causative agents of persistent infections in breast implants. *PLoS One* 11:e0146668.
doi: 10.1371/journal.pone.0146668

Chong, J., Wishart, D. S., and Xia, J. (2019). Using metaboanalyst 4.0 for comprehensive and integrative metabolomics data analysis. *Curr. Protoc. Bioinformatics* 68:e86.

Christgen, S. L., and Becker, D. F. (2019). Role of proline in pathogen and host interactions. *Antioxid. Redox Signal.* 30, 683–709.

Conlan, S., Mijares, L. A., Nisc Comparative Sequencing Program, Becker, J., Blakesley, R. W., Bouffard, G. G., et al. (2012). *Staphylococcus epidermidis* pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates. *Genome Biol.* 13:R64. doi: 10.1186/gb-2012-13-7-r64

Connolly, J., Boldock, E., Prince, L. R., Renshaw, S. A., Whyte, M. K., and Foster, S. J. (2017). Identification of *Staphylococcus aureus* factors required for pathogenicity and growth in human blood. *Infect. Immun.* 85, e00337–e00417.
doi: 10.1128/IAI.00337-17

Cotter, P. D., and Hill, C. (2003). Surviving the acid test: responses of gram-
positive bacteria to low pH. *Microbiol. Mol. Biol. Rev.* 67, 429–453. doi: 10.1128/
MMBR.67.3.429–453.2003

Deplano, A., Vandendriessche, S., Nonhoff, C., Dodémont, M., Roisin, S., and Denis, O. (2016). National surveillance of *Staphylococcus epidermidis* recovered from bloodstream infections in Belgian hospitals. *J. Antimicrob. Chemother.* 71, 1815–1819. doi: 10.1093/jac/dkw086

Durand, J. M., Dagberg, B., Uhlin, B. E., and Björk, G. R. (2000). Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of *Shigella flexneri*: the expression of the virF gene. *Mol. Microbiol.* 35, 924–935. doi: 10.1046/j.1365-2958.20000.01767.x

Edwards, A. M., Addo, M. A., and Dos Santos, P. C. (2020). Extracurricular functions of tRNA Modifications in Microorganisms. *Genes* 11:907. doi: 10.3390/
genes11080907

Espadinha, D., Sobral, R. G., Mendes, C. I., Méric, G., Sheppard, S. K., Carrico, J. A., et al. (2019). Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of *Staphylococcus epidermidis* clonal lineages. *Front. Microbiol.* 10:1971. doi: 10.3389/fmicb.2019.01971

Figueroa-Soto, C. G., and Valenzuela-Soto, E. M. (2018). Glycine betaine rather than acting only as an osmolyte also plays a role as regulator in cellular metabolism. *Biochimie* 147, 89–97. doi: 10.1016/j.biochi.2018.01.002

Gaupp, R., Ledala, N., and Somerville, G. A. (2012). *Staphylococcal* response to oxidative stress. *Front. Cell. Infect. Microbiol.* 2:33. doi: 10.3389/fcimb.2012.00033

Gill, S. R., Fouts, D. E., Archer, G. L., Mongodin, E. F., Deboy, R. T., Ravel, J., et al. (2005). Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant *Staphylococcus aureus* strain and a biofilm-producing methicillin-resistant *Staphylococcus epidermidis* strain. *J. Bacteriol.* 187, 2426–2438. doi: 10.1128/JB.187.7.2426–2438.2005

Graham, J. E., and Wilkinson, B. J. (1992). *Staphylococcus aureus* osmoregulation: roles for choline, glycine betaine, proline, and taurine. *J. Bacteriol.* 174, 2711–2716. doi: 10.1128/jb.174.8.2711–2716.1992

Gu, L., Liu, X., Wang, Y.-Q., Zhou, Y. T., Zhu, H. W., Huang, J., et al. (2020).
Revelation of AbF in regulation of mismatch repair and energy metabolism in
S. epidermidis by integrated proteomic and metabolomic analysis. *J. Proteomics*
226:103900. doi: 10.1016/j.jprot.2020.103900

Halsey, C. R., Lei, S., Wax, J. K., Lehman, M. K., Nuxoll, A. S., Steinke, L., et al. (2017). Amino acid catabolism in *Staphylococcus aureus* and the function of carbon catabolite repression. *mBio* 8, e1434–e1516.

