R. Ricciardi, D. A. Rothenberger, R. D. Madoff, and N. N. Baxter, Increasing Prevalence and Severity of Clostridium difficile Colitis in Hospitalized Patients in the United States, Archives of Surgery, vol.142, issue.7, pp.624-631, 2007.
DOI : 10.1001/archsurg.142.7.624

V. G. Loo, L. Poirier, M. A. Miller, M. Oughton, M. D. Libman et al., ???Associated Diarrhea with High Morbidity and Mortality, New England Journal of Medicine, vol.353, issue.23, pp.2442-2449, 2005.
DOI : 10.1056/NEJMoa051639

J. G. Bartlett, Narrative Review: The New Epidemic of Clostridium difficile???Associated Enteric Disease, Annals of Internal Medicine, vol.145, issue.10, pp.758-764, 2006.
DOI : 10.7326/0003-4819-145-10-200611210-00008

T. Akerlund, B. Svenungsson, A. Lagergren, and L. G. Burman, Correlation of Disease Severity with Fecal Toxin Levels in Patients with Clostridium difficile-Associated Diarrhea and Distribution of PCR Ribotypes and Toxin Yields In Vitro of Corresponding Isolates, Journal of Clinical Microbiology, vol.44, issue.2, pp.353-358, 2006.
DOI : 10.1128/JCM.44.2.353-358.2006

C. Deneve, C. Janoir, I. Poilane, C. Fantinato, and A. Collignon, New trends in Clostridium difficile virulence and pathogenesis, International Journal of Antimicrobial Agents, vol.33, pp.24-28, 2009.
DOI : 10.1016/S0924-8579(09)70012-3

I. Just, J. Selzer, M. Wilm, C. Von-eichel-streiber, M. Mann et al., Glucosylation of Rho proteins by Clostridium difficile toxin B, Nature, vol.375, issue.6531, pp.500-503, 1995.
DOI : 10.1038/375500a0

I. Just, M. Wilm, J. Selzer, G. Rex, C. Von-eichel-streiber et al., The Enterotoxin from Clostridium difficile (ToxA) Monoglucosylates the Rho Proteins, Journal of Biological Chemistry, vol.270, issue.23, pp.13932-13936, 1995.
DOI : 10.1074/jbc.270.23.13932

N. Mani, D. Lyras, L. Barroso, P. Howarth, T. Wilkins et al., Environmental Response and Autoregulation of Clostridium difficile TxeR, a Sigma Factor for Toxin Gene Expression, Journal of Bacteriology, vol.184, issue.21, pp.5971-5978, 2002.
DOI : 10.1128/JB.184.21.5971-5978.2002

S. Matamouros, P. England, and B. Dupuy, Clostridium difficile toxin expression is inhibited by the novel regulator TcdC, Molecular Microbiology, vol.180, issue.Part 7, pp.1274-1288, 2007.
DOI : 10.1111/j.1365-2958.2007.05739.x

R. Govind and B. Dupuy, Secretion of Clostridium difficile Toxins A and B Requires the Holin-like Protein TcdE, PLoS Pathogens, vol.38, issue.Pt 1, p.1002727, 2012.
DOI : 10.1371/journal.ppat.1002727.s001

C. Schwan, B. Stecher, T. Tzivelekidis, M. Van-ham, M. Rohde et al., Clostridium difficile Toxin CDT Induces Formation of Microtubule-Based Protrusions and Increases Adherence of Bacteria, PLoS Pathogens, vol.23, issue.12, p.1000626, 2009.
DOI : 10.1371/journal.ppat.1000626.s010

S. V. Seddon, I. Hemingway, and S. P. Borriello, Hydrolytic enzyme production by Clostridium difficile and its relationship to toxin production and virulence in the hamster model, Journal of Medical Microbiology, vol.31, issue.3, pp.169-174, 1990.
DOI : 10.1099/00222615-31-3-169

J. M. Kirby, H. Ahern, A. K. Roberts, V. Kumar, Z. Freeman et al., Cwp84, a Surface-associated Cysteine Protease, Plays a Role in the Maturation of the Surface Layer of Clostridium difficile, Journal of Biological Chemistry, vol.284, issue.50, pp.34666-34673, 2009.
DOI : 10.1074/jbc.M109.051177

