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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/79547完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 李昆達(Kung-Ta Lee) | |
| dc.contributor.author | Yu-Chieh Lin | en |
| dc.contributor.author | 林雨頡 | zh_TW |
| dc.contributor.author | f05b22007 | |
| dc.date.accessioned | 2022-11-23T09:03:22Z | - |
| dc.date.available | 2024-09-22 | |
| dc.date.available | 2022-11-23T09:03:22Z | - |
| dc.date.copyright | 2021-11-08 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2021-09-24 | |
| dc.identifier.citation | 1. Ventola, C. L. (2015) The antibiotic resistance crisis: part 1: causes and threats. P T 40, 277-283. 2. von Wintersdorff, C. J., Penders, J., van Niekerk, J. M., Mills, N. D., Majumder, S., van Alphen, L. B., Savelkoul, P. H., and Wolffs, P. F. (2016) Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer. Front Microbiol 7, 173. DOI: 10.3389/fmicb.2016.00173. 3. Graf, F. E., Palm, M., Warringer, J., and Farewell, A. (2019) Inhibiting conjugation as a tool in the fight against antibiotic resistance. Drug Dev Res 80, 19-23. DOI: 10.1002/ddr.21457. 4. Bergstrom, C. T., Lipsitch, M., and Levin, B. R. (2000) Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155, 1505-1519. 5. CDC (2013) Antibiotic resistance threats in the United States. 6. Paulsen, I. T., Banerjei, L., Myers, G. S., Nelson, K. E., Seshadri, R., Read, T. D., Fouts, D. E., Eisen, J. A., Gill, S. R., Heidelberg, J. F., Tettelin, H., Dodson, R. J., Umayam, L., Brinkac, L., Beanan, M., Daugherty, S., DeBoy, R. T., Durkin, S., Kolonay, J., Madupu, R., Nelson, W., Vamathevan, J., Tran, B., Upton, J., Hansen, T., Shetty, J., Khouri, H., Utterback, T., Radune, D., Ketchum, K. A., Dougherty, B. A., and Fraser, C. M. (2003) Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299, 2071-2074. DOI: 10.1126/science.1080613. 7. Aakra, A., Vebo, H., Snipen, L., Hirt, H., Aastveit, A., Kapur, V., Dunny, G., Murray, B. E., and Nes, I. F. (2005) Transcriptional response of Enterococcus faecalis V583 to erythromycin. Antimicrob Agents Chemother 49, 2246-2259. DOI: 10.1128/AAC.49.6.2246-2259.2005. 8. Hanchi, H., Mottawea, W., Sebei, K., and Hammami, R. (2018) The Genus Enterococcus: Between Probiotic Potential and Safety Concerns-An Update. Front Microbiol 9, 1791. DOI: 10.3389/fmicb.2018.01791. 9. Lindenstrauss, A. G., Ehrmann, M. A., Behr, J., Landstorfer, R., Haller, D., Sartor, R. B., and Vogel, R. F. (2014) Transcriptome analysis of Enterococcus faecalis toward its adaption to surviving in the mouse intestinal tract. Arch Microbiol 196, 423-433. DOI: 10.1007/s00203-014-0982-2. 10. Arias, C. A., and Murray, B. E. (2012) The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol 10, 266-278. DOI: 10.1038/nrmicro2761. 11. Jones, M. E., Draghi, D. C., Thornsberry, C., Karlowsky, J. A., Sahm, D. F., and Wenzel, R. P. (2004) Emerging resistance among bacterial pathogens in the intensive care unit–a European and North American Surveillance study (2000–2002). Annals of Clinical Microbiology and Antimicrobials 3, 1-11. 12. Arias, C. A., Contreras, G. A., and Murray, B. E. (2010) Management of multidrug-resistant enterococcal infections. Clin Microbiol Infect 16, 555-562. DOI: 10.1111/j.1469-0691.2010.03214.x. 13. Geldart, K. G., Kommineni, S., Forbes, M., Hayward, M., Dunny, G. M., Salzman, N. H., and Kaznessis, Y. N. (2018) Engineered E. coli Nissle 1917 for the reduction of vancomycin-resistant Enterococcus in the intestinal tract. Bioeng Transl Med 3, 197-208. DOI: 10.1002/btm2.10107. 14. Clewell, D. B., Francia, M. V., Flannagan, S. E., and An, F. Y. (2002) Enterococcal plasmid transfer: sex pheromones, transfer origins, relaxases, and the Staphylococcus aureus issue. Plasmid 48, 193-201. DOI: 10.1016/s0147-619x(02)00113-0. 15. Manson, J. M., Hancock, L. E., and Gilmore, M. S. (2010) Mechanism of chromosomal transfer of Enterococcus faecalis pathogenicity island, capsule, antimicrobial resistance, and other traits. Proc Natl Acad Sci U S A 107, 12269-12274. DOI: 10.1073/pnas.1000139107. 16. Willems, R. J., Hanage, W. P., Bessen, D. E., and Feil, E. J. (2011) Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance. FEMS Microbiol Rev 35, 872-900. DOI: 10.1111/j.1574-6976.2011.00284.x. 17. Liu, L., Chen, X., Skogerbo, G., Zhang, P., Chen, R., He, S., and Huang, D. W. (2012) The human microbiome: a hot spot of microbial horizontal gene transfer. Genomics 100, 265-270. DOI: 10.1016/j.ygeno.2012.07.012. 18. Dunny, G. M. (2007) The peptide pheromone-inducible conjugation system of Enterococcus faecalis plasmid pCF10: cell-cell signalling, gene transfer, complexity and evolution. Philos Trans R Soc Lond B Biol Sci 362, 1185-1193. DOI: 10.1098/rstb.2007.2043. 