ESCHERICHIA COLI AT THE INTESTINAL MUCOSAL SURFACE

4th Edition: Virulence Mechanisms of Bacterial Pathogens

Volumn , Issue , 2022, Pages 175-196

  Conway, Tyrrell ^a   Cohen, Paul S ^b  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b UNIVERSITY OF RHODE ISLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85134673979     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1128/9781555815851.ch12     Document Type: Chapter

References (162)

1. Allan, A. 1981. Structure and function of gastrointestinal mucus, p. 637-639. In L. R. Johnson (ed.), Physiology of the Gastrointestinal Tract. Raven Press, New York, NY.
2. Allen, A. 1984. The structure and function of gastrointestinal mucus, p. 3-11. In E. C. Boedecker (ed.), Attachment of Organisms to the Gut Mucosa, vol. II. CRC Press, Inc., Boca Raton, FL.
3. Anderson, J. D., W. A. Gillespie, and M. H. Richmond. 1973. Chemotherapy and antibioticresistance transfer between Enterobacteria in the human gastro-intestinal tract. J. Med. Microbiol. 6:461-473.
4. Anderson, K. L., and A. A. Salyers. 1989. Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starchdegrading enzymes. J. Bacteriol. 171:3192-3198.
5. Anderson, K. L., and A. A. Salyers. 1989. Genetic evidence that outer membrane binding of starch is required for starch utilization by. Bacteroides thetaiotaomicron. J. Bacteriol. 171:3199-3204.
6. Angelichio, M. J., and A. Camilli. 2002. In vivo expression technology. Infect. Immun. 70:6518-6523.
7. Apperloo-Renkema, H. Z., B. D. Van der Waaij, and D. Van der Waaij. 1990. Determination of colonization resistance of the digestive tract by biotyping of Enterobacteriaceae. Epidemiol. Infect. 105:355-361.
8. Atuma, C., V. Strugala, A. Allen, and L. Holm. 2001. The adherent gastrointestinal mucus gel layer: thickness and physical state in vivo. Am. J. Physiol. Gastrointest. Liver Physiol. 280:G922-G929.
9. Barker, C. S., B. M. Prüss, and P. Matsumura. 2004. Increased motility of Escherichia coli by insertion sequence element integration into the regulatory region of the flhD operon. J. Bacteriol. 186:7529-7537.
10. Bartlett, D. H., B. B. Frantz, and P. Matsumura. 1988. Flagellar transcriptional activators FlbB and FlaI: gene sequences and 5' consensus sequences of operons under FlbB and FlaI control. J. Bacteriol. 170:1575-1581.
11. Baughn, A. D., and M. H. Malamy. 2004. The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen. Nature 427:441-444.
12. Blaso, F., C. Iobbi, and J. Ratouchniak. 1990. Nitrate reductase of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon. Mol. Gen. Genet. 222:104-111.
13. Blattner, F. R., G. Plunkett III, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
14. Bleves, S., M. Marie-Noëlle, G. Detry, and G. R. Cornelis. 2002. Up-regulation of the Yersinia enterocolitica yop regulon by deletion of the flagellum master operon flhDC. J. Bacteriol. 184:3214-3223.
15. Bohnhoff, M., B. L. Drake, and C. P. Miller. 1954. Effect of streptomycin on susceptibility of intestinal tract to experimental Salmonella infection. Proc. Soc. Exp. Biol. Med. 86:132-137.
16. Brunder, W., H. Schmidt, and H. Karch. 1997. EspP, a novel extracellular serine protease of enterohaemorrhagic Escherichia coli O157:H7 cleaves human coagulation factor V. Mol. Microbiol. 24:767-778.
17. Cecchini, G., I. Schroder, R. P. Gunsalus, and E. Maklashina. 2002. Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim. Biophys. Acta 1553:140-157.
18. Celli, J., W. Deng, and B. B. Finlay. 2000. Enteropathogenic Escherichia coli (EPEC) attachment to epithelial cells: exploiting the host cell cytoskeleton from the outside. Cell. Microbiol. 2:1-9.
19. Chang, D. E., D. J. Smalley, D. L. Tucker, M. P. Leatham, W. E. Norris, S. J. Stevenson, A. B. Anderson, J. E. Grissom, D. C. Laux, P. S. Cohen, and T. Conway. 2004. Carbon nutrition of Escherichia coli in the mouse intestine. Proc. Natl. Acad. Sci. USA 101:7427-7432.
20. Clarke, M. B., and V. Sperandio. 2005. Events at the host-microbial interface of the gastrointestinal tract. III. Cell-to-cell signaling among microbial flora, host, and pathogens: there is a whole lot of talking going on. Am. J. Physiol. Gastrointest. Liver Physiol. 288:G1105-G1109.
