A. E. Abo-amer, J. Munn, K. Jackson, M. Aktas, P. Golby et al., DNA interaction and phosphotransfer of the C4-dicarboxylateresponsive DcuS-DcuR two-component regulatory system from Escherichia coli, J. Bacteriol, vol.186, pp.1879-1889, 2004.

C. Alcantara, A. Revilla-guarinos, and M. Zuniga, Influence of twocomponent signal transduction systems of Lactobacillus casei BL23 on tolerance to stress conditions, Appl. Environ. Microbiol, vol.77, pp.1516-1519, 2011.

S. Arioli, R. Koirala, V. Taverniti, W. Fiore, and S. Guglielmetti, Quantitative recovery of viable Lactobacillus paracasei CNCM I-1572 (L. casei DG R ) after gastrointestinal passage in healthy adults, Front. Microbiol, vol.9, p.1720, 2018.

M. Arumugam, J. Raes, E. Pelletier, D. Le-paslier, T. Yamada et al., Enterotypes of the human gut microbiome, Nature, vol.473, pp.174-180, 2011.
URL : https://hal.archives-ouvertes.fr/cea-00903625

G. Balandino, I. Milazzo, and D. Fazio, Antibiotic susceptibility of bacterial isolates from probiotic products available in Italy, Microbial. Ecol. Health Dis, vol.20, pp.199-203, 2008.

C. Bauerl, G. Perez-martinez, F. Yan, D. B. Polk, and V. Monedero, Functional analysis of the p40 and p75 proteins from Lactobacillus casei BL23, J. Mol. Microbiol. Biotechnol, vol.19, pp.231-241, 2010.

M. Bellon-fontaine, J. Rault, and C. J. Van-oss, Microbial adhesion to solvents: a novel method to determine the electron-donor/electron-accpetor or Lewis acid-base properties of microbial cells, Colloids Surf B Biointerfaces, vol.7, pp.47-53, 1996.

E. Bernard, T. Rolain, P. Courtin, A. Guillot, P. Langella et al., Characterization of O-acetylation of N-acetylglucosamine: a novel structural variation of bacterial peptidoglycan, J. Biol. Chem, vol.286, pp.23950-23958, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01004335

D. Billot-klein, R. Legrand, B. Schoot, J. Van-heijenoort, and L. Gutmann, Peptidoglycan structure of Lactobacillus casei, a species highly resistant to glycopeptide antibiotics, J. Bacteriol, vol.179, pp.6208-6212, 1997.

P. Bisicchia, D. Noone, E. Lioliou, A. Howell, S. Quigley et al., The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis, Mol. Microbiol, vol.65, pp.180-200, 2007.

H. Cai, R. Thompson, M. F. Budinich, J. R. Broadbent, and J. L. Steele, Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution, Genome Biol. Evol, vol.1, pp.239-257, 2009.

M. Chapot-chartier and S. Kulakauskas, Cell wall structure and function in lactic acid bacteria, Microbial. Cell Factories, vol.13, p.9, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01204431

I. J. Claes, G. Schoofs, K. Regulski, P. Courtin, M. P. Chapot-chartier et al., Genetic and biochemical characterization of the cell wall hydrolase activity of the major secreted protein of Lactobacillus rhamnosus GG, PLoS One, vol.7, p.31588, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01189702

J. C. Clemente, L. K. Ursell, L. W. Parfrey, and R. Knight, The impact of the gut microbiota on human health: an integrative view, Cell, vol.148, pp.1258-1270, 2012.

S. N. Cohen, A. C. Chang, and L. Hsu, Nonchromosomal antibiotic resistance in bacteria: genetic transformation of Escherichia coli by R-factor DNA, Proc. Natl. Acad. Sci. U.S.A, vol.69, pp.2110-2114, 1972.

P. Courtin, G. Miranda, A. Guillot, F. Wessner, C. Mezange et al., Peptidoglycan structure analysis of Lactococcus lactis reveals the presence of an L,D-carboxypeptidase involved in peptidoglycan maturation, J. Bacteriol, vol.188, pp.5293-5298, 2006.

B. L. De-jonge, Y. S. Chang, D. Gage, and A. Tomasz, Peptidoglycan composition of a highly methicillin-resistant Staphylococcus aureus strain. The role of penicillin binding protein 2A, J. Biol. Chem, vol.267, pp.11248-11254, 1992.