Handke, L. D., Rogers, K. L., Olson, M. E., Somerville, G. A., Jerrells, T. J., Rupp, M. E., et al. (2008). *Staphylococcus epidermidis* saeR is an effector of anaerobic growth and a mediator of acute inflammation. *Infect. Immun.* 76, 141–152. doi: 10.1128/IAI.00556-07

Harris, L. G., Murray, S., Pascoe, B., Bray, J., Meric, G., Mageiros, L., et al. (2016). Biofilm morphotypes and population structure among *Staphylococcus epidermidis* from commensal and clinical samples. *PLoS One* 11:e0151240. doi: 10.1371/journal.pone.0151240

Hayoun, K., Gouveia, D., Grenga, L., Pible, O., Armengaud, J. and Alpha-Bazin, B. (2019). Evaluation of sample preparation methods for fast proteotyping of microorganisms by tandem mass spectrometry. *Front. Microbiol.* 10:1985. doi: 10.3389/fmicb.2019.01985

Hegde, S. S., and Shrader, T. E. (2001). FemABX family members are novel nonribosomal peptidyltransferases and important pathogen-specific drug targets. *J. Biol. Chem.* 276, 6998–7003. doi: 10.1074/jbc.M008591200

Iyer, V., Raut, J., and Dasgupta, A. (2021). Impact of pH on growth of *Staphylococcus epidermidis* and *Staphylococcus aureus* *in vitro*. *J. Med. Microbiol.* 70. doi: 10.1099/jmm.0.001421

Jean Beltran, P. M., Federspiel, J. D., Sheng, X., and Cristea, I. M. (2017). Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. *Mol. Syst. Biol.* 13:922.

Kammeyer, A., and Luiten, R. M. (2015). Oxidation events and skin aging. *Ageing Res. Rev.* 21, 16–29.

Kantyka, T., Pyrc, K., Gruca, M., Smagur, J., Plaza, K., Guzik, K., et al. (2013). *Staphylococcus aureus* proteases degrade lung surfactant protein A potentially impairing innate immunity of the lung. *J. Innate Immun.* 5, 251–260. doi: 10.1159/000345417

Kaur, I., Purves, J., Harwood, M., Ketley, J. M., Andrew, P. W., Waldron, K. J., et al. (2022). Role of horizontally transferred copper resistance genes in *Staphylococcus aureus* and *Listeria monocytogenes*. *Microbiology* 168:1162. doi: 10.1099/mic.0.001162

Kinkel, T. L., Ramos-Montañez, S., Pando, J. M., Tadeo, D. V., Strom, E. N., Libby, S. J., et al. (2016). An essential role for bacterial nitric oxide synthase in *Staphylococcus aureus* electron transfer and colonization. *Nat. Microbiol.* 2:16224. doi: 10.1038/nmicrobiol.2016.224

Klein, G., Mathé, C., Biola-Clier, M., Devineau, S., Drouineau, E., Hatem, E., et al. (2016). RNA-binding proteins are a major target of silica nanoparticles in cell extracts. *Nanotoxicology* 10, 1555–1564. doi: 10.1080/17435390.2016.1244299

Kleinschmidt, S., Huygens, F., Faoagali, J., Rathnayake, I. U., and Hafner, L. M. (2015). *Staphylococcus epidermidis* as a cause of bacteremia. *Future Microbiol.* 10, 1859–1879.

Koch, G., Wermser, C., Acosta, I. C., Kricks, L., Stengel, S. T., Yepes, A., et al. (2017). Attenuating *Staphylococcus aureus* virulence by targeting flotillin protein scaffold activity. *Cell Chem. Biol.* 24, 845–857. doi: 10.1016/j.chembiol.2017.05.027

Kocianova, S., Vuong, C., Yao, Y., Voyich, J. M., Fischer, E. R., DeLeo, F. R., et al. (2005). Key role of poly-gamma-DL-glutamic acid in immune evasion and virulence of *Staphylococcus epidermidis*. *J. Clin. Invest.* 115, 688–694. doi: 10.1172/JCI23523

Korem, M., Gov, Y., and Rosenberg, M. (2010). Global gene expression in *Staphylococcus aureus* following exposure to alcohol. *Microb. Pathog.* 48, 74–84.

Kunin, C. M., and Rudy, J. (1991). Effect of NaCl-induced osmotic stress on intracellular concentrations of glycine betaine and potassium in *Escherichia coli*. *Enterococcus faecalis*, and *staphylococci*. *J. Lab. Clin. Med.* 118, 217–224.

Lambers, H., Piessens, S., Bloem, A., Pronk, H., and Finkel, P. (2006). Natural skin surface pH is on average below 5, which is beneficial for its resident flora. *Int. J. Cosmet. Sci.* 28, 359–370. doi: 10.1111/j.1467-2494.2006.00344.x

Lee, E., and Anjum, F. (2022). *Staphylococcus Epidermidis*. Treasure Island, FL: StatPearls Publishing.

