a ROS-inducing bacterial species in the stomach, Inflammation Research, vol.44, issue.Suppl 1, pp.997-1003, 2010.
DOI : 10.1007/s00011-010-0245-x

C. Sears and W. Garrett, Microbes, Microbiota, and Colon Cancer, Cell Host & Microbe, vol.15, issue.3, pp.317-328, 2014.
DOI : 10.1016/j.chom.2014.02.007
URL : http://doi.org/10.1016/j.chom.2014.02.007

L. Proctor, The Human Microbiome Project in 2011 and Beyond, Cell Host & Microbe, vol.10, issue.4, pp.287-291, 2011.
DOI : 10.1016/j.chom.2011.10.001

J. Weisburger, B. Reddy, T. Narisawa, and E. Wynder, Germ-Free Status and Colon Tumor Induction by N-Methyl-N'-Nitro-N-Nitrosoguanidine, Experimental Biology and Medicine, vol.148, issue.4, pp.1119-1121, 1975.
DOI : 10.3181/00379727-148-38700

L. Vannucci, R. Stepankova, H. Kozakova, A. Fiserova, P. Rossmann et al., Colorectal carcinogenesis in germ-free and conventionally reared rats: Different intestinal environments affect the systemic immunity, International Journal of Oncology, vol.32, pp.609-617, 2008.
DOI : 10.3892/ijo.32.3.609

H. Tjalsma, A. Boleij, J. Marchesi, and B. Dutilh, A bacterial driver???passenger model for colorectal cancer: beyond the usual suspects, Nature Reviews Microbiology, vol.184, issue.8, pp.575-582, 1038.
DOI : 10.1038/nrmicro2819

A. 55-couturier-maillard, T. Secher, A. Rehman, N. S. , D. Arcangelis et al., NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer, Journal of Clinical Investigation, vol.123, pp.700-711, 1172.
DOI : 10.1172/JCI62236DS1

B. Hu, E. Elinav, S. Huber, T. Strowig, L. Hao et al., Microbiota-induced activation of epithelial IL-6 signaling links inflammasome-driven inflammation with transmissible cancer, ] 57 Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome, pp.9862-9867, 1038.
DOI : 10.1073/pnas.1307575110

R. Schwabe and C. Jobin, The microbiome and cancer, Nature Reviews Cancer, vol.109, issue.11, pp.800-812, 2013.
DOI : 10.1038/nrc3610

G. Hajishengallis, R. Darveau, and M. Curtis, The keystone-pathogen hypothesis, Nature Reviews Microbiology, vol.10, issue.10, pp.717-725, 2012.
DOI : 10.1038/nrmicro2873

N. Sanapareddy, R. Legge, B. Jovov, A. Mccoy, L. Burcal et al., Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans, The ISME Journal, vol.308, issue.10, pp.1858-1868, 2012.
DOI : 10.1111/j.1523-5378.2006.00381.x

I. Sobhani, J. Tap, F. Roudot-thoraval, J. Roperch, S. Letulle et al., Microbial Dysbiosis in Colorectal Cancer (CRC) Patients, PLoS ONE, vol.228, issue.1, p.16393, 2011.
DOI : 10.1371/journal.pone.0016393.s001
URL : https://hal.archives-ouvertes.fr/hal-01190486

T. Wang, G. Cai, Y. Qiu, N. Fei, M. Zhang et al., Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers, The ISME Journal, vol.70, issue.2, pp.320-329, 2012.
DOI : 10.1038/ismej.2011.109

J. Ahn, R. Sinha, Z. Pei, C. Dominianni, J. Wu et al., Human Gut Microbiome and Risk for Colorectal Cancer, JNCI Journal of the National Cancer Institute, vol.105, issue.24, pp.1907-1911, 2013.
DOI : 10.1093/jnci/djt300

N. Wu, X. Yang, R. Zhang, J. Li, X. Xiao et al., Dysbiosis Signature of Fecal Microbiota in Colorectal Cancer Patients, Microbial Ecology, vol.15, issue.8, pp.462-470, 2013.
DOI : 10.1007/s00248-013-0245-9

A. Abdulamir, R. Hafidh, A. Bakar, and F. , The association of Streptococcus bovis/gallolyticus with colorectal tumors: The nature and the underlying mechanisms of its etiological role, Journal of Experimental & Clinical Cancer Research, vol.30, issue.1, p.11, 2011.
DOI : 10.1186/1756-9966-30-11

R. Klein, R. Recco, M. Catalano, S. Edberg, J. Casey et al., with Carcinoma of the Colon, New England Journal of Medicine, vol.297, issue.15, pp.800-802, 1977.
DOI : 10.1056/NEJM197710132971503

N. Grahn, M. Hmani-aifa, K. Fransén, P. Söderkvist, and H. Monstein, Molecular identification of Helicobacter DNA present in human colorectal adenocarcinomas by 16S rDNA PCR amplification and pyrosequencing analysis, Journal of Medical Microbiology, vol.54, issue.11, pp.1031-1035, 2005.
DOI : 10.1099/jmm.0.46122-0

M. Jones, P. Helliwell, C. Pritchard, J. Tharakan, and J. Mathew, Helicobacter pylori in colorectal neoplasms: is there an aetiological relationship?, World Journal of Surgical Oncology, vol.5, issue.1, pp.511477-7819, 2007.
DOI : 10.1186/1477-7819-5-51

N. Zumkeller, H. Brenner, M. Zwahlen, and D. Rothenbacher, Helicobacter pylori Infection and Colorectal Cancer Risk: A Meta-Analysis, Helicobacter, vol.106, issue.2, pp.75-80, 2006.
DOI : 10.1093/jnci/83.23.1734

F. Housseau and C. Sears, ) mice: a human commensal-based murine model of colon carcinogenesis, Cell Cycle, vol.9, issue.1, pp.3-5, 2010.
DOI : 10.4161/cc.9.1.10352

