J. Aas, B. J. Paster, L. N. Stokes, I. Olsen, and F. E. Dewhirst, Defining the Normal Bacterial Flora of the Oral Cavity, Journal of Clinical Microbiology, vol.43, issue.11, pp.5721-5753, 2005.
DOI : 10.1128/JCM.43.11.5721-5732.2005

C. Ambroset, C. Coluzzi, G. Guédon, M. Devignes, V. Loux et al., New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration, Frontiers in Microbiology, vol.8, issue.31, 2016.
DOI : 10.1038/nrmicro2382

URL : https://hal.archives-ouvertes.fr/hal-01262284

C. Augeron and C. L. Laboisse, Emergence of permanently differentiated cell clones in a human colonic cancer cell line in culture after treatment with sodium butyrate, Cancer Research, vol.44, issue.9, pp.3961-96744312, 1984.

P. Ayoubi, A. O. Kilic, and M. N. Vijayakumar, Tn5253, the pneumococcal omega (cat tet) BM6001 element, is a composite structure of two conjugative transposons, Tn5251 and Tn5252., Journal of Bacteriology, vol.173, issue.5, pp.1617-1639, 1991.
DOI : 10.1128/jb.173.5.1617-1622.1991

A. Bateman, M. T. Holden, and C. Yeats, The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation, Bioinformatics, vol.69, issue.5, pp.1301-1303, 2005.
DOI : 10.1128/IAI.69.5.3013-3020.2001

A. Bateman, M. T. Holden, and C. Yeats, The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation, Bioinformatics, vol.69, issue.5, pp.1301-1304, 2005.
DOI : 10.1128/IAI.69.5.3013-3020.2001

J. W. Beaber, B. Hochhut, and M. K. Waldor, SOS response promotes horizontal dissemination of antibiotic resistance genes, Nature, vol.53, issue.6969, pp.72-76, 2004.
DOI : 10.1073/pnas.120163297

A. M. Beg, M. N. Jones, T. Miller-torbert, and R. G. Holt, Binding of Streptococcus mutans to extracellular matrix molecules and fibrinogen, Biochemical and Biophysical Research Communications, vol.298, issue.1, pp.75-84, 2002.
DOI : 10.1016/S0006-291X(02)02390-2

X. Bellanger, C. Morel, B. Decaris, and G. Guédon, Derepression of Excision of Integrative and Potentially Conjugative Elements from Streptococcus thermophilus by DNA Damage Response: Implication of a cI-Related Repressor, Journal of Bacteriology, vol.189, issue.4, pp.1478-81, 2007.
DOI : 10.1128/JB.01125-06

URL : https://hal.archives-ouvertes.fr/hal-01659457

X. Bellanger, C. Morel, F. Gonot, A. Puymege, B. Decaris et al., Site-specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture, Molecular Microbiology, vol.21, issue.4, pp.912-937, 2011.
DOI : 10.1111/j.1574-6976.1998.tb00355.x

URL : https://hal.archives-ouvertes.fr/hal-01659267

X. Bellanger, S. Payot, N. Leblond-bourget, and G. Guédon, Conjugative and mobilizable genomic islands in bacteria: evolution and diversity, FEMS Microbiology Reviews, vol.38, issue.4, pp.720-60, 2014.
DOI : 10.1371/journal.pone.0014016

URL : https://hal.archives-ouvertes.fr/hal-01474898

X. Bellanger, A. P. Roberts, C. Morel, F. Choulet, G. Pavlovic et al., Conjugative Transfer of the Integrative Conjugative Elements ICESt1 and ICESt3 from Streptococcus thermophilus, Journal of Bacteriology, vol.191, issue.8, pp.2764-751001412, 1128.
DOI : 10.1128/JB.01412-08

URL : https://hal.archives-ouvertes.fr/hal-01659303

J. D. Bendtsen, H. Nielsen, G. Von-heijne, and S. Brunak, Improved Prediction of Signal Peptides: SignalP 3.0, Journal of Molecular Biology, vol.340, issue.4, pp.783-95, 2004.
DOI : 10.1016/j.jmb.2004.05.028

B. A. Bensing, R. Seepersaud, Y. T. Yen, and P. M. Sullam, Selective transport by SecA2: An expanding family of customized motor proteins, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1843, issue.8, pp.1843-1674, 2014.
DOI : 10.1016/j.bbamcr.2013.10.019

B. A. Bensing, I. R. Siboo, and P. M. Sullam, Glycine Residues in the Hydrophobic Core of the GspB Signal Sequence Route Export toward the Accessory Sec Pathway, Journal of Bacteriology, vol.189, issue.10, pp.3846-54, 2007.
DOI : 10.1128/JB.00027-07

B. A. Bensing and P. M. Sullam, Transport of Preproteins by the Accessory Sec System Requires a Specific Domain Adjacent to the Signal Peptide, Journal of Bacteriology, vol.192, issue.16, pp.4223-4255, 2010.
DOI : 10.1128/JB.00373-10

B. A. Bensing, Y. T. Yen, R. Seepersaud, and P. M. Sullam, A Specific Interaction between SecA2 and a Region of the Preprotein Adjacent to the Signal Peptide Occurs during Transport via the Accessory Sec System, Journal of Biological Chemistry, vol.58, issue.29, pp.24438-24485, 2012.
DOI : 10.1038/nature07335

S. B. Beres and J. M. Musser, Contribution of Exogenous Genetic Elements to the Group A Streptococcus Metagenome, PLoS ONE, vol.21, issue.8, 2007.
DOI : 10.1371/journal.pone.0000800.s001

M. Bhatty, L. Gomez, J. A. Christie, and P. J. , The expanding bacterial type IV secretion lexicon, Research in Microbiology, vol.164, issue.6, 2013.
DOI : 10.1016/j.resmic.2013.03.012

D. Bhaya, M. Davison, and R. Barrangou, CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation, Annual Review of Genetics, vol.45, issue.1, pp.273-97, 2011.
DOI : 10.1146/annurev-genet-110410-132430

E. M. Bik, C. D. Long, G. C. Armitage, P. Loomer, J. Emerson et al., Bacterial diversity in the oral cavity of 10 healthy individuals, The ISME Journal, vol.26, issue.8, pp.962-74, 2010.
DOI : 10.1186/1471-2180-9-259

S. Blanquet-diot, S. Denis, S. Chalancon, F. Chaira, J. Cardot et al., Use of Artificial Digestive Systems to Investigate the Biopharmaceutical Factors Influencing the Survival of Probiotic Yeast During Gastrointestinal Transit in Humans, Pharmaceutical Research, vol.54, issue.4, pp.1444-53, 2012.
DOI : 10.2323/jgam.54.221

B. Bose, J. M. Auchtung, C. A. Lee, and A. D. Grossman, A conserved anti-repressor controls horizontal gene transfer by proteolysis, Molecular Microbiology, vol.59, issue.3, 2008.
DOI : 10.1128/9781555817954.ch10

B. Bose and A. D. Grossman, Regulation of Horizontal Gene Transfer in Bacillus subtilis by Activation of a Conserved Site-Specific Protease, Journal of Bacteriology, vol.193, issue.1, pp.22-31, 2011.
DOI : 10.1128/JB.01143-10

S. Brega, E. Caliot, P. Trieu-cuot, and S. Dramsi, SecA Localization and SecA-Dependent Secretion Occurs at New Division Septa in Group B Streptococcus, PLoS ONE, vol.182, issue.(5), 2013.
DOI : 10.1371/journal.pone.0065832.s004

URL : https://hal.archives-ouvertes.fr/pasteur-01300164

A. Brenciani, E. Tiberi, E. Tili, M. Mingoia, C. Palmieri et al., Genetic determinants and elements associated with antibiotic resistance in viridans group streptococci, Journal of Antimicrobial Chemotherapy, vol.302, issue.7-8, pp.1197-204, 2014.
DOI : 10.1016/j.ijmm.2012.09.001

M. Brochet, E. Couvé, P. Glaser, G. Guédon, and S. Payot, Integrative Conjugative Elements and Related Elements Are Major Contributors to the Genome Diversity of Streptococcus agalactiae, Journal of Bacteriology, vol.190, issue.20, pp.6913-6920, 2008.
DOI : 10.1128/JB.00824-08

URL : https://hal.archives-ouvertes.fr/hal-01637762

M. Brochet, V. Da-cunha, E. Couvé, C. Rusniok, P. Trieu-cuot et al., Atypical association of DDE transposition with conjugation specifies a new family of mobile elements, Molecular Microbiology, vol.144, issue.4, pp.948-59, 2009.
DOI : 10.1099/00221287-147-5-1243

M. Burmølle, M. I. Bahl, L. B. Jensen, S. J. Sørensen, and L. H. Hansen, Type 3 fimbriae, encoded by the conjugative plasmid pOLA52, enhance biofilm formation and transfer frequencies in Enterobacteriaceae strains, Microbiology, vol.154, issue.1, pp.187-95010454, 2007.
DOI : 10.1099/mic.0.2007/010454-0