19. Breuer, R. J., Hirt, H., and Dunny, G. M. (2018) Mechanistic Features of the Enterococcal pCF10 Sex Pheromone Response and the Biology of Enterococcus faecalis in Its Natural Habitat. J Bacteriol 200. DOI: 10.1128/JB.00733-17. 20. Dunny, G., Funk, C., and Adsit, J. (1981) Direct stimulation of the transfer of antibiotic resistance by sex pheromones in Streptococcus faecalis. Plasmid 6, 270-278. DOI: 10.1016/0147-619x(81)90035-4. 21. Torres, O. R., Korman, R. Z., Zahler, S. A., and Dunny, G. M. (1991) The conjugative transposon Tn925: enhancement of conjugal transfer by tetracycline in Enterococcus faecalis and mobilization of chromosomal genes in Bacillus subtilis and E. faecalis. Mol Gen Genet 225, 395-400. DOI: 10.1007/bf00261679. 22. Carniol, K., and Gilmore, M. S. (2004) Signal transduction, quorum-sensing, and extracellular protease activity in Enterococcus faecalis biofilm formation. J Bacteriol 186, 8161-8163. DOI: 10.1128/JB.186.24.8161-8163.2004. 23. Nakayama, J., Ruhfel, R. E., Dunny, G. M., Isogai, A., and Suzuki, A. (1994) The prgQ gene of the Enterococcus faecalis tetracycline resistance plasmid pCF10 encodes a peptide inhibitor, iCF10. J Bacteriol 176, 7405-7408. DOI: 10.1128/jb.176.23.7405-7408.1994. 24. Leonard, B. A., Podbielski, A., Hedberg, P. J., and Dunny, G. M. (1996) Enterococcus faecalis pheromone binding protein, PrgZ, recruits a chromosomal oligopeptide permease system to import sex pheromone cCF10 for induction of conjugation. Proc Natl Acad Sci U S A 93, 260-264. DOI: 10.1073/pnas.93.1.260. 25. Shi, K., Brown, C. K., Gu, Z. Y., Kozlowicz, B. K., Dunny, G. M., Ohlendorf, D. H., and Earhart, C. A. (2005) Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis. Proc Natl Acad Sci U S A 102, 18596-18601. DOI: 10.1073/pnas.0506163102. 26. Bensing, B. A., and Dunny, G. M. (1993) Cloning and molecular analysis of genes affecting expression of binding substance, the recipient-encoded receptor(s) mediating mating aggregate formation in Enterococcus faecalis. J Bacteriol 175, 7421-7429. DOI: 10.1128/jb.175.22.7421-7429.1993. 27. Bhatty, M., Cruz, M. R., Frank, K. L., Gomez, J. A., Andrade, F., Garsin, D. A., Dunny, G. M., Kaplan, H. B., and Christie, P. J. (2015) Enterococcus faecalis pCF10-encoded surface proteins PrgA, PrgB (aggregation substance) and PrgC contribute to plasmid transfer, biofilm formation and virulence. Mol Microbiol 95, 660-677. DOI: 10.1111/mmi.12893. 28. Dunny, G. M. (2013) Enterococcal sex pheromones: signaling, social behavior, and evolution. Annu Rev Genet 47, 457-482. DOI: 10.1146/annurev-genet-111212-133449. 29. Chen, Y., Staddon, J. H., and Dunny, G. M. (2007) Specificity determinants of conjugative DNA processing in the Enterococcus faecalis plasmid pCF10 and the Lactococcus lactis plasmid pRS01. Mol Microbiol 63, 1549-1564. DOI: 10.1111/j.1365-2958.2007.05610.x. 30. Staddon, J. H., Bryan, E. M., Manias, D. A., Chen, Y., and Dunny, G. M. (2006) Genetic characterization of the conjugative DNA processing system of enterococcal plasmid pCF10. Plasmid 56, 102-111. DOI: 10.1016/j.plasmid.2006.05.001. 31. Chen, Y., Bandyopadhyay, A., Kozlowicz, B. K., Haemig, H. A. H., Tai, A., Hu, W. S., and Dunny, G. M. (2017) Mechanisms of peptide sex pheromone regulation of conjugation in Enterococcus faecalis. Microbiologyopen 6. DOI: 10.1002/mbo3.492. 32. Chatterjee, A., Cook, L. C., Shu, C. C., Chen, Y., Manias, D. A., Ramkrishna, D., Dunny, G. M., and Hu, W. S. (2013) Antagonistic self-sensing and mate-sensing signaling controls antibiotic-resistance transfer. Proc Natl Acad Sci U S A 110, 7086-7090. DOI: 10.1073/pnas.1212256110. 33. Clewell, D. B., An, F. Y., Flannagan, S. E., Antiporta, M., and Dunny, G. M. (2000) Enterococcal sex pheromone precursors are part of signal sequences for surface lipoproteins. Mol Microbiol 35, 246-247. DOI: 10.1046/j.1365-2958.2000.01687.x. 34. Antiporta, M. H., and Dunny, G. M. (2002) ccfA, the genetic determinant for the cCF10 peptide pheromone in Enterococcus faecalis OG1RF. J Bacteriol 184, 1155-1162. DOI: 10.1128/jb.184.4.1155-1162.2002. 35. Cabezon, E., de la Cruz, F., and Arechaga, I. (2017) Conjugation Inhibitors and Their Potential Use to Prevent Dissemination of Antibiotic Resistance Genes in Bacteria. Front Microbiol 8, 2329. DOI: 10.3389/fmicb.2017.02329. 36. Getino, M., and de la Cruz, F. (2018) Natural and Artificial Strategies To Control the Conjugative Transmission of Plasmids. Microbiol Spectr 6. DOI: 10.1128/microbiolspec.MTBP-0015-2016. 