N. Toprak, A. Yagci, B. Gulluoglu, M. Akin, P. Demirkalem et al., A possible role of Bacteroides fragilis enterotoxin in the aetiology of colorectal cancer, Clinical Microbiology and Infection, vol.12, issue.8, pp.782-786, 2006.
DOI : 10.1111/j.1469-0691.2006.01494.x

S. Wu, P. Morin, D. Maouyo, and C. Sears, Bacteroides fragilis enterotoxin induces c-Myc expression and cellular proliferation, Gastroenterology, vol.124, issue.2, pp.392-400, 2003.
DOI : 10.1053/gast.2003.50047

R. Balamurugan, E. Rajendiran, S. George, G. Samuel, B. Ramakrishna et al., in the feces of patients with colorectal cancer, Journal of Gastroenterology and Hepatology, vol.160, issue.1, pp.1298-1303, 2001.
DOI : 10.1111/j.1440-1746.2008.05490.x

J. Hermsen, M. Schurr, K. Kudsk, and L. Faucher, Phenotyping Clostridium septicum Infection: A Surgeon's Infectious Disease, Journal of Surgical Research, vol.148, issue.1, pp.67-76, 2008.
DOI : 10.1016/j.jss.2008.02.027

N. Mirza, J. Mccloud, and M. Cheetham, Clostridium septicum sepsis and colorectal cancer - a reminder, World Journal of Surgical Oncology, vol.7, issue.1, pp.731477-7819, 2009.
DOI : 10.1186/1477-7819-7-73

A. Kostic, E. Chun, L. Robertson, J. Glickman, C. Gallini et al., Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment, Cell Host & Microbe, vol.14, issue.2, pp.207-215, 2013.
DOI : 10.1016/j.chom.2013.07.007

A. Mccoy, F. Araújo-pérez, A. Azcárate-peril, J. Yeh, R. Sandler et al., Fusobacterium Is Associated with Colorectal Adenomas, PLoS ONE, vol.7, issue.1, p.53653, 2013.
DOI : 10.1371/journal.pone.0053653.s001

M. Rubinstein, X. Wang, W. Liu, Y. Hao, G. Cai et al., Fusobacterium nucleatum Promotes Colorectal Carcinogenesis by Modulating E-Cadherin/??-Catenin Signaling via its FadA Adhesin, Cell Host & Microbe, vol.14, issue.2, pp.195-206, 2013.
DOI : 10.1016/j.chom.2013.07.012

H. Martin, B. Campbell, C. Hart, C. Mpofu, M. Nayar et al., Enhanced Escherichia coli adherence and invasion in Crohn???s disease and colon cancer 1 1The authors thank Professor T. K. Korhonen (Division of General Microbiology, University of Helsinki, Finland), who kindly donated Escherichia coli IH11165; Professor J.-F. Colombel (Laboratoire de Recherche sur les Maladies Inflammatoire de l???Intestine, Centre Hospitalier Universitaire, Lille, France) and Professor A. Darfeuille-Michaud (Faculte de Pharmacie, Clermont-Ferrand, France), who kindly donated the Crohn???s disease ileal isolates LF10 and LF82; and Dr. Keith Leiper (Gastroenterology Unit, Royal Liverpool & Broadgreen University Hospitals Trust, Liverpool, UK) for his cooperation in obtaining colorectal tissue specimens.As a consequence of the work described herein, a patent application has been filed by the University of Liverpool regarding the use of soluble plantain fiber in Crohn???s disease., Gastroenterology, vol.127, issue.1, pp.80-93, 2004.
DOI : 10.1053/j.gastro.2004.03.054

A. Swidsinski, M. Khilkin, D. Kerjaschki, S. Schreiber, M. Ortner et al., Association between intraepithelial Escherichia coli and colorectal cancer, Gastroenterology, vol.115, issue.2, pp.281-286, 1998.
DOI : 10.1016/S0016-5085(98)70194-5

J. Arthur, E. Perez-chanona, M. Mühlbauer, S. Tomkovich, J. Uronis et al., Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota, Science, vol.338, issue.6103, pp.120-123, 2012.
DOI : 10.1126/science.1224820

W. Mccoy and J. Mason, Enterococcal endocarditis associated with carcinoma of the sigmoid; report of a case, J Med Assoc State Ala, vol.21, pp.162-166, 1951.

W. Hoppes and P. Lerner, Nonenterococcal Group-D Streptococcal Endocarditis Caused by Streptococcus bovis, Annals of Internal Medicine, vol.81, issue.5, pp.588-593, 1974.
DOI : 10.7326/0003-4819-81-5-588

R. Klein, M. Catalano, S. Edberg, J. Casey, and N. Steigbigel, Streptococcus bovis Septicemia and Carcinoma of the Colon, Annals of Internal Medicine, vol.91, issue.4, pp.560-5620003, 1979.
DOI : 10.7326/0003-4819-91-4-560

R. Dubrow, S. Edberg, E. Wikfors, D. Callan, F. Troncale et al., Fecal carriage of Streptococcus bovis and colorectal adenomas A prospective controlled study of the association of Streptococcus bovis with colorectal carcinoma, Gastroenterology J Clin Pathol, vol.101, issue.51, pp.721-725, 1991.

A. Boleij, M. Van-gelder, D. Swinkels, H. Tjalsma, A. Wright et al., Clinical Importance of Streptococcus gallolyticus infection among colorectal cancer patients: systematic review and meta-analysis Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces, Clin Infect Dis Appl Environ Microbiol, vol.53, issue.68, pp.870-878, 2002.

