The complex world of gastrointestinal bacteria

Canadian Journal of Animal Science

Volumn 83, Issue 3, 2003, Pages 409-427

  Anderson, K L ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Bacteria; Biofilms; Colonic bacteria; Gastrointestinal bacteria; Gastrointestinal tract; Quorum sensing; Ruminal bacteria

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 0344531483     PISSN: 00083984     EISSN: None     Source Type: Journal    
DOI: 10.4141/A02-066     Document Type: Review

References (228)

1. Actis, L. A., Tolmasky, M. E. and Crosa, J. H. 1999. Bacterial plasmids: replication of extrachromosomal genetic elements encoding resistance to antimicrobial compounds. Front. Biosci. 4: D43-D62.
2. Adlerberth, I., Carlsson, B., de Man, P., Jalil, F., Khan, S. R., Larsson, P., Mellander, L., Svanborg, C., Wold, A. E. and Hansson, L. Å. 1991. Intestinal colonization of Enterobacteriaceae in Pakistani and Swedish hospital delivered children. Acta Pediatr. Scand. 80: 602-610.
3. Akin, D. E. 1976. Ultrastructure of rumen bacterial attachment to forage cell walls. Appl. Environ. Microbiol. 31: 562-568.
4. Alakomi, H.-L., Skyttä, E., Saarela, M., Mattila-Sandholm, T., Latva-Kala, K. and Helander, I. M. 2000. Lactic acid permeabilizes gram-negative bacteria by disrupting the outer membrane. Appl. Environ. Microbiol. 66: 2001-2005.
5. Allan-Wojtas, P., Farnworth, E. R., Modler, H. W. and Carbyn, S. 1997. A solvent-based fixative for electron microscopy to improve retention and visualization of the intestinal mucus blanket for probiotics studies. Microscopy Res. Tech. 36: 390-399.
6. Amann, R. I., Ludwig, W. and Schleifer, K.-H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169.
7. Anderson, K. L. 1995. Biochemical analysis of starch degradation by Ruminobacter amylophilus 70. Appl. Environ. Microbiol. 61: 1488-1491.
8. Anderson, K. L. 2000. Degradation of cellulose and starch by anaerobic bacteria. Pages 359-386 in R. J. Doyle, ed. Glycomicrobiology. Kluwer Academic/Plenum Publishers, New York, NY.
9. Anderson, K. L. and Salyers, A. A. 1989. Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes. J. Bacteriol. 171: 3192-3198.
10. Anderson, K. L., Megehee, J. A. and Varel, V. H. 1998. Conjugal transfer of transposon Tn1545 into the cellulolytic bacterium Eubacterium cellulosolvens. Lett. Appl. Microbiol. 26: 35-37.
11. Anderson, K. L., Nagaraja, T. G., Morrill, J. L., Avery, T. B., Galitzer, S. J. and Boyer, J. E. 1987. Ruminal microbial development in conventionally or early-weaned calves. J. Anim. Sci. 64: 1215-1226.
12. Anderson, K. L., Nagaraja, T. G., Morrill, J. L., Reddy, P. G., Avery, T. B. and Anderson, N. V. 1988. Performance and ruminal changes of early-weaned calves fed lasalocid. J. Anim. Sci. 66: 806-813.
13. Apajalahti, J. H., Kettunen, A., Bedford, M. R. and Holben, W. E. 2001. Percent G + C profiling accurately reveals diet-related differences in the gastrointestinal microbial community of broiler chickens. Appl. Environ. Microbiol. 67: 5656-5667.
14. Avelar, K. E., Pinto, L. J., Antunes, L. C., Lobo, L. A., Basto, M. C., Domingues, R. M. and Ferreira, M. C. 1999. Production of bacteriocin by Bacteroides fragilis and partial characterization. Lett. Appl. Microbiol. 29: 264-268.
15. Bassler, B. L., Greenberg, E. P. and Stevens, A. M. 1997. Cross-species induction of luminescence in the quorum-sensing bacterium Vibrio harveyi. J. Bacteriol. 179: 4043-4045.
16. Bayer, E. A., Sholam, Y. and Lamed, R. 2000. An exocellular organelle for degrading plant cell wall polysaccharides. Pages 387-439 in R. J. Doyle, ed. Glycomicrobiology. Kluwer Academic/Plenum Publishers, New York, NY.
17. Beckwith, J. 1987. The lactose operon. Pages 1444-1452 in F. C. Neidhart, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger, eds. Escherichia coli and Salmonella typhimurium. Cellular and molecular biology. American Society for Microbiology, Washington, DC.
18. Behall, K. M. and Howe, J. C. 1995. Contribution of fiber and resistant starch to metabolizable energy. Am. J. Clin. Nutr. 62: 1158S-1160S.
19. Bennet, R., Eriksson, M., Nord, C. E. and Zetterström, R. 1986. Fecal bacterial microflora of newborn infants during intensive care management and treatment with five antibiotic regimens. Pediatr. Infect. Dis. 5: 533-539.
20. Booth, I. R. 1999. The regulation of intracellular pH in bacteria. Pages 19-27 in J. C. Derek and G. Gardner, eds. Bacterial response to pH. John Wiley and Sons, Ltd., New York, NY.