37. Lujan, S. A., Guogas, L. M., Ragonese, H., Matson, S. W., and Redinbo, M. R. (2007) Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase. Proc Natl Acad Sci U S A 104, 12282-12287. DOI: 10.1073/pnas.0702760104. 38. Keyser, P., Elofsson, M., Rosell, S., and Wolf-Watz, H. (2008) Virulence blockers as alternatives to antibiotics: type III secretion inhibitors against Gram-negative bacteria. J Intern Med 264, 17-29. DOI: 10.1111/j.1365-2796.2008.01941.x. 39. Getino, M., Sanabria-Rios, D. J., Fernandez-Lopez, R., Campos-Gomez, J., Sanchez-Lopez, J. M., Fernandez, A., Carballeira, N. M., and de la Cruz, F. (2015) Synthetic Fatty Acids Prevent Plasmid-Mediated Horizontal Gene Transfer. MBio 6, e01032-01015. DOI: 10.1128/mBio.01032-15. 40. Saarela, M., Lahteenmaki, L., Crittenden, R., Salminen, S., and Mattila-Sandholm, T. (2002) Gut bacteria and health foods--the European perspective. Int J Food Microbiol 78, 99-117. DOI: 10.1016/s0168-1605(02)00235-0. 41. Gourbeyre, P., Denery, S., and Bodinier, M. (2011) Probiotics, prebiotics, and synbiotics: impact on the gut immune system and allergic reactions. J Leukoc Biol 89, 685-695. DOI: 10.1189/jlb.1109753. 42. Martin, R., and Langella, P. (2019) Emerging Health Concepts in the Probiotics Field: Streamlining the Definitions. Front Microbiol 10, 1047. DOI: 10.3389/fmicb.2019.01047. 43. Elshaghabee, F. M. F., Rokana, N., Gulhane, R. D., Sharma, C., and Panwar, H. (2017) Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives. Front Microbiol 8, 1490. DOI: 10.3389/fmicb.2017.01490. 44. Majeed, M., Nagabhushanam, K., Natarajan, S., Sivakumar, A., Ali, F., Pande, A., Majeed, S., and Karri, S. K. (2016) Bacillus coagulans MTCC 5856 supplementation in the management of diarrhea predominant Irritable Bowel Syndrome: a double blind randomized placebo controlled pilot clinical study. Nutr J 15, 21. DOI: 10.1186/s12937-016-0140-6. 45. Anukam, K. C., Osazuwa, E. O., Osadolor, H. B., Bruce, A. W., and Reid, G. (2008) Yogurt containing probiotic Lactobacillus rhamnosus GR-1 and L. reuteri RC-14 helps resolve moderate diarrhea and increases CD4 count in HIV/AIDS patients. J Clin Gastroenterol 42, 239-243. DOI: 10.1097/MCG.0b013e31802c7465. 46. Zhang, F., Li, X. Y., Park, H. J., and Zhao, M. (2013) Effect of microencapsulation methods on the survival of freeze-dried Bifidobacterium bifidum. J Microencapsul 30, 511-518. DOI: 10.3109/02652048.2012.758178. 47. Spinler, J. K., Taweechotipatr, M., Rognerud, C. L., Ou, C. N., Tumwasorn, S., and Versalovic, J. (2008) Human-derived probiotic Lactobacillus reuteri demonstrate antimicrobial activities targeting diverse enteric bacterial pathogens. Anaerobe 14, 166-171. DOI: 10.1016/j.anaerobe.2008.02.001. 48. Piewngam, P., Zheng, Y., Nguyen, T. H., Dickey, S. W., Joo, H. S., Villaruz, A. E., Glose, K. A., Fisher, E. L., Hunt, R. L., Li, B., Chiou, J., Pharkjaksu, S., Khongthong, S., Cheung, G. Y. C., Kiratisin, P., and Otto, M. (2018) Pathogen elimination by probiotic Bacillus via signalling interference. Nature 562, 532-537. DOI: 10.1038/s41586-018-0616-y. 49. Jett, B. D., Huycke, M. M., and Gilmore, M. S. (1994) Virulence of enterococci. Clin Microbiol Rev 7, 462-478. DOI: 10.1128/cmr.7.4.462. 50. McCormick, J. K., Tripp, T. J., Dunny, G. M., and Schlievert, P. M. (2002) Formation of vegetations during infective endocarditis excludes binding of bacterial-specific host antibodies to Enterococcus faecalis. J Infect Dis 185, 994-997. DOI: 10.1086/339604. 51. Carniol, K., and Gilmore, M. S. (2004) Signal transduction, quorum-sensing, and extracellular protease activity in Enterococcus faecalis biofilm formation. J Bacteriol 186, 8161–8163. DOI: 10.1128/JB.186.24.8161-8163.2004. 52. Murray, B. E. (1997) Vancomycin-resistant enterococci. Am J Med 102, 284-293. DOI: 10.1016/S0002-9343(99)80270-8. 53. Klevens, R. M., Edwards, J. R., Richards, C. L., Jr., Horan, T. C., Gaynes, R. P., Pollock, D. A., and Cardo, D. M. (2007) Estimating health care-associated infections and deaths in U.S. hospitals, 2002. Public Health Rep 122, 160-166. DOI: 10.1177/003335490712200205. 54. Frieden, T. (2013) Antibiotic resistance threats in the United States, US Department of Health Human Services, Washington, DC. 55. Bandyopadhyay, A., O'Brien, S., Frank, K. L., Dunny, G. M., and Hu, W. S. (2016) Antagonistic Donor Density Effect Conserved in Multiple Enterococcal Conjugative Plasmids. Appl Environ Microbiol 82, 4537-4545. DOI: 10.1128/AEM.00363-16. 56. Breuer, R. J., Hirt, H., and Dunny, G. M. (2018) Mechanistic features of the enterococcal pCF10 sex pheromone response and the biology of Enterococcus faecalis in its natural habitat. J Bacteriol 200, e00733–00717. DOI: 10.1128/JB.00733-17. 