O. Connor, J. R. Johnson, S. Gerding, and D. N. , Clostridium difficile Infection Caused by the Epidemic BI/NAP1/027 Strain, Gastroenterology, vol.136, issue.6, pp.1913-1924, 2009.
DOI : 10.1053/j.gastro.2009.02.073

B. Dupuy and A. L. Sonenshein, toxin genes, Molecular Microbiology, vol.27, issue.1, pp.107-120, 1998.
DOI : 10.1046/j.1365-2958.1998.00663.x

J. Deutscher, C. Francke, and P. W. Postma, How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria, Microbiology and Molecular Biology Reviews, vol.70, issue.4, pp.939-1031, 2006.
DOI : 10.1128/MMBR.00024-06
URL : https://hal.archives-ouvertes.fr/hal-00164056

H. M. Blencke, G. Homuth, H. Ludwig, U. Mader, M. Hecker et al., Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways, Metabolic Engineering, vol.5, issue.2, pp.133-149, 2003.
DOI : 10.1016/S1096-7176(03)00009-0

M. S. Moreno, B. L. Schneider, R. R. Maile, W. Weyler, M. H. Saier et al., Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses, Molecular Microbiology, vol.181, issue.5, pp.1366-1381, 2001.
DOI : 10.1111/j.1365-2958.2001.02328.x

A. L. Zomer, G. Buist, R. Larsen, J. Kok, and O. P. Kuipers, Time-Resolved Determination of the CcpA Regulon of Lactococcus lactis subsp. cremoris MG1363, Journal of Bacteriology, vol.189, issue.4, pp.1366-1381, 2007.
DOI : 10.1128/JB.01013-06

M. Van-der-voort, O. P. Kuipers, G. Buist, W. M. De-vos, and T. Abee, Assessment of CcpA-mediated catabolite control of gene expression in Bacillus cereus ATCC 14579, BMC Microbiology, vol.8, issue.1, p.62, 2008.
DOI : 10.1186/1471-2180-8-62

C. Ren, Y. Gu, S. Hu, Y. Wu, P. Wang et al., Identification and inactivation of pleiotropic regulator CcpA to eliminate glucose repression of xylose utilization in Clostridium acetobutylicum, Metabolic Engineering, vol.12, issue.5, pp.446-454, 2010.
DOI : 10.1016/j.ymben.2010.05.002

S. M. Carvalho, T. G. Kloosterman, O. P. Kuipers, and A. R. Neves, CcpA Ensures Optimal Metabolic Fitness of Streptococcus pneumoniae, PLoS ONE, vol.6, issue.10, p.26707, 2011.
DOI : 10.1371/journal.pone.0026707.s008

C. Li, F. Sun, H. Cho, V. Yelavarthi, C. Sohn et al., CcpA Mediates Proline Auxotrophy and Is Required for Staphylococcus aureus Pathogenesis, Journal of Bacteriology, vol.192, issue.15, pp.3883-3892, 2010.
DOI : 10.1128/JB.00237-10

K. Seidl, M. Stucki, M. Ruegg, C. Goerke, C. Wolz et al., Staphylococcus aureus CcpA Affects Virulence Determinant Production and Antibiotic Resistance, Antimicrobial Agents and Chemotherapy, vol.50, issue.4, pp.1183-1194, 2006.
DOI : 10.1128/AAC.50.4.1183-1194.2006

J. Varga, V. L. Stirewalt, and S. B. Melville, The CcpA Protein Is Necessary for Efficient Sporulation and Enterotoxin Gene (cpe) Regulation in Clostridium perfringens, Journal of Bacteriology, vol.186, issue.16, pp.5221-5229, 2004.
DOI : 10.1128/JB.186.16.5221-5229.2004

J. J. Varga, B. Therit, and S. B. Melville, Type IV Pili and the CcpA Protein Are Needed for Maximal Biofilm Formation by the Gram-Positive Anaerobic Pathogen Clostridium perfringens, Infection and Immunity, vol.76, issue.11, pp.4944-4951, 2008.
DOI : 10.1128/IAI.00692-08