21. Cohen, P. S., and D. C. Laux. 1994. The role of interactions between fimbriae and the intestinal mucus layer in bacterial colonization and enteric pathogenesis, p. 213-225. In P. Klemm (ed.), Fimbriae: Adhesion, Biogenesis, Genetics, and Vaccines. CRC Press, Inc., Boca Raton, FL.
22. Cole, A. M., and T. Ganz. 2005. Defensins and other antimicrobial peptides: innate defense of mucosal surfaces, p. 17-34. In J. P. Nataro, P. S. Cohen, H. L. T. Mobley, and J. N. Weiser (ed.), Colonization of Mucosal Surfaces. ASM Press, Washington, DC.
23. Conway, P. L., A. Welin, and P. S. Cohen. 1990. Presence of K88-specific receptors in porcine ileal mucus is age dependent. Infect. Immun. 58:3178-3182.
24. Conway, T., and G. K. Schoolnik. 2003. Micro array expression profiling: capturing a genome-wide portrait of the transcriptome. Mol. Microbiol. 47:879-889.
25. Cotter, P. A., S. B. Melville, J. A. Albrecht, and R. P. Gunsalus. 1997. Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation. Mol. Microbiol. 25:605-615.
26. Craven, S. E. 1994. Altered colonizing ability for the ceca of broiler chicks by lipopolysaccharidedeficient mutants of Salmonella typhimurium. Avian Dis. 38:401-408.
27. Croft, C. N., and P. B. Cotton. 1973. Gastrointestinal cell loss in man. Digestion 8:144-160.
28. Das, A., R. Silaghi-Dumitrescu, L. G. Ljungdahl, and D. M. Kurtz, Jr. 2005. Cytochrome bd oxidase, oxidative stress, and dioxygen tolerance of the strictly anaerobic bacterium. Moorella thermoacetica. J. Bacteriol. 187:2020-2029.
29. Datsenko, K. A., and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97:6640-6645.
30. Dean, E. A. 1990. Comparison of receptors for 987P pili of enterotoxigenic Escherichia coli in the small intestines of neonatal and older pigs. Infect. Immun. 58:4030-4035.
31. Drumm, B., A. M. Roberton, and P. M. Sherman. 1988. Inhibition of attachment of Escherichia coli RDEC-1 to intestinal microvillus membranes by rabbit ileal mucus and mucin in vitro. Infect. Immun. 56:2437-2442.
32. Dutta, P. R., R. Cappello, F. Navarro-Garcia, and J. P. Nataro. 2002. Functional comparison of serine protease autotransporters of enterobacteriaceae. Infect. Immun. 70:7105-7113.
33. Eriksson, S., S. Lucchini, A. Thompson, M. Rhen, and J. C. Hinton. 2003. Unravelling the biology of macrophage infection by gene expression profiling of intracellular. Salmonella enterica. Mol. Microbiol. 47:103-118.
34. Falk, P. G., L. V. Hooper, T. Midtvedt, and J. I. Gordon. 1998. Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology. Microbiol. Mol. Biol. Rev. 62:1157-1170.
35. Favre-Bonte, S., T. R. Licht, C. Forestier, and K. A. Krogfelt. 1999. Klebsiella pneumoniae capsule expression is necessary for colonization of large intestines of streptomycin-treated mice. Infect. Immun. 67:6152-6156.
36. Favre-Bonte, S., B. Joly, and C. Forestier. 1999. Consequences of reduction of Klebsiella pneumoniae capsule expression on interactions of this bacterium with epithelial cells. Infect. Immun. 67:554-561.
37. Finegold, S. M., V. L. Sutter, and G. E. Mathisen. 1983. Normal indigenous intestinal flora, p. 3-31. In D. J. Hentges (ed.), Human Intestinal Microflora in Health and Disease. Academic Press, New York, NY.
38. Fioramonti, J., and L. Bueno. 1980. Motor activity in the large intestine of the pig related to dietary fiber and retention time. Br. J. Nutr. 43:155-162.
39. 14C]glucosamine incorporation by subcellular fractions of small intestine mucosa. J. Biol. Chem. 245:3584-3592.
40. Foynes, S., N. Dorrell, S. J. Ward, R. A. Stabler, A. A. McColm, A. N. Rycroft, and B. W. Wren. 2000. Helicobacter pylori possesses two CheY response regulators and a histidine kinase sensor, CheA, which are essential for chemotaxis and colonization of the gastric mucosa. Infect. Immun. 68:2016-2023.
41. Franchini, A. G., and T. Egli. 2006. Global gene expression in Escherichia coli K-12 during short-term and long-term adaptation to glucoselimited continuous culture conditions. Microbiology 152:2111-2127.
42. Franklin, D. P., D. C. Laux, T. J. Williams, M. C. Falk, and P. S. Cohen. 1990. Growth of Salmonella typhimurium SL5319 and Escherichia coli F-18 in mouse cecal mucus: role of peptides and iron. FEMS Microbiol. Ecol. 74:229-240.