21. Borriella, S. P. 1986. Microbial flora of the gastrointestinal tract. Pages 2-16 in M. J. Hill, ed. Microbial metabolism in the digestive tract. CRC Press, Inc., Boca Raton, FL.
22. Bogosian, G., Morris, P. J. L. and O'Neil, J. P. 1998. A mixed culture recovery method indicates that enteric bacteria do not enter the viable but nonculturable state. Appl. Environ. Microbiol. 64: 1736-1742.
23. Bogosian, G., Sammons, L. E., Morris, P. J. L., O'Neil, J. P., Heitkamp, M. A. and Weber, D. B. 1996. Death of the Escherichia coli K-12 strain W3110 in soil and water. Appl. Environ. Microbiol. 62: 4114-4120.
24. Campanac, C., Pineau, L., Payard, A., Baziard-Mouysset, G. and Roques, C. 2002. Interactions between biocide cationic agents and bacterial biofilms. Antimicrob. Ag. Chemo. 46: 1469-1474.
25. Campbell, J. M., Fahey, G. C. and Wolf, B. W. 1997. Selected indigestible oligosaccharides affect large bowel mass, cecal and fecal short-chain fatty acids, pH and microflora in rats. J. Nutr. 127: 130-136.
26. Casiano-Colón, A. and Marquis, R. E. 1988. Role of the arginine deaminase system in protecting oral bacteria and an enzymatic basis for acid tolerance. Appl. Environ. Microbiol. 54: 1318-1324.
27. Cerba, J. J. 1999. Influences of microbiota on intestinal immune system development. Am. J. Clin. Nutr. 69: 1046S-1051S.
28. Chee-Sanford, J. C., Aminov, R. I., Krapac, I. J., Garrigues-Jeanjean, N. and Mackie, R. I. 2001. Occurrence and diversity of tetracycline resistance genes in lagoons and groundwater underlying two swine production facilities. Appl. Environ. Microbiol. 67: 1494-1502.
29. Christensen, B. B., Sternberg, C., Andersen, J. B., Eberl, L., Møller, S., Givskov, M. and Molin, S. 1998. Establishment of new genetic traits in a microbial biofilm community. Appl. Environ. Microbiol. 64: 2247-2255.
30. Cochran, W. L., McFeters, G. A. and Stewart, P. S. 2000. Reduced susceptibility of thin Pseudomonas aeruginosa biofilms to hydrogen peroxide and monochloramine. J. Appl. Microbiol. 88: 22-30.
31. Coe, M. L., Nagaraja, T. G., Sun, Y. D., Wallace, N., Towne, E. G., Kemp, K. E. and Hutcheson, J. P. 1999. Effect of virginiamycin on ruminal fermentation in cattle during adaptation to a high concentrate diet and during an induced acidosis. J. Anim. Sci. 77: 2259-2268.
32. Clewell, D. B. 1999. Sex pheromone systems in enterococci. Pages 47-65 in G. M. Dunny and S. C. Winans, eds. Cell-cell signaling in bacteria. ASM Press, Washington DC.
33. Clewell, D. B., Flannagan, S. E. and Jaworski, D. B. 1995. Unconstrained bacterial promiscuity: the Tn916-Tn1545 family of conjugative transposons. Trends Microbiol. 3: 229-236.
34. Cooperstock, M. S. and Zedd A. J. 1983. Intestinal flora of infants. Pages 79-99 in D. J. Hentges, ed. Human intestinal microflora in health and disease. Academic Press, New York, NY.
35. Danese, P. N., Pratt, L. A. and Kolter, R. 2000. Exopolysaccharide production is required for development of Escherichia coli K-12 biofilm architecture. J. Bacteriol. 182: 3593-3596.
36. Davies, D. G., Parsek, M. R., Pearson, J. P., Iglewski, B. H., Costerton, J. W. and Greenberg, E. P. 1998. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 280: 295-298.
37. Davey, M. E. and O'Toole, G. A. 2000. Microbial biofilms: from ecology to molecular genetics. Microbiol Mol. Biol. Rev. 64: 847-867.
38. deBeer, D., Stoodley, P., Roe, F. and Lewandowski, Z. 1993. Oxygen distribution and mass transport in biofilms. Biotechnol. Bioeng. 43: 1131-1138.
39. de Kievit, T. R., Gillis, R., Marx, S. Brown, C. and Iglewski, B. H. 2001. Quorum-sensing genes in Pseudomonas aeroginosa biofilms: their role and expression patterns. Appl. Environ. Microbiol. 67: 1865-1873.
40. de Vov, V. M., Kuipers, O. P., van der Meer, J. R. and Siezen, R. J. 1995. Maturation pathway of nisin and other lantibiotics: post-translationally modified antimicrobial peptides exported by gram-positive bacteria. Mol. Microbiol. 17: 427-437.
41. Dong, Y. H., Xu, J. L.,. Li, X. Z. and Zhang, L. H. 2000. AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Proc. Nat. Acad. Sci. USA. 97: 3526-3531.
42. Dorman, C. J. 1995. DNA topology and the global control of bacterial gene expression: implications for the regulation of virulence gene expression. Microbiology 141: 1271-1280.
43. Ducluzeau, R. 1988. Role of experimental microbial ecology in gastrointerology. Pages 7-26 in E. Bergone-Berezin, ed. Microbial ecology and intestinal infections. Springer-Verlag, Berlin, Germany.