A. Abdulamir, R. Hafidh, and F. Bakar, Molecular detection, quantification, and isolation of Streptococcus gallolyticus bacteria colonizing colorectal tumors: inflammation-driven potential of carcinogenesis via IL-1, COX-2, and IL-8, Molecular Cancer, vol.9, issue.1, pp.249-20846456, 2010.
DOI : 10.1186/1476-4598-9-249

A. Boleij and H. Tjalsma, The itinerary of Streptococcus gallolyticus infection in patients with colonic malignant disease, The Lancet Infectious Diseases, vol.13, issue.8, pp.719-724, 2013.
DOI : 10.1016/S1473-3099(13)70107-5

Y. Guo and H. Li, Association between Helicobacter pylori infection and colorectal neoplasm risk: A meta-analysis Based on East Asian population, Journal of Cancer Research and Therapeutics, vol.10, issue.8, pp.263-266, 2014.
DOI : 10.4103/0973-1482.151482

H. Higashi, R. Tsutsumi, A. Fujita, S. Yamazaki, M. Asaka et al., Biological activity of the Helicobacter pylori virulence factor CagA is determined by variation in the tyrosine phosphorylation sites, Proceedings of the National Academy of Sciences, vol.99, issue.22, pp.14428-14433, 2002.
DOI : 10.1073/pnas.222375399

H. Shmuely, D. Passaro, A. Figer, Y. Niv, S. Pitlik et al., Relationship between Helicobacter pylori CagA status and colorectal cancer, The American Journal of Gastroenterology, vol.15, issue.12, pp.3406-3410, 2001.
DOI : 10.1046/j.1523-5378.1999.99316.x

J. Huang, S. Lee, and S. Mazmanian, The human commensal Bacteroides fragilis binds intestinal mucin, Anaerobe, vol.17, issue.4, pp.137-141, 2011.
DOI : 10.1016/j.anaerobe.2011.05.017

S. Macfarlane, E. Woodmansey, and G. Macfarlane, Colonization of Mucin by Human Intestinal Bacteria and Establishment of Biofilm Communities in a Two-Stage Continuous Culture System, Applied and Environmental Microbiology, vol.71, issue.11, pp.7483-7492, 2005.
DOI : 10.1128/AEM.71.11.7483-7492.2005

N. Zitomersky, M. Coyne, and L. Comstock, Longitudinal Analysis of the Prevalence, Maintenance, and IgA Response to Species of the Order Bacteroidales in the Human Gut, Infection and Immunity, vol.79, issue.5, pp.2012-2020, 2011.
DOI : 10.1128/IAI.01348-10

A. Boleij, E. Hechenbleikner, A. Goodwin, R. Badani, E. Stein et al., The Bacteroides fragilis Toxin Gene Is Prevalent in the Colon Mucosa of Colorectal Cancer Patients, Clinical Infectious Diseases, vol.60, issue.2, pp.208-215, 2015.
DOI : 10.1093/cid/ciu787

K. Rhee, S. Wu, X. Wu, D. Huso, B. Karim et al., Induction of Persistent Colitis by a Human Commensal, Enterotoxigenic Bacteroides fragilis, in Wild-Type C57BL/6 Mice, Infection and Immunity, vol.77, issue.4, pp.1708-171800814, 2009.
DOI : 10.1128/IAI.00814-08

C. Pillar and M. Gilmore, Enterococcal virulence - pathogenicity island of E. Faecalis, Frontiers in Bioscience, vol.9, issue.1-3, pp.2335-2346, 2004.
DOI : 10.2741/1400

M. Huycke, D. Moore, J. W. Wise, P. Shepard, L. Kotake et al., Extracellular superoxide production by Enterococcus faecalis requires demethylmenaquinone and is attenuated by functional terminal quinol oxidases, Molecular Microbiology, vol.93, issue.3, pp.729-740, 2001.
DOI : 10.1046/j.1365-2958.2001.02638.x

M. Huycke and D. Moore, In vivo production of hydroxyl radical by enterococcus faecalis colonizing the intestinal tract using aromatic hydroxylation, Free Radical Biology and Medicine, vol.33, issue.6, pp.818-826, 2002.
DOI : 10.1016/S0891-5849(02)00977-2

E. Balish and T. Warner, Enterococcus faecalis Induces Inflammatory Bowel Disease in Interleukin-10 Knockout Mice, The American Journal of Pathology, vol.160, issue.6, pp.2253-2257, 2002.
DOI : 10.1016/S0002-9440(10)61172-8

J. Dylewski and L. Luterman, Septic arthritis and Clostridium septicum: a clue to colon cancer, Canadian Medical Association Journal, vol.182, issue.13, pp.1446-1447, 2010.
DOI : 10.1503/cmaj.091946

A. Kostic, D. Gevers, C. Pedamallu, M. Michaud, F. Duke et al., Genomic analysis identifies association of Fusobacterium with colorectal carcinoma, Genome Research, vol.22, issue.2, pp.292-298, 2012.
DOI : 10.1101/gr.126573.111

J. Marchesi, B. Dutilh, N. Hall, W. Peters, R. Roelofs et al., Towards the Human Colorectal Cancer Microbiome, PLoS ONE, vol.6, issue.1, p.20447, 2011.
DOI : 10.1371/journal.pone.0020447.s008

M. Bonnet, E. Buc, P. Sauvanet, C. Darcha, D. Dubois et al., Colonization of the Human Gut by E. coli and Colorectal Cancer Risk, Clinical Cancer Research, vol.20, issue.4, pp.859-867, 2014.
DOI : 10.1158/1078-0432.CCR-13-1343

K. Viljoen, A. Dakshinamurthy, P. Goldberg, and J. Blackburn, Quantitative Profiling of Colorectal Cancer-Associated Bacteria Reveals Associations between Fusobacterium spp., Enterotoxigenic Bacteroides fragilis (ETBF) and Clinicopathological Features of Colorectal Cancer, PLOS ONE, vol.27, issue.3, p.119462, 2015.
DOI : 10.1371/journal.pone.0119462.s003

A. 110-darfeuille-michaud, J. Boudeau, P. Bulois, C. Neut, A. Glasser et al., High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn???s disease, Gastroenterology, vol.127, issue.2, pp.412-421, 2004.
DOI : 10.1053/j.gastro.2004.04.061