57. Akhtar, M., Hirt, H., and Zurek, L. (2009) Horizontal transfer of the tetracycline resistance gene tetM mediated by pCF10 among Enterococcus faecalis in the house fly (Musca domestica L.) alimentary canal. Microb Ecol 58, 509-518. DOI: 10.1007/s00248-009-9533-9. 58. Kamada, N., Chen, G. Y., Inohara, N., and Nunez, G. (2013) Control of pathogens and pathobionts by the gut microbiota. Nat Immunol 14, 685-690. DOI: 10.1038/ni.2608. 59. Macpherson, A. J., and Harris, N. L. (2004) Interactions between commensal intestinal bacteria and the immune system. Nat Rev Immunol 4, 478-485. DOI: 10.1038/nri1373. 60. Bermudez-Brito, M., Plaza-Diaz, J., Munoz-Quezada, S., Gomez-Llorente, C., and Gil, A. (2012) Probiotic mechanisms of action. Ann Nutr Metab 61, 160-174. DOI: 10.1159/000342079. 61. Dunny, G. M., Antiporta, M. H., and Hirt, H. (2001) Peptide pheromone-induced transfer of plasmid pCF10 in Enterococcus faecalis: probing the genetic and molecular basis for specificity of the pheromone response. Peptides 22, 1529-1539. DOI: 10.1016/s0196-9781(01)00489-2. 62. Kuo, L. C., Cheng, W. Y., Wu, R. Y., Huang, C. J., and Lee, K. T. (2006) Hydrolysis of black soybean isoflavone glycosides by Bacillus subtilis natto. Appl Microbiol Biotechnol 73, 314-320. DOI: 10.1007/s00253-006-0474-7. 63. Kuo, L. C., and Lee, K. T. (2008) Cloning, expression, and characterization of two beta-glucosidases from isoflavone glycoside-hydrolyzing Bacillus subtilis natto. J Agric Food Chem 56, 119-125. DOI: 10.1021/jf072287q. 64. Atlas, R. M. (2010) Handbook of microbiological media, CRC press, 65. Dunny, G. M., Brown, B. L., and Clewell, D. B. (1978) Induced cell aggregation and mating in Streptococcus faecalis: evidence for a bacterial sex pheromone. Proc Natl Acad Sci U S A 75, 3479-3483. DOI: 10.1073/pnas.75.7.3479. 66. Kristich, C. J., Chandler, J. R., and Dunny, G. M. (2007) Development of a host-genotype-independent counterselectable marker and a high-frequency conjugative delivery system and their use in genetic analysis of Enterococcus faecalis. Plasmid 57, 131-144. DOI: 10.1016/j.plasmid.2006.08.003. 67. Barnes, A. M. T., Dale, J. L., Chen, Y., Manias, D. A., Greenwood Quaintance, K. E., Karau, M. K., Kashyap, P. C., Patel, R., Wells, C. L., and Dunny, G. M. (2017) Enterococcus faecalis readily colonizes the entire gastrointestinal tract and forms biofilms in a germ-free mouse model. Virulence 8, 282-296. DOI: 10.1080/21505594.2016.1208890. 68. Ruhfel, R. E., Manias, D. A., and Dunny, G. M. (1993) Cloning and characterization of a region of the Enterococcus faecalis conjugative plasmid, pCF10, encoding a sex pheromone-binding function. J Bacteriol 175, 5253-5259. DOI: 10.1128/jb.175.16.5253-5259.1993. 69. Erickson, R. J. B., Bandyopadhyay, A. A., Barnes, A. M. T., O'Brien, S. A., Hu, W. S., and Dunny, G. M. (2020) Single-Cell Analysis Reveals that the Enterococcal Sex Pheromone Response Results in Expression of Full-Length Conjugation Operon Transcripts in All Induced Cells. J Bacteriol 202. DOI: 10.1128/JB.00685-19. 70. Hsieh, C. W., Chiu, Y. C., Wang, P. S., and Lin, J. H. (2016) Determining probiotic potential of lactic acid bacteria isolated from traditional Taiwan fermented vegetables. Journal of Agriculture and Forestry, National Chiayi University 13, 81-93. 71. Davis, G. H. (1955) The classification of Lactobacilli from the human mouth. J Gen Microbiol 13, 481-493. DOI: 10.1099/00221287-13-3-481. 72. Kandler, O., Stetter, K.-O., and Köhl, R. (1980) Lactobacillus reuteri sp. nov., a new species of heterofermentative lactobacilli. Zentralblatt Für Bakteriologie: I. Abt. Originale C: Allgemeine, Angewandte Und Ökologische Mikrobiologie 1, 264-269. 73. Gordon, R. E., Haynes, W. C., and Pang, C. H.-N. (1973) The genus bacillus, Agricultural Research Service, US Department of Agriculture. 74. Zeigler, D. R., Pragai, Z., Rodriguez, S., Chevreux, B., Muffler, A., Albert, T., Bai, R., Wyss, M., and Perkins, J. B. (2008) The origins of 168, W23, and other Bacillus subtilis legacy strains. J Bacteriol 190, 6983-6995. DOI: 10.1128/JB.00722-08. 75. Koo, B. M., Kritikos, G., Farelli, J. D., Todor, H., Tong, K., Kimsey, H., Wapinski, I., Galardini, M., Cabal, A., Peters, J. M., Hachmann, A. B., Rudner, D. Z., Allen, K. N., Typas, A., and Gross, C. A. (2017) Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis. Cell Syst 4, 291-305 e297. DOI: 10.1016/j.cels.2016.12.013. 76. Seki, H., Shiohara, M., Matsumura, T., Miyagawa, N., Tanaka, M., Komiyama, A., and Kurata, S. (2003) Prevention of antibiotic-associated diarrhea in children by Clostridium butyricum MIYAIRI. Pediatr Int 45, 86-90. DOI: 10.1046/j.1442-200x.2003.01671.x. 77. Lin, X., Chen, X., Chen, Y., Jiang, W., and Chen, H. (2015) The effect of five probiotic lactobacilli strains on the growth and biofilm formation of Streptococcus mutans. Oral Dis 21, e128-134. DOI: 10.1111/odi.12257. 