C. Chiang, C. Bongiorni, and M. Perego, Glucose-Dependent Activation of Bacillus anthracis Toxin Gene Expression and Virulence Requires the Carbon Catabolite Protein CcpA, Journal of Bacteriology, vol.193, issue.1, 2011.
DOI : 10.1128/JB.01656-09

M. B. Mendez, A. Goni, W. Ramirez, and R. R. Grau, Sugar inhibits the production of the toxins that trigger clostridial gas gangrene, Microbial Pathogenesis, vol.52, issue.1, pp.85-91, 2012.
DOI : 10.1016/j.micpath.2011.10.008

A. Antunes, I. Martin-verstraete, and B. Dupuy, CcpA-mediated repression of Clostridium difficile toxin gene expression, Molecular Microbiology, vol.44, issue.1, pp.882-899, 2011.
DOI : 10.1111/j.1365-2958.2010.07495.x

M. Sebaihia, B. W. Wren, P. Mullany, N. F. Fairweather, N. Minton et al., The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome, Nature Genetics, vol.21, issue.7, pp.779-786, 2006.
DOI : 10.1038/ng1830

O. Connor, J. R. Lyras, D. Farrow, K. A. Adams, V. Powell et al., Construction and analysis of chromosomal Clostridium difficile mutants, Molecular Microbiology, vol.23, issue.5, pp.1335-1351, 2006.
DOI : 10.1016/S0140-6736(05)67420-X

K. H. Wilson, M. J. Kennedy, and F. R. Fekety, Use of sodium taurocholate to enhance spore recovery on a medium selective for Clostridium difficile, J. Clin. Microbiol, vol.15, pp.443-446, 1982.

J. P. Carlier and N. Sellier, Gas chromatographic-mass spectral studies after methylation of metabolites produced by some anaerobic bacteria in spent media, Journal of Chromatography B: Biomedical Sciences and Applications, vol.493, pp.257-273, 1989.
DOI : 10.1016/S0378-4347(00)82733-4

L. Saujet, M. Monot, B. Dupuy, O. Soutourina, and I. Martin-verstraete, The Key Sigma Factor of Transition Phase, SigH, Controls Sporulation, Metabolism, and Virulence Factor Expression in Clostridium difficile, Journal of Bacteriology, vol.193, issue.13, pp.3186-3196, 2011.
DOI : 10.1128/JB.00272-11
URL : https://hal.archives-ouvertes.fr/pasteur-01370840

J. M. Rouillard, M. Zuker, and E. Gulari, OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach, Nucleic Acids Research, vol.31, issue.12, pp.3057-3062, 2003.
DOI : 10.1093/nar/gkg426

D. C. Grainger, T. W. Overton, N. Reppas, J. T. Wade, E. Tamai et al., Genomic Studies with Escherichia coli MelR Protein: Applications of Chromatin Immunoprecipitation and Microarrays, Journal of Bacteriology, vol.186, issue.20, pp.6938-6943, 2004.
DOI : 10.1128/JB.186.20.6938-6943.2004

M. E. Ritchie, J. Silver, A. Oshlack, M. Holmes, D. Diyagama et al., A comparison of background correction methods for two-colour microarrays, Bioinformatics, vol.23, issue.20, pp.2700-2707, 2007.
DOI : 10.1093/bioinformatics/btm412

G. K. Smyth and T. Speed, Normalization of cDNA microarray data, Methods, vol.31, issue.4, pp.265-273, 2003.
DOI : 10.1016/S1046-2023(03)00155-5

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and poweful approach to multiple testing, J. R. Stat. Soc. Series B Stat. Methodol, vol.57, pp.289-300, 1995.