S. C. De-keersmaecker, K. Braeken, T. L. Verhoeven, M. Perea-velez, S. Lebeer et al., Flow cytometric testing of green fluorescent protein-tagged Lactobacillus rhamnosus GG for response to defensins, Appl. Environ. Microbiol, vol.72, pp.4923-4930, 2006.

A. Delaune, O. Poupel, A. Mallet, Y. M. Coic, T. Msadek et al., Peptidoglycan crosslinking relaxation plays an important role in Staphylococcus aureus WalKR-dependent cell viability, PLoS One, vol.6, p.17054, 2011.

A. Delhaye, J. F. Collet, and G. Laloux, A Fly on the wall: how stress response systems can sense and respond to damage to peptidoglycan. Front, Cell Infect Microbiol, vol.9, p.380, 2019.

T. Di-renzo, A. Reale, F. Boscaino, and M. C. Messia, Flavoring production in kamut R . quinoa and wheat doughs fermented by Lactobacillus paracasei, Lactobacillus plantarum, and Lactobacillus brevis: a SPME-GC/MS study, Front. Microbiol, vol.9, p.429, 2018.

W. J. Dower, J. F. Miller, and C. W. Ragsdale, High efficiency transformation of E. coli by high voltage electroporation, Nucleic Acids Res, vol.16, pp.6127-6145, 1988.

S. Dubrac, I. G. Boneca, O. Poupel, and T. Msadek, New insights into the WalK/WalR (YycG/YycF) essential signal transduction pathway reveal a major role in controlling cell wall metabolism and biofilm formation in Staphylococcus aureus, J. Bacteriol, vol.189, pp.8257-8269, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00189231

S. Fehlbaum, C. Chassard, C. Schwab, M. Voolaid, C. Fourmestraux et al., In vitro study of Lactobacillus paracasei CNCM I-1518 in healthy and Clostridium difficile colonized elderly gut microbiota, Front. Nutr, vol.6, p.184, 2019.

T. Ferain, J. N. Hobbs, J. Richardson, N. Bernard, and D. Garmyn, Knockout of the two ldh genes has a major impact on peptidoglycan precursor synthesis in Lactobacillus plantarum, J. Bacteriol, vol.178, pp.5431-5437, 1996.

D. Fiocco, A. Longo, M. P. Arena, P. Russo, G. Spano et al., How probiotics face food stress: they get by with a little help, Crit. Rev. Food Sci. Nutr, vol.18, pp.1-29, 2019.

T. Gensollen, S. S. Iyer, D. L. Kasper, and R. S. Blumberg, How colonization by microbiota in early life shapes the immune system, Science, vol.352, pp.539-544, 2016.

T. J. Gibson, Studies on the Epstein-Barr Virus Genome, 1984.

S. E. Girardin, I. G. Boneca, J. Viala, M. Chamaillard, A. Labigne et al., Nod2 is a general sensor of peptidoglycan through muramyl dipeptide (MDP) detection, J. Biol. Chem, vol.278, pp.8869-8872, 2003.

B. Glauner, Separation and quantification of muropeptides with highperformance liquid chromatography, Anal. Biochem, vol.172, issue.88, p.90468, 1988.

J. Gury, L. Barthelmebs, N. P. Tran, C. Divies, and J. F. Cavin, Cloning, deletion, and characterization of PadR, the transcriptional repressor of the phenolic acid decarboxylase-encoding padA gene of Lactobacillus plantarum, 2004.

, Appl. Environ. Microbiol, vol.70, pp.2146-2153

J. Gury, H. Seraut, N. P. Tran, L. Barthelmebs, S. Weidmann et al., Inactivation of PadR, the repressor of the phenolic acid stress response, by molecular interaction with Usp1, a universal stress protein from Lactobacillus plantarum, in Escherichia coli, Appl. Environ. Microbiol, vol.75, pp.5273-5283, 2009.

S. Handwerger, M. J. Pucci, K. J. Volk, J. Liu, and M. S. Lee, Vancomycin-resistant Leuconostoc mesenteroides and Lactobacillus casei synthesize cytoplasmic peptidoglycan precursors that terminate in lactate, J. Bacteriol, vol.176, pp.260-264, 1994.