78. Wasfi, R., Abd El-Rahman, O. A., Zafer, M. M., and Ashour, H. M. (2018) Probiotic Lactobacillus sp. inhibit growth, biofilm formation and gene expression of caries-inducing Streptococcus mutans. J Cell Mol Med 22, 1972-1983. DOI: 10.1111/jcmm.13496. 79. Breuer, R. J., Bandyopadhyay, A., O'Brien, S. A., Barnes, A. M. T., Hunter, R. C., Hu, W. S., and Dunny, G. M. (2017) Stochasticity in the enterococcal sex pheromone response revealed by quantitative analysis of transcription in single cells. PLoS Genet 13, e1006878. DOI: 10.1371/journal.pgen.1006878. 80. Hirt, H., Greenwood-Quaintance, K. E., Karau, M. J., Till, L. M., Kashyap, P. C., Patel, R., and Dunny, G. M. (2018) Enterococcus faecalis Sex Pheromone cCF10 Enhances Conjugative Plasmid Transfer In Vivo. MBio 9. DOI: 10.1128/mBio.00037-18. 81. Shokryazdan, P., Sieo, C. C., Kalavathy, R., Liang, J. B., Alitheen, N. B., Faseleh Jahromi, M., and Ho, Y. W. (2014) Probiotic potential of Lactobacillus strains with antimicrobial activity against some human pathogenic strains. Biomed Res Int 2014, 927268. DOI: 10.1155/2014/927268. 82. Mukherjee, P. K., Chandra, J., Retuerto, M., Sikaroodi, M., Brown, R. E., Jurevic, R., Salata, R. A., Lederman, M. M., Gillevet, P. M., and Ghannoum, M. A. (2014) Oral mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi. PLoS Pathog 10, e1003996. DOI: 10.1371/journal.ppat.1003996. 83. Grintzalis, K., Georgiou, C. D., and Schneider, Y. J. (2015) An accurate and sensitive Coomassie Brilliant Blue G-250-based assay for protein determination. Anal Biochem 480, 28-30. DOI: 10.1016/j.ab.2015.03.024. 84. Cai, D., Wang, H., He, P., Zhu, C., Wang, Q., Wei, X., Nomura, C. T., and Chen, S. (2017) A novel strategy to improve protein secretion via overexpression of the SppA signal peptide peptidase in Bacillus licheniformis. Microb Cell Fact 16, 70. DOI: 10.1186/s12934-017-0688-7. 85. Hsu, R. L., Lee, K. T., Wang, J. H., Lee, L. Y., and Chen, R. P. (2009) Amyloid-degrading ability of nattokinase from Bacillus subtilis natto. J Agric Food Chem 57, 503-508. DOI: 10.1021/jf803072r. 86. Friberger, P., Knos, M., Gustavsson, S., Aurell, L., and Claeson, G. (1978) Methods for determination of plasmin, antiplasmin and plasminogen by means of substrate S-2251. Haemostasis 7, 138-145. DOI: 10.1159/000214252. 87. Bolger, A. M., Lohse, M., and Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120. DOI: 10.1093/bioinformatics/btu170. 88. Kim, D., Langmead, B., and Salzberg, S. L. (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357-360. DOI: 10.1038/nmeth.3317. 89. Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., and Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28, 511-515. DOI: 10.1038/nbt.1621. 90. Yu, G., Wang, L. G., Han, Y., and He, Q. Y. (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284-287. DOI: 10.1089/omi.2011.0118. 91. Livak, K. J., and Schmittgen, T. D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25, 402-408. DOI: 10.1006/meth.2001.1262. 92. Wu, S., Liu, Y., Lei, L., and Zhang, H. (2021) Endogenous antisense walR RNA modulates biofilm organization and pathogenicity of Enterococcus faecalis. Exp Ther Med 21, 69. DOI: 10.3892/etm.2020.9501. 93. Letourneau, J., Levesque, C., Berthiaume, F., Jacques, M., and Mourez, M. (2011) In vitro assay of bacterial adhesion onto mammalian epithelial cells. J Vis Exp. DOI: 10.3791/2783. 94. Dale, J. L., Cagnazzo, J., Phan, C. Q., Barnes, A. M., and Dunny, G. M. (2015) Multiple roles for Enterococcus faecalis glycosyltransferases in biofilm-associated antibiotic resistance, cell envelope integrity, and conjugative transfer. Antimicrob Agents Chemother 59, 4094-4105. DOI: 10.1128/AAC.00344-15. 95. Liu, F., Jin, P., Gong, H., Sun, Z., Du, L., and Wang, D. (2020) Antibacterial and antibiofilm activities of thyme oil against foodborne multiple antibiotics-resistant Enterococcus faecalis. Poult Sci 99, 5127-5136. DOI: 10.1016/j.psj.2020.06.067. 96. Liu, F., Sun, Z., Wang, F., Liu, Y., Zhu, Y., Du, L., Wang, D., and Xu, W. (2020) Inhibition of biofilm formation and exopolysaccharide synthesis of Enterococcus faecalis by phenyllactic acid. Food Microbiol 86, 103344. DOI: 10.1016/j.fm.2019.103344. 97. Dubois, M., Gilles, K., Hamilton, J. K., Rebers, P. A., and Smith, F. (1951) A colorimetric method for the determination of sugars. Nature 168, 167. DOI: 10.1038/168167a0. 98. Nakayama, J., Ruhfel, R. E., Dunny, G. M., Isogai, A., and Suzuki, A. (1994) The prgQ gene of the Enterococcus faecalis tetracycline resistance plasmid pCF10 encodes a peptide inhibitor, iCF10. J Bacteriol 176, 7405–7408. DOI: 10.1128/jb.176.23.7405-7408.1994. 