43. Fredrickson, A. G. 1977. Behavior of mixed cultures of microorganisms. Annu. Rev. Microbiol. 31:63-87.
44. Freter, R. 1983. Mechanisms that control the microflora in the large intestine, p. 33-54. In D. J. Hentges (ed.), Human Intestinal Microflora in Health and Disease. Academic Press, New York, NY.
45. Freter, R. 1992. Factors affecting the microecology of the gut, p. 111-144. In R. Fuller (ed.), Probiotics: the Scientific Basis. Chapman and Hall, London, United Kingdom.
46. Freter, R., H. Brickner, M. Botney, D. Cleven, and A. Aranki. 1983. Mechanisms that control bacterial populations in continuous-flow culture models or mouse large intestinal flora. Infect. Immun. 39:676-685.
47. Freter, R., H. Brickner, J. Fekete, M. M. Vickerman, and K. E. Carey. 1983. Survival and implantation of Escherichia coli in the intestinal tract. Infect. Immun. 39:686-703.
48. Freter, R., P. C. O’Brien, and M. S. Macsai. 1981. Role of chemotaxis in the association of motile bacteria with intestinal mucosa: in vivo studies. Infect. Immun. 34:234-240.
49. Gennis, R., and V. Stewart. 1996. Respiration, p. 217-261. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, vol. 1. American Society for Microbiology, Washington, DC.
50. Gibbons, R. J., and B. Kapsimalis. 1967. Estimates of the overall rate of growth of the intestinal microflora of hamsters, guinea pigs, and mice. J. Bacteriol. 93:510-512.
51. Girón, J. A. 2005. Role of flagella in mucosal colonization, p. 213-235. In J. P. Nataro, P. S. Cohen, H. L. T. Mobley, and J. N. Weiser (ed.), Colonization of Mucosal Surfaces. ASM Press, Washington, DC.
52. Gries, D. M., N. J. Pultz, and C. J. Donskey. 2005. Growth in cecal mucus facilitates colonization of the mouse intestinal tract by methicillin-resistant. Staphylococcus aureus. J. Infect. Dis. 192:1621-1627.
53. Grovum, W., and G. D. Phillips. 1973. Rate of passage of digesta in sheep. 5. Theoretical considerations based on a physical model and computer simulation. Br. J. Nutr. 30:377-390.
54. Grozdanov, L., C. Raasch, J. Schulze, U. Sonnenborn, G. Gottschalk, J. Hacker, and U. Dobrindt. 2004. Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. J. Bacteriol. 186:5432-5441.
55. He, G., R. A. Shankar, M. Chzhan, A. Samouilov, P. Kuppusamy, and J. L. Zweier. 1999. Noninvasive measurement of anatomic structure and intraluminal oxygenation in the gastrointestinal tract of living mice with spatial and spectral EPR imaging. Proc. Natl. Acad. Sci. USA 96:4586-4591.
56. Heithoff, D. M., C. P. Conner, P. C. Hanna, S. M. Julio, U. Hentschel, and M. J. Mahan. 1997. Bacterial infection as assessed by in vivo gene expression. Proc. Natl. Acad. Sci. USA 94:934-939.
57. Henderson, I. R., J. Czeczulin, C. Eslava, F. Noriega, and J. P. Nataro. 1999. Characterization of Pic, a secreted protease of Shigella flexneri and enteroaggregative Escherichia coli. Infect. Immun. 67:5587-5596.
58. Henderson, I. R., and J. P. Nataro. 2001. Virulence functions of autotransporter proteins. Infect. Immun. 69:1231-1243.
59. Hensel, M., J. E. Shea, C. Gleeson, M. D. Jones, E. Dalton, and D. W. Holden. 1995. Simultaneous identification of bacterial virulence genes by negative selection. Science 269:400-403.
60. Hentges, D. J. 1983. Role of the intestinal microflora in host defense against infection, p. 311-331. In D. J. Hentges (ed.), Human Intestinal Microflora in Health and Disease. Academic Press, New York, NY.
61. Hentges, D. J., J. U. Que, S. W. Casey, and A. J. Stein. 1984. The influence of streptomycin on colonization resistance in mice. Microecol. Ther. 14:53-62.
62. Herbert, M. A., S. Hayes, M. E. Deadman, C. M. Tang, D. W. Hood, and E. R. Moxon. 2002. Signature tagged mutagenesis of Haemophilus influenzae identifies genes required for in vivo survival. Microb. Pathog. 33:211-223.
63. Hooper, L. V., T. Midtvedt, and J. I. Gordon. 2002. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu. Rev. Nutr. 22:283-307.
64. Hooper, L. V., T. S. Stoppenbeck, C. V. Hong, and J. I. Gordon. 2003. Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat. Immunol. 4:269-273.
65. Hooper, L. V., M. H. Wong, A. Thelin, L. Hansson, P. G. Falk, and J. I. Gordon. 2001. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291:881-884.