Lekshmi, M., Ammini, P., Adjei, J., Sanford, L. M., Shrestha, U., Kumar, S., et al. (2018). Modulation of antimicrobial efflux pumps of the major facilitator superfamily in *Staphylococcus aureus*. *AIMS Microbiol.* 4, 1–18. doi: 10.3934/microbiol.2018.1.1

Li, L., Abdelhady, W., Donegan, N. P., Seidl, K., Cheung, A., Zhou, Y. F., et al. (2018). Role of purine biosynthesis in persistent methicillin-resistant *Staphylococcus aureus* infection. *J. Infect. Dis.* 218, 1367–1377. doi: 10.1093/infdis/jiy340

Lindahl, T., and Nyberg, B. (1972). Rate of depurination of native deoxyribonucleic acid. *Biochemistry* 11, 3610–3618.

Liu, H., Sadygov, R. G., and Yates, J. R. (2004). A model for random sampling and estimation of relative protein abundance in shotgun proteomics. *Anal. Chem.* 76, 4193–4201. doi: 10.1021/ac0498563

Lou, Q., Zhu, T., Hu, J., Ben, H., Yang, J., Yu, F., et al. (2011). Role of the SaeRS two-component regulatory system in *Staphylococcus epidermidis* autolysis and biofilm formation. *BMC Microbiol.* 11:146. doi: 10.1186/1471-2180-11-146

Manna, A. C., Ingavale, S. S., Maloney, M., van Wamel, W., and Cheung, A. L. (2004). Identification of sarV (SA2062), a new transcriptional regulator, is repressed by SarA and MgrA (SA0641) and involved in the regulation of autolysis in *Staphylococcus aureus*. *J. Bacteriol.* 186, 5267–5280. doi: 10.1128/JB.186.16.5267–5280.2004

Martínez-García, S., Peralta, H., Betanzos-Cabrera, G., Chavez-Galan, L., Rodriguez-Martínez, S., Cancino-Diaz, M. E., et al. (2021). Proteomic comparison of biofilm vs. planktonic *Staphylococcus epidermidis* cells suggests key metabolic differences between these conditions. *Res. Microbiol.* 172:103796. doi: 10.1016/j.resmic.2020.103796

Mielich-Süss, B., Wagner, R. M., Mietrach, N., Hertlein, T., Marincola, G., Ohlsen, K., et al. (2017). Flotillin scaffold activity contributes to type VII secretion system assembly in *Staphylococcus aureus*. *PLoS Pathog.* 13:e1006728. doi: 10.1371/journal.ppat.1006728
causative agents of persistent infections in breast implants. *PLoS One* 11:e0146668.
doi: 10.1371/journal.pone.0146668

Chong, J., Wishart, D. S., and Xia, J. (2019). Using metaboanalyst 4.0 for comprehensive and integrative metabolomics data analysis. *Curr. Protoc. Bioinformatics* 68:e86.

Christgen, S. L., and Becker, D. F. (2019). Role of proline in pathogen and host interactions. *Antioxid. Redox Signal.* 30, 683–709.

Conlan, S., Mijares, L. A., Nisc Comparative Sequencing Program, Becker, J., Blakesley, R. W., Bouffard, G. G., et al. (2012). *Staphylococcus epidermidis* pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates. *Genome Biol.* 13:R64. doi: 10.1186/gb-2012-13-7-r64

Connolly, J., Boldock, E., Prince, L. R., Renshaw, S. A., Whyte, M. K., and Foster, S. J. (2017). Identification of *Staphylococcus aureus* factors required for pathogenicity and growth in human blood. *Infect. Immun.* 85, e00337–e00417.
doi: 10.1128/IAI.00337-17

Cotter, P. D., and Hill, C. (2003). Surviving the acid test: responses of gram-
positive bacteria to low pH. *Microbiol. Mol. Biol. Rev.* 67, 429–453. doi: 10.1128/
MMBR.67.3.429–453.2003

Deplano, A., Vandendriessche, S., Nonhoff, C., Dodémont, M., Roisin, S., and Denis, O. (2016). National surveillance of *Staphylococcus epidermidis* recovered from bloodstream infections in Belgian hospitals. *J. Antimicrob. Chemother.* 71, 1815–1819. doi: 10.1093/jac/dkw086

Durand, J. M., Dagberg, B., Uhlin, B. E., and Björk, G. R. (2000). Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of *Shigella flexneri*: the expression of the virF gene. *Mol. Microbiol.* 35, 924–935. doi: 10.1046/j.1365-2958.20000.01767.x

Edwards, A. M., Addo, M. A., and Dos Santos, P. C. (2020). Extracurricular functions of tRNA Modifications in Microorganisms. *Genes* 11:907. doi: 10.3390/
genes11080907

Espadinha, D., Sobral, R. G., Mendes, C. I., Méric, G., Sheppard, S. K., Carrico, J. A., et al. (2019). Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of *Staphylococcus epidermidis* clonal lineages. *Front. Microbiol.* 10:1971. doi: 10.3389/fmicb.2019.01971