J. Hellemans, G. Mortier, A. De-paepe, F. Speleman, and J. Vandesompele, qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data, Genome Biol, vol.8, p.19, 2007.

A. A. Hugo, E. E. Tymczyszyn, A. Gomez-zavaglia, and P. F. Perez, Effect of human defensins on lactobacilli and liposomes, J. Appl. Microbiol, vol.113, pp.1491-1497, 2012.

M. I. Hutchings, H. J. Hong, and M. J. Buttner, The vancomycin resistance VanRS two-component signal transduction system of Streptomyces coelicolor, Mol. Microbiol, vol.59, pp.923-935, 2006.

M. Ito, Y. G. Kim, H. Tsuji, T. Takahashi, M. Kiwaki et al., Transposon mutagenesis of probiotic Lactobacillus casei identifies asnH, an asparagine synthetase gene involved in its immune-activating capacity, PLoS One, vol.9, p.83876, 2014.

B. R. Johnson, J. Hymes, R. Sanozky-dawes, E. D. Henriksen, R. Barrangou et al., Conserved S-Layer-associated proteins revealed by exoproteomic survey of S-Layer-forming lactobacilli, Appl. Environ. Microbiol, vol.82, pp.134-145, 2016.

I. Klare, C. Konstabel, G. Werner, G. Huys, V. Vankerckhoven et al., Antimicrobial susceptibilities of Lactobacillus, Pediococcus and Lactococcus human isolates and cultures intended for probiotic or nutritional use, J. Antimicrob. Chemother, vol.59, pp.900-912, 2007.

A. Koh, F. De-vadder, P. Kovatcheva-datchary, and F. Bäckhed, From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites, Cell, vol.165, pp.1332-1345, 2016.

J. Koponen, K. Laakso, K. Koskenniemi, M. Kankainen, K. Savijoki et al., Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG, J. Proteomics, vol.75, pp.1357-1374, 2012.

S. Layec, B. Decaris, and N. Leblond-bourget, Diversity of Firmicutes peptidoglycan hydrolases and specificities of those involved in daughter cell separation, Res. Microbiol, vol.159, pp.507-515, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01204247

S. Lebeer, I. J. Claes, C. I. Balog, G. Schoofs, T. L. Verhoeven et al., The major secreted protein Msp1/p75 is O-glycosylated in Lactobacillus rhamnosus GG, Microb. Cell Fact, vol.11, p.15, 2012.

I. Letunic, T. Doerks, and P. Bork, SMART: recent updates, new developments and status in 2015, Nucleic Acids Res, vol.43, 2014.

H. Licandro-seraut, S. Brinster, M. Van-de-guchte, H. Scornec, E. Maguin et al., Development of an efficient in vivo system (Pjunc-TpaseIS1223) for random transposon mutagenesis of Lactobacillus casei, Appl. Environ. Microbiol, vol.78, pp.5417-5423, 2012.

H. Licandro-seraut, J. Gury, N. P. Tran, L. Barthelmebs, and J. F. Cavin, Kinetics and intensity of the expression of genes involved in the stress response tightly induced by phenolic acids in Lactobacillus plantarum, J. Mol. Microbiol. Biotechnol, vol.14, pp.41-47, 2008.

H. Licandro-seraut, H. Scornec, T. Pedron, J. F. Cavin, and P. J. Sansonetti, Functional genomics of Lactobacillus casei establishment in the gut, Proc. Natl. Acad. Sci. U.S.A, vol.111, pp.3101-3109, 2014.

C. A. Lozupone, J. I. Stombaugh, J. I. Gordon, J. K. Jansson, and R. Knight, Diversity, stability and resilience of the human gut microbiota, Nature, vol.489, pp.220-230, 2012.

T. Mackey, V. Lejeune, M. Janssens, and G. Wauters, Identification of vancomycin-resistant lactic bacteria isolated from humans, J. Clin. Microbiol, vol.31, pp.2499-2501, 1993.

K. Makarova, A. Slesarev, Y. Wolf, A. Sorokin, B. Mirkin et al., Comparative genomics of the lactic acid bacteria, Proc. Natl. Acad .Sci. U.S.A, vol.103, pp.15611-15616, 2006.