66. Hooper, L. V., J. Xu, P. G. Falk, T. Midtvedt, and J. I. Gordon. 1999. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc. Natl. Acad. Sci. USA 96:9833-9838.
67. Horne, S. M., and B. M. Prüss. 2006. Global gene regulation in Yersinia enterocolitica: effect of FliA on the expression levels of flagellar and plasmid-encoded virulence genes. Arch. Microbiol. 185:115-126.
68. Hoskins, L. 1984. Mucin degradation by enteric bacteria: ecological aspects and implications for bacterial attachment to gut mucosa, p. 51-65. In E. C. Boedecker (ed.), Attachment of Organisms to the Gut Mucosa, vol. II. CRC Press, Inc., Boca Raton, FL.
69. Hoskins, L. C., M. Agustines, W. B. McKee, E. T. Boulding, M. Kriaris, and G. Niedermeyer. 1985. Mucin degradation in human colon ecosystems. Isolation and properties of fecal strains that degrade ABH blood group antigens and oligosaccharides from mucin glycoproteins. J. Clin. Investig. 75:944-953.
70. Hull, R., D. Rudy, W. Donovan, C. Svanborg, I. Wieser, C. Stewart, and R. Darouiche. 2000. Urinary tract infection prophylaxis using Escherichia coli 83972 in spinal cord injured patients. J. Urol. 163:872-877.
71. Jin, L. Z., and X. Zhao. 2000. Intestinal receptors for adhesive fimbriae of enterotoxigenic Escherichia coli (ETEC) K88 in swine: a review. Appl. Microbiol. Biotechnol. 54:311-318.
72. Kaper, J. B., S. Elliot, V. Sperandio, N. T. Perna, F. Mayhew, and F. R. Blattner. 1998. Attaching-and-effacing intestinal histopathology and the locus of enterocyte effacement, p. 163-182. In J. P. Kaper and A. D. O’Brien (ed.), Escherichia coli O157:H7 and Other Shiga Toxin-Producing E. coli Strains. American Society for Microbiology, Washington, DC.
73. Kaper, J. B., and V. Sperandio. 2005. Bacterial cell-to-cell signaling in the gastrointestinal tract. Infect. Immun. 73:3197-3209.
74. Kim, Y. S., A. Morita, S. Miura, and B. Siddiqui. 1984. Structure of glycoconjugates of intestinal mucosal membranes. Role of bacterial adherence, p. 99-109. In E. C. Boedecker (ed.), Attachment of Organisms to the Gut Mucosa, vol. II. CRC Press, Inc., Boca Raton, FL.
75. Klemm, P., and K. A. K. Krogfelt. 1994. Type 1 fimbriae of Escherichia coli, p. 9-26. In P. Klemm (ed.), Fimbriae: Adhesion, Biogenesis, Genetics, and Vaccines. CRC Press, Inc., Boca Raton, FL.
76. Krogfelt, K. A. 1991. Bacterial adhesion: genetics, biogenesis, and role in pathogenesis of fimbrial adhesions of Escherichia coli. Rev. Infect. Dis. 13:721-735.
77. Krogfelt, K. A., B. A. McCormick, R. L. Burghoff, D. C. Laux, and P. S. Cohen. 1991. Expression of Escherichia coli F-18 type 1 fimbriae in the streptomycin-treated mouse large intestine. Infect. Immun. 59:1567-1568.
78. Lai, Y. C., H. L. Peng, and H. Y. Chang. 2001. Identification of genes induced in vivo during Klebsiella pneumoniae CG43 infection. Infect. Immun. 69:7140-7145.
79. Leatham, M. P., S. J. Stevenson, E. J. Gauger, K. A. Krogfelt, J. J. Lins, T. L. Haddock, S. M. Autieri, T. Conway, and P. S. Cohen. 2005. The mouse intestine selects non-motile flhDC mutants of Escherichia coli MG1655 with increased colonizing ability and better utilization of carbon sources. Infect. Immun. 73:8039-8049.
80. Lee, A. 1980. Normal flora of animal intestinal surfaces, p. 145-173. In G. Bitton and K. C. Marshall (ed.), Adsorption of Microorganisms to Surfaces. Wiley, New York, NY.
81. Lee, A. 1985. Neglected niches, the microbial ecology of the gastrointestinal tract. Adv. Microb. Ecol. 8:115-162.
82. Lemos, R. S., C. M. Gomes, M. Santana, J. LeGall, A. V. Xavier, and M. Teixeira. 2001. The “strict” anaerobe Desulfovibrio gigas contains a membrane-bound oxygen-reducing respiratory chain. FEBS Lett. 496:40-43.
83. Lendenmann, U., M. Snozzi, and T. Egli. 1996. Kinetics of the simultaneous utilization of sugar mixtures by Escherichia coli in continuous culture. Appl. Environ. Microbiol. 62:1493-1499.