99. Ling Lin, F., Zi Rong, X., Wei Fen, L., Jiang Bing, S., Ping, L., and Chun Xia, H. (2007) Protein secretion pathways in Bacillus subtilis: implication for optimization of heterologous protein secretion. Biotechnol Adv 25, 1-12. DOI: 10.1016/j.biotechadv.2006.08.002. 100. Contesini, F. J., Melo, R. R., and Sato, H. H. (2018) An overview of Bacillus proteases: from production to application. Crit Rev Biotechnol 38, 321–334. DOI: 10.1080/07388551.2017.1354354. 101. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessieres, P., Bolotin, A., Borchert, S., Borriss, R., Boursier, L., Brans, A., Braun, M., Brignell, S. C., Bron, S., Brouillet, S., Bruschi, C. V., Caldwell, B., Capuano, V., Carter, N. M., Choi, S. K., Cordani, J. J., Connerton, I. F., Cummings, N. J., Daniel, R. A., Denziot, F., Devine, K. M., Dusterhoft, A., Ehrlich, S. D., Emmerson, P. T., Entian, K. D., Errington, J., Fabret, C., Ferrari, E., Foulger, D., Fritz, C., Fujita, M., Fujita, Y., Fuma, S., Galizzi, A., Galleron, N., Ghim, S. Y., Glaser, P., Goffeau, A., Golightly, E. J., Grandi, G., Guiseppi, G., Guy, B. J., Haga, K., Haiech, J., Harwood, C. R., Henaut, A., Hilbert, H., Holsappel, S., Hosono, S., Hullo, M. F., Itaya, M., Jones, L., Joris, B., Karamata, D., Kasahara, Y., Klaerr-Blanchard, M., Klein, C., Kobayashi, Y., Koetter, P., Koningstein, G., Krogh, S., Kumano, M., Kurita, K., Lapidus, A., Lardinois, S., Lauber, J., Lazarevic, V., Lee, S. ., Levine, A., Liu, H., Masuda, S., Mauel, C., Medigue, C., Medina, N., Mellado, R. P., Mizuno, M., Moestl, D., Nakai, S., Noback, M., Noone, D., O'Reilly, M., Ogawa, K., Ogiwara, A., Oudega, B., Park, S. H., Parro, V., Pohl, T. M., Portelle, D., Porwollik, S., Prescott, A. M., Presecan, E., Pujic, P., Purnelle, B., Rapoport, G., Rey, M., Reynolds, S., Rieger, M., Rivolta, C., Rocha, E., Roche, B., Rose, M., Sadaie, Y., Sato, T., Scanlan, E., Schleich, S., Schroeter, R., Scoffone, F., Sekiguchi, J., Sekowska, A., Seror, S. J., Serror, P., Shin, B. S., Soldo, B., Sorokin, A., Tacconi, E., Takagi, T., Takahashi, H., Takemaru, K., Takeuchi, M., Tamakoshi, A., Tanaka, T., Terpstra, P., Togoni, A., Tosato, V., Uchiyama, S., Vandebol, M., Vannier, F., Vassarotti, A., Viari, A., Wambutt, R., Wedler, H., Weitzenegger, T., Winters, P., Wipat, A., Yamamoto, H., Yamane, K., Yasumoto, K., Yata, K., Yoshida, K., Yoshikawa, H. F., Zumstein, E., Yoshikawa, H., and Danchin, A. (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390, 249-256. DOI: 10.1038/36786. 102. Nishito, Y., Osana, Y., Hachiya, T., Popendorf, K., Toyoda, A., Fujiyama, A., Itaya, M., and Sakakibara, Y. (2010) Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics 11, 243. DOI: 10.1186/1471-2164-11-243. 103. Sloma, A., Rufo, G. A., Jr., Theriault, K. A., Dwyer, M., Wilson, S. W., and Pero, J. (1991) Cloning and characterization of the gene for an additional extracellular serine protease of Bacillus subtilis. J Bacteriol 173, 6889-6895. DOI: 10.1128/jb.173.21.6889-6895.1991. 104. Showsh, S. A., De Boever, E. H., and Clewell, D. B. (2001) Vancomycin resistance plasmid in Enterococcus faecalis that encodes sensitivity to a sex pheromone also produced by Staphylococcus aureus. Antimicrob Agents Chemother 45, 2177-2178. DOI: 10.1128/aac.45.7.2177-2178.2001. 105. De Boever, E. H., Clewell, D. B., and Fraser, C. M. (2000) Enterococcus faecalis conjugative plasmid pAM373: complete nucleotide sequence and genetic analyses of sex pheromone response. Mol Microbiol 37, 1327-1341. DOI: 10.1046/j.1365-2958.2000.02072.x. 106. Clewell, D. B., An, F. Y., Flannagan, S. E., Antiporta, M., and Dunny, G. M. (2000) Enterococcal sex pheromone precursors are part of signal sequences for surface lipoproteins. Mol Microbiol 35, 246–247. DOI: 10.1046/j.1365-2958.2000.01687.x. 107. Nakayama, J., Igarashi, S., Nagasawa, H., Clewell, D. B., An, F. Y., and Suzuki, A. (1996) Isolation and structure of staph-cAM373 produced by Staphylococcus aureus that induces conjugal transfer of Enterococcus faecalis plasmid pAM373. Biosci Biotechnol Biochem 60, 1038-1039. DOI: 10.1271/bbb.60.1038. 108. Vickerman, M. M., Flannagan, S. E., Jesionowski, A. M., Brossard, K. A., Clewell, D. B., and Sedgley, C. M. (2010) A genetic determinant in Streptococcus gordonii Challis encodes a peptide with activity similar to that of enterococcal sex pheromone cAM373, which facilitates intergeneric DNA transfer. J Bacteriol 192, 2535-2545. DOI: 10.1128/JB.01689-09. 109. Priest, F. G. (1993) Systematics and ecology of Bacillus. Bacillus subtilis and other gram‐positive bacteria: Biochemistry, physiology, and molecular genetics 1-16. 