44. Dukan, S., Lévi, Y. and Touati, D. 1997. Recovery of culturability of an HOCL-stressed population of Escherichia coli after incubation in phosphate buffer: resuscitation or regrowth? Appl. Environ. Microbiol. 63: 4204-4209.
45. Dunny, G. M. 1997. Cell-cell communication in gram-positive bacteria. Ann. Rev. Microbiol. 51: 527-564.
46. Dunny, G. M. and Winans, S. C. 1999. Bacterial life: neither lonely nor boring. Pages 1-5 in G. M. Dunny and S. C. Winans, eds. Cell-cell signaling in bacteria. ASM Press, Washington, DC.
47. Drury, W. J., Stewart, P. S. and Characklis, W. G. 1993. Transport of 1-μm latex particles in Pseudomonas aeruginosa biofilms. Biotechnol. Bioeng. 42: 111-117.
48. Dykes, G. A. 1995. Bacteriocins: ecological and evolutionary significance. Trends Ecol. Evol. 10: 186-189.
49. Ennahar, S., Sashihara, T., Sonomoto, K. and Ishizaki, A. 2000. ClassIIa bacteriocins: biosynthesis, structure and activity. FEMS Microbiol. Rev. 24: 85-106.
50. Erickson, D. L., Nsereko, V. L., Morgavi, D. P., Selinger, L. B., Rode, L. M. and Beauchemin, K. A. 2002. Evidence of quorum sensing in the rumen ecosystem: detection of N-acyl homoserine lactone autoinducers in ruminal contents. Can. J. Microbiol. 48: 374-378.
51. Falk, P. G., Hooper, L. V., Midtvedt, T. and Gordon, J. I. 1998. Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology. Microbiol. Mol. Biol. Rev. 62: 1157-1170.
52. Favier, C. F., Vaughan, E. E., De Vos, W. M. and Akkermans, A. D. L. 2002. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68: 219-226.
53. Finegold, S. M., Sutter, V. L. and Mathisen, G. E. 1983. Normal indigenous intestinal flora. Pages 3-31 in D. J. Hentges, ed. Human intestinal microflora in health and disease. Academic Press, New York, NY.
54. Firth, N., Rideway, K. P., Byrne, M. E., Fink, P. D., Johnson, L., Paulsen, I. T. and Skurray, R. A. 1993. Analysis of a transfer region from the staphylococcal conjugative plasmid pSK41. Gene 136: 13-25.
55. Fleming , S. E., Fitch, M. D. and De Vries, S. 1992. The influence of dietary fiber on proliferation of intestinal mucosal cells in miniature swine may not be mediated by fermentation. J. Nutr. 122: 906-916.
56. Fondevila, M. and Dehority, B. A. 1996. Interactions between Fibrobacter succinogenes, Prevotella ruminicola, and Ruminococcus flavefaciens in the digestion of cellulose from forages. J. Anim. Sci. 74: 678-684.
57. Fonty, G., Jouany, J. P., Senaud, J., Gouet P. and Grain, J. 1984. The evolution of microflora, microfauna and digestion in the rumen of lambs from birth to 4 months. Can. J. Anim. Sci. 64 (Suppl.): 165-166.
58. Foster, J. W. 2000. Microbial responses to acid stress. Pages 99-115 in G. Storz and R. Hengge-Aronis, eds. Bacterial stress response. ASM Press, Washington DC.
59. Fujimoto, S. and Clewell, D. B. 1998. Regulation of the pAd1 sex pheromone response of Enterococcus faecalis by direct interaction between the cAD1 peptide mating signal and the negatively regulating, DNA-binding TraA protein. Proc. Nat. Acad. Sci. 95: 6430-6435.
60. Fuqua, W. C., Winans, S. C. and Greensberg, E. P. 1994. Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J. Bacteriol. 176: 269-275.
61. Garrigues-Jeanjean, N., Wittmer, A., Ouriet, M. F., Duval-Iflah, Y. 1999. Transfer of the shuttle vector pRRI207 between Escherichia coli and Bacteroides spp. in vitro and in vivo in the digestive tract of axenic mice and in gnotoxenic mice inoculated with a human microflora. FEMS Microbiol. Ecol. 29: 33-43.
62. Gauthier, M. J. 2000. Environmental parameters associated with the viable but nonculturable state. Pages 87-112 in R. R. Colwell and D. J. Grimes, ed. Nonculturable microorganisms in the environment. ASM Press, Washington DC.
63. Genz, A.-K., Engelhardt, W. and Busche, R. 1999. Maintenance and regulation of the pH microclimate at the luminal surface of the distal colon of guinea-pig. J. Physiol. 517: 507-519.
64. Ghigo, J. M. 2001. Natural conjugative plasmids induce bacterial biofilm development. Nature 412: 442-445.
65. Giraud, A., Matic, I., Randman, M., Fons, M. and Taddei, F. 2002. Mutator bacteria as a risk factor in treatment of infectious diseases. Antimicrob. Ag. Chemother. 46: 863-865.
66. Giraud, A., Matic, I., Tenaillon, O., Clara, A., Randman, M., Fons, M. and Taddei, F. 2001. Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut. Science 291: 2606-2608.