V. Burrus, C. Bontemps, B. Decaris, and G. Guédon, Characterization of a Novel Type II Restriction-Modification System, Sth368I, Encoded by the Integrative Element ICESt1 of Streptococcus thermophilus CNRZ368, Applied and Environmental Microbiology, vol.67, issue.4, pp.1522-1530, 2001.
DOI : 10.1128/AEM.67.4.1522-1528.2001

V. Burrus, G. Pavlovic, B. Decaris, and G. Guédon, Conjugative transposons: the tip of the iceberg, Molecular Microbiology, vol.67, issue.3, 2002.
DOI : 10.1128/AEM.67.8.3488-3495.2001

URL : https://hal.archives-ouvertes.fr/hal-01659089

V. Burrus, G. Pavlovic, B. Decaris, and G. Guédon, The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration, Plasmid, vol.48, issue.2, pp.77-97, 2002.
DOI : 10.1016/S0147-619X(02)00102-6

URL : https://hal.archives-ouvertes.fr/hal-01659496

V. Burrus, Y. Roussel, B. Decaris, and G. Guédon, Characterization of a Novel Integrative Element, ICESt1, in the Lactic Acid Bacterium Streptococcus thermophilus, Applied and Environmental Microbiology, vol.66, issue.4, pp.1749-53, 2000.
DOI : 10.1128/AEM.66.4.1749-1753.2000

URL : https://hal.archives-ouvertes.fr/hal-01659518

J. P. Burton, P. Wescombe, J. M. Macklaim, M. H. Chai, K. Macdonald et al., Persistence of the Oral Probiotic Streptococcus salivarius M18 Is Dose Dependent and Megaplasmid Transfer Can Augment Their Bacteriocin Production and Adhesion Characteristics, PLoS ONE, vol.76, issue.6, 2013.
DOI : 10.1371/journal.pone.0065991.t003

H. J. Busscher, B. Van-de-belt-gritter, R. J. Dijkstra, W. Norde, F. C. Petersen et al., Intermolecular Forces and Enthalpies in the Adhesion of Streptococcus mutans and an Antigen I/II-Deficient Mutant to Laminin Films, Journal of Bacteriology, vol.189, issue.8, pp.2988-951001731, 1128.
DOI : 10.1128/JB.01731-06

J. Carlsson, H. Grahnén, G. Jonsson, and S. Wikner, Early Establishment of Streptococcus salivarius in the Mouths of Infants, Journal of Dental Research, vol.19, issue.2, pp.415-423, 1970.
DOI : 10.1016/0003-9969(69)90226-X

N. Carraro, V. Libante, C. Morel, B. Decaris, F. Charron-bourgoin et al., Differential regulation of two closely related integrative and conjugative elements from Streptococcus thermophilus, BMC Microbiology, vol.11, issue.1, 2011.
DOI : 10.1007/s00203-004-0712-2

URL : https://hal.archives-ouvertes.fr/hal-01659072

J. Celli and P. Trieu-cuot, Circularization of Tn916 is required for expression of the transposon-encoded transfer functions: characterization of long tetracycline-inducible transcripts reading through the attachment site, Molecular Microbiology, vol.28, issue.1, pp.103-179593300, 1998.
DOI : 10.1126/science.2468181

F. Chaffanel, F. Charron-bourgoin, V. Libante, N. Leblond-bourget, and S. Payot, ABSTRACT, Applied and Environmental Microbiology, vol.81, issue.12, pp.415-430, 2015.
DOI : 10.1128/AEM.00415-15

S. T. Chancey, S. Agrawal, M. R. Schroeder, M. M. Farley, H. Tettelin et al., Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae, Frontiers in Microbiology, vol.69, issue.124, 2015.
DOI : 10.1093/jac/dku019

I. Chen, P. J. Christie, and D. Dubnau, The Ins and Outs of DNA Transfer in Bacteria, Science, vol.310, issue.5753, pp.310-1456, 2005.
DOI : 10.1126/science.1114021

Q. Cheng, D. Stafslien, S. S. Purushothaman, P. Cleary, I. Chmouryguina et al., The Group B Streptococcal C5a Peptidase Is Both a Specific Protease and an Invasin, Infection and Immunity, vol.70, issue.5, pp.2408-2421, 1996.
DOI : 10.1128/IAI.70.5.2408-2413.2002

S. Chuzeville, A. Puymège, J. Madec, M. Haenni, and S. Payot, Characterization of a New CAMP Factor Carried by an Integrative and Conjugative Element in Streptococcus agalactiae and Spreading in Streptococci, PLoS ONE, vol.50, issue.3, 2012.
DOI : 10.1371/journal.pone.0048918.s005

URL : https://hal.archives-ouvertes.fr/hal-01637786

L. Ciric, M. Ellatif, P. Sharma, R. Patel, X. Song et al., Tn916-like elements from human, oral, commensal streptococci possess a variety of antibiotic and antiseptic resistance genes, International Journal of Antimicrobial Agents, vol.39, issue.4, pp.360-361, 2012.
DOI : 10.1016/j.ijantimicag.2011.12.007

P. P. Cleary, U. Prahbu, J. B. Dale, D. E. Wexler, and J. Handley, Streptococcal C5a peptidase is a highly specific endopeptidase, Infection and Immunity, vol.60, issue.12, pp.5219-5242, 1992.

D. B. Clewell, D. D. Jaworski, S. E. Flannagan, L. A. Zitzow, and Y. A. Su, The conjugative transposon Tn916 of Enterococcus faecalis: structural analysis and some key factors involved in movement, Developments in Biological Standardization, vol.85, pp.11-78586160, 1995.

I. Cochetti, E. Tili, M. Vecchi, A. Manzin, M. Mingoia et al., New Tn916-related elements causing erm(B)-mediated erythromycin resistance in tetracycline-susceptible pneumococci, Journal of Antimicrobial Chemotherapy, vol.49, issue.1, pp.127-158, 2007.
DOI : 10.1128/AAC.49.6.2454-2459.2005

J. C. Corredoira, M. P. Alonso, J. F. García, E. Casariego, A. Coira et al., Clinical characteristics and significance of Streptococcus salivarius bacteremia and Streptococcus bovis bacteremia: a prospective 16-year study, European Journal of Clinical Microbiology & Infectious Diseases, vol.277, issue.4, pp.250-255, 2005.
DOI : 10.1128/AAC.39.10.2243

C. Cosseau, D. Devine, E. Dullaghan, J. L. Gardy, A. Chikatamarla et al., The Commensal Streptococcus salivarius K12 Downregulates the Innate Immune Responses of Human Epithelial Cells and Promotes Host-Microbe Homeostasis, Infection and Immunity, vol.76, issue.9, pp.4163-751000188, 1128.
DOI : 10.1128/IAI.00188-08

N. J. Croucher, D. Walker, P. Romero, N. Lennard, G. K. Paterson et al., Role of Conjugative Elements in the Evolution of the Multidrug-Resistant Pandemic Clone Streptococcus pneumoniaeSpain23F ST81, Journal of Bacteriology, vol.191, issue.5, pp.1480-1489, 2009.
DOI : 10.1128/JB.01343-08

D. G. Cvitkovitch, Y. Li, and R. P. Ellen, Quorum sensing and biofilm formation in Streptococcal infections, Journal of Clinical Investigation, vol.112, issue.11, pp.1626-1632, 2003.
DOI : 10.1172/JCI200320430

R. E. Dalbey, P. Wang, and A. Kuhn, Assembly of Bacterial Inner Membrane Proteins, Annual Review of Biochemistry, vol.80, issue.1, pp.161-87, 2011.
DOI : 10.1146/annurev-biochem-060409-092524

M. R. Davies, J. Shera, G. H. Van-domselaar, K. S. Sriprakash, and D. J. Mcmillan, A Novel Integrative Conjugative Element Mediates Genetic Transfer from Group G Streptococcus to Other ??-Hemolytic Streptococci, Journal of Bacteriology, vol.191, issue.7, pp.2257-651001624, 1128.
DOI : 10.1128/JB.01624-08

F. De-la-cruz, L. S. Frost, R. J. Meyer, and E. L. Zechner, Conjugative DNA metabolism in Gramnegative bacteria, FEMS Microbiology Reviews, vol.34, issue.1, 2010.