Figueroa-Soto, C. G., and Valenzuela-Soto, E. M. (2018). Glycine betaine rather than acting only as an osmolyte also plays a role as regulator in cellular metabolism. *Biochimie* 147, 89–97. doi: 10.1016/j.biochi.2018.01.002

Gaupp, R., Ledala, N., and Somerville, G. A. (2012). *Staphylococcal* response to oxidative stress. *Front. Cell. Infect. Microbiol.* 2:33. doi: 10.3389/fcimb.2012.00033

Gill, S. R., Fouts, D. E., Archer, G. L., Mongodin, E. F., Deboy, R. T., Ravel, J., et al. (2005). Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant *Staphylococcus aureus* strain and a biofilm-producing methicillin-resistant *Staphylococcus epidermidis* strain. *J. Bacteriol.* 187, 2426–2438. doi: 10.1128/JB.187.7.2426–2438.2005

Graham, J. E., and Wilkinson, B. J. (1992). *Staphylococcus aureus* osmoregulation: roles for choline, glycine betaine, proline, and taurine. *J. Bacteriol.* 174, 2711–2716. doi: 10.1128/jb.174.8.2711–2716.1992

Gu, L., Liu, X., Wang, Y.-Q., Zhou, Y. T., Zhu, H. W., Huang, J., et al. (2020).
Revelation of AbF in regulation of mismatch repair and energy metabolism in
S. epidermidis by integrated proteomic and metabolomic analysis. *J. Proteomics*
226:103900. doi: 10.1016/j.jprot.2020.103900

Halsey, C. R., Lei, S., Wax, J. K., Lehman, M. K., Nuxoll, A. S., Steinke, L., et al. (2017). Amino acid catabolism in *Staphylococcus aureus* and the function of carbon catabolite repression. *mBio* 8, e1434–e1516.

Handke, L. D., Rogers, K. L., Olson, M. E., Somerville, G. A., Jerrells, T. J., Rupp, M. E., et al. (2008). *Staphylococcus epidermidis* saeR is an effector of anaerobic growth and a mediator of acute inflammation. *Infect. Immun.* 76, 141–152. doi: 10.1128/IAI.00556-07

Harris, L. G., Murray, S., Pascoe, B., Bray, J., Meric, G., Mageiros, L., et al. (2016). Biofilm morphotypes and population structure among *Staphylococcus epidermidis* from commensal and clinical samples. *PLoS One* 11:e0151240. doi: 10.1371/journal.pone.0151240

Hayoun, K., Gouveia, D., Grenga, L., Pible, O., Armengaud, J. and Alpha-Bazin, B. (2019). Evaluation of sample preparation methods for fast proteotyping of microorganisms by tandem mass spectrometry. *Front. Microbiol.* 10:1985. doi: 10.3389/fmicb.2019.01985

Hegde, S. S., and Shrader, T. E. (2001). FemABX family members are novel nonribosomal peptidyltransferases and important pathogen-specific drug targets. *J. Biol. Chem.* 276, 6998–7003. doi: 10.1074/jbc.M008591200

Iyer, V., Raut, J., and Dasgupta, A. (2021). Impact of pH on growth of *Staphylococcus epidermidis* and *Staphylococcus aureus* *in vitro*. *J. Med. Microbiol.* 70. doi: 10.1099/jmm.0.001421

Jean Beltran, P. M., Federspiel, J. D., Sheng, X., and Cristea, I. M. (2017). Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. *Mol. Syst. Biol.* 13:922.

Kammeyer, A., and Luiten, R. M. (2015). Oxidation events and skin aging. *Ageing Res. Rev.* 21, 16–29.

Kantyka, T., Pyrc, K., Gruca, M., Smagur, J., Plaza, K., Guzik, K., et al. (2013). *Staphylococcus aureus* proteases degrade lung surfactant protein A potentially impairing innate immunity of the lung. *J. Innate Immun.* 5, 251–260. doi: 10.1159/000345417

Kaur, I., Purves, J., Harwood, M., Ketley, J. M., Andrew, P. W., Waldron, K. J., et al. (2022). Role of horizontally transferred copper resistance genes in *Staphylococcus aureus* and *Listeria monocytogenes*. *Microbiology* 168:1162. doi: 10.1099/mic.001162

Kinkel, T. L., Ramos-Montañez, S., Pando, J. M., Tadeo, D. V., Strom, E. N., Libby, S. J., et al. (2016). An essential role for bacterial nitric oxide synthase in *Staphylococcus aureus* electron transfer and colonization. *Nat. Microbiol.* 2:16224. doi: 10.1038/nmicrobiol.2016.224

Klein, G., Mathé, C., Biola-Clier, M., Devineau, S., Drouineau, E., Hatem, E., et al. (2016). RNA-binding proteins are a major target of silica nanoparticles in cell extracts. *Nanotoxicology* 10, 1555–1564. doi: 10.1080/17435390.2016.1244299

Kleinschmidt, S., Huygens, F., Faoagali, J., Rathnayake, I. U., and Hafner, L. M. (2015). *Staphylococcus epidermidis* as a cause of bacteremia. *Future Microbiol.* 10, 1859–1879.