67. Gomez, A., Ladiré, M., Marcille, F. and Fons, M. 2002. Trypsin mediates growth phase-dependent transcriptional regulation of genes involved in biosynthesis of ruminococcin A, a lantibiotic produced by a Ruminococcus gnavus strain from a human intestinal microbiota. J. Bacteriol. 184: 18-28.
68. Gong, J., Forster, R. J., Yu, H., Chambers, Wheatcroft, R., Sabour, P. M. and Chen, S. 2002a. Molecular analysis of bacterial populations in the ileum of broiler chickens and comparison with bacteria in the cecum. FEMS Microbiol. Ecol. 41: 171-179.
69. Gong, J., Forster, R. J., Yu, H., Chambers, J. R., Sabour, P. M. Wheatcroft, R. and Chen, S. 2002b. Diversity and phylogenetic analysis of bacteria in the mucosa of chicken ceca and comparison with bacteria in the cecal lumen. FEMS Microbiol. Lett. 208: 1-7.
70. Grey, B. and Steck, T. R. 2001. Concentrations of copper thought to be toxic to Escherichia coli can induce the viable but nonculturable condition. Appl. Environ. Microbiol. 67: 5325-5327.
71. Grönlund, M. M., Arvilommi, H., Kero, P., Lethtonen, O. P. and Isolauri, E. 2000. Importance of intestinal colonisation in the maturation of humoral immunity in early infancy: a prospective follow up study of healthy infants aged 0-6 months. Arch. Dis. Child Fetal Neonatal Ed. 83: F186-F192.
72. Herrick, J. B., Stuart-Keil, K. G., Ghiorse, W. C. and Madsen, E. L. 1997. Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site. Appl. Environ. Microbiol. 63: 2330-2337.
73. Hespell, R. B. and Whitehead, T. R. 1991a. Conjugal transfer of Tn916, Tn916 delta E, and pAM beta 1 from Enterococcus fibrisolvens strains. Appl. Environ. Microbiol. 57: 2703-2709.
74. Hespell, R. B. and Whitehead, T. R. 1991b. Introduction of Tn916 and pAM beta 1 into Streptococcus bovis JB1 by conjugation. Appl. Environ. Microbiol. 57: 2710-2713.
75. Higgins, C. F., Dorman, C. J., Stirling, D. A., Waddell, L., Booth, I. R., May, G. and Bremer, E. 1988. A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli. Cell 52: 569-584.
76. Holdeman, L. V., Cato, E. P. and Moore, W. E. C. 1977. Anaerobe laboratory manual. 4th ed. Virginia Polytechnic Institute and State University, Blacksburg, VA.
77. Hooper, L. V., Stappenbeck, T. S., Hong, C. V. and Gordon, J. I. 2003. Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nature Immunol. (in press).
78. Huber, B., Riedel, K., Hentzer, M., Heydorn, A., Gotschlich, A., Givskov, M., Molin, S. and Eberl, L. 2001. The cep quorum-sensing system of Burkholderia cepacia H111 controls biofilm formation and swarming motility. Microbiol. 147: 2517-2518.
79. Hugendieck, I. and Meyer, O. 1992. The structural genes encoding CO dehydrogenase subunits (cox L, M and S) in Pseudomonas carboxydovorans OM5 reside on plasmid in pHCG3 and are, with the exception of Streptomyces thermoautotrophicus, conserved in carboxydotrophic bacteria. Arch. Microbiol. 157: 301-304.
80. Hughes, J. B., Hellmann, J. J., Ricketts, T. H. and Bohannan, B. J. M. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67: 4399-4406.
81. Hwa, V. and Salyers, A. A. 1992. Analysis of two chrondroitin sulfate utilization mutants of Bacteroides thetaiotaomicron that differ in their abilities to compete with the wild type in the gastrointestinal tracts of germfree mice. Appl. Environ. Microbiol. 58: 869-876.
82. Jack, R. W., Tagg, J. R. and Ray, B. 1995. Bacteriocins of gram-positive bacteria. Microbiol. Rev. 59: 171-200.
83. Jackson, D. W., Suzuki, K., Oakford, L., Simecka, J. W., Hart, M. E. and Romeo, T. 2002. Biofilm formation and dispersal under the influence of the global regulator CsrA of Escherichia coli. J. Bacteriol. 184: 290-301.
84. Jalc, D. and Laukavá, A. 2002. Effect of nisin and monensin on rumen fermentation in artificial rumen. Berl. Munch. Tierarztl. Wochenschr. 115: 6-10.
85. Jensen, B. B. and Jørgensen, H. 1994. Effect of dietary fiber on microbial activity and microbial gas production in various regions of the gastrointestinal tract of pigs. Appl. Environ. Microbiol. 60: 1897-1904.
86. Jensen, E. T., Kharazmi, A., Lam, K., Costerton, J. W. and Hoiby, N. 1990. Human polymorphonuclear leukocyte response to Pseudomonas aeruginosa grown in biofilms. Infect. Immun. 58: 2383-2385.
87. Kalmokoff, M. L. and Teather, R. M. 1997. Isolation and characterization of bacteriocin (Butyrivibriocin AR10) from the ruminal anaerobe Butyrivibrio fibrisolvens AR10: evidence in support of the widespread occurrence of bacteriocin-like activity among ruminal isolates of B. fibrisolvens. Appl. Environ. Microbiol. 63: 394-402.