N. Pons, J. M. Batto, S. D. Ehrlich, and P. Renault, Development of Software Facilities to Characterize Regulatory Binding Motifs and Application to Streptococcaceae, Journal of Molecular Microbiology and Biotechnology, vol.14, issue.1-3, pp.67-73, 2008.
DOI : 10.1159/000106084

T. L. Bailey, M. Boden, F. A. Buske, M. Frith, C. E. Grant et al., MEME SUITE: tools for motif discovery and searching, Nucleic Acids Research, vol.37, issue.Web Server, pp.202-208, 2009.
DOI : 10.1093/nar/gkp335

P. S. Novichkov, D. A. Rodionov, E. D. Stavrovskaya, E. S. Novichkova, A. E. Kazakov et al., RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach, Nucleic Acids Research, vol.38, issue.Web Server, pp.299-307, 2010.
DOI : 10.1093/nar/gkq531

B. Gorke and J. Stulke, Carbon catabolite repression in bacteria: many ways to make the most out of nutrients, Nature Reviews Microbiology, vol.280, issue.8, pp.613-624, 2008.
DOI : 10.1038/nrmicro1932

C. C. Kietzman and M. G. Caparon, Distinct Time-Resolved Roles for Two Catabolite-Sensing Pathways during Streptococcus pyogenes Infection, Infection and Immunity, vol.79, issue.2, pp.812-821, 2011.
DOI : 10.1128/IAI.01026-10

K. Seidl, S. Muller, P. Francois, C. Kriebitzsch, J. Schrenzel et al., Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus, BMC Microbiology, vol.9, issue.1, p.95, 2009.
DOI : 10.1186/1471-2180-9-95

M. A. Schumacher, M. Sprehe, M. Bartholomae, W. Hillen, and R. G. Brennan, Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element, Nucleic Acids Research, vol.40, issue.21, p.10717, 2011.

J. D. Partridge, D. M. Bodenmiller, M. S. Humphrys, and S. Spiro, genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility, Molecular Microbiology, vol.47, issue.4, pp.680-694, 2009.
DOI : 10.1111/j.1365-2958.2009.06799.x

S. Anbalagan, W. M. Mcshan, P. M. Dunman, and M. S. Chaussee, Identification of Rgg Binding Sites in the Streptococcus pyogenes Chromosome, Journal of Bacteriology, vol.193, issue.18, pp.4933-4942, 2011.
DOI : 10.1128/JB.00429-11

C. A. Suarez, V. S. Blancato, S. Poncet, J. Deutscher, and C. Magni, CcpA represses the expression of the divergent cit operons of Enterococcus faecalis through multiple cre sites, BMC Microbiology, vol.11, issue.1, p.227, 2011.
DOI : 10.1128/JB.186.14.4543-4555.2004

Y. Miwa and Y. Fujita, Involvement of Two Distinct Catabolite-Responsive Elements in Catabolite Repression of the Bacillus subtilis myo-Inositol (iol) Operon, Journal of Bacteriology, vol.183, issue.20, pp.5877-5884, 2001.
DOI : 10.1128/JB.183.20.5877-5884.2001

S. Karlsson, A. Lindberg, E. Norin, L. G. Burman, and T. Akerlund, Toxins, Butyric Acid, and Other Short-Chain Fatty Acids Are Coordinately Expressed and Down-Regulated by Cysteine in Clostridium difficile, Infection and Immunity, vol.68, issue.10, pp.5881-5888, 2000.
DOI : 10.1128/IAI.68.10.5881-5888.2000

S. Jackson, M. Calos, A. Myers, and W. T. Self, Analysis of Proline Reduction in the Nosocomial Pathogen Clostridium difficile, Journal of Bacteriology, vol.188, issue.24, pp.8487-8495, 2006.
DOI : 10.1128/JB.01370-06

J. Kim, D. Darley, T. Selmer, and W. Buckel, Characterization of (R)-2-Hydroxyisocaproate Dehydrogenase and a Family III Coenzyme A Transferase Involved in Reduction of L-Leucine to Isocaproate by Clostridium difficile, Applied and Environmental Microbiology, vol.72, issue.9, pp.6062-6069, 2006.
DOI : 10.1128/AEM.00772-06

N. Fonknechten, S. Chaussonnerie, S. Tricot, A. Lajus, J. R. Andreesen et al., Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence, BMC Genomics, vol.11, issue.1, p.555, 2010.
DOI : 10.1186/1471-2164-11-555
URL : https://hal.archives-ouvertes.fr/pasteur-00670622