E. Del-amo, C. Esteva, S. Hernandez-bou, C. Galles, M. Navarro et al., Serotypes and Clonal Diversity of Streptococcus pneumoniae Causing Invasive Disease in the Era of PCV13 in Catalonia, Spain, PLOS ONE, vol.38, issue.12, 2016.
DOI : 10.1371/journal.pone.0151125.t002

D. Grosso, M. Camilli, R. Barbabella, G. Blackman-northwood, J. Farrell et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.7, pp.3226-301001713, 1128.
DOI : 10.1128/AAC.01713-10

D. Grosso, M. Scotto-d-'abusco, A. Iannelli, F. Pozzi, G. Pantosti et al., Tn2009, a Tn916-Like Element Containing mef(E) in Streptococcus pneumoniae, Antimicrobial Agents and Chemotherapy, vol.48, issue.6, pp.2037-2079, 2004.
DOI : 10.1128/AAC.48.6.2037-2042.2004

C. Delorme, A. Abraham, P. Renault, and E. Guédon, Genomics of Streptococcus salivarius, a major human commensal, Infection, Genetics and Evolution, vol.33, 2014.
DOI : 10.1016/j.meegid.2014.10.001

URL : https://hal.archives-ouvertes.fr/hal-01154007

C. Delorme, C. Bartholini, A. Bolotine, S. D. Ehrlich, and P. Renault, Emergence of a Cell Wall Protease in the Streptococcus thermophilus Population, Applied and Environmental Microbiology, vol.76, issue.2, pp.451-60, 2010.
DOI : 10.1128/AEM.01018-09

URL : https://hal.archives-ouvertes.fr/hal-01204329

C. Delorme, C. Poyart, S. D. Ehrlich, and P. Renault, Extent of Horizontal Gene Transfer in Evolution of Streptococci of the Salivarius Group, Journal of Bacteriology, vol.189, issue.4, pp.1330-1371, 2007.
DOI : 10.1128/JB.01058-06

URL : https://hal.archives-ouvertes.fr/hal-01204331

R. P. Dempster and J. R. Tagg, The production of bacteriocin-link substances by the oral bacterium Streptococcus salivarius, Archives of Oral Biology, vol.27, issue.2, pp.151-77044350, 1982.
DOI : 10.1016/0003-9969(82)90136-4

M. Desvaux, E. Dumas, I. Chafsey, and M. Hébraud, Protein cell surface display in Grampositive bacteria: from single protein to macromolecular protein structure, FEMS Microbiology Letters, vol.256, issue.1, 2006.

K. P. Dierksen, M. Inglis, and J. R. Tagg, High pharyngeal carriage rates of Streptococcus pyogenes in Dunedin school children with a low incidence of rheumatic fever. The New Zealand Medical Journal, pp.496-505, 1122.

C. D. Doern and C. D. Burnham, It's Not Easy Being Green: the Viridans Group Streptococci, with a Focus on Pediatric Clinical Manifestations, Journal of Clinical Microbiology, vol.48, issue.11, pp.3829-3864, 2010.
DOI : 10.1128/JCM.01563-10

D. J. Du-plessis, N. Nouwen, and A. J. Driessen, The Sec translocase, Biochimica et Biophysica Acta (BBA) - Biomembranes, vol.1808, issue.3, 2011.
DOI : 10.1016/j.bbamem.2010.08.016

P. B. Eckburg, E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen et al., Diversity of the Human Intestinal Microbial Flora, Science, vol.308, issue.5728, pp.308-1635, 2005.
DOI : 10.1126/science.1110591

M. C. Enright and B. G. Spratt, Multilocus sequence typing, Trends in Microbiology, vol.7, issue.12, pp.482-489, 1999.
DOI : 10.1016/S0966-842X(99)01609-1

C. F. Favier, E. E. Vaughan, W. M. De-vos, A. D. Akkermans, L. Feld et al., Molecular Monitoring of Succession of Bacterial Communities in Human Neonates, Applied and Environmental Microbiology, vol.68, issue.1, pp.219-245, 2002.
DOI : 10.1128/AEM.68.1.219-226.2002

J. Fogh, J. M. Fogh, and T. Orfeo, One Hundred and Twenty-Seven Cultured Human Tumor Cell Lines Producing Tumors in Nude Mice23, JNCI: Journal of the National Cancer Institute, vol.59, issue.1, pp.221-227, 1977.
DOI : 10.1093/jnci/59.1.221

L. Fontaine, C. Boutry, M. H. De-frahan, B. Delplace, C. Fremaux et al., A Novel Pheromone Quorum-Sensing System Controls the Development of Natural Competence in Streptococcus thermophilus and Streptococcus salivarius, Journal of Bacteriology, vol.192, issue.5, pp.1444-541001251, 1128.
DOI : 10.1128/JB.01251-09

L. Fontaine, A. Wahl, M. Fléchard, J. Mignolet, and P. Hols, Regulation of competence for natural transformation in streptococci, Infection, Genetics and Evolution, vol.33, pp.343-60, 2015.
DOI : 10.1016/j.meegid.2014.09.010

A. E. Franke and D. B. Clewell, Evidence for a chromosome-borne resistance transposon (Tn916) in Streptococcus faecalis that is capable of " conjugal " transfer in the absence of a conjugative plasmid, Journal of Bacteriology, vol.145, issue.1, pp.494-502, 1981.

M. B. Frankel, B. M. Wojcik, A. C. Dedent, D. M. Missiakas, and O. Schneewind, ABI domaincontaining proteins contribute to surface protein display and cell division in Staphylococcus aureus, Molecular Microbiology, vol.78, issue.1, pp.238-52, 2010.

R. Freudl, Leaving home ain't easy: protein export systems in Gram-positive bacteria, Research in Microbiology, vol.164, issue.6, 2013.
DOI : 10.1016/j.resmic.2013.03.014

J. Geng, S. Huang, S. Li, S. Hu, and . Chen, Complete Genome Sequence of the Ureolytic Streptococcus salivarius Strain 57.I, Journal of Bacteriology, vol.193, issue.19, pp.5596-5603, 2011.
DOI : 10.1128/JB.05670-11

M. G. Ghinet, E. Bordeleau, J. Beaudin, R. Brzezinski, S. Roy et al., Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria, PLoS ONE, vol.147, issue.Pt 3, 2011.
DOI : 10.1371/journal.pone.0027846.s013

P. Glaser, C. Rusniok, C. Buchrieser, F. Chevalier, L. Frangeul et al., Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease, Molecular Microbiology, vol.181, issue.6, pp.1499-513, 2002.
DOI : 10.1074/jbc.271.31.18892

N. Goessweiner-mohr, K. Arends, W. Keller, and E. Grohmann, Conjugative type IV secretion systems in Gram-positive bacteria, Plasmid, vol.70, issue.3, 2013.
DOI : 10.1016/j.plasmid.2013.09.005

N. Goessweiner-mohr, K. Arends, W. Keller, and E. Grohmann, Conjugation in Gram-Positive Bacteria, Microbiology Spectrum, vol.2, issue.4, 2014.

N. Goessweiner-mohr, L. Grumet, K. Arends, T. Pavkov-keller, C. C. Gruber et al., Conjugation Protein TraM resembles VirB8 Type IV Secretion Proteins, Journal of Biological Chemistry, vol.84, issue.3, pp.2018-2046, 2013.
DOI : 10.1021/bi300298v

URL : http://www.jbc.org/content/288/3/2018.full.pdf

P. K. Gopal, J. Prasad, J. Smart, and H. S. Gill, In vitro adherence properties of Lactobacillus rhamnosus DR20 and Bifidobacterium lactis DR10 strains and their antagonistic activity against an enterotoxigenic Escherichia coli, International Journal of Food Microbiology, vol.67, issue.3, pp.207-223, 2001.
DOI : 10.1016/S0168-1605(01)00440-8

B. Govindarajan, B. B. Menon, S. Spurr-michaud, K. Rastogi, M. S. Gilmore et al., A Metalloproteinase Secreted by Streptococcus pneumoniae Removes Membrane Mucin MUC16 from the Epithelial Glycocalyx Barrier, PLoS ONE, vol.78, issue.3, pp.1-12, 2012.
DOI : 10.1371/journal.pone.0032418.s003

F. Griffith, A. C. Groth, and M. P. Calos, The Significance of Pneumococcal Types, Journal of Hygiene, vol.27, issue.02, pp.113-59, 1928.
DOI : 10.1017/S0022172400031879

R. Guérillot, V. Da-cunha, E. Sauvage, C. Bouchier, and P. Glaser, Modular Evolution of TnGBSs, a New Family of Integrative and Conjugative Elements Associating Insertion Sequence Transposition, Plasmid Replication, and Conjugation for Their Spreading, Journal of Bacteriology, vol.195, issue.9, pp.1979-901001745, 1128.
DOI : 10.1128/JB.01745-12

J. Guglielmini, B. Néron, S. S. Abby, M. P. Garcillán-barcia, F. De-la-cruz et al., Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Research, vol.12, issue.R237, pp.5715-5742, 2014.
DOI : 10.1186/1471-2180-12-172

URL : https://hal.archives-ouvertes.fr/pasteur-01374962

J. Guglielmini, L. Quintais, M. P. Garcillán-barcia, F. De-la-cruz, and E. P. Rocha, The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation, PLoS Genetics, vol.22, issue.8, 2011.
DOI : 10.1371/journal.pgen.1002222.s002