110. Espinosa-de-los-Monteros, J., Martinez, A., and Valle, F. (2001) Metabolic profiles and aprE expression in anaerobic cultures of Bacillus subtilis using nitrate as terminal electron acceptor. Appl Microbiol Biotechnol 57, 379-384. DOI: 10.1007/s002530100749. 111. Bourgogne, A., Garsin, D. A., Qin, X., Singh, K. V., Sillanpaa, J., Yerrapragada, S., Ding, Y., Dugan-Rocha, S., Buhay, C., Shen, H., Chen, G., Williams, G., Muzny, D., Maadani, A., Fox, K. A., Gioia, J., Chen, L., Shang, Y., Arias, C. A., Nallapareddy, S. R., Zhao, M., Prakash, V. P., Chowdhury, S., Jiang, H., Gibbs, R. A., Murray, B. E., Highlander, S. K., and Weinstock, G. M. (2008) Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol 9, R110. DOI: 10.1186/gb-2008-9-7-r110. 112. Vollmer, W., Blanot, D., and de Pedro, M. A. (2008) Peptidoglycan structure and architecture. FEMS Microbiol Rev 32, 149-167. DOI: 10.1111/j.1574-6976.2007.00094.x. 113. Bucher, T., Oppenheimer-Shaanan, Y., Savidor, A., Bloom-Ackermann, Z., and Kolodkin-Gal, I. (2015) Disturbance of the bacterial cell wall specifically interferes with biofilm formation. Environ Microbiol Rep 7, 990-1004. DOI: 10.1111/1758-2229.12346. 114. Theilacker, C., Sanchez-Carballo, P., Toma, I., Fabretti, F., Sava, I., Kropec, A., Holst, O., and Huebner, J. (2009) Glycolipids are involved in biofilm accumulation and prolonged bacteraemia in Enterococcus faecalis. Mol Microbiol 71, 1055-1069. DOI: 10.1111/j.1365-2958.2009.06587.x 115. Dubrac, S., Bisicchia, P., Devine, K. M., and Msadek, T. (2008) A matter of life and death: cell wall homeostasis and the WalKR (YycGF) essential signal transduction pathway. Mol Microbiol 70, 1307-1322. DOI: 10.1111/j.1365-2958.2008.06483.x. 116. Watanabe, T., Igarashi, M., Okajima, T., Ishii, E., Kino, H., Hatano, M., Sawa, R., Umekita, M., Kimura, T., Okamoto, S., Eguchi, Y., Akamatsu, Y., and Utsumi, R. (2012) Isolation and characterization of signermycin B, an antibiotic that targets the dimerization domain of histidine kinase WalK. Antimicrob Agents Chemother 56, 3657-3663. DOI: 10.1128/AAC.06467-11. 117. Baldassarri, L., Cecchini, R., Bertuccini, L., Ammendolia, M. G., Iosi, F., Arciola, C. R., Montanaro, L., Di Rosa, R., Gherardi, G., Dicuonzo, G., Orefici, G., and Creti, R. (2001) Enterococcus spp. produces slime and survives in rat peritoneal macrophages. Med Microbiol Immunol 190, 113-120. DOI: 10.1007/s00430-001-0096-8. 118. Monte, J., Abreu, A. C., Borges, A., Simoes, L. C., and Simoes, M. (2014) Antimicrobial Activity of Selected Phytochemicals against Escherichia coli and Staphylococcus aureus and Their Biofilms. Pathogens 3, 473-498. DOI: 10.3390/pathogens3020473. 119. Flemming, H. C., and Wingender, J. (2010) The biofilm matrix. Nat Rev Microbiol 8, 623-633. DOI: 10.1038/nrmicro2415. 120. Haussler, S., Ziegler, I., Lottel, A., Gotz, F. V., Rohde, M., Wehmhohner, D., Saravanamuthu, S., Tummler, B., and Steinmetz, I. (2003) Highly adherent small-colony variants of Pseudomonas aeruginosa in cystic fibrosis lung infection. J Med Microbiol 52, 295-301. DOI: 10.1099/jmm.0.05069-0. 121. Kragh, K. N., Hutchison, J. B., Melaugh, G., Rodesney, C., Roberts, A. E., Irie, Y., Jensen, P. O., Diggle, S. P., Allen, R. J., Gordon, V., and Bjarnsholt, T. (2016) Role of Multicellular Aggregates in Biofilm Formation. mBio 7, e00237. DOI: 10.1128/mBio.00237-16. 122. Choi, N.-Y., Bae, Y.-M., and Lee, S.-Y. (2015) Cell……… | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/79547 | - |
| dc.description.abstract | 糞腸球菌 (Enterococcus faecalis) 是引發院內感染的重要病原菌，它已被發現對多種臨床使用的抗生素產生抗藥性，包括以往用於治療腸球菌感染的最後一線抗生素–萬古黴素 (Vancomycin)。此外，攜帶抗藥性之糞腸球菌可藉由信息素反應式接合質體轉移 (pheromone-inducible conjugative plasmid transfer) 將抗藥性基因進一步傳遞給不具抗藥性之糞腸球菌，這樣的特性使得防範該類感染變得更加困難。為了減緩糞腸球菌抗藥性基因的散播，本研究探討益生菌對糞腸球菌抗生素抗藥性質體 pCF10 轉移之影響。納豆菌 (Bacillus subtilis subsp. natto) 是自日本納豆發酵食品分離出之益生菌，我們發現其培養液可藉由影響糞腸球菌胜肽信息素 cCF10 之活性而有效抑制質體 pCF10 轉移，且不會影響糞腸球菌之生長。該抑制效果來自納豆菌所分泌介於 30 至 50 kDa 分子量的熱不穩定物質，我們推測可能為其胞外蛋白酶。進一步，我們發現納豆激酶 (nattokinase) 於此抑制效果中扮演著重要角色，其可將 cCF10 (LVTLVFV) 水解為 ”LVTL+VFV” 片段，使其失去活性。此外，納豆激酶所水解出之cCF10片段 “LVTL” (命名為 L 胜肽) 也具有抑制質體 pCF10 轉移的效果。除了cCF10之外，抗萬古黴素糞腸球菌之胜肽信息素 faecalis-cAM373 和 gordonii-cAM373 也會被納豆激酶水解，此結果顯示納豆菌可能具有干擾糞腸球菌傳遞萬古黴素抗藥性的潛力。除了抑制糞腸球菌之抗生素抗藥性質體轉移，我們也發現納豆菌的培養液會抑制糞腸球菌細胞外膜 (cell envelope) 合成相關之基因表現，進而影響其生物膜 (biofilm) 之形成。我們的研究顯示了可將納豆菌發酵產物和 L 胜肽應用於對抗抗生素抗藥性糞腸球菌的可行性。 | zh_TW |