88. Karthikeyan, S., Korber, D. R., Wolfaardt, G. M. and Caldwell, D. E. 2001. Adaptation of bacterial communities to environmental transitions from labile to refractory substrates. Int. Microbiol. 4: 73-80.
89. Kashket, E. 1987. Bioenergetics of lactic acid bacteria: cytoplasmic pH and osmotolerance. FEMS Microbiol. Rev. 46: 233-244.
90. Kinniment, S. L. and Wimpenny, J. W. 1992. Measurement of the distribution of adenylate concentrations and adenylate energy charge across Pseudomonas aeruginosa biofilms. Appl. Environ. Microbiol. 58: 1629-1635.
91. Kirjavainen, P. V., Ouwehand, A. C., Isolauri, E. and Salminen, S. J. 1998. The ability of probiotic bacteria to bind to human intestinal mucus. FEMS Micribiol. Lett. 167: 185-189.
92. Kjelleberg, S. and Molin, S. 2002. Is there a role for quorum sensing signals in bacterial biofilms? Curr. Opin. Microbiol. 5: 254-258.
93. Klaenhammer, T. R. 1993. Genetics of bacteriocins produced by lactic acid bacteria. FEMS Microbiol. Rev. 12: 39-86.
94. Kleerebezem, M., de Vos, W. M. and Kuipers, O. P. 1999. The lantibiotics nisin and subtilin act as extracellular regulators of their own synthesis. Pages 159-174 in G. M. Dunny and S. C. Winans, eds. Cell-cell signaling in bacteria. ASM Press, Washington DC.
95. Kolenbrander, P. E., Andersen, R. N., Kaz,erzak, K. M. and Palmer, R. J. 2000. Coaggregation and coadhesion in oral biofilms. Pages 65-85 in D. G. Allison, H. M. Lappin-Scott, and M. Wilson, eds. Community structure and co-operation in biofilms. Cambridge University Press, Cambridge, UK.
96. Kolter, R. 1999. Growth in studying the cessation of growth. J. Bacteriol. 181: 697-699.
97. Korber, D. R., James, G. and Costerton, J. W. 1994. Evaluation of fleroxacin activity against established Pseudomonas fluorescens biofilms. Appl. Environ. Microbiol. 60: 1663-1669.
98. Kudo, H., Cheng, K. J. and Costerton, J. W. 1987. Interactions between Treponema bryantii and cellulolytic bacteria in the in vitro digestion of straw cellulose. Can. J. Microbiol. 33: 241-248.
99. Leadbetter, J. D. and Greenberg, E. P. 2000. Metabolism of acylhomoserine lactone quorum-sensing signals by Variovorax paradoxus. J. Bacteriol. 182: 6921-6926.
100. Lebaron, P., Bauda, P., Lett, M. C., Duval-Iflah, Y., Simonet, P., Jacq, E., Frank, N., Roux, B., Baleux, B., Faurie, G., Hubert, J. C., Normand, P., Prieur, D., Schmitt, S. and Block, J.C. 1997. Recombinant plasmid mobilization between E. coli strains in seven sterile microcosms. Can. J. Microbiol. 43: 534-540.
101. LeClerc, J. E., Li, B., Payne, W. L. and Cebula, T. A. 1996. High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274: 1208-1211.
102. Lee, J. Y., Boman, A., Chuanxin, S., Andersson, M., Jörnvall, H., Mutt, V. and Boman, H. G. 1989. Antibacterial peptides from pig intestine: isolation of a mammalian cecropin. Proc. Nat. Acad. Sci. USA 86: 9159-9163.
103. Leer, R. J., van der Vossen, M. B. M., Van Giezen, N., van Noort, J. M. and Pouwels, P. H. 1995. Genetic analysis of acidocin B, a novel bacteriocin produced by Lactobacillus acidophilus. Microbiology 141: 1629-1635.
104. Leser, T. D., Amenuvor, J. Z., Jensen, T. K., Lindecrona, R. H. and Møller, K. 2002. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl. Environ. Microbiol. 68: 673-690.
105. Lewis, K. 2001. Riddle of biofilm resistance. Antimicrob. Ag. Chemother. 45: 999-1007.
106. Licht, T. R., Christensen, B. B., Krogfelt, K. A. and Molin, S. 1999a. Plasmid transfer in the animal intestine and other dynamic bacterial populations: the role of community structure and environment. Microbiology 145: 2615-2622.
107. Licht, T. R., Hammerum, A. M., Jensen, L. B. and Jacobsen, B. L. 2001. Effect of pheromone induction on transfer of the Enterococcus faecalis plasmid pCF10 in intestinal mucus ex vivo. FEMS Microbiol. Lett. 204: 305-309.
108. Licht, T. R., Laugesen, D., Jensen, L. B. and Jacobsen, B. L. 2002. Transfer of the pheromone-inducible plasmid pCF10 among Enterococcus faecalis microorganisms colonizing the intestine of mini-pigs. Appl. Environ. Microbiol. 68: 187-193.
109. Licht, T. R., Tolker-Nielsen, T., Holmstrøm, K., Krogfelt, K. A. and Molin, S. 1999b. Inhibition of Escherichia coli precursor-16S processing by mouse intestinal contents. Environ. Microbiol. 1: 23-32.