Koch, G., Wermser, C., Acosta, I. C., Kricks, L., Stengel, S. T., Yepes, A., et al. (2017). Attenuating *Staphylococcus aureus* virulence by targeting flotillin protein scaffold activity. *Cell Chem. Biol.* 24, 845–857. doi: 10.1016/j.chembiol.2017.05.027

Kocianova, S., Vuong, C., Yao, Y., Voyich, J. M., Fischer, E. R., DeLeo, F. R., et al. (2005). Key role of poly-gamma-DL-glutamic acid in immune evasion and virulence of *Staphylococcus epidermidis*. *J. Clin. Invest.* 115, 688–694. doi: 10.1172/JCI23523

Korem, M., Gov, Y., and Rosenberg, M. (2010). Global gene expression in *Staphylococcus aureus* following exposure to alcohol. *Microb. Pathog.* 48, 74–84.

Kunin, C. M., and Rudy, J. (1991). Effect of NaCl-induced osmotic stress on intracellular concentrations of glycine betaine and potassium in *Escherichia coli*. *Enterococcus faecalis*, and *staphylococci*. *J. Lab. Clin. Med.* 118, 217–224.

Lambers, H., Piessens, S., Bloem, A., Pronk, H., and Finkel, P. (2006). Natural skin surface pH is on average below 5, which is beneficial for its resident flora. *Int. J. Cosmet. Sci.* 28, 359–370. doi: 10.1111/j.1467-2494.2006.00344.x

Lee, E., and Anjum, F. (2022). *Staphylococcus Epidermidis*. Treasure Island, FL: StatPearls Publishing.

Lekshmi, M., Ammini, P., Adjei, J., Sanford, L. M., Shrestha, U., Kumar, S., et al. (2018). Modulation of antimicrobial efflux pumps of the major facilitator superfamily in *Staphylococcus aureus*. *AIMS Microbiol.* 4, 1–18. doi: 10.3934/microbiol.2018.1.1

Li, L., Abdelhady, W., Donegan, N. P., Seidl, K., Cheung, A., Zhou, Y. F., et al. (2018). Role of purine biosynthesis in persistent methicillin-resistant *Staphylococcus aureus* infection. *J. Infect. Dis.* 218, 1367–1377. doi: 10.1093/infdis/jiy340

Lindahl, T., and Nyberg, B. (1972). Rate of depurination of native deoxyribonucleic acid. *Biochemistry* 11, 3610–3618.

Liu, H., Sadygov, R. G., and Yates, J. R. (2004). A model for random sampling and estimation of relative protein abundance in shotgun proteomics. *Anal. Chem.* 76, 4193–4201. doi: 10.1021/ac0498563

Lou, Q., Zhu, T., Hu, J., Ben, H., Yang, J., Yu, F., et al. (2011). Role of the SaeRS two-component regulatory system in *Staphylococcus epidermidis* autolysis and biofilm formation. *BMC Microbiol.* 11:146. doi: 10.1186/1471-2180-11-146

Manna, A. C., Ingavale, S. S., Maloney, M., van Wamel, W., and Cheung, A. L. (2004). Identification of sarV (SA2062), a new transcriptional regulator, is repressed by SarA and MgrA (SA0641) and involved in the regulation of autolysis in *Staphylococcus aureus*. *J. Bacteriol.* 186, 5267–5280. doi: 10.1128/JB.186.16.5267–5280.2004

Martínez-García, S., Peralta, H., Betanzos-Cabrera, G., Chavez-Galan, L., Rodriguez-Martínez, S., Cancino-Diaz, M. E., et al. (2021). Proteomic comparison of biofilm vs. planktonic *Staphylococcus epidermidis* cells suggests key metabolic differences between these conditions. *Res. Microbiol.* 172:103796. doi: 10.1016/j.resmic.2020.103796

Mielich-Süss, B., Wagner, R. M., Mietrach, N., Hertlein, T., Marincola, G., Ohlsen, K., et al. (2017). Flotillin scaffold activity contributes to type VII secretion system assembly in *Staphylococcus aureus*. *PLoS Pathog.* 13:e1006728. doi: 10.1371/journal.ppat.1006728
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Sabaté Brescó, M., Harris, L. G., Thompson, K., Stanic, B., Morgenstern, M., O’Mahony, L., et al. (2017). Pathogenic mechanisms and host interactions in *Staphylococcus epidermidis* device-related infection. *Front. Microbiol.* 8:1401. doi: 10.3389/fmicb.2017.01401