A. Darfeuille-michaud, C. Neut, N. Barnich, E. Lederman, D. Martino et al., Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease, Gastroenterology, vol.115, issue.6, pp.1405-1413, 1998.
DOI : 10.1016/S0016-5085(98)70019-8

O. Maddocks, A. Short, M. Donnenberg, S. Bader, and D. Harrison, Attaching and Effacing Escherichia coli Downregulate DNA Mismatch Repair Protein In Vitro and Are Associated with Colorectal Adenocarcinomas in Humans, PLoS ONE, vol.65, issue.5, p.5517, 2009.
DOI : 10.1371/journal.pone.0005517.g006

S. Martins, D. Prazeres, J. Cabral, and G. Monteiro, Comparison of real-time polymerase chain reaction and hybridization assays for the detection of Escherichia coli genomic DNA in process samples and pharmaceutical-grade plasmid DNA products, Analytical Biochemistry, vol.322, issue.1, pp.127-129, 2003.
DOI : 10.1016/j.ab.2003.07.004

J. Arthur and C. Jobin, The complex interplay between inflammation, the microbiota and colorectal cancer, Gut Microbes, vol.19, issue.3, pp.253-258, 2013.
DOI : 10.1016/j.jmb.2012.09.017

E. Buc, D. Dubois, P. Sauvanet, J. Raisch, J. Delmas et al., High Prevalence of Mucosa-Associated E. coli Producing Cyclomodulin and Genotoxin in Colon Cancer, PLoS ONE, vol.57, issue.2, p.56964, 2013.
DOI : 10.1371/journal.pone.0056964.s005

M. Prorok-hamon, M. Friswell, A. Alswied, C. Roberts, F. Song et al., are increased in inflammatory bowel disease and colon cancer, Gut, vol.317, issue.5, pp.761-770, 2014.
DOI : 10.1136/gutjnl-2013-304739

J. Raisch, E. Buc, M. Bonnet, P. Sauvanet, E. Vazeille et al., colonize gut mucosa and promote cell proliferation, World Journal of Gastroenterology, vol.20, issue.21, pp.6560-6572, 2014.
DOI : 10.3748/wjg.v20.i21.6560
URL : https://hal.archives-ouvertes.fr/hal-01211998

G. Cuevas-ramos, C. Petit, I. Marcq, M. Boury, E. Oswald et al., Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells, Proceedings of the National Academy of Sciences, vol.107, issue.25, pp.11537-11542, 2010.
DOI : 10.1073/pnas.1001261107

J. Nougayrède, S. Homburg, F. Taieb, M. Boury, E. Brzuszkiewicz et al., Escherichia coli Induces DNA Double-Strand Breaks in Eukaryotic Cells, Science, vol.313, issue.5788, pp.848-851, 2006.
DOI : 10.1126/science.1127059

A. Cougnoux, G. Dalmasso, R. Martinez, E. Buc, J. Delmas et al., Bacterial genotoxin colibactin promotes colon tumour growth by inducing a senescence-associated secretory phenotype, Gut, vol.63, issue.12, pp.1932-1942, 2014.
DOI : 10.1136/gutjnl-2013-305257
URL : https://hal.archives-ouvertes.fr/hal-01101227

O. Maddocks, K. Scanlon, and M. Donnenberg, An Escherichia coli Effector Protein Promotes Host Mutation via Depletion of DNA Mismatch Repair Proteins, mBio, vol.4, issue.3, pp.152-0011300152, 2013.
DOI : 10.1128/mBio.00152-13

P. Escobar-páramo, K. Grenet, L. Menac-'h, A. Rode, L. Salgado et al., Large-Scale Population Structure of Human Commensal Escherichia coli Isolates, Applied and Environmental Microbiology, vol.70, issue.9, pp.5698-5700, 2004.
DOI : 10.1128/AEM.70.9.5698-5700.2004

L. Gall, T. Clermont, O. Gouriou, S. Picard, B. Nassif et al., Extraintestinal Virulence Is a Coincidental By-Product of Commensalism in B2 Phylogenetic Group Escherichia coli Strains, Molecular Biology and Evolution, vol.24, issue.11, pp.2373-2384, 2007.
DOI : 10.1093/molbev/msm172
URL : https://hal.archives-ouvertes.fr/hal-00554748

Y. Han, A. Ikegami, C. Rajanna, H. Kawsar, Y. Zhou et al., Identification and Characterization of a Novel Adhesin Unique to Oral Fusobacteria, Journal of Bacteriology, vol.187, issue.15, pp.5330-53405330, 2005.
DOI : 10.1128/JB.187.15.5330-5340.2005

J. Fox and T. Wang, Inflammation, atrophy, and gastric cancer, Journal of Clinical Investigation, vol.117, issue.1, pp.60-69, 2007.
DOI : 10.1172/JCI30111

N. Ohnishi, H. Yuasa, S. Tanaka, H. Sawa, M. Miura et al., Transgenic expression of Helicobacter pylori CagA induces gastrointestinal and hematopoietic neoplasms in mouse, Proceedings of the National Academy of Sciences, vol.105, issue.3, pp.1003-1008, 2008.
DOI : 10.1073/pnas.0711183105

S. Wu, K. Rhee, E. Albesiano, S. Rabizadeh, X. Wu et al., A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses, Nature Medicine, vol.124, issue.9, pp.1016-1022, 2009.
DOI : 10.1038/nm.2015

J. Moncrief, R. Obiso, L. Barroso, J. Kling, R. Wright et al., The enterotoxin of Bacteroides fragilis is a metalloprotease, Infect Immun, vol.63, pp.175-181, 1995.