84. Ley, R. E., D. A. Peterson, and J. I. Gordon. 2006. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:837-848.
85. Licht, T. R., K. A. Krogfelt, P. S. Cohen, L. K. Poulsen, J. Urbance, and S. Molin. 1996. Role of lipopolysaccharide in colonization of the mouse intestine by Salmonella typhimurium studied by in situ hybridization. Infect. Immun. 64:3811-3817.
86. Licht, T. R., T. Tolker-Nielsen, K. Holmstrom, K. A. Krogfelt, and S. Molin. 1999. Inhibition of Escherichia coli precursor-16S rRNA processing by mouse intestinal contents. Environ. Microbiol. 1:23-32.
87. Liévin-Le Moal, V., and A. L. Servin. 2006. The front line of enteric host defense against unwelcome intrusion of harmful microorganisms: mucins, antimicrobial peptides, and microbiota. Clin. Microbiol. Rev. 19:315-337.
88. Lorenz, M. C., and G. R. Fink. 2002. Life and death in a macrophage: role of the glyoxylate cycle in virulence. Eukaryot. Cell 1:657-662.
89. Macnab, R. M. 1996. Flagella and motility, p. 123-145. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella, 2nd ed., vol. 1. ASM Press, Washington, DC.
90. Mahan, M. J., J. M. Slauch, and J. J. Mekalanos. 1993. Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259:686-688.
91. Mahan, M. J., J. W. Tobias, J. M. Slauch, P. C. Hanna, R. J. Collier, and J. J. Mekalanos. 1995. Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host. Proc. Natl. Acad. Sci. USA 92:669-673.
92. Markowitz, S. M., J. M. Veazey, Jr., F. L. Macrina, C. G. Mayhall, and V. A. Lamb. 1980. Sequential outbreaks of infection due to Klebsiella pneumoniae in a neonatal intensive care unit: implication of a conjugative R plasmid. Infect. Dis. 142:106-112.
93. Maroncle, N., D. Balestrino, C. Rich, and C. Forestier. 2002. Identification of Klebsiella pneumoniae genes involved in intestinal colonization and adhesion using signature-tagged mutagenesis. Infect. Immun. 70:4729-4734.
94. Martindale, J., D. Stroud, E. R. Moxon, and C. M. Tang. 2000. Genetic analysis of Escherichia coli K1 gastrointestinal colonization. Mol. Microbiol. 37:1293-1305.
95. McCormick, B. A., D. P. Franklin, D. C. Laux, and P. S. Cohen. 1989. Type 1 pili are not necessary for colonization of the streptomycintreated mouse large intestine by type 1-piliated Escherichia coli F-18 and E. coli K-12. Infect. Immun. 57:3022-3029.
96. McCormick, B. A., P. Klemm, K. A. Krogfelt, R. L. Burghoff, L. Pallesen, D. C. Laux, and P. S. Cohen. 1993. Escherichia coli F-18 phase locked “ON” for expression of type 1 fimbriae is a poor colonizer of the streptomycintreated mouse large intestine. Microb. Pathog. 14:33-43.
97. McCormick, B. A., D. C. Laux, and P. S. Cohen. 1990. Neither motility nor chemotaxis plays a role in the ability of Escherichia coli F-18 to colonize the streptomycin-treated mouse large intestine. Infect. Immun. 58:2957-2961.
98. McCormick, B. A., B. A. D. Stocker, D. C. Laux, and P. S. Cohen. 1988. The role of motility, chemotaxis, penetration through, and growth in intestinal mucus in the ability of an avirulent strain of Salmonella typhimurium to colonize the large intestines of streptomycintreated mice. Infect. Immun. 56:2209-2217.
99. McKinney, J. D., K. Honerzu Bentrup, E. J. Munoz-Elias, A. Miczak, B. Chen, W. T. Chan, D. Swenson, J. C. Sacchettini, W. R. Jacobs, Jr., and D. G. Russell. 2000. Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature 406:735-738.
100. Mejean, V., C. Iobbi-Nivol, M. Lepelletier, G. Giordano, M. Chippaux, and M. C. Pascal. 1994. TMAO anaerobic respiration in Escherichia coli: involvement of the tor operon. Mol. Microbiol. 11:1169-1179.
101. Merrell, D. S., S. M. Butler, F. Qadri, N. A. Dolganov, A. Alam, M. B. Cohen, S. B. Calderwood, G. K. Schoolnik, and A. Camilli. 2002. Host-induced epidemic spread of the cholera bacterium. Nature 417:642-645.
102. Merrell, D. S., D. L. Hava, and A. Camilli. 2002. Identification of novel factors involved in colonization and acid tolerance of Vibrio cholerae. Mol. Microbiol. 43:1471-1491.