110. Lithium, M. J., Brooker, B. E., Pettipher, G. L. and Harris, P. J. 1978. Ruminococcus flavefaciens cell coat and adhesion to cotton cellulose and to cell walls in leaves of perennial ryegrass (Lolium perenne). Appl. Environ. Microbiol. 35: 156-165.
111. Lu, L. and Walker, W. A. 2001. Pathologic and physiologic interactions of bacteria with the gastrointestinal epithelium. Am. J. Clin. Nutr. 73 (Suppl.): 1124S-1130S.
112. Macfarlane, G. T. and Macfarlane, S. 1997. Human colonic microbiota: ecology, physiology and metabolic potential of intestinal bacteria. Scand. J. Gastrointerol. 222 (Suppl.): 3-9.
113. Mackie, R. I., Sghir, A. and Gaskins, H. R. 1999. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr. 69: 1035S-1045S.
114. Maglione, G. and Russell, J. B. 1997. The adverse effect of ammonia limitations and excess-cellobiose on Fibrobacter succinogenes S85. Appl. Microbiol. Biotechnol. 48: 720-725.
115. Magnuson, R., Solomon, J. and Grossman, A. D. 1994. Biochemical and genetic characterization of a competence pheromone from B. subtilus. Cell 77: 207-216.
116. Mah, T. F. and O'Toole, G. A. 2001. Mechanisms of biofilm resistance to antimicrobial agents. Trends Microbiol. 9: 34-39.
117. Mantovani, H. C. and Russell, J. B. 2001. Nisin resistance of Streptococcus bovis. Appl. Environ. Microbiol. 67: 808-813.
118. Marshall, K. C. 2000. Starved and nonculturable microorganisms in biofilms. Pages 113-129 in R. R. Colwell and D. J. Grimes, eds. Nonculturable microorganisms in the environment. ASM Press, Washington DC.
119. Marteau, P., Pochart, P., Doré, J., Béra-Maillet, C., Bernaller, A. and Cortheir, G. 2001. Comparative study of bacterial groups within the human cecal and fecal microbiota. Appl. Environ. Microbiol. 67: 4939-4942.
120. Massey, R. C., Rainey, P. B., Sheehan, B. J., Keane, O. M. and Dorman, C. J. 1999. Environmentally constrained mutation and adaptive evolution in Salmonella. Curr. Biol. 9: 1477-1480.
121. Massol-Deyá, A. A., Whallon, J., Hickey, R. F. and Tiedje, J. M. 1995. Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater. Appl. Environ. Microbiol. 61: 769-777.
122. Mayer, C., Moritz, R., Kirschner, C., Borchard, W., Mailbaum, R., Wingender, J. and Flemming, H. C. 1999. The role of intermolecular interactions: studies on model systems of bacterial biofilms. Int. J. Biol. Macromol. 26: 3-16.
123. Mazel, D. and Davies, J. 1999. Antibiotic resistance in microbes. Cell. Mol. Life Sci. 56: 742-754.
124. McAllister, T. A., Bae, H. D., Jones, G. A. and Cheng, K. G. 1994. Microbial attachment and feed digestion in the rumen. J. Anim. Sci. 72: 3004-3018.
125. McAuliffe, O., Ryan, M. P., Ross, R. P., Hill, C., Breeuwer, P. and Abee, T. 1998. Lacticin 3147, a broad-spectrum bacteriocin which selectively dissipates the membrane potential. Appl. Environ. Microbiol. 64: 439-445.
126. McLean, R. J. C., Whiteley, M., Stickler, D. J. and Fuqua, W. C. 1997. Evidence of autoinducer activity in naturally occurring biofilms. FEMS Microbiol. Lett. 154: 259-263.
127. Melville, C. M., Scott, K. P., Mercer, D. K. and Flint, H. J. 2001. Novel tetracycline resistance gene, tet(32), in the Clostridium-related human colonic anaerobe K10 and its transmission in vitro to the rumen anaerobe Butyrivibrio fibrisolvens. Antimicrob. Ag. Chemother. 45: 3246-3249.
128. Miranda, C. M., Farias, S. L. M., Carvalho, M. A. R., Damasceno, C. A. V., Totola, A. H., Tavares, C. A. P., Cisalpino, E. O. and Vieira, E. C. 1993. Purification and partial characterization of a bacteriocin isolated from Bacteroides ovatus H47. Can. J. Microbiol. 39: 169-174.
129. Misra, T. K. 1992. Bacterial resistance to inorganic mercury salts and organomercurials. Plasmid 27: 4-16.
130. Møller, S., Pedersen, A. R., Poulsen, L. K., Arvin, E. and Molin, S. 1996. Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy. Appl. Environ. Microbiol. 62: 4632-4640.
131. Møller, S., Sternberg, C., Andersen, J. B., Christensen, B. B., Ramos, J. L., Givskov, M. and Molin, S. 1998. In situ gene expression in mixed-culture biofilms: evidence of metabolic interactions between community members. Appl. Environ. Microbiol. 64: 721-732.
132. Montville, T. J. and Chen, Y. 1998. Mechanistic action of pediocin and nisin: recent progress and unresolved questions. Appl. Microbiol. Biotechnol. 50: 511-519.
133. Moore, W. E. C. and Holdeman, L. V. 1974. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl. Microbiol. 27: 961-979.