R. C. Matos, M. Schwarzer, H. Gervais, P. Courtin, P. Joncour et al., D-Alanylation of teichoic acids contributes to Lactobacillus plantarummediated Drosophila growth during chronic undernutrition, Nat. Microbiol, vol.2, pp.1635-1647, 2017.

M. Meyrand, A. Boughammoura, P. Courtin, C. Mezange, A. Guillot et al., Peptidoglycan N-acetylglucosamine deacetylation decreases autolysis in Lactococcus lactis, Microbiology, vol.153, pp.3275-3285, 2007.

C. Milani, S. Duranti, F. Bottacini, E. Casey, F. Turroni et al., The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol, Mol. Biol. Rev, vol.81, pp.36-53, 2017.

V. Molle and M. J. Buttner, Different alleles of the response regulator gene bldM arrest Streptomyces coelicolor development at distinct stages, Mol. Microbiol, vol.36, pp.1265-1278, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00314426

D. Munoz-provencio, M. Llopis, M. Antolin, I. De-torres, F. Guarner et al., Adhesion properties of Lactobacillus casei strains to resected intestinal fragments and components of the extracellular matrix, Arch. Microbiol, vol.191, pp.153-161, 2009.

F. C. Neuhaus and J. Baddiley, A continuum of anionic charge: structures and functions of D-alanyl-teichoic acids in gram-positive bacteria. Microbiol, Mol. Biol. Rev, vol.67, pp.686-723, 2003.

A. Palud, H. Scornec, J. F. Cavin, and H. Licandro, New genes involved in mild stress response identified by transposon mutagenesis, Front. Microbiol, vol.9, p.535, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01907759

E. Palumbo, M. Deghorain, P. S. Cocconcelli, M. Kleerebezem, A. Geyer et al., D-alanyl ester depletion of teichoic acids in Lactobacillus plantarum results in a major modification of lipoteichoic acid composition and cell wall perforations at the septum mediated by the Acm2 autolysin, J. Bacteriol, vol.188, pp.3709-3715, 2006.

P. Velez, M. Verhoeven, T. L. Draing, C. Von-aulock, S. Pfitzenmaier et al., Functional analysis of D-alanylation of lipoteichoic acid in the probiotic strain Lactobacillus rhamnosus GG, Appl. Environ. Microbiol, vol.73, pp.3595-3604, 2007.

G. Perpetuini, B. N. Pham-hoang, H. Scornec, R. Tofalo, M. Schirone et al., In Lactobacillus pentosus, the olive brine adaptation genes are required for biofilm formation, Int. J. Food Microbiol, vol.216, pp.104-109, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01498614

D. Raychaudhuri and A. N. Chatterjee, Use of resistant mutants to study the interaction of triton X-100 with Staphylococcus aureus, J. Bacteriol, vol.164, pp.1337-1349, 1985.

K. Regulski, P. Courtin, M. Meyrand, I. J. Claes, S. Lebeer et al., Analysis of the peptidoglycan hydrolase complement of Lactobacillus casei and characterization of the major gamma-D-glutamyl-Llysyl-endopeptidase, PLoS One, vol.7, 2012.

J. Rico, M. J. Yebra, G. Pérez-martínez, J. Deutscher, and V. Monedero, Analysis of ldh genes in Lactobacillus casei BL23: role on lactic acid production, J. Ind. Microbiol. Biotechnol, vol.35, pp.579-586, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00315470

T. Rolain, E. Bernard, A. Beaussart, H. Degand, P. Courtin et al., O-glycosylation as a novel control mechanism of peptidoglycan hydrolase activity, J. Biol. Chem, vol.288, pp.22233-22247, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01204414

L. Rossetti, D. Carminati, M. Zago, and G. Giraffa, A qualified presumption of safety approach for the safety assessment of grana padano whey starters, Int. J. Food Microbiol, vol.130, pp.70-73, 2009.

J. Sambrook, E. F. Fritsch, and T. Maniatis, Molecular Cloning: a Laboratory Manual, Cold Sring Harbor, 1989.

H. Scornec, M. Tichit, C. Bouchier, T. Pedron, J. F. Cavin et al., Rapid 96-well plates DNA extraction and sequencing procedures to identify genome-wide transposon insertion sites in a difficult to lyse bacterium: Lactobacillus casei, J. Microbiol. Methods, vol.106, pp.78-82, 2014.