103. Miranda, R. L., T. Conway, M. P. Leatham, D. E. Chang, W. E. Norris, J. H. Allen, S. J. Stevenson, D. C. Laux, and P. S. Cohen. 2004. Glycolytic and gluconeogenic growth of Escherichia coli O157:H7 (EDL933) and E. coli K-12 (MG1655) in the mouse intestine. Infect. Immun. 72:1666-1676.
104. Møller, A. K., M. P. Leatham, T. Conway, P. J. M. Nuijten, L. A. M. de Haan, K. A. Krogfelt, and P. S. Cohen. 2003. An Escherichia coli MG1655 lipopolysaccharide deeprough core mutant grows and survives in mouse cecal mucus but fails to colonize the mouse large intestine. Infect. Immun. 71:2142-2152.
105. -strains. J. Bacteriol. 186:2319-2327.
106. Moore, W. E. C., and L. V. Holdeman. 1974. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl. Microbiol. 27:961-979.
107. Mouricout, M., J. M. Petit, J. R. Carias, and R. Julien. 1990. Glycoprotein glycans that inhibit adhesion of Escherichia coli mediated by K99 fimbriae: treatment of experimental colibacillosis. Infect. Immun. 58:98-106.
108. Neidhardt, F. C., and B. Magasanik. 1960. Studies on the role of ribonucleic acid in bacteria. Biochim. Biophys. Acta 42:99-116.
109. Neill, M. A. 1998. Treatment of disease due to Shiga toxin-producing Escherichia coli: infectious disease management, p. 357-363. In J. B. Kaper and A. D. O’Brien (ed.), Escherichia coli O157:H7 and Other Shiga Toxin-Producing E. coli Strains. ASM Press, Washington, DC.
110. Neutra, M. R. 1984. The mechanism of intestinal mucus secretion, p. 33-41. In E. C. Boedecker (ed.), Attachment of Organisms to the Gut Mucosa, vol. II. CRC Press, Inc., Boca Raton, FL.
111. Nevola, J. J., D. C. Laux, and P. S. Cohen. 1987. In vivo colonization of the mouse large intestine and in vitro penetration of intestinal mucus by an avirulent strain of Salmonella typhimurium and its lipopolysaccharide-deficient mutant. Infect. Immun. 55:2884-2890.
112. Newman, J. V., R. Kolter, D. C. Laux, and P. S. Cohen. 1994. The role of leuX in Escherichia coli colonization of the streptomycintreated mouse large intestine. Microb. Pathog. 17:301-311.
113. Nishi, J., J. Sheikh, K. Mizuguchi, B. Luisi, V. Burland, A. Boutin, D. J. Rose, F. R. Blattner, and J. P. Nataro. 2003. The export of coat protein from enteroaggregative Escherichia coli by a specific ATP-binding cassette transporter system. J. Biol. Chem. 278:45680-45689.
114. Oh, M. K., L. Rohlin, K. C. Kao, and J. C. Liao. 2002. Global expression profiling of acetate-grown Escherichia coli. J. Biol. Chem. 277:13175-13178.
115. Okeke, I. N., and J. P. Nataro. 2001. Enteroaggregative Escherichia coli. Lancet Infect. Dis. 1:304-313.
116. Osorio, C. G., J. A. Crawford, J. Michalski, H. Martinez-Wilson, J. B. Kaper, and A. Camilli. 2005. Second-generation recombination-based in vivo expression technology for large-scale screening for Vibrio cholerae genes induced during infection of the mouse small intestine. Infect. Immun. 73:972-980.
117. Paerregaard, A., F. Espersen, O. M. Jensen, and M. Skurnik. 1991. Interactions between Yersinia enterocolitica and rabbit ileal mucus: growth, adhesion, penetration, and subsequent changes in surface hydrophobicity and ability to adhere to ileal brush border membrane vesicles. Infect. Immun. 59:253-260.
118. Pasetti, M. F., R. Salerno-Goncalves, and M. B. Sztein. 2005. Mechanisms of adaptive immunity that prevent colonization of mucosal surfaces, p. 35-47. In J. P. Nataro, P. S. Cohen, H. L. T. Mobley, and J. N. Weiser (ed.), Colonization of Mucosal Surfaces. ASM Press, Washington, DC.
119. Peekhaus, N., and T. Conway. 1998. What’s for dinner?: Entner-Doudoroffmetabolism in Escherichia coli. J. Bacteriol. 180:3495-3502.
120. Potten, C. S., and T. D. Allen. 1977. Ultrastruc ture of cell loss in intestinal mucosa. J. Ultrastruct. Res. 60:272-277.
121. Poulsen, L. K., F. Lan, C. S. Kristensen, P. Hobolth, S. Molin, and K. A. Krogfelt. 1994. Spatial distribution of Escherichia coli in the mouse large intestine inferred from rRNA in situ hybridization. Infect. Immun. 62:5191-5194.
122. Poulsen, L. K., T. R. Licht, C. Rang, K. A. Krogfelt, and S. Molin. 1995. Physiological state of Escherichia coli BJ4 growing in the large intestines of streptomycin-treated mice. J. Bacteriol. 177:5840-5845.