Sadykov, M. R., Zhang, B., Halouska, S., Nelson, J. L., Kreimer, L. W., Zhu, Y., et al. (2010). Using NMR metabolomics to investigate tricarboxylic acid cycle-dependent signal transduction in *Staphylococcus epidermidis*. *J. Biol. Chem.* 285, 36616–36624. doi: 10.1074/jbc.M110152843

Samant, S., Lee, H., Ghassemi, M., Chen, J., Cook, J. L., Mankin, A. S., et al. (2008). Nucleotide biosynthesis is critical for growth of bacteria in human blood. *PLoS Pathog.* 4:e37. doi: 10.1371/journal.ppat.0040037

Savijoki, K., Iivanainen, A., Siljamäki, P., Laine, P. K., Paulin, L., Karonen, T., et al. (2014). Genomics and proteomics provide new insight into the commensal and pathogenic lifestyles of bovine- and human-associated *Staphylococcus epidermidis* strains. *J. Proteome Res.* 13, 3748–3762. doi: 10.1021/pr500322d

Schmid-Wendtner, M. H., and Korting, H. C. (2006). The pH of the skin surface and its impact on the barrier function. *Skin Pharmacol. Physiol.* 19, 296–302. doi: 10.1159/000094670

Siljamäki, P., Varmanen, P., Kankainen, M., Pyörälä, S., Karonen, T., Iivanainen, A., et al. (2014). Comparative proteome profiling of bovine and human *Staphylococcus epidermidis* strains for screening specifically expressed virulence and adaptation proteins. *Proteomics* 14, 1890–1894. doi: 10.1002/pmic.201300275

Somerville, G. A., and Powers, R. (2014). Growth and preparation of *Staphylococcus epidermidis* for NMR metabolomic analysis. *Methods Mol. Biol.* 1106, 71–91. doi: 10.1007/978-1-62703-736-5_6

Souza, B. S. V., de Silva, K. C. S., Parente, A. F. A., Borges, C. L., Paccez, J. D., Pereira, M., et al. (2019). The influence of pH on *Staphylococcus saprophyticus* iron metabolism and the production of siderophores. *Microb. Infect.* 21, 456–463.

Steinert, M., Ramming, I., and Bergmann, S. (2020). Impact of von willebrand factor on bacterial pathogenesis. *Front. Med.* 7:543. doi: 10.3389/fmed.2020.0543

Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., et al. (2019). STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. *Nucleic Acids Res.* 47, D607–D613. doi: 10.1093/nar/gky1131

Takada, H., and Yoshikawa, H. (2018). Essentiality and function of WalK/WalR two-component system: the past, present, and future of research. *Biosci. Biotechnol. Biochem.* 82, 1–11. doi: 10.1080/09168451.2018.1444466

Tran, H.-K. R., Grebenc, D. W., Klein, T. A., and Whitney, J. C. (2021). Bacterial type VII secretion: an important player in host-microbe and microbe-microbe interactions. *Mol. Microbiol.* 115, 478–489. doi: 10.1111/mmi.14680

Uribe-Alvarez, C., Chiquete-Félix, N., Contreras-Zentella, M., Guerrero-Castillo, S., Peña, A., and Uribe-Carvajal, S. (2016). *Staphylococcus epidermidis*: metabolic adaptation and biofilm formation in response to different oxygen concentrations. *Pathog. Dis.* 74:ftv111. doi: 10.1093/femspd/ftv111

van Dalen, R., Peschel, A., and van Sorge, N. M. (2020). Wall teichoic acid in *Staphylococcus aureus* host interaction. *Trends Microbiol.* 28, 985–998.

Vanzieleghem, T., Herman-Bausier, P., Dufrene, Y. F., and Mahillon, J. (2015). *Staphylococcus epidermidis* affinity for fibrinogen-coated surfaces correlates with the abundance of the SdrG adhesin on the cell surface. *Langmuir* 31, 4713–4721. doi: 10.1021/acs.langmuir.5b00360

Vasu, D., Sunitha, M. M., Srikanth, L., Swarupa, V., Prasad, U. V., Sireesha, K., et al. (2015). In *Staphylococcus aureus* the regulation of pyruvate kinase activity by serine/threonine protein kinase favors biofilm formation. *3 Biotech* 5, 505–512. doi: 10.1007/s13205-014-0248-3

Viela, F., Speziale, P., Pietrocola, G., and Dufrêne, Y. F. (2019). Bacterial pathogens under high-tension: *Staphylococcus aureus* adhesión to von Willebrand factor is activated by force. *Microb. Cell* 6, 321–323. doi: 10.15698/mic2019.07.684