URL : https://hal.archives-ouvertes.fr/pasteur-00647077

M. Haenni, E. Saras, S. Bertin, P. Leblond, J. Madec et al., Diversity and Mobility of Integrative and Conjugative Elements in Bovine Isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis, Applied and Environmental Microbiology, vol.76, issue.24, pp.76-7957, 1128.
DOI : 10.1128/AEM.00805-10

URL : https://hal.archives-ouvertes.fr/hal-01637787

E. Hakalehto, T. Vilpponen-salmela, K. Kinnunen, and A. Wright, Lactic Acid Bacteria Enriched from Human Gastric Biopsies, ISRN Gastroenterology, vol.21, issue.1, pp.109183-109193, 2011.
DOI : 10.1097/MEG.0b013e32830d0eff

X. Y. Han, M. Kamana, and K. V. Rolston, Viridans Streptococci Isolated by Culture from Blood of Cancer Patients: Clinical and Microbiologic Analysis of 50 Cases, Journal of Clinical Microbiology, vol.44, issue.1, 2006.
DOI : 10.1128/JCM.44.1.160-165.2006

P. S. Handley, F. F. Correia, K. Russell, B. Rosan, and J. M. Dirienzo, Association of a novel high molecular weight, serine-rich protein (SrpA) with fibril-mediated adhesion of the oral biofilm bacterium Streptococcus cristatus, Oral Microbiology and Immunology, vol.165, issue.3, pp.131-171, 2005.
DOI : 10.1046/j.1365-2958.1999.01670.x

W. Hao and Y. Lee, Microflora of the Gastrointestinal Tract: A Review, Methods in Molecular Biology, vol.268, issue.3, pp.491-502, 2004.
DOI : 10.1385/1-59259-766-1:491

D. L. Hartl and E. W. Jones, Génétique, Les grands principes. (Dunod Retrieved from http://www.dunod.com/sciences-techniques/sciences-fondamentales/sciences-de-la-vie-et- sante, 2003.

D. L. Hasty, I. Ofek, H. S. Courtney, and R. J. Doyle, Multiple adhesins of streptococci, Infection and Immunity, vol.60606, issue.6, pp.2147-2152, 1992.

M. Hausner and S. Wuertz, High Rates of Conjugation in Bacterial Biofilms as Determined by Quantitative In Situ Analysis, Applied and Environmental Microbiology, vol.65, issue.8, pp.3710-3713, 1999.

D. G. Heath and P. P. Cleary, Fc-receptor and M-protein genes of group A streptococci are products of gene duplication., Proceedings of the National Academy of Sciences, vol.86, issue.12, pp.4741-4746, 1989.
DOI : 10.1073/pnas.86.12.4741

Z. Heather, M. T. Holden, K. F. Steward, J. Parkhill, L. Song et al., A novel streptococcal integrative conjugative element involved in iron acquisition, Molecular Microbiology, vol.179, issue.Part 5, pp.1274-92, 2008.
DOI : 10.1128/jb.176.1.213-220.1994

A. P. Hendrickx, J. M. Budzik, S. Oh, and O. Schneewind, Architects at the bacterial surface ??? sortases and the assembly of pili with isopeptide bonds, Nature Reviews Microbiology, vol.77, issue.3, pp.166-7610, 1038.
DOI : 10.1128/IAI.00772-08

A. P. Hendrickx, R. J. Willems, M. J. Bonten, and W. Van-schaik, LPxTG surface proteins of enterococci, Trends in Microbiology, vol.17, issue.9, pp.423-453, 2009.
DOI : 10.1016/j.tim.2009.06.004

P. W. Hermans, P. V. Adrian, A. , C. Estevão, S. Hoogenboezem et al., The Streptococcal Lipoprotein Rotamase A (SlrA) Is a Functional Peptidyl-prolyl Isomerase Involved in Pneumococcal Colonization, Journal of Biological Chemistry, vol.7, issue.2, pp.968-76, 2006.
DOI : 10.1128/IAI.72.4.2416-2419.2004

H. Hirt, D. A. Manias, E. M. Bryan, J. R. Klein, J. K. Marklund et al., Characterization of the Pheromone Response of the Enterococcus faecalis Conjugative Plasmid pCF10: Complete Sequence and Comparative Analysis of the Transcriptional and Phenotypic Responses of pCF10-Containing Cells to Pheromone Induction, Journal of Bacteriology, vol.187, issue.3, pp.1044-54, 2005.
DOI : 10.1128/JB.187.3.1044-1054.2005

O. Hyink, P. A. Wescombe, M. Upton, N. Ragland, J. P. Burton et al., Salivaricin A2 and the Novel Lantibiotic Salivaricin B Are Encoded at Adjacent Loci on a 190-Kilobase Transmissible Megaplasmid in the Oral Probiotic Strain Streptococcus salivarius K12, Applied and Environmental Microbiology, vol.73, issue.4, pp.1107-11131002265, 1128.
DOI : 10.1128/AEM.02265-06

A. Ilangovan, S. Connery, and G. Waksman, Structural biology of the Gram-negative bacterial conjugation systems, Trends in Microbiology, vol.23, issue.5, 2015.
DOI : 10.1016/j.tim.2015.02.012

N. S. Jakubovics, J. L. Brittan, L. C. Dutton, and H. F. Jenkinson, Multiple adhesin proteins on the cell surface of Streptococcus gordonii are involved in adhesion to human fibronectin, Microbiology, vol.189, issue.8, pp.3572-80, 2009.
DOI : 10.1128/JB.01808-06

N. S. Jakubovics, S. W. Kerrigan, A. H. Nobbs, N. Strömberg, C. J. Van-dolleweerd et al., Functions of Cell Surface-Anchored Antigen I/II Family and Hsa Polypeptides in Interactions of Streptococcus gordonii with Host Receptors, Infection and Immunity, vol.73, issue.10, pp.73-6629, 2005.
DOI : 10.1128/IAI.73.10.6629-6638.2005

H. F. Jenkinson and D. R. Demuth, Structure, function and immunogenicity of streptococcal antigen I/II polypeptides, Molecular Microbiology, vol.23, issue.2, pp.183-909044252, 1997.
DOI : 10.1046/j.1365-2958.1997.2021577.x

H. F. Jenkinson and R. Lamont, Streptococcal Adhesion and Colonization, Critical Reviews in Oral Biology & Medicine, vol.8, issue.2, pp.175-200, 1997.
DOI : 10.1111/j.1399-302X.1996.tb00334.x

H. F. Jenkinson, S. D. Terry, R. Mcnab, and G. W. Tannock, Inactivation of the gene encoding surface protein SspA in Streptococcus gordonii DL1 affects cell interactions with human salivary agglutinin and oral actinomyces, Infection and Immunity, issue.8, pp.61-3199, 1993.

M. Jönsson and G. Swedberg, Macrolide resistance can be transferred by conjugation from viridans streptococci to Streptococcus pyogenes, International Journal of Antimicrobial Agents, vol.28, issue.2, 2006.
DOI : 10.1016/j.ijantimicag.2006.02.023

N. Juge, Microbial adhesins to gastrointestinal mucus, Trends in Microbiology, vol.20, issue.1, pp.30-39, 2012.
DOI : 10.1016/j.tim.2011.10.001

G. Kaci, D. Goudercourt, V. Dennin, B. Pot, J. Doré et al., ABSTRACT, Applied and Environmental Microbiology, vol.80, issue.3, pp.928-341003133, 1128.
DOI : 10.1128/AEM.03133-13

URL : https://hal.archives-ouvertes.fr/lirmm-00929825

S. Kawabata, Y. Tamura, J. Murakami, Y. Terao, I. Nakagawa et al., A novel, anchorless streptococcal surface protein that binds to human immunoglobulins, Biochemical and Biophysical Research Communications, vol.296, issue.5, pp.1329-1362, 2002.
DOI : 10.1016/S0006-291X(02)02078-8

M. Kebouchi, W. Galia, M. Genay, C. Soligot, X. Lecomte et al., Implication of sortase-dependent proteins of Streptococcus thermophilus in adhesion to human intestinal epithelial cell lines and bile salt tolerance, Applied Microbiology and Biotechnology, vol.94, issue.Suppl 1, pp.10-1007, 2016.
DOI : 10.1002/jsfa.6395

URL : https://hal.archives-ouvertes.fr/hal-01329214

S. L. King and C. M. Dekaney, Small intestinal stem cells, Current Opinion in Gastroenterology, vol.29, issue.2, pp.140-145, 2013.
DOI : 10.1097/MOG.0b013e32835cf253

T. Kitten, C. L. Munro, N. Q. Zollar, S. P. Lee, and R. D. Patel, Oral Streptococcal Bacteremia in Hospitalized Patients: Taxonomic Identification and Clinical Characterization, Journal of Clinical Microbiology, vol.50, issue.3, pp.1039-421006438, 1128.
DOI : 10.1128/JCM.06438-11