S. Karlsson, L. G. Burman, and T. Akerlund, Induction of toxins in Clostridium difficile is associated with dramatic changes of its metabolism, Microbiology, vol.154, issue.11, pp.3430-3436, 2008.
DOI : 10.1099/mic.0.2008/019778-0

J. Meyer, Clostridial iron-sulphur proteins, J. Mol. Microbiol. Biotechnol, vol.2, pp.9-14, 2000.

J. E. Emerson, R. A. Stabler, B. W. Wren, and N. F. Fairweather, Microarray analysis of the transcriptional responses of Clostridium difficile to environmental and antibiotic stress, Journal of Medical Microbiology, vol.57, issue.6, pp.757-764, 2008.
DOI : 10.1099/jmm.0.47657-0

T. Zotta, A. Ricciardi, A. Guidone, M. Sacco, L. Muscariello et al., Inactivation of ccpA and aeration affect growth, metabolite production and stress tolerance in Lactobacillus plantarum WCFS1, International Journal of Food Microbiology, vol.155, issue.1-2, pp.51-59, 2012.
DOI : 10.1016/j.ijfoodmicro.2012.01.017

C. Leboeuf, L. Leblanc, Y. Auffray, and A. Hartke, Characterization of the ccpA Gene of Enterococcus faecalis: Identification of Starvation-Inducible Proteins Regulated by CcpA, Journal of Bacteriology, vol.182, issue.20, pp.5799-5806, 2000.
DOI : 10.1128/JB.182.20.5799-5806.2000

E. Camiade, J. Peltier, I. Bourgeois, E. Couture-tosi, P. Courtin et al., Characterization of Acp, a Peptidoglycan Hydrolase of Clostridium perfringens with N-Acetylglucosaminidase Activity That Is Implicated in Cell Separation and Stress-Induced Autolysis, Journal of Bacteriology, vol.192, issue.9, pp.2373-2384, 2010.
DOI : 10.1128/JB.01546-09

T. D. Lawley, N. J. Croucher, L. Yu, S. Clare, M. Sebaihia et al., Proteomic and Genomic Characterization of Highly Infectious Clostridium difficile 630 Spores, Journal of Bacteriology, vol.191, issue.17, pp.5377-5386, 2009.
DOI : 10.1128/JB.00597-09

S. Underwood, S. Guan, V. Vijayasubhash, S. D. Baines, L. Graham et al., Characterization of the Sporulation Initiation Pathway of Clostridium difficile and Its Role in Toxin Production, Journal of Bacteriology, vol.191, issue.23, pp.7296-7305, 2009.
DOI : 10.1128/JB.00882-09

T. Doan and S. Aymerich, Regulation of the central glycolytic genes in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate, Molecular Microbiology, vol.182, issue.6, pp.1709-1721, 2003.
DOI : 10.1046/j.1365-2958.2003.03404.x

H. Ludwig, N. Rebhan, H. M. Blencke, M. Merzbacher, and J. Stulke, Control of the glycolytic gapA operon by the catabolite control protein A in Bacillus subtilis: a novel mechanism of CcpA-mediated regulation, Molecular Microbiology, vol.29, issue.2, pp.543-553, 2002.
DOI : 10.1046/j.1432-1327.1998.2510538.x

S. S. Dineen, S. M. Mcbride, and A. L. Sonenshein, Integration of Metabolism and Virulence by Clostridium difficile CodY, Journal of Bacteriology, vol.192, issue.20, pp.5350-5362, 2010.
DOI : 10.1128/JB.00341-10

A. Goelzer, F. Brikci, I. Martin-verstraete, P. Noirot, P. Bessieres et al., Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis, BMC Systems Biology, vol.2, issue.1, p.20, 2008.
DOI : 10.1186/1752-0509-2-20
URL : https://hal.archives-ouvertes.fr/hal-00315553

G. A. Somerville and R. A. Proctor, At the Crossroads of Bacterial Metabolism and Virulence Factor Synthesis in Staphylococci, Microbiology and Molecular Biology Reviews, vol.73, issue.2, pp.233-248, 2009.
DOI : 10.1128/MMBR.00005-09