A. Goodwin, D. Shields, C. Wu, S. Huso, D. Wu et al., Polyamine catabolism contributes to enterotoxigenic Bacteroides fragilis-induced colon tumorigenesis, Proceedings of the National Academy of Sciences, vol.108, issue.37, pp.15354-15359, 2011.
DOI : 10.1073/pnas.1010203108

S. Wu, K. Lim, J. Huang, R. Saidi, and C. Sears, Bacteroides fragilis enterotoxin cleaves the zonula adherens protein, E-cadherin, Proceedings of the National Academy of Sciences, vol.95, issue.25, pp.14979-14984, 1998.
DOI : 10.1073/pnas.95.25.14979

S. Wu, J. Shin, G. Zhang, M. Cohen, A. Franco et al., The Bacteroides fragilis Toxin Binds to a Specific Intestinal Epithelial Cell Receptor, Infection and Immunity, vol.74, issue.9, pp.5382-5390, 2006.
DOI : 10.1128/IAI.00060-06

D. Nesi?, Y. Hsu, and C. Stebbins, Assembly and function of a bacterial genotoxin, Nature, vol.7, issue.6990, pp.429-433, 2004.
DOI : 10.1006/jmbi.1996.0703

J. Nougayrède, F. Taieb, J. De-rycke, and E. Oswald, Cyclomodulins: bacterial effectors that modulate the eukaryotic cell cycle, Trends in Microbiology, vol.13, issue.3, pp.103-110, 2005.
DOI : 10.1016/j.tim.2005.01.002

E. Oswald, J. Nougayrède, F. Taieb, and M. Sugai, Bacterial toxins that modulate host cell-cycle progression, Current Opinion in Microbiology, vol.8, issue.1, pp.83-91, 2005.
DOI : 10.1016/j.mib.2004.12.011

S. Travaglione, A. Fabbri, and C. Fiorentini, The Rho-activating CNF1 toxin from pathogenic E. coli: A risk factor for human cancer development?, Infectious Agents and Cancer, vol.3, issue.1, pp.41750-9378, 2008.
DOI : 10.1186/1750-9378-3-4

J. Smith and D. Bayles, The Contribution of Cytolethal Distending Toxin to Bacterial Pathogenesis, Critical Reviews in Microbiology, vol.275, issue.4, pp.227-248, 2006.
DOI : 10.1080/10408410601023557

Z. Ge, A. Rogers, Y. Feng, A. Lee, S. Xu et al., Bacterial cytolethal distending toxin promotes the development of dysplasia in a model of microbially induced hepatocarcinogenesis, Cellular Microbiology, vol.68, issue.8, pp.2070-2080, 2007.
DOI : 10.1128/IAI.72.5.2521-2527.2004

Z. Ge, D. Schauer, and J. Fox, virulence properties of bacterial cytolethal-distending toxin, Cellular Microbiology, vol.72, issue.8, pp.1599-1607, 2008.
DOI : 10.1111/j.1462-5822.2008.01173.x

W. Garrett, C. Gallini, T. Yatsunenko, M. Michaud, A. Dubois et al., Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis, Cell Host & Microbe, vol.8, issue.3, pp.292-300, 2010.
DOI : 10.1016/j.chom.2010.08.004

W. Garrett, S. Punit, C. Gallini, M. Michaud, D. Zhang et al., Colitis-Associated Colorectal Cancer Driven by T-bet Deficiency in Dendritic Cells, Cancer Cell, vol.16, issue.3, pp.208-219, 2009.
DOI : 10.1016/j.ccr.2009.07.015

J. Putze, C. Hennequin, J. Nougayrède, W. Zhang, S. Homburg et al., Genetic Structure and Distribution of the Colibactin Genomic Island among Members of the Family Enterobacteriaceae, Infection and Immunity, vol.77, issue.11, pp.4696-470300522, 2009.
DOI : 10.1128/IAI.00522-09

B. Dutilh, L. Backus, S. Van-hijum, and H. Tjalsma, Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer, Best Practice & Research Clinical Gastroenterology, vol.27, issue.1, pp.85-99, 2013.
DOI : 10.1016/j.bpg.2013.03.008

P. Louis, G. Hold, and H. Flint, The gut microbiota, bacterial metabolites and colorectal cancer, Nature Reviews Microbiology, vol.4, issue.10, pp.661-672, 2014.
DOI : 10.1038/nrmicro3344

J. Barrasa, N. Olmo, M. Lizarbe, and J. Turnay, Bile acids in the colon, from healthy to cytotoxic molecules, Toxicology in Vitro, vol.27, issue.2, pp.964-977, 2013.
DOI : 10.1016/j.tiv.2012.12.020

H. Bernstein, C. Bernstein, C. Payne, and K. Dvorak, Bile acids as endogenous etiologic agents in gastrointestinal cancer, World Journal of Gastroenterology, vol.15, issue.27, pp.3329-3340, 2009.
DOI : 10.3748/wjg.15.3329

J. Ou, J. Delany, M. Zhang, S. Sharma, O. Keefe et al., Association Between Low Colonic Short-Chain Fatty Acids and High Bile Acids in High Colon Cancer Risk Populations, Nutrition and Cancer, vol.10, issue.1, pp.34-40, 2012.
DOI : 10.1136/gut.28.10.1221

B. Philipp, Bacterial degradation of bile salts, Applied Microbiology and Biotechnology, vol.182, issue.4, pp.903-915, 2011.
DOI : 10.1007/s00253-010-2998-0

H. Bernstein, C. Bernstein, C. Payne, K. Dvorakova, and H. Garewal, Bile acids as carcinogens in human gastrointestinal cancers, Mutation Research/Reviews in Mutation Research, vol.589, issue.1, pp.47-65, 2005.
DOI : 10.1016/j.mrrev.2004.08.001

K. Dvorak, C. Payne, M. Chavarria, L. Ramsey, B. Dvorakova et al., Bile acids in combination with low pH induce oxidative stress and oxidative DNA damage: relevance to the pathogenesis of Barrett's oesophagus, Gut, vol.56, issue.6, pp.763-771, 2006.
DOI : 10.1136/gut.2006.103697

S. Yoshimoto, T. Loo, K. Atarashi, H. Kanda, S. Sato et al., Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome, Nature, vol.45, issue.7456, pp.97-101, 1038.
DOI : 10.1002/jcp.22598

H. Takada, T. Hirooka, Y. Hiramatsu, and M. Yamamoto, Effect of beta-glucuronidase inhibitor on azoxymethane-induced colonic carcinogenesis in rats, Cancer Res, vol.42, pp.331-334, 1982.