123. Prüss, B. M., J. W. Campbell, T. K. Van Dyk, C. Zhu, Y. Kogan, and P. Matsumura. 2003. FlhD/FlhC is a regulator of anaerobic respiration and the Entner-Doudoroffpathway through induction of the methylaccepting chemotaxis protein Aer. J. Bacteriol. 185:534-543.
124. Prüss, B. M., X. Liu, W. Hendrickson, and P. Matsumura. 2001. FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions. FEMS Microbiol. Lett. 197:91-97.
125. Pultz, N. J., U. Stiefel, S. Subramanyan, M. S. Helfand, and C. J. Donskey. 2005. Mechanisms by which anaerobic microbiota inhibit the establishment in mice of intestinal colonization by vancomycin-resistant. Enterococcus. J. Infect. Dis. 191:949-956.
126. Quastler, H., and F. G. Sherman. 1959. Cell population in the intestinal epithelium of the mouse. Exp. Cell Res. 17:420-438.
127. Rang, C. U., T. R. Licht, T. Midtvedt, P. L. Conway, L. Chao, K. A. Krogfelt, P. S. Cohen, and S. Molin. 1999. Estimation of growth rates of Escherichia coli BJ4 in streptomycin-treated and previously germfree mice by in situ rRNA hybridization. Clin. Diagn. Lab. Immunol. 6:434-436.
128. Rediers, H., P. B. Rainey, J. Vanderleyden, and R. De Mot. 2005. Unraveling the secret lives of bacteria: use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring nichespecific gene expression. Microbiol. Mol. Biol. Rev. 69:217-261.
129. Revel, A. T., A. M. Talaat, and M. V. Norgard. 2002. DNA microarray analysis of differential gene expression in Borrelia burgdorferi, the Lyme disease spirochete. Proc. Natl. Acad. Sci. USA 99:1562-1567.
130. Robertson, J. M., G. Grant, E. Allen-Bercoe, M. J. Woodward, A. Pusztai, and H. J. Flint. 2000. Adhesion of Salmonella enterica var. Enteritidis strains lacking fimbriae and flagella to rat ileal explants cultured at the air interface or submerged in tissue culture medium. J. Med. Microbiol. 49:691-696.
131. Roos, V., and P. Klemm. 2006. Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract. Infect. Immun. 74:3565-3575.
132. Salyers, A. A., and J. A. Z. Leedle. 1983. Carbohydrate metabolism in the human colon, p. 129-146. In D. J. Hentges (ed.), Human Intestinal Microflora in Health and Disease. Academic Press, Inc., New York, NY.
133. Sansonetti, P. J. 2004. War and peace at mucosal surfaces. Nat. Rev. Immunol. 4:953-964.
134. Sartor, R. B. 2005. Probiotic therapy of intestinal inflammation and infections. Curr. Opin. Gastroenterol. 21:44-50.
135. Savage, D. C. 1977. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 31:107-133.
136. Savageau, M. A. 1983. Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am. Nat. 122:732-744.
137. Schmitt, C. K., J. S. Ikeda, S. C. Darnell, P. R. Watson, J. Bispham, T. S. Wallis, D. L. Weinstein, E. S. Metcalf, and A. D. O’Brien. 2001. Absence of all components of the flagellar export and synthesis machinery differentially alters virulence of Salmonella enterica serovar Typhimurium in models of typhoid fever, survival in macrophages, tissue culture invasiveness, and calf enterocolitis. Infect. Immun. 69:5619-5625.
138. Sheikh, J., J. R. Czeczulin, S. Harrington, S. Hicks, I. R. Henderson, C. Le Bouguenec, P. Gounon, A. Phillips, and J. P. Nataro. 2002. A novel dispersin protein in enteroaggregative Escherichia coli. J. Clin. Investig. 110:1329-1337.
139. Silva, A. J., K. Pham, and J. A. Benitez. 2003. Haemagglutinin/protease expression and mucin gel penetration in El Tor biotype Vibrio cholerae. Microbiology 149:1883-1891.
140. Slomiany, A., S. Yano, B. I. Slomiany, and G. B. J. Glass. 1978. Lipid composition of the gastric mucus barrier in the rat. J. Biol. Chem. 253:3785-3791.
141. Snyder, J., B. Haugen, E. Buckles, C. Lockatell, D. Johnson, M. Donnenberg, R. Welch, and H. Mobley. 2004. Transcriptome of uropathogenic Escherichia coli during urinary tract infection. Infect. Immun. 72:6373-6381.
142. Stathopoulos, C., D. L. Provence, and R. Curtiss III. 1999. Characterization of the avian pathogenic Escherichia coli hemagglutinin Tsh, a member of the immunoglobulin A proteasetype family of autotransporters. Infect. Immun. 67:772-781.