M. Kleerebezem, P. Hols, E. Bernard, T. Rolain, M. Zhou et al., The extracellular biology of the lactobacilli, FEMS Microbiology Reviews, vol.61, issue.2, pp.199-230, 2010.
DOI : 10.1038/nprot.2006.143

P. E. Kolenbrander, R. J. Palmer, S. Periasamy, and N. S. Jakubovics, Oral multispecies biofilm development and the key role of cell???cell distance, Nature Reviews Microbiology, vol.66, issue.7, pp.471-8010, 1038.
DOI : 10.1111/j.1399-302X.2008.00489.x

A. Kovacs-simon, R. W. Titball, and S. L. Michell, ABSTRACT, Infection and Immunity, vol.79, issue.2, pp.548-61, 2011.
DOI : 10.1128/IAI.00682-10

E. R. Krah and F. L. Macrina, Identification of a region that influences host range of the streptococcal conjugative plasmid pIP501, Plasmid, vol.25, issue.1, pp.64-73, 1991.
DOI : 10.1016/0147-619X(91)90007-J

V. Krishnan and S. V. Narayana, Crystallography of Gram-Positive Bacterial Adhesins, Advances in Experimental Medicine and Biology, vol.715, pp.175-95, 2011.
DOI : 10.1007/978-94-007-0940-9_11

J. E. Król, H. D. Nguyen, L. M. Rogers, H. Beyenal, S. M. Krone et al., ABSTRACT, Applied and Environmental Microbiology, vol.77, issue.15, pp.77-5079, 1128.
DOI : 10.1128/AEM.00090-11

B. Kurenbach, C. Bohn, J. Prabhu, M. Abudukerim, U. Szewzyk et al., Intergeneric transfer of the Enterococcus faecalis plasmid pIP501 to Escherichia coli and Streptomyces lividans and sequence analysis of its tra region, Plasmid, vol.50, issue.1, pp.86-93, 2003.
DOI : 10.1016/S0147-619X(03)00044-1

R. Leclercq, Mechanisms of resistance to macrolides and lincosamides: nature of the resistance elements and their clinical implications. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America, pp.482-92, 2002.

X. Lecomte, V. Gagnaire, V. Briard-bion, J. Jardin, S. Lortal et al., The naturally competent strain Streptococcus thermophilus LMD-9 as a new tool to anchor heterologous proteins on the cell surface, Microbial Cell Factories, vol.13, issue.1, pp.82-92, 2014.
DOI : 10.1186/1475-2859-13-82

URL : https://hal.archives-ouvertes.fr/hal-01209649

J. Lederberg, Plasmid (1952???1997), Plasmid, vol.39, issue.1, 1998.
DOI : 10.1006/plas.1997.1320

L. , J. Tatum, and E. L. , Gene recombination in Escherichia coli, Nature, vol.158, issue.558, p.21001945, 1946.

T. Lesuffleur, A. Barbat, E. Dussaulx, and A. Zweibaum, Growth adaptation to methotrexate of HT-29 human colon carcinoma cells is associated with their ability to differentiate into columnar absorptive and mucus-secreting cells, Cancer Research, vol.50, issue.19, pp.6334-432205381, 1990.

T. R. Licht and A. Wilcks, Conjugative Gene Transfer in the Gastrointestinal Environment, Advances in Applied Microbiology, vol.58, issue.05, pp.77-9510, 2005.
DOI : 10.1016/S0065-2164(05)58002-X

V. Liévin-le-moal and A. L. Servin, The Front Line of Enteric Host Defense against Unwelcome Intrusion of Harmful Microorganisms: Mucins, Antimicrobial Peptides, and Microbiota, Clinical Microbiology Reviews, vol.19, issue.2, pp.315-352, 2006.
DOI : 10.1128/CMR.19.2.315-337.2006

V. Liévin-le-moal and A. L. Servin, Pathogenesis of Human Enterovirulent Bacteria: Lessons from Cultured, Fully Differentiated Human Colon Cancer Cell Lines, Microbiology and Molecular Biology Reviews, vol.77, issue.3, pp.380-439, 2013.
DOI : 10.1128/MMBR.00064-12

L. Liu, X. Chen, G. Skogerbø, P. Zhang, R. Chen et al., The human microbiome: A hot spot of microbial horizontal gene transfer, Genomics, vol.100, issue.5, pp.265-70, 2012.
DOI : 10.1016/j.ygeno.2012.07.012

M. Lopez-sanchez, E. Sauvage, V. Da-cunha, D. Clermont, R. Hariniaina et al., controls the diversity of its mobilome, Molecular Microbiology, vol.18, issue.6, pp.1057-71, 2012.
DOI : 10.1101/gr.074492.107

F. Lorenzo-díaz and M. Espinosa, Large-scale filter mating assay for intra- and inter-specific conjugal transfer of the promiscuous plasmid pMV158 in Gram-positive bacteria, Plasmid, vol.61, issue.1, pp.65-70, 2009.
DOI : 10.1016/j.plasmid.2008.09.005

R. M. Love, M. D. Mcmillan, and H. F. Jenkinson, Invasion of dentinal tubules by oral streptococci is associated with collagen recognition mediated by the antigen I/II family of polypeptides, Infection and Immunity, vol.65, issue.12, pp.5157-64, 1997.

J. Luki?, I. Strahini?, B. Jov?i?, B. Filipi?, L. Topisirovi? et al., ABSTRACT, Applied and Environmental Microbiology, vol.78, issue.22, pp.78-7993, 1128.
DOI : 10.1128/AEM.02141-12

H. Luo, K. Wan, and H. H. Wang, High-frequency conjugation system facilitates biofilm formation and pAMbeta1 transmission by Lactococcus lactis, Applied and Environmental Microbiology, vol.71, issue.6, 2005.

A. Lycklama, J. A. Nijeholt, and A. J. Driessen, The bacterial Sec-translocase: structure and mechanism, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.279, issue.14, pp.1016-1044, 1592.
DOI : 10.1074/jbc.M312892200

H. Machiyama, T. Yamaguchi, Y. Sawada, T. M. Watanabe, and H. Fujita, SH3 domain of c-Src governs its dynamics at focal adhesions and the cell membrane, FEBS Journal, vol.92, issue.20, 2015.
DOI : 10.1529/biophysj.106.094649

S. Malhotra-kumar, C. Lammens, A. Martel, C. Mallentjer, S. Chapelle et al., Oropharyngeal carriage of macrolide-resistant viridans group streptococci: a prevalence study among healthy adults in Belgium, Journal of Antimicrobial Chemotherapy, vol.53, issue.2, pp.271-277, 2004.
DOI : 10.1093/jac/dkh026

J. Marrero and M. K. Waldor, Interactions between Inner Membrane Proteins in Donor and Recipient Cells Limit Conjugal DNA Transfer, Developmental Cell, vol.8, issue.6, 2005.
DOI : 10.1016/j.devcel.2005.05.004

M. A. Mcguckin, S. K. Lindén, P. Sutton, and T. H. Florin, Mucin dynamics and enteric pathogens, Nature Reviews Microbiology, vol.154, issue.4, pp.265-7810, 1038.
DOI : 10.1099/mic.0.2008/019380-0

B. B. Menon and B. Govindarajan, Identification of an atypical zinc metalloproteinase, ZmpC, from an epidemic conjunctivitis-causing strain of Streptococcus pneumoniae, Microbial Pathogenesis, vol.56, 2013.
DOI : 10.1016/j.micpath.2012.11.006

M. R. Millar, C. J. Linton, A. Cade, D. Glancy, M. Hall et al., Application of 16S rRNA gene PCR to study bowel flora of preterm infants with and without necrotizing enterocolitis, Journal of Clinical Microbiology, vol.34, issue.10, pp.2506-2516, 1996.

M. Mingoia, E. Morici, A. Brenciani, E. Giovanetti, and P. E. Varaldo, Genetic basis of the association of resistance genes mef(I) (macrolides) and catQ (chloramphenicol) in streptococci, Frontiers in Microbiology, vol.14, issue.500, 2014.
DOI : 10.1186/1471-2164-14-500

M. Mingoia, E. Morici, G. Morroni, E. Giovanetti, D. Grosso et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.58, issue.10, pp.5886-931003638, 1128.
DOI : 10.1128/AAC.03638-14

M. Mingoia, M. Vecchi, I. Cochetti, E. Tili, L. A. Vitali et al., Composite structure of Streptococcus pneumoniae containing the erythromycin efflux resistance gene mefI and the chloramphenicol resistance gene catQ, Antimicrobial Agents and Chemotherapy, issue.11, pp.51-3983, 2007.