D. Kim and Y. Jin, Intestinal bacterial ??-glucuronidase activity of patients with colon cancer, Archives of Pharmacal Research, vol.34, issue.6, pp.564-567, 2001.
DOI : 10.1007/BF02975166

H. Haiser and P. Turnbaugh, Is It Time for a Metagenomic Basis of Therapeutics?, Science, vol.336, issue.6086, pp.1253-1255, 2012.
DOI : 10.1126/science.1224396

B. Wallace, H. Wang, K. Lane, J. Scott, J. Orans et al., Alleviating cancer drug toxicity by inhibiting a bacterial enzyme Gut microbial activity, implications for health and disease: the potential role of metabolite analysis, Science J Proteome Res, vol.330, issue.11, pp.831-835, 1021.

W. Russell, S. Gratz, S. Duncan, G. Holtrop, J. Ince et al., High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health, American Journal of Clinical Nutrition, vol.93, issue.5, pp.1062-1072, 2011.
DOI : 10.3945/ajcn.110.002188

R. Hughes, A. Cross, J. Pollock, and S. Bingham, Dose-dependent effect of dietary meat on endogenous colonic N-nitrosation, Carcinogenesis, vol.22, issue.1, pp.199-202, 2001.
DOI : 10.1093/carcin/22.1.199

A. Belcheva, T. Irrazabal, S. Robertson, C. Streutker, H. Maughan et al., Gut Microbial Metabolism Drives Transformation of Msh2-Deficient Colon Epithelial Cells, Cell, vol.158, issue.2, pp.288-299, 2014.
DOI : 10.1016/j.cell.2014.04.051

N. Singh, A. Gurav, S. Sivaprakasam, E. Brady, R. Padia et al., Activation of Gpr109a, Receptor for Niacin and the Commensal Metabolite Butyrate, Suppresses Colonic Inflammation and Carcinogenesis, Immunity, vol.40, issue.1, pp.128-139, 2014.
DOI : 10.1016/j.immuni.2013.12.007

C. Gill and I. Rowland, Diet and cancer: assessing the risk, British Journal of Nutrition, vol.23, issue.S1, pp.73-87, 2002.
DOI : 10.1007/BF00341276

W. Russell, S. Duncan, L. Scobbie, G. Duncan, L. Cantlay et al., Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein, Molecular Nutrition & Food Research, vol.104, issue.Suppl 3, pp.523-535, 2013.
DOI : 10.1002/mnfr.201200594

Y. Loh, P. Jakszyn, R. Luben, A. Mulligan, P. Mitrou et al., N-nitroso compounds and cancer incidence: the European Prospective Investigation into Cancer and Nutrition (EPIC)-Norfolk Study, American Journal of Clinical Nutrition, vol.93, issue.5, pp.1053-1061, 2011.
DOI : 10.3945/ajcn.111.012377

E. Magee, C. Richardson, R. Hughes, and J. Cummings, Contribution of dietary protein to sulfide production in the large intestine: an in vitro and a controlled feeding study in humans, Am J Clin Nutr, vol.72, pp.1488-1494, 2000.

W. Roediger, J. Moore, and W. Babidge, Colonic sulfide in pathogenesis and treatment of ulcerative colitis, Digestive Diseases and Sciences, vol.42, issue.8, pp.1571-1579, 1997.
DOI : 10.1023/A:1018851723920

M. Attene-ramos, G. Nava, M. Muellner, E. Wagner, M. Plewa et al., DNA damage and toxicogenomic analyses of hydrogen sulfide in human intestinal epithelial FHs 74 Int cells, Environmental and Molecular Mutagenesis, vol.81, issue.Database issue, pp.304-314, 2010.
DOI : 10.1002/em.20546

M. Attene-ramos, E. Wagner, H. Gaskins, and M. Plewa, Hydrogen Sulfide Induces Direct Radical-Associated DNA Damage, Molecular Cancer Research, vol.5, issue.5, pp.455-459, 2007.
DOI : 10.1158/1541-7786.MCR-06-0439

H. Seitz and F. Stickel, Molecular mechanisms of alcohol-mediated carcinogenesis, Nature Reviews Cancer, vol.22, issue.8, pp.599-612, 2007.
DOI : 10.1038/nrc2191

N. Homann, Alcohol and upper gastrointestinal tract cancer: the role of local acetaldehyde production, Addiction Biology, vol.98, issue.4, pp.309-323, 2001.
DOI : 10.1016/S0304-3835(99)00343-2

S. Hooper, M. Wilson, and S. Crean, Exploring the link between microorganisms and oral cancer: A systematic review of the literature, Head & Neck, vol.43, issue.2/3, pp.1228-1239, 2009.
DOI : 10.1002/hed.21140

S. Choi, Y. Kim, J. Weitzel, and J. Mason, Folate depletion impairs DNA excision repair in the colon of the rat, Gut, vol.43, issue.1, pp.93-99, 1998.
DOI : 10.1136/gut.43.1.93

N. Homann, J. Tillonen, and M. Salaspuro, Microbially produced acetaldehyde from ethanol may increase the risk of colon cancer via folate deficiency, International Journal of Cancer, vol.19, issue.2, pp.169-173, 2000.
DOI : 10.1002/(SICI)1097-0215(20000415)86:2<169::AID-IJC4>3.0.CO;2-3