134. Mori, M., Sakagami, Y., Ishii, Y., Isogai, A., Kitada, C., Fujino, M., Adsit, C. J., Dunny, G. M. and Suzuki, A. 1988. Structure of cCF10, a peptide sex pheromone which induces conjugative transfer of the Streptococcus faecalis tetracycline resistance plasmid, pCF10. J. Biol. Chem. 263: 14574-14578.
135. Morovskyl, M., Pristas, P., Czikková, S. and Javorsky, P. 1998. A bacteriocin-mediated antagonism by Enterococcus faecium BC25 against ruminal Streptococcus bovis. Microbiol. Res. 153: 277-281.
136. Negri, M.-C., Morosini, M.-I., Baquero, M.-R., del Campo, R., Blazquez, J. and Baquero, F. 2002. Very low cefotaxime concentrations select for hypermutable Streptococcus pneumoniae populations. Antimicrob. Ag. Chemother. 46: 528-530.
137. Nilsson, L., Oliver, J. D. and Kjelleberg, S. 1991. Resuscitation of Vibrio vulnificus from the viable but nonculturable state. J. Bacteriol. 173: 5054-5059.
138. Nes, I. F. and Eijsink, V. G. H. 1999. Regulation of group II peptide bacteriocin synthesis by quorum-sensing mechanisms. Pages 175-192 in G. M. Dunny and S. C. Winans, eds. Cell-cell signaling in bacteria. ASM Press, Washington DC.
139. Netherwood, T., Bowden, R., Harrison, P., O'Donnell, A. G., Parker, D. S. and Gilbert, H. J. 1999. Gene transfer in the gastrointestinal tract. Appl. Environ. Microbiol. 65: 5139-5141.
140. Nielsen, A. T., Tolker-Nielsen, T., Barken, K. B. and Molin, S. 2000. Role of commensal relationships on the spatial structure of a surface-attached microbial consortium. Environ. Microbiol. 2: 59-68.
141. Nikolich, M. P., Hong, G., Shoemaker, N. B. and Salyers, A. A. 1994. Evidence for natural transfer of tetQ between bacteria that normally colonize humans and bacteria that normally colonize livestock. Appl. Environ. Microbiol. 60: 3255-3260.
142. Odenyo, A. A., Mackie, R. I., Stahl, D. A. and White, B. A. 1994. The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: development of probes for Ruminococcus species and evidence for bacteriocin production. Appl. Environ. Microbiol. 60: 3688-3696.
143. Oliver, A., Canton, R., Campo, P., Baquero, F. and Blazquez, J. 2000. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288: 1251-1254.
144. Osborne, J. M. and Dehority, B. A. 1989. Synergism in degradation and utilization of intact forage cellulose, hemicellulose, and pectin by three pure cultures of ruminal bacteria. Appl. Environ. Microbiol. 55: 2247-2250.
145. O'Toole, G. A. and Kolter, R. 1998a. Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signaling pathways: a genetic analysis. Mol. Microbiol. 28: 449-461.
146. O'Toole, G. A. and Kolter, R. 1998b. Flagellar and twitching motility are necessary for Pseudomonas aeroginosa biofilm development. Mol. Microbiol. 30: 295-305.
147. O'Toole, G. A., Gibbs, K. A., Hager, P. W., Phibbs, Jr., P. V. and Kolter, R. 2000. The global carbon metabolism regulator Crc is a component of a signal transduction pathway required for biofilm development by Pseudomonas aeruginosa. J. Bacteriol. 182: 425-431.
148. Palva, T. K., Holstrom, K. O., Heino, P. and Palva, E. T. 1993. Induction of plant defense response by exoenzymes of Erwinia carotovora subsp. carotovora. Mol. Plant-Microbe Interact. 6: 190-196.
149. Pereira, M. O., Kuehn, M., Wuertz, S., Neu, T. and Melo, L. F. 2002. Effect of flow regime on the architecture of a Pseudomonas fluorescens biofilm. Biotechnol. Bioeng. 78: 164-171.
150. Picioreanu, C., van Loosdrecht, M. C. and Heijnen, J. J. 1998. Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automation approach. Biotech. Bioeng. 58: 101-116.
151. Pirhonen, M., Flego, D., Heikinheima, R. and Palva, E. T. 1993. A small diffusible signal molecule is responsible for the global control of virulence and exoenzyme production by the plant pathogen Erwinia carotovora. EMBO J. 17: 2467-2476.
152. Poulsen, L. K., Ballard, G. and Stahl, D. A. 1993. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol. 59: 1354-1360.
153. Poulsen, L. K., Licht, T. R., Rang, C., Krogfelt, K. A. and Molin, S. 1995. Physiological state of Escherichia coli BJ4 growing in the large intestines of streptomycin-treated mice. J. Bacteriol. 177: 5840-5845.
154. Pratt, L. A. and Kolter, R. 1998. Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type 1 Pili. Mol. Microbiol. 30: 285-293.
155. Prigent-Combaret, C., Vidal, O., Dorel, C. and Lejeune, P. 1999. Abiotic surface sensing and biofilm-dependent regulation of gene expression in Escherichia coli. J. Bacteriol. 181: 5993-6002.
156. Prigent-Combaret, C., Brombacher, E., Vidal, O., Ambert, A., Lejeune, P., Landini, P. and Dorel, C. 2001. Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene. J. Bacteriol. 183: 7213-7223.