S. Molin and T. Tolker-nielsen, Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure, Current Opinion in Biotechnology, vol.14, issue.3, pp.255-261, 2003.
DOI : 10.1016/S0958-1669(03)00036-3

C. J. Morton and I. D. Campbell, SH3 Domains: Molecular ???Velcro???, Current Biology, vol.4, issue.7, pp.615-617, 1994.
DOI : 10.1016/S0960-9822(00)00134-2

P. Mullany, A. P. Roberts, and H. Wang, Mechanism of integration and excision in conjugative transposons, Cellular and Molecular Life Sciences (CMLS), vol.59, issue.12, pp.2017-2039, 2002.
DOI : 10.1007/s000180200001

K. L. Nielsen, A. M. Hammerum, L. M. Lambertsen, C. H. Lester, M. Arpi et al., Characterization and transfer studies of macrolide resistance genes in Streptococcus pneumoniae from Denmark, Scandinavian Journal of Infectious Diseases, vol.51, issue.15, pp.42-586, 2010.
DOI : 10.1128/AAC.00790-07

A. H. Nobbs, R. J. Lamont, and H. F. Jenkinson, Streptococcus Adherence and Colonization, Microbiology and Molecular Biology Reviews, vol.73, issue.3, pp.407-5000014, 2009.
DOI : 10.1128/MMBR.00014-09

R. Novak, E. Charpentier, J. S. Braun, E. Park, S. Murti et al., Extracellular targeting of choline-binding proteins in Streptococcus pneumoniae by a zinc metalloprotease, Molecular Microbiology, vol.176, issue.2, pp.366-76, 2000.
DOI : 10.1128/jb.176.10.2976-2985.1994

I. Ofek and R. J. Doyle, Bacterial Adhesion to Cells and Tissues, pp.10-1007, 1994.
DOI : 10.1007/978-1-4684-6435-1

L. Oligino and P. Fives-taylor, Overexpression and purification of a fimbria-associated adhesin of Streptococcus parasanguis, Infection and Immunity, vol.61, issue.3, pp.1016-1038, 1993.

M. B. Oliver, M. P. Van-der-linden, S. A. Küntzel, J. S. Saad, and M. H. Nahm, Serotype 6 Variants with Glycosyltransferases Synthesizing Two Differing Repeating Units, Journal of Biological Chemistry, vol.123, issue.36, pp.25976-85, 2013.
DOI : 10.1128/JCM.43.6.2656-2661.2005

C. Y. Ong, S. A. Beatson, A. G. Mcewan, and M. A. Schembri, Conjugative Plasmid Transfer and Adhesion Dynamics in an Escherichia coli Biofilm, Applied and Environmental Microbiology, vol.75, issue.21, pp.6783-911000974, 1128.
DOI : 10.1128/AEM.00974-09

R. Otto, B. Brink, H. Veldkamp, and W. N. Konings, The relation between growth rate and electrochemical proton gradient of Streptococcus cremoris, FEMS Microbiology Letters, vol.140, issue.1, 1983.
DOI : 10.1099/00221287-23-3-457

H. Park, S. Shim, S. Kim, J. Park, S. Park et al., Molecular analysis of colonized bacteria in a human newborn infant gut, Journal of Microbiology, vol.43, issue.4, pp.345-53, 2005.

K. A. Patras, P. A. Wescombe, B. Rösler, J. D. Hale, J. R. Tagg et al., Streptococcus salivarius K12 Limits Group B Streptococcus Vaginal Colonization, Infection and Immunity, vol.83, issue.9, pp.3438-3444, 2015.
DOI : 10.1128/IAI.00409-15

G. Pavlovic, V. Burrus, B. Gintz, B. Decaris, and G. Guédon, Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus, Microbiology, vol.150, issue.4, pp.759-74, 2004.
DOI : 10.1099/mic.0.26883-0

URL : https://hal.archives-ouvertes.fr/hal-01659488

T. Pawson and J. Schlessingert, SH2 and SH3 domains, Current Biology, vol.3, issue.7, pp.434-44210, 1993.
DOI : 10.1016/0960-9822(93)90350-W

E. Pérez-trallero, D. Vicente, M. Montes, J. M. Marimon, and L. Piñeiro, High proportion of pharyngeal carriers of commensal streptococci resistant to erythromycin in Spanish adults, Journal of Antimicrobial Chemotherapy, vol.48, issue.2, pp.225-234, 2001.
DOI : 10.1093/jac/48.2.225

F. C. Petersen, S. Assev, H. C. Van-der-mei, H. J. Busscher, and A. A. Scheie, Functional Variation of the Antigen I/II Surface Protein in Streptococcus mutans and Streptococcus intermedius, Infection and Immunity, vol.70, issue.1, pp.249-56, 2002.
DOI : 10.1128/IAI.70.1.249-256.2002

F. C. Petersen, S. Pasco, J. Ogier, J. P. Klein, S. Assev et al., Expression and Functional Properties of the Streptococcus intermedius Surface Protein Antigen I/II, Infection and Immunity, vol.69, issue.7, pp.4647-53, 2001.
DOI : 10.1128/IAI.69.7.4647-4653.2001

O. E. Petrova and K. Sauer, Sticky Situations: Key Components That Control Bacterial Surface Attachment, Journal of Bacteriology, vol.194, issue.10, pp.2413-2438, 2012.
DOI : 10.1128/JB.00003-12

C. Possoz, J. Gagnat, G. Sezonov, M. Guérineau, and J. Pernodet, Conjugal immunity of Streptomyces strains carrying the integrative element pSAM2 is due to the pif gene (pSAM2 immunity factor), Molecular Microbiology, vol.9, issue.57, pp.1385-93, 2003.
DOI : 10.1101/gad.9.11.1316

A. Puymège, S. Bertin, G. Guédon, and S. Payot, Analysis of Streptococcus agalactiae pangenome for prevalence, diversity and functionality of integrative and conjugative or mobilizable elements integrated in the tRNA(Lys CTT) gene. Molecular Genetics and Genomics : MGG. doi:10, pp.438-453, 1007.

J. Qin, R. Li, J. Raes, M. Arumugam, K. S. Burgdorf et al., A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.13, issue.7285, pp.464-59, 1038.
DOI : 10.1101/gr.229202. Article published online before March 2002

URL : https://hal.archives-ouvertes.fr/cea-00908974

L. Rajeev, K. Malanowska, and J. F. Gardner, Challenging a Paradigm: the Role of DNA Homology in Tyrosine Recombinase Reactions, Microbiology and Molecular Biology Reviews, vol.73, issue.2, pp.300-309, 2009.
DOI : 10.1128/MMBR.00038-08

P. J. Rauch, W. M. De-vos, D. J. Reinscheid, C. Stößer, K. Ehlert et al., Characterization of the novel nisin-sucrose conjugative transposon Tn5276 and its insertion in Lactococcus lactis., Journal of Bacteriology, vol.174, issue.4, pp.1280-1287, 1992.
DOI : 10.1128/jb.174.4.1280-1287.1992

V. P. Richards, S. R. Palmer, P. D. Pavinski-bitar, X. Qin, G. M. Weinstock et al., Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus, Genome Biology and Evolution, vol.16, issue.4, pp.741-753, 2014.
DOI : 10.1007/s10911-011-9236-y

A. P. Roberts, G. Cheah, D. Ready, J. Pratten, M. Wilson et al., Transfer of Tn916-Like Elements in Microcosm Dental Plaques, Antimicrobial Agents and Chemotherapy, vol.45, issue.10, pp.2943-2946, 2001.
DOI : 10.1128/AAC.45.10.2943-2946.2001

A. P. Roberts and P. Mullany, A modular master on the move: the Tn916 family of mobile genetic elements, Trends in Microbiology, vol.17, issue.6, 2009.
DOI : 10.1016/j.tim.2009.03.002

A. P. Roberts and P. Mullany, -like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance, FEMS Microbiology Reviews, vol.8, issue.(suppl 1), 2011.
DOI : 10.1038/nrmicro2382

M. C. Roberts, Update on acquired tetracycline resistance genes, FEMS Microbiology Letters, vol.64, issue.2, pp.195-203, 2005.
DOI : 10.1093/infdis/162.6.1309

D. Roche, M. Fléchard, N. Lallier, M. Répérant, A. Brée et al., ICEEc2, a New Integrative and Conjugative Element Belonging to the pKLC102/PAGI-2 Family, Identified in Escherichia coli Strain BEN374, Journal of Bacteriology, vol.192, issue.19, pp.5026-361000609, 1128.
DOI : 10.1128/JB.00609-10

URL : https://hal.archives-ouvertes.fr/hal-01129464

J. D. Rogers, E. M. Haase, A. E. Brown, C. W. Douglas, J. P. Gwynn et al., Identification and analysis of a gene (abpA) encoding a major amylase-binding protein in Streptococcus gordonii, Microbiology, vol.144, issue.5, pp.144-1223, 1998.
DOI : 10.1099/00221287-144-5-1223

K. F. Ross, C. W. Ronson, and J. R. Tagg, Isolation and characterization of the lantibiotic salivaricin A and its structural gene salA from Streptococcus salivarius 20P3, Applied and Environmental Microbiology, vol.59, issue.7, pp.2014-2035, 1993.