E. Cario, BACTERIAL INTERACTIONS WITH CELLS OF THE INTESTINAL MUCOSA: TOLL-LIKE RECEPTORS AND NOD2, Gut, vol.54, issue.8, pp.1182-1193, 2004.
DOI : 10.1136/gut.2004.062794

M. Karin and F. Greten, NF-??B: linking inflammation and immunity to cancer development and progression, Nature Reviews Immunology, vol.100, issue.10, pp.749-759, 2005.
DOI : 10.1038/nri1703

S. 175-rakoff-nahoum and R. Medzhitov, Regulation of Spontaneous Intestinal Tumorigenesis Through the Adaptor Protein MyD88, Science, vol.317, issue.5834, pp.124-127, 2007.
DOI : 10.1126/science.1140488

J. Uronis, M. Mühlbauer, H. Herfarth, T. Rubinas, G. Jones et al., Modulation of the Intestinal Microbiota Alters Colitis-Associated Colorectal Cancer Susceptibility, PLoS ONE, vol.4, issue.6, p.6026, 2009.
DOI : 10.1371/journal.pone.0006026.g007

T. Irrazábal, A. Belcheva, S. Girardin, A. Martin, and D. Philpott, The Multifaceted Role of the Intestinal Microbiota in Colon Cancer, Molecular Cell, vol.54, issue.2, pp.309-320, 2014.
DOI : 10.1016/j.molcel.2014.03.039

G. Chen, M. Shaw, G. Redondo, and G. Núñez, The Innate Immune Receptor Nod1 Protects the Intestine from Inflammation-Induced Tumorigenesis, Cancer Research, vol.68, issue.24, pp.10060-10067, 2008.
DOI : 10.1158/0008-5472.CAN-08-2061

B. Chassaing and A. Darfeuille-michaud, The Commensal Microbiota and Enteropathogens in the Pathogenesis of Inflammatory Bowel Diseases, Gastroenterology, vol.140, issue.6, pp.1720-1728, 2011.
DOI : 10.1053/j.gastro.2011.01.054

D. Cunningham, W. Atkin, H. Lenz, H. Lynch, B. Minsky et al., Colorectal cancer, The Lancet, vol.375, issue.9719, pp.1030-1047, 2010.
DOI : 10.1016/S0140-6736(10)60353-4

C. Manichanh, N. Borruel, F. Casellas, and F. Guarner, The gut microbiota in IBD, Nature Reviews Gastroenterology & Hepatology, vol.252, issue.10, pp.599-608, 2012.
DOI : 10.1038/nrgastro.2012.152

J. Zackular, N. Baxter, K. Iverson, W. Sadler, J. Petrosino et al., The Gut Microbiome Modulates Colon Tumorigenesis, mBio, vol.4, issue.6, pp.692-0061300692, 2013.
DOI : 10.1128/mBio.00692-13

J. Raisch, N. Rolhion, A. Dubois, A. Darfeuille-michaud, and M. Bringer, Intracellular colon cancer-associated Escherichia coli promote protumoral activities of human macrophages by inducing sustained COX-2 expression, Laboratory Investigation, vol.191, issue.3, pp.296-307, 2015.
DOI : 10.1124/mol.104.005199
URL : https://hal.archives-ouvertes.fr/hal-01222408

M. Cooke, M. Evans, M. Dizdaroglu, and J. Lunec, Oxidative DNA damage: mechanisms, mutation, and disease, The FASEB Journal, vol.17, issue.10, pp.1195-1214, 2003.
DOI : 10.1096/fj.02-0752rev

M. Evans, M. Dizdaroglu, and M. Cooke, Oxidative DNA damage and disease: induction, repair and significance, Mutation Research/Reviews in Mutation Research, vol.567, issue.1, pp.1-61, 2004.
DOI : 10.1016/j.mrrev.2003.11.001

D. Wang, D. Kreutzer, and J. Essigmann, Mutagenicity and repair of oxidative DNA damage: insights from studies using defined lesions, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, vol.400, issue.1-2, pp.99-115, 1998.
DOI : 10.1016/S0027-5107(98)00066-9

H. Bartsch and J. Nair, Potential role of lipid peroxidation derived DNA damage in human colon carcinogenesis: studies on exocyclic base adducts as stable oxidative stress markers, Cancer Detection and Prevention, vol.26, issue.4, pp.308-312, 2002.
DOI : 10.1016/S0361-090X(02)00093-4

A. Keshavarzian, D. Zapeda, T. List, and S. Mobarhan, High levels of reactive oxygen metabolites in colon cancer tissue: Analysis by chemiluminescence probe, Nutrition and Cancer, vol.90, issue.3, pp.243-249, 1080.
DOI : 10.1056/NEJM198902093200606

A. Roessner, D. Kuester, P. Malfertheiner, and R. Schneider-stock, Oxidative stress in ulcerative colitis-associated carcinogenesis, Pathology - Research and Practice, vol.204, issue.7, pp.511-524, 2008.
DOI : 10.1016/j.prp.2008.04.011

J. Lundberg, E. Weitzberg, J. Cole, and N. Benjamin, Opinion: Nitrate, bacteria and human health, Nature Reviews Microbiology, vol.349, issue.7, pp.593-602, 2004.
DOI : 10.1080/00365520310007152

T. Sobko, L. Huang, T. Midtvedt, E. Norin, L. Gustafsson et al., Generation of NO by probiotic bacteria in the gastrointestinal tract, Free Radical Biology and Medicine, vol.41, issue.6, pp.985-991, 2006.
DOI : 10.1016/j.freeradbiomed.2006.06.020

T. Sobko, C. Reinders, E. Jansson, E. Norin, T. Midtvedt et al., Gastrointestinal bacteria generate nitric oxide from nitrate and nitrite, Nitric Oxide, vol.13, issue.4, pp.272-278, 2005.
DOI : 10.1016/j.niox.2005.08.002

S. Grivennikov, F. Greten, and K. M. , Immunity, Inflammation, and Cancer, Cell, vol.140, issue.6, pp.883-899, 2010.
DOI : 10.1016/j.cell.2010.01.025

J. Klaunig, L. Kamendulis, and B. Hocevar, Oxidative Stress and Oxidative Damage in Carcinogenesis, Toxicologic Pathology, vol.38, issue.1, pp.96-109, 2010.
DOI : 10.1177/0192623309356453

W. Dröge, Free Radicals in the Physiological Control of Cell Function, Physiological Reviews, vol.82, issue.1, pp.47-95, 2001.
DOI : 10.1152/physrev.00018.2001

F. Hazane-puch, M. Bonnet, K. Valenti, S. Schnebert, R. Kurfurst et al., Study of fibroblast gene expression in response to oxidative stress induced by hydrogen peroxide or UVA with skin aging, Eur J Dermatol, vol.20, pp.308-320, 2010.