R. Sengupta, E. Altermann, R. C. Anderson, W. C. Mcnabb, P. J. Moughan et al., The role of cell surface architecture of lactobacilli in host-microbe interactions in the gastrointestinal tract, Mediators Inflamm, p.237921, 2013.

A. Seth, F. Yan, D. B. Polk, and R. K. Rao, Probiotics ameliorate the hydrogen peroxide-induced epithelial barrier disruption by a PKC-and MAP kinase-dependent mechanism, Am. J. Physiol. Gastrointest Liver Physiol, vol.294, pp.1060-1069, 2008.

E. Smit, F. Oling, R. Demel, B. Martinez, and P. H. Pouwels, The S-layer protein of Lactobacillus acidophilus ATCC 4356: identification and characterisation of domains responsible for S-protein assembly and cell wall binding, J. Mol. Biol, vol.305, pp.245-257, 2001.

F. Sommer, J. M. Anderson, R. Bharti, J. Raes, and P. Rosenstiel, The resilience of the intestinal microbiota influences health and disease, Nat. Rev. Microbiol, vol.15, pp.630-638, 2017.

J. L. Sonnenburg and F. Bäckhed, Diet-microbiota interactions as moderators of human metabolism, Nature, vol.535, pp.56-64, 2016.

A. Steen, E. Palumbo, M. Deghorain, P. S. Cocconcelli, J. Delcour et al., Autolysis of Lactococcus lactis is increased upon D-alanine depletion of peptidoglycan and lipoteichoic acids, J. Bacteriol, vol.187, pp.114-124, 2005.

E. Stefanovic, K. N. Kilcawley, C. Roces, M. C. Rea, M. O'sullivan et al., Evaluation of the potential of Lactobacillus paracasei adjuncts for flavor compounds development and diversification in short-aged cheddar cheese, Front. Microbiol, vol.9, p.1506, 2018.

A. M. Stock, V. L. Robinson, and P. N. Goudreau, Two-component signal transduction, Annu. Rev. Biochem, vol.69, pp.183-215, 2000.

O. Takeuchi, A. , and S. , Pattern recognition receptors and inflammation, Cell, vol.140, pp.805-820, 2010.

, Structure, function and diversity of the healthy human microbiome, The Human Microbiome Project Consortium, vol.486, pp.207-214, 2012.

J. Thiéry, Mise en évidence des polysaccharides sur coupes fines en microscopie électronique, J. Microscopie, vol.6, pp.987-1018, 1967.

M. Van-de-guchte, P. Serror, C. Chervaux, T. Smokvina, S. D. Ehrlich et al., Stress responses in lactic acid bacteria, Antonie Van Leeuwenhoek, vol.82, pp.187-216, 2002.

M. Wilks, R. Wiggins, A. Whiley, E. Hennessy, S. Warwick et al., Identification and H2O2 production of vaginal lactobacilli from pregnant women at high risk of preterm birth and relation with outcome, J. Clin. Microbiol, vol.42, pp.713-717, 2004.

F. Yan, H. Cao, T. L. Cover, R. Whitehead, M. K. Washington et al., Soluble proteins produced by probiotic bacteria regulate intestinal epithelial cell survival and growth, Gastroenterology, vol.132, pp.562-575, 2007.

F. Yan, L. Liu, P. J. Dempsey, Y. H. Tsai, E. W. Raines et al., , 2013.

, A Lactobacillus rhamnosus GG-derived soluble protein, p40, stimulates ligand release from intestinal epithelial cells to transactivate epidermal growth factor receptor, J. Biol. Chem, vol.288, pp.30742-30751

M. R. Yeaman and N. Y. Yount, Mechanisms of antimicrobial peptide action and resistance, Pharmacol. Rev, vol.55, pp.27-55, 2003.

Y. C. Zhang, L. W. Zhang, Y. F. Tuo, C. F. Guo, H. X. Yi et al., Inhibition of Shigella sonnei adherence to HT-29 cells by lactobacilli from Chinese fermented food and preliminary characterization of S-layer protein involvement, Res. Microbiol, vol.161, pp.667-672, 2010.

L. Zitvogel, R. Daillère, M. P. Roberti, B. Routy, and G. Kroemer, Anticancer effects of the microbiome and its products, Nat. Rev. Microbiol, vol.15, pp.465-478, 2017.