M. Rousset, The human colon carcinoma cell lines HT-29 and Caco-2: Two in vitro models for the study of intestinal differentiation, Biochimie, vol.68, issue.9, pp.1035-403096381, 1986.
DOI : 10.1016/S0300-9084(86)80177-8

M. W. Russell and B. Mansson-rahemtulla, Interaction between surface protein antigens of Streptococcus mutans and human salivary components, Oral Microbiology and Immunology, vol.55, issue.2, pp.106-112762013, 1989.
DOI : 10.1177/00220345760550020801

J. Sampath and M. N. Vijayakumar, Identification of a DNA Cytosine Methyltransferase Gene in Conjugative Transposon Tn5252, Plasmid, vol.39, issue.1, pp.63-76, 1997.
DOI : 10.1006/plas.1997.1316

M. Santagati, F. Iannelli, M. R. Oggioni, S. Stefani, and G. Pozzi, Characterization of a Genetic Element Carrying the Macrolide Efflux Gene mef(A) in Streptococcus pneumoniae, Antimicrobial Agents and Chemotherapy, vol.44, issue.9, pp.2585-2592, 2000.
DOI : 10.1128/AAC.44.9.2585-2587.2000

F. Santoro, M. E. Vianna, and A. P. Roberts, Variation on a theme; an overview of the Tn916/Tn1545 family of mobile genetic elements in the oral and nasopharyngeal streptococci, Frontiers in Microbiology, vol.69, issue.228, 2014.
DOI : 10.1093/jac/dku019

Y. Sasaki, N. Taketomo, and T. Sasaki, Factors affecting transfer frequency of pAM beta 1 from Streptococcus faecalis to Lactobacillus plantarum., Journal of Bacteriology, vol.170, issue.12, pp.5939-5981, 1988.
DOI : 10.1128/jb.170.12.5939-5942.1988

Y. Sato, Y. Yamamoto, and H. Kizaki, Cloning and sequence analysis of the gbpC gene encoding a novel glucan-binding protein of Streptococcus mutans The genomics and proteomics of biofilm formation, Infection and Immunity, vol.65, issue.2, pp.668-75, 1997.

D. R. Schaberg, D. B. Clewell, L. L. Glatzer, A. J. Ligtenberg, E. C. Veerman et al., Conjugative transfer of R-plasmids from Streptococcus faecalis to Staphylococcus aureus., Antimicrobial Agents and Chemotherapy, vol.22, issue.2, pp.204-211, 1982.
DOI : 10.1128/AAC.22.2.204

O. Schneewind and D. M. Missiakas, Protein secretion and surface display in Gram-positive bacteria, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.454, issue.7205, pp.1123-1162, 1592.
DOI : 10.1038/nature07219

S. Schubert, S. Dufke, J. Sorsa, and J. Heesemann, A novel integrative and conjugative element (ICE) of Escherichia coli: the putative progenitor of the Yersinia high-pathogenicity island, Molecular Microbiology, vol.178, issue.3, pp.837-885, 2004.
DOI : 10.1128/jb.178.14.4157-4165.1996

S. Schwarz, C. Kehrenberg, B. Doublet, and A. Cloeckaert, Molecular basis of bacterial resistance to chloramphenicol and florfenicol, FEMS Microbiology Reviews, vol.46, issue.5, pp.519-561, 2004.
DOI : 10.1016/S0934-8840(11)80440-8

R. Seepersaud, B. A. Bensing, Y. T. Yen, and P. M. Sullam, Asp3 mediates multiple protein-protein interactions within the accessory Sec system of Streptococcus gordonii, Molecular Microbiology, vol.455, issue.2, pp.490-505, 2010.
DOI : 10.1111/j.1365-2958.2010.07346.x

D. Serfiotis-mitsa, G. A. Roberts, L. P. Cooper, J. H. White, M. Nutley et al., The Orf18 Gene Product from Conjugative Transposon Tn916 Is an ArdA Antirestriction Protein that Inhibits Type I DNA Restriction???Modification Systems, Journal of Molecular Biology, vol.383, issue.5, pp.970-81, 2008.
DOI : 10.1016/j.jmb.2008.06.005

T. Shirokawa, J. Nakajima, K. Hirose, H. Suzuki, S. Nagaoka et al., Spontaneous Meningitis Due to Streptococcus salivarius Subsp. salivarius: Cross-reaction in an Assay with a Rapid Diagnostic Kit that Detected Streptococcus pneumoniae Antigens, Internal Medicine, vol.53, issue.3, pp.279-307, 2014.
DOI : 10.2169/internalmedicine.53.0803

I. Sliepen, J. Van-damme, M. Van-essche, G. Loozen, M. Quirynen et al., Microbial Interactions Influence Inflammatory Host Cell Responses, Journal of Dental Research, vol.88, issue.11, pp.1026-3010, 2009.
DOI : 10.1006/cyto.2001.0863

I. Sliepen, M. Van-essche, G. Loozen, J. Van-eldere, M. Quirynen et al., : colonization of epithelial cells under hydrodynamic conditions, Oral Microbiology and Immunology, vol.41, issue.suppl 4, pp.390-395, 2009.
DOI : 10.1111/j.1399-302X.2007.00388.x

C. Smillie, M. P. Garcillán-barcia, M. V. Francia, E. P. Rocha, and F. Cruz, Mobility of Plasmids, Microbiology and Molecular Biology Reviews, vol.74, issue.3, pp.434-521000020, 1128.
DOI : 10.1128/MMBR.00020-10

URL : https://hal.archives-ouvertes.fr/pasteur-01374958

M. D. Smith and W. R. Guild, Improved method for conjugative transfer by filter mating of Streptococcus pneumoniae, Journal of Bacteriology, vol.144, issue.1, pp.457-466, 1980.

C. Stadler and M. Teuber, The Macrolide Efflux Genetic Assembly of Streptococcus pneumoniae Is Present in Erythromycin-Resistant Streptococcus salivarius, Antimicrobial Agents and Chemotherapy, vol.46, issue.11, pp.3690-3691, 2002.
DOI : 10.1128/AAC.46.11.3690-3691.2002

R. Stentz, M. Gasson, and C. Shearman, The Tra Domain of the Lactococcal CluA Surface Protein Is a Unique Domain That Contributes to Sex Factor DNA Transfer, Journal of Bacteriology, vol.188, issue.6, 2006.
DOI : 10.1128/JB.188.6.2106-2114.2006

J. P. Suljak, G. Reid, S. M. Wood, R. J. Mcconnell, H. C. Van-der-mei et al., Bacterial adhesion to dental amalgam and three resin composites, Journal of Dentistry, vol.23, issue.3, pp.171-67782529, 1995.
DOI : 10.1016/0300-5712(95)93575-M

P. Suntharalingam and D. G. Cvitkovitch, Quorum sensing in streptococcal biofilm formation, Trends in Microbiology, vol.13, issue.1, 2005.
DOI : 10.1016/j.tim.2004.11.009

J. Sutcliffe, A. Tait-kamradt, and L. Wondrack, Streptococcus pneumoniae and Streptococcus pyogenes resistant to macrolides but sensitive to clindamycin: a common resistance pattern mediated by an efflux system, Antimicrobial Agents and Chemotherapy, vol.40, issue.8, pp.1817-1841, 1996.

J. R. Tagg and K. P. Dierksen, Bacterial replacement therapy: adapting ???germ warfare??? to infection prevention, Trends in Biotechnology, vol.21, issue.5, pp.217-240, 2003.
DOI : 10.1016/S0167-7799(03)00085-4

H. Tamura, A. Yamada, and H. Kato, Identification and Characterization of an Antigen I/II Homologous Gene, pah, from Streptococcus downei, Current Microbiology, vol.74, issue.5, pp.518-541, 2008.
DOI : 10.1007/s00284-008-9117-9

F. Tang and C. Lu, [Lytic phages and prophages of Streptococcus suis--a review], Wei Sheng Wu Xue Bao = Acta Microbiologica Sinica, vol.55, issue.4, pp.389-94, 2015.

P. M. Tendolkar, A. S. Baghdayan, and N. Shankar, Putative Surface Proteins Encoded within a Novel Transferable Locus Confer a High-Biofilm Phenotype to Enterococcus faecalis, Journal of Bacteriology, vol.188, issue.6, pp.2063-72, 2006.
DOI : 10.1128/JB.188.6.2063-2072.2006

B. E. Terzaghi and W. E. Sandine, Improved medium for lactic streptococci and their bacteriophages, Applied Microbiology, vol.29, issue.6, pp.807-820, 1975.

H. Tettelin, V. Masignani, M. J. Cieslewicz, J. Eisen, S. Peterson et al., Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae, Proceedings of the National Academy of Sciences, vol.342, issue.3, pp.99-12391, 2002.
DOI : 10.1056/NEJM200001203420319

A. Toussaint and C. Merlin, Mobile Elements as a Combination of Functional Modules, Plasmid, vol.47, issue.1, 2002.
DOI : 10.1006/plas.2001.1552

T. Tsukazaki, H. Mori, Y. Echizen, R. Ishitani, S. Fukai et al., Structure and function of a membrane component SecDF that enhances protein export, Nature, vol.273, issue.7350, pp.474-235, 1038.
DOI : 10.1074/jbc.273.30.18835

A. M. Vacca-smith, C. A. Jones, M. J. Levine, M. W. Stinson, B. Bogert et al., Glucosyltransferase mediates adhesion of Streptococcus gordonii to human endothelial cells in vitro Retrieved from http Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem, Infection and Immunity PloS One, vol.62, issue.812, pp.2187-94, 1994.