157. Probert, H. M. and Gibson, G. R. 2002. Bacterial biofilms in the human gastrointestinal tract. Curr. Issues Intest. Microbiol. 3: 23-27.
158. Pryde, S. E., Richardson, A. J., Stewart, C. S. and Flint, H. J. 1999. Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig. Appl. Environ. Microbiol. 65: 5372-5377.
159. Rada, V. and Dlabal, J. 1998. Susceptibility of bifidobacteria to nisin. Lett. Appl. Microbiol. 26: 123-125.
160. Rang, C. U., Licht, T. R., Midtvedt, T., Conway, P. L., Chao, L., Krogfelt, K. A., Cohen, P. S. and Molin, S. 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.
161. Rang, C. U., Mikkola, R., Molin, S. and Conway, P. L. 1997. Ribosomal efficiency and growth rates of freshly isolated Escherichia coli strains originating from the gastrointestinal tract. FEBS Lett. 418: 27-29.
162. Rasmussen, K. and Lewandowski, Z. 1998. Microelectrode measurements of local mass transport rates in heterogeneous biofilms. Biotechnol. Bioeng. 59: 302-309.
163. Ravatn, R., Zehnder, A. J. B. and van der Meer, J. R. 1998. Low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from Pseudomonas sp. strain B13 to Pseudomonas putida F1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms. Appl. Environ. Microbiol. 64: 2126-2132.
164. Robinson, P. H. and McQueen, R. E. 1994. Influence of supplemental protein source and feeding frequency on rumen fermentation and performance in dairy cows. J. Dairy Sci. 77: 1340-1353.
165. Robinson, I. M., Whipp, S. C., Bucklin, J. A. and Allison, M. J. 1984. Characteristics of predominant bacteria from the colons of normal and dysenteric pigs. Appl. Environ. Microbiol. 48: 964-969.
166. Roos, S., Karner, F., Axelsson, L. and Jonsson, H. 2000. Lactobacillus mucosae sp. nov., a new species with in vitro mucusbinding activity isolated from pig intestine. Internat. J. Syst. Evol. Microbiol. 50: 251-258.
167. Roth, L. A. and Keenan, D. 1971. Acid injury in Escherichia coli. Can. J. Microbiol. 17: 1005-1008.
168. Rozee, K. R., Cooper, K., Lam, K. and Costerton, J. W. 1982. Microbial flora of the mouse ileum mucous layer and epithelial surface. Appl. Environ. Microbiol. 43: 1451-1463.
169. Russell, A. D. 1997. Plasmids and bacterial resistance to biocides. J. Appl. Microbiol. 83: 155-165.
170. Russell, J. B. 1991. Intracellular pH of acid-tolerant ruminal bacteria. Appl. Environ. Microbiol. 57: 3383-3384.
171. Russell, J. B. 1992. Glucose toxicity and the inability of Bacteroides ruminicola to regulate glucose transport and utilization. Appl. Environ. Microbiol. 58: 2040-2045.
172. Russell, J. B. 1993. The glucose toxicity of Prevotella ruminicola: Methylglyoxal accumulation and its effect on membrane physiology. Appl. Environ. Microbiol. 58: 2844-2850.
173. Russell, J. B. 1998. Strategies that ruminal bacteria use to handle excess carbohydrate. J. Amin. Sci. 76: 1955-1963.
174. Rychlik, J. L. and Russell, J. B. 2002. Bacteriocin-like activity of Butyrivibrio fibrisolvens JL5 and its effect on other ruminal bacteria and ammonia production. Appl. Environ. Microbiol. 68: 1040-1046.
175. Salyers, A. A. 1990. Polysaccharide utilization by human colonic bacteria. Adv. Exp. Med. Biol. 270: 151-158.
176. Salyers, A. A. and Guthrie, E. P. 1988. A deletion in the chromosome of Bacteroides thetaiotaomicron that abolishes production of chondroitinase II does not affect survival of the organism in gastrointestinal tracts of exgremfree mice. Appl. Environ. Microbiol. 54: 1964-1969.
177. Salyers, A. A. and McCarthy, R. E. 1989. Assessing the importance of host-derived polysaccharides as carbon sources for bacteria growing in the human colon. Anim. Feed Sci. Technol. 23: 109-120.
178. Salyers, A. A. and Pajeau, M. 1989. Competitiveness of different polysaccharide utilization mutants of Bacteroides thetaiotaomicron in the intestinal tracts of germfree mice. Appl. Environ. Microbiol. 55: 2572-2578.
179. Salyers, A. A. and Pajeau, M. and McCarthy, R. E. 1988. Importance of mucopolysaccharides as substrates for Bacteroides thetaiotaomicron growing in intestinal tracts of exgremfree mice. Appl. Environ. Microbiol. 54: 1970-1976.
180. Salyers, A. A., Shoemaker, N. B., Stevens, A. M. and Lhing-Yew, L. 1995. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol. Rev. 59: 579-590.
181. Sauer, K., Camper, A. K., Ehrlich, G. D., Costerton, J. W. and Davies, D. G. 2002. Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm. J. Bacteriol. 184: 1140-1154.
182. Savage, D. C. 1977. Microbial ecology of the gastrointestinal tract. Ann. Rev. Microbiol. 31: 107-133.
183. Schell, M. A., Karmirantzou, M., Snel, B., Vilanova, D., Berger, B., Pessi, G., Zwahlen, M