Wang, L., Li, M., Dong, D., Bach, T. H., Sturdevant, D. E., Vuong, C., et al. (2008). SarZ is a key regulator of biofilm formation and virulence in *Staphylococcus epidermidis*. *J. Infect. Dis.* 197, 1254–1262. doi: 10.1086/586714

Wargo, M. J. (2013). Homeostasis and catabolism of choline and glycine betaine: lessons from *Pseudomonas aeruginosa*. *Appl. Environ. Microbiol.* 79, 2112–2120. doi: 10.1128/AEM.03565-12

Weiss, G., and Schaible, U. E. (2015). Macrophage defense mechanisms against intracellular bacteria. *Immunol. Rev.* 264, 182–203.

Willdigg, J. R., and Helmann, J. D. (2021). Mini review: bacterial membrane composition and its modulation in response to stress. *Front. Mol. Biosci.* 8:634438. doi: 10.3389/fmolb.2021.634438

Xia, J., and Wishart, D. S. (2010). MetPA: a web-based metabolomics tool for pathway analysis and visualization. *Bioinformatics* 26, 2342–2344.

Yee, R., Feng, J., Wang, J., Chen, J., and Zhang, Y. (2019). Identification of genes regulating cell death in *Staphylococcus aureus*. *Front. Microbiol.* 10:2199. doi: 10.3389/fmicb.2019.02199

Zhang, B., Halouska, S., Schiaffo, C. E., Sadykov, M. R., Somerville, G. A. and Powers, R. (2011). NMR analysis of a stress response metabolic signaling network. *J. Proteome Res.* 10, 3743–3754.

Zhang, Y.-M., and Rock, C. O. (2008). Thematic review series: glycerolipids. Acyltransferases in bacterial glycerophospholipid synthesis. *J. Lipid Res.* 49, 1867–1874. doi: 10.1194/jlr.R800005-JLR200

Zhu, Y., Weiss, E. C., Otto, M., Fey, P. D., Smeltzer, M. S., and Somerville, G. A. (2007). *Staphylococcus aureus* biofilm metabolism and the influence of arginine on polysaccharide intercellular adhesin synthesis, biofilm formation, and pathogenesis. *Infect. Immun.* 75, 4219–4226. doi: 10.1128/IAI.00509-07
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Sabaté Brescó, M., Harris, L. G., Thompson, K., Stanic, B., Morgenstern, M., O’Mahony, L., et al. (2017). Pathogenic mechanisms and host interactions in *Staphylococcus epidermidis* device-related infection. *Front. Microbiol.* 8:1401. doi: 10.3389/fmicb.2017.01401

Sadykov, M. R., Zhang, B., Halouska, S., Nelson, J. L., Kreimer, L. W., Zhu, Y., et al. (2010). Using NMR metabolomics to investigate tricarboxylic acid cycle-dependent signal transduction in *Staphylococcus epidermidis*. *J. Biol. Chem.* 285, 36616–36624. doi: 10.1074/jbc.M110.152843

Samant, S., Lee, H., Ghassemi, M., Chen, J., Cook, J. L., Mankin, A. S., et al. (2008). Nucleotide biosynthesis is critical for growth of bacteria in human blood. *PLoS Pathog.* 4:e37. doi: 10.1371/journal.ppat.0040037

Savijoki, K., Iivanainen, A., Siljamäki, P., Laine, P. K., Paulin, L., Karonen, T., et al. (2014). Genomics and proteomics provide new insight into the commensal and pathogenic lifestyles of bovine- and human-associated *Staphylococcus epidermidis* strains. *J. Proteome Res.* 13, 3748–3762. doi: 10.1021/pr500322d

Schmid-Wendtner, M. H., and Korting, H. C. (2006). The pH of the skin surface and its impact on the barrier function. *Skin Pharmacol. Physiol.* 19, 296–302. doi: 10.1159/000094670

Siljamäki, P., Varmanen, P., Kankainen, M., Pyörälä, S., Karonen, T., Iivanainen, A., et al. (2014). Comparative proteome profiling of bovine and human *Staphylococcus epidermidis* strains for screening specifically expressed virulence and adaptation proteins. *Proteomics* 14, 1890–1894. doi: 10.1002/pmic.201300275

Somerville, G. A., and Powers, R. (2014). Growth and preparation of *Staphylococcus epidermidis* for NMR metabolomic analysis. *Methods Mol. Biol.* 1106, 71–91. doi: 10.1007/978-1-62703-736-5_6

Souza, B. S. V., de Silva, K. C. S., Parente, A. F. A., Borges, C. L., Paccez, J. D., Pereira, M., et al. (2019). The influence of pH on *Staphylococcus saprophyticus* iron metabolism and the production of siderophores. *Microb. Infect.* 21, 456–463.