C. G. Van-hoogmoed, G. I. Geertsema-doornbusch, W. Teughels, M. Quirynen, H. J. Busscher et al., Reduction of periodontal pathogens adhesion by antagonistic strains, Oral Microbiology and Immunology, vol.33, issue.1, pp.43-51, 2008.
DOI : 10.1902/jop.1994.65.5s.498

M. L. Van-tassell and M. J. Miller, Lactobacillus Adhesion to Mucus, Nutrients, vol.4, issue.5, pp.613-3610, 2011.
DOI : 10.1371/journal.pone.0004927

J. R. Verani, L. Mcgee, and S. J. Schrag, Prevention of perinatal group B streptococcal disease-revised guidelines from CDC, MMWR. Recommendations and Reports : Morbidity and Mortality Weekly Report. Recommendations and Reports Centers for Disease Control, vol.59, issue.10, pp.1-36, 2010.

J. E. Vidal, H. P. Ludewick, R. M. Kunkel, D. Zähner, and K. P. Klugman, ABSTRACT, Infection and Immunity, vol.79, issue.10, pp.4050-406005186, 2011.
DOI : 10.1128/IAI.05186-11

I. Von-ossowski, R. Satokari, J. Reunanen, S. Lebeer, S. C. De-keersmaecker et al., ABSTRACT, Applied and Environmental Microbiology, vol.77, issue.13, pp.77-4465, 1128.
DOI : 10.1128/AEM.02497-10

F. Wan and M. J. Lenardo, The nuclear signaling of NF-??B: current knowledge, new insights and future perspectives, Cell Research, vol.179, issue.1, pp.24-33, 2010.
DOI : 10.1038/sj.onc.1209982

H. Wang, M. C. Smith, and P. Mullany, The Conjugative Transposon Tn5397 Has a Strong Preference for Integration into Its Clostridium difficile Target Site, Journal of Bacteriology, vol.188, issue.13, pp.4871-4879, 2006.
DOI : 10.1128/JB.00210-06

M. Wang, S. Ahrne, B. Jeppsson, and G. Molin, Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes Analysis of functional domains of the Enterococcus faecalis pheromone-induced surface protein aggregation substance, Journal of Bacteriology, vol.183, issue.19, pp.5659-67, 2001.

C. M. Waters, H. Hirt, J. K. Mccormick, P. M. Schlievert, C. L. Wells et al., An amino-terminal domain of Enterococcus faecalis aggregation substance is required for aggregation, bacterial internalization by epithelial cells and binding to lipoteichoic acid, Molecular Microbiology, vol.28, issue.4, pp.1159-71, 2004.
DOI : 10.1111/j.1574-695X.1999.tb01371.x

C. M. Waters, C. L. Wells, and G. M. Dunny, The Aggregation Domain of Aggregation Substance, Not the RGD Motifs, Is Critical for Efficient Internalization by HT-29 Enterocytes, Infection and Immunity, vol.71, issue.10, pp.5682-5691, 2003.
DOI : 10.1128/IAI.71.10.5682-5689.2003

A. H. Weerkamp, H. C. Van-der-mei, and J. W. Slot, Relationship of cell surface morphology and composition of Streptococcus salivarius K+ to adherence and hydrophobicity, Infection and Immunity, vol.55, issue.2, pp.438-483, 1987.

P. A. Wescombe, M. Upton, K. P. Dierksen, N. L. Ragland, S. Sivabalan et al., Production of the Lantibiotic Salivaricin A and Its Variants by Oral Streptococci and Use of a Specific Induction Assay To Detect Their Presence in Human Saliva, Applied and Environmental Microbiology, vol.72, issue.2, pp.1459-66, 2006.
DOI : 10.1128/AEM.72.2.1459-1466.2006

P. A. Wescombe, M. Upton, P. Renault, R. E. Wirawan, D. Power et al., Salivaricin 9, a new lantibiotic produced by Streptococcus salivarius, Microbiology, vol.72, issue.2, pp.1290-1299, 2011.
DOI : 10.1128/AEM.72.2.1148-1156.2006

URL : https://hal.archives-ouvertes.fr/hal-01001439

M. Wilson, R. Martin, S. T. Walk, C. Young, S. Grossman et al., Clinical and Laboratory Features of Streptococcus salivarius Meningitis: A Case Report and Literature Review, Clinical Medicine & Research, vol.10, issue.1, pp.15-25, 2012.
DOI : 10.3121/cmr.2011.1001

R. Wozniak, F. Fouts, D. E. Spagnoletti, M. Colombo, M. M. Ceccarelli et al., Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs, PLoS Genetics, vol.40, issue.12, 2009.
DOI : 10.1371/journal.pgen.1000786.s002

R. Wozniak, F. Waldor, and M. K. , Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nature Reviews Microbiology, vol.5, issue.8, pp.552-6310, 1038.
DOI : 10.1128/jb.173.22.7136-7141.1991

P. Xu, J. M. Alves, T. Kitten, A. Brown, Z. Chen et al., Genome of the Opportunistic Pathogen Streptococcus sanguinis, Journal of Bacteriology, vol.189, issue.8, pp.3166-751001808, 1128.
DOI : 10.1128/JB.01808-06

Y. T. Yen, R. Seepersaud, B. A. Bensing, and P. M. Sullam, Asp2 and Asp3 Interact Directly with GspB, the Export Substrate of the Streptococcus gordonii Accessory Sec System, Journal of Bacteriology, vol.193, issue.13, pp.3165-741000057, 1128.
DOI : 10.1128/JB.00057-11

J. Yu, Z. Sun, W. Liu, X. Xi, Y. Song et al., Multilocus sequence typing of Streptococcus thermophilus from naturally fermented dairy foods in China and Mongolia, BMC Microbiology, vol.8, issue.9, p.236, 2015.
DOI : 10.1371/journal.pone.0073253

W. Yu and F. Götz, Cell Wall Antibiotics Provoke Accumulation of Anchored mCherry in the Cross Wall of Staphylococcus aureus, PLoS ONE, vol.50, issue.1, 2012.
DOI : 10.1371/journal.pone.0030076.s003

L. Zhou, X. Ma, W. Gao, K. Yao, A. Shen et al., Molecular characteristics of erythromycin-resistant Streptococcus pneumoniae from pediatric patients younger than five years in Beijing, 2010, BMC Microbiology, vol.12, issue.1, pp.228-238, 2010.
DOI : 10.1128/JCM.39.7.2565-2571.2001

W. R. Zückert, Secretion of Bacterial Lipoproteins: Through the Cytoplasmic Membrane, the Periplasm and Beyond, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1843, issue.8, p.1843, 2014.
DOI : 10.1016/j.bbamcr.2014.04.022

M. Zúñiga, I. Pardo, and S. Ferrer, Conjugative plasmid pIP501 undergoes specific deletions after transfer from Lactococcus lactis to Oenococcus oeni, Archives of Microbiology, vol.180, issue.5, pp.367-73, 2003.
DOI : 10.1007/s00203-003-0599-3

C. Delorme, C. Poyart, S. Ehrlich, and R. P. , Extent of Horizontal Gene Transfer in Evolution of Streptococci of the Salivarius Group, Journal of Bacteriology, vol.189, issue.4, pp.1330-1371, 2007.
DOI : 10.1128/JB.01058-06

URL : https://hal.archives-ouvertes.fr/hal-01204331

D. Grosso, M. Camilli, R. Barbabella, G. , B. Northwood et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.7, pp.3226-3256, 2011.
DOI : 10.1128/AAC.01713-10

S. Malhotra-kumar, C. Lammens, J. Piessens, and H. Goossens, Multiplex PCR for Simultaneous Detection of Macrolide and Tetracycline Resistance Determinants in Streptococci, Antimicrobial Agents and Chemotherapy, vol.49, issue.11, pp.4798-800, 2005.
DOI : 10.1128/AAC.49.11.4798-4800.2005

M. Haenni, E. Saras, S. Bertin, P. Leblond, J. Madec et al., Diversity and Mobility of Integrative and Conjugative Elements in Bovine Isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis, Applied and Environmental Microbiology, vol.76, issue.24, pp.7957-65, 2010.
DOI : 10.1128/AEM.00805-10

URL : https://hal.archives-ouvertes.fr/hal-01637787

D. Marra, B. Pethel, G. Churchward, and J. Scott, The frequency of conjugative transposition of Tn916 is not determined by the frequency of excision, J Bacteriol, vol.181, pp.5414-5422, 1999.