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| dc.description.tableofcontents | "口試委員會審定書.....i 誌謝.....ii 中文摘要.....iii Abstract.....iv List of Abbreviation and Full Name.....v Contents.....vii List of Figures.....x List of Tables.....xii Chapter 1 Background.....1 1. The antibiotic resistance crisis.....1 2. Enterococcus faecalis.....2 3. Conjugative plasmid pCF10 of E. faecalis.....4 3.1 Overview of plasmid pCF10.....4 3.2 Regulation of conjugation.....6 4. Conjugation inhibitors (COINs).....8 5. Probiotics.....9 Chapter 2 Objective.....12 Chapter 3 Materials Methods.....16 1. Bacterial strains, medium and growth conditions.....16 2. Preparation of probiotic spent culture supernatants (SCSs).....18 3. In vitro mating assay with spent probiotic culture supernatants.....19 4. Characterization of pCF10 transfer-inhibiting substances in the spent probiotic culture supernatants.....20 5. Supernatant fractionation through different molecular weight (MW) cutoff (MWCO) membranes.....21 6. Determination of the total protein concentration in the probiotic culture supernatant.....21 7. GFP induction assay and analysis.....22 8. Analysis of peptide pheromones using HPLC and MS.....23 9. RNA purification and sequencing.....24 10. RNA-sequencing data analysis.....25 11. Quantitative real-time polymerase chain reaction (qRT-PCR).....26 12. Cell culture.....26 13. In vitro assay of bacterial adhesion onto human intestinal Caco-2 cell line.....27 14. Biofilm growth.....28 15. Experimental setup for microscopy.....29 16. Extraction and analysis of exopolysaccharide from biofilm.....30 17. HPAEC analysis of the carbohydrate composition of polysaccharides obtained from the E. faecalis cell envelope.....31 18. Statistics.....32 Chapter 4 Results.....34 4.1. Screening of potent pCF10 transfer-inhibiting probiotic spent culture supernatant.....34 1. Properties of probiotic cultures.....34 2. Effect of probiotic spent culture supernatants on pCF10 transfer.....35 4.2. Characterization and isolation of pCF10 transfer-inhibiting substances in probiotic spent culture supernatant.....35 1. Effect of chemical and physical treated probiotic spent culture supernatant on pCF10 transfer.....36 2. At least one 30-50 kDa protein in B. subtilis natto supernatant inhibits pCF10 transfer.....37 4.3. Mechanism of pCF10 transfer-inhibiting effect of B. subtilis natto supernatant.....38 1. Inhibitory effect of B. subtilis natto supernatant on the conjugative transfer of pCF10.....38 2. B. subtilis natto supernatant affects the activity of cCF10.....39 3. An extracellular protease of B. subtilis natto cleaves cCF10 and inhibits pCF10 transfer.....39 4. B. subtilis natto supernatant maintains pCF10 transfer-inhibiting activity after acid treatment.....43 5. Small amounts of cCF10 fragments interfere with the conjugative transfer of pCF10.....44 6. B. subtilis natto supernatant cleaves the mating inducer of vancomycin-resistant E. faecalis.....45 4.4. Anaerobic growth of B. subtilis natto.....46 1. B. subtilis natto grows and secrets proteases under anaerobic conditions.....46 4.5. Transcriptome analysis of E. faecalis in response to B. subtilis natto culture supernatant treatment.....47 1. RNA-seq analysis of E. faecalis in response to B. subtilis natto supernatant.....48 2. Inhibitory effect of B. subtilis natto supernatant on E. faecalis peptidoglycan biosynthesis pathway and WalK/WalR two-component system.....50 3. B. subtilis natto supernatant affects E. faecalis adhesion onto human intestinal Caco-2 cells.....51 4. Inhibition of E. faecalis biofilm production by B. subtilis natto supernatant.....52 5. E. faecalis biofilm architecture is impacted by B. subtilis natto supernatant.....53 6. Inhibition of E. faecalis biofilm polysaccharide production by B. subtilis natto supernatant.....54 7. B. subtilis natto supernatant restructures carbohydrates in E. faecalis cell envelope.....55 Chapter 5 Discussion Conclusion.....57 Figures.....64 Tables.....92 References.....107 Appendix.....121 " | |
| dc.language.iso | en | |
| dc.title | 益生菌於干擾糞腸球菌抗藥性轉移之研究與應用 | zh_TW |
| dc.title | Study and application of probiotics in interfering antibiotic resistance transfer of Enterococcus faecalis | en |
| dc.date.schoolyear | 109-2 | |
| dc.description.degree | 博士 | |
| dc.contributor.oralexamcommittee | 楊健志(Hsin-Tsai Liu),陳俊任(Chih-Yang Tseng),劉啟德,陳佩燁 | |
| dc.subject.keyword | 糞腸球菌,抗生素抗藥性,信息素反應式接合質體轉移,納豆菌,納豆激酶, | zh_TW |
| dc.subject.keyword | Enterococcus faecalis,antibiotic resistance,pheromone-inducible conjugative plasmid transfer,Bacillus subtilis natto,nattokinase, | en |
| dc.relation.page | 126 | |
| dc.identifier.doi | 10.6342/NTU202103284 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2021-09-24 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 生化科技學系 | zh_TW |
| dc.date.embargo-lift | 2024-09-22 | - |
| 顯示於系所單位： | 生化科技學系 | |
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