Steinert, M., Ramming, I., and Bergmann, S. (2020). Impact of von willebrand factor on bacterial pathogenesis. *Front. Med.* 7:543. doi: 10.3389/fmed.2020.05043

Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., et al. (2019). STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. *Nucleic Acids Res.* 47, D607–D613. doi: 10.1093/nar/gky1131

Takada, H., and Yoshikawa, H. (2018). Essentiality and function of WalK/WalR two-component system: the past, present, and future of research. *Biosci. Biotechnol. Biochem.* 82, 1–11. doi: 10.1080/09168451.2018.1444466

Tran, H.-K. R., Grebenc, D. W., Klein, T. A., and Whitney, J. C. (2021). Bacterial type VII secretion: an important player in host-microbe and microbe-microbe interactions. *Mol. Microbiol.* 115, 478–489. doi: 10.1111/mmi.14680

Uribe-Alvarez, C., Chiquete-Félix, N., Contreras-Zentella, M., Guerrero-Castillo, S., Peña, A., and Uribe-Carvajal, S. (2016). *Staphylococcus epidermidis*: metabolic adaptation and biofilm formation in response to different oxygen concentrations. *Pathog. Dis.* 74:ftv111. doi: 10.1093/femspd/ftv111

van Dalen, R., Peschel, A., and van Sorge, N. M. (2020). Wall teichoic acid in *Staphylococcus aureus* host interaction. *Trends Microbiol.* 28, 985–998.

Vanzieleghem, T., Herman-Bausier, P., Dufrene, Y. F., and Mahillon, J. (2015). *Staphylococcus epidermidis* affinity for fibrinogen-coated surfaces correlates with the abundance of the SdrG adhesin on the cell surface. *Langmuir* 31, 4713–4721. doi: 10.1021/acs.langmuir.5b00360

Vasu, D., Sunitha, M. M., Srikanth, L., Swarupa, V., Prasad, U. V., Sireesha, K., et al. (2015). In *Staphylococcus aureus* the regulation of pyruvate kinase activity by serine/threonine protein kinase favors biofilm formation. *3 Biotech* 5, 505–512. doi: 10.1007/s13205-014-0248-3

Viela, F., Speziale, P., Pietrocola, G., and Dufrêne, Y. F. (2019). Bacterial pathogens under high-tension: *Staphylococcus aureus* adhesión to von Willebrand factor is activated by force. *Microb. Cell* 6, 321–323. doi: 10.15698/mic2019.07.684

Wang, L., Li, M., Dong, D., Bach, T. H., Sturdevant, D. E., Vuong, C., et al. (2008). SarZ is a key regulator of biofilm formation and virulence in *Staphylococcus epidermidis*. *J. Infect. Dis.* 197, 1254–1262. doi: 10.1086/586714

Wargo, M. J. (2013). Homeostasis and catabolism of choline and glycine betaine: lessons from *Pseudomonas aeruginosa*. *Appl. Environ. Microbiol.* 79, 2112–2120. doi: 10.1128/AEM.03565-12

Weiss, G., and Schaible, U. E. (2015). Macrophage defense mechanisms against intracellular bacteria. *Immunol. Rev.* 264, 182–203.

Willdigg, J. R., and Helmann, J. D. (2021). Mini review: bacterial membrane composition and its modulation in response to stress. *Front. Mol. Biosci.* 8:634438. doi: 10.3389/fmolb.2021.634438

Xia, J., and Wishart, D. S. (2010). MetPA: a web-based metabolomics tool for pathway analysis and visualization. *Bioinformatics* 26, 2342–2344.

Yee, R., Feng, J., Wang, J., Chen, J., and Zhang, Y. (2019). Identification of genes regulating cell death in *Staphylococcus aureus*. *Front. Microbiol.* 10:2199. doi: 10.3389/fmicb.2019.02199

Zhang, B., Halouska, S., Schiaffo, C. E., Sadykov, M. R., Somerville, G. A. and Powers, R. (2011). NMR analysis of a stress response metabolic signaling network. *J. Proteome Res.* 10, 3743–3754.

Zhang, Y.-M., and Rock, C. O. (2008). Thematic review series: glycerolipids. Acyltransferases in bacterial glycerophospholipid synthesis. *J. Lipid Res.* 49, 1867–1874. doi: 10.1194/jlr.R800005-JLR200

Zhu, Y., Weiss, E. C., Otto, M., Fey, P. D., Smeltzer, M. S., and Somerville, G. A. (2007). *Staphylococcus aureus* biofilm metabolism and the influence of arginine on polysaccharide intercellular adhesin synthesis, biofilm formation, and pathogenesis. *Infect. Immun.* 75, 4219–4226. doi: 10.1128/IAI.00509-07