V. Moreno, F. Gemignani, S. Landi, L. Gioia-patricola, A. Chabrier et al., Polymorphisms in Genes of Nucleotide and Base Excision Repair: Risk and Prognosis of Colorectal Cancer, Clinical Cancer Research, vol.12, issue.7, pp.2101-2108, 2006.
DOI : 10.1158/1078-0432.CCR-05-1363

P. Peltomäki, Role of DNA Mismatch Repair Defects in the Pathogenesis of Human Cancer, Journal of Clinical Oncology, vol.21, issue.6, pp.1174-1179, 2003.
DOI : 10.1200/JCO.2003.04.060

A. Mangerich, C. Knutson, N. Parry, S. Muthupalani, W. Ye et al., Infection-induced colitis in mice causes dynamic and tissue-specific changes in stress response and DNA damage leading to colon cancer, Analysis of structurefunction relationships in the colibactin-maturating enzyme ClbP, pp.1820-1829, 2012.
DOI : 10.1073/pnas.1207829109

D. Dubois, O. Baron, A. Cougnoux, J. Delmas, N. Pradel et al., ClbP Is a Prototype of a Peptidase Subgroup Involved in Biosynthesis of Nonribosomal Peptides, Journal of Biological Chemistry, vol.286, issue.41, pp.35562-35570, 2011.
DOI : 10.1074/jbc.M111.221960
URL : https://hal.archives-ouvertes.fr/hal-00748957

D. Reimer, K. Pos, M. Thines, P. Grün, and H. Bode, A natural prodrug activation mechanism in nonribosomal peptide synthesis, Nature Chemical Biology, vol.71, issue.12, pp.888-890, 2011.
DOI : 10.1038/nchembio.688

A. Cougnoux, J. Delmas, L. Gibold, T. Faïs, C. Romagnoli et al., Small-molecule inhibitors prevent the genotoxic and protumoural effects induced by colibactin-producing bacteria Epub ahead of print, Gut, pp.25588406-25588416, 2015.

P. Licciardi, S. Wong, M. Tang, and T. Karagiannis, Epigenome targeting by probiotic metabolites, Gut Pathogens, vol.2, issue.1, pp.241757-4749, 2010.
DOI : 10.1186/1757-4749-2-24

M. Ritchie and T. Romanuk, A Meta-Analysis of Probiotic Efficacy for Gastrointestinal Diseases, PLoS ONE, vol.16, issue.5599, p.34938, 2012.
DOI : 10.1371/journal.pone.0034938.s003

K. Khazaie, M. Zadeh, M. Khan, P. Bere, F. Gounari et al., Abating colon cancer polyposis by Lactobacillus acidophilus deficient in lipoteichoic acid, Proceedings of the National Academy of Sciences, vol.109, issue.26, pp.10462-10467, 2012.
DOI : 10.1073/pnas.1207230109

M. Mohamadzadeh, E. Pfeiler, J. Brown, M. Zadeh, M. Gramarossa et al., Regulation of induced colonic inflammation by Lactobacillus acidophilus deficient in lipoteichoic acid, Proceedings of the National Academy of Sciences, vol.108, issue.Supplement_1, pp.4623-4630, 2011.
DOI : 10.1073/pnas.1005066107

R. Saber, M. Zadeh, K. Pakanati, P. Bere, T. Klaenhammer et al., regulates downstream signals, Immunotherapy, vol.3, issue.3, pp.337-347, 2011.
DOI : 10.2217/imt.10.119

Y. Lightfoot, T. Yang, B. Sahay, and M. Mohamadzadeh, Targeting aberrant colon cancer-specific DNA methylation with lipoteichoic acid-deficient Lactobacillus acidophilus, Gut Microbes, vol.4, issue.1, pp.84-88, 2013.
DOI : 10.1146/annurev.pathol.4.110807.092311

D. Ghadimi, U. Helwig, J. Schrezenmeir, K. Heller, and M. De-vrese, Epigenetic imprinting by commensal probiotics inhibits the IL-23/IL-17 axis in an in vitro model of the intestinal mucosal immune system, Journal of Leukocyte Biology, vol.92, issue.4, pp.895-911, 2012.
DOI : 10.1189/jlb.0611286

C. Hedin, K. Whelan, and J. Lindsay, Evidence for the use of probiotics and prebiotics in inflammatory bowel disease: a review of clinical trials, Proceedings of the Nutrition Society, vol.22, issue.03, pp.307-315, 2007.
DOI : 10.1136/gut.32.10.1166

P. Marteau, M. De-vrese, C. Cellier, and J. Schrezenmeir, Protection from gastrointestinal diseases with the use of probiotics, Am J Clin Nutr, vol.73, pp.430-436, 2001.

Q. Feng, S. Liang, H. Jia, A. Stadlmayr, L. Tang et al., Gut microbiome development along the colorectal adenoma???carcinoma sequence, Nature Communications, vol.102, p.6528, 2015.
DOI : 10.1038/ncomms7528

J. Gagnière, Microbiota and colorectal cancer © 2016 Baishideng Publishing Group Inc. All rights reserved