143. Struve, C., C. Forestier, and K. A. Krogfelt. 2003. Application of a novel multiscreening signature-tagged mutagenesis assay for identification of Klebsiella pneumoniae genes essential in colonization and infection. Microbiology 149:167-176.
144. Sun, J., F. Gunzer, A. M. Westendorf, J. Buer, M. Scharfe, M. Jarek, F. Gossling, H. Blocker, and A. P. Zeng. 2005. Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data. J. Biotechnol. 117:147-161.
145. Sweeney, N. J., P. Klemm, B. A. McCormick, E. Moller-Nielsen, M. Utley, M. A. Schembri, D. C. Laux, and P. S. Cohen. 1996. The Escherichia coli K-12 gntP gene allows E. coli F-18 to occupy a distinct nutritional niche in the streptomycin-treated mouse large intestine. Infect. Immun. 64:3497-3503.
146. Sweeney, N. J., D. C. Laux, and P. S. Cohen. 1996. Escherichia coli F-18 and K-12 eda mutants do not colonize the streptomycintreated mouse large intestine. Infect. Immun. 64:3504-3511.
147. Syed, S. S., G. D. Abrams, and R. Freter. 1970. Efficiency of various intestinal bacteria in assuming normal functions of enteric flora after association with germ-free mice. Infect. Immun. 2:376-386.
148. Takata, T., S. Fujimoto, and K. Amako. 1992. Isolation of nonchemotactic mutants of Campylobacter jejuni and their colonization of the mouse intestinal tract. Infect. Immun. 60:3596-3600.
149. Taylor, P. A., and P. J. Williams. 1975. Theoretical studies on the coexistence of competing species under continuous-flow conditions. Can. J. Microbiol. 21:90-98.
150. Tchawa Yimga, M., M. P. Leatham, J. H. Allen, D. C. Laux, T. Conway, and P. S. Cohen. 2006. The role of gluconeogenesis and the TCA cycle in the virulence of Salmonella enterica serovar Typhimurium in BALB/c mice. Infect. Immun. 74:1130-1140.
151. Tominaga, A., R. Lan, and P. R. Reeves. 2005. Evolutionary changes of the flhDC flagellar master operon in Shigella strains. J. Bacteriol. 187:4295-4302.
152. Tseng, C. P., J. Albrecht, and R. P. Gunsalus. 1996. Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli. J. Bacteriol. 178:1094-1098.
153. van der Waaij, D., J. M. Berghuis de Vries, and J. E. C. Lekkerkerk. 1971. Colonization resistance of the digestive tract in conventional and antibiotic-treated mice. J. Hyg. 69:405-441.
154. Wadolkowski, E. A., D. C. Laux, and P. S. Cohen. 1988. Colonization of the streptomycin-treated mouse large intestine by a human fecal Escherichia coli strain: role of growth in mucus. Infect. Immun. 56:1030-1035.
155. Wadolkowski, E. A., D. C. Laux, and P. S. Cohen. 1988. Colonization of the streptomycintreated mouse large intestine by a human fecal Escherichia coli strain: role of adhesion to mucosal receptors. Infect. Immun. 56:1036-1043.
156. Walter, J., N. C. Heng, W. P. Hammes, D. M. Loach, G. W. Tannock, and C. Hertel. 2003. Identification of Lactobacillus reuteri genes specifically induced in the mouse gastrointestinal tract. Appl. Environ. Microbiol. 69:2044-2051.
157. Way, S. S., S. Sallustio, R. S. Magliozzo, and M. B. Goldberg. 1999. Impact of either elevated or decreased levels of cytochrome bd expression on Shigella flexneri virulence. J. Bacteriol. 181:1229-1237.
158. Welch, R. A., V. Burland, G. Plunkett III, P. Redford, P. Roesch, D. Rasko, E. L. Buckles, S. R. Liou, A. Boutin, J. Hackett, D. Stroud, G. F. Mayhew, D. J. Rose, S. Zhou, D. C. Schwartz, N. T. Perna, H. L. Mobley, M. S. Donnenberg, and F. R. Blattner. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99:17020-17024.
159. Wilson, K. H., and R. B. Blitchington. 1996. Human biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62:2273-2278.
160. Worton, K. J., D. C. Candy, T. S. Wallis, G. J. Clarke, M. P. Osborne, S. J. Haddon, and J. Stephen. 1989. Studies on early association of Salmonella typhimurium with intestinal mucosa in vivo and in vitro: relationship to virulence. J. Med. Microbiol. 29:283-294.
161. Xu, J., and J. I. Gordon. 2003. Honor thy symbionts. Proc. Natl. Acad. Sci. USA 100:10452-10459.
162. Xu, Q., M. Dziejman, and J. J. Mekalanos. 2003. Determination of the transcriptome of Vibrio cholerae during intraintestinal growth and midexponential phase in vitro. Proc. Natl. Acad. Sci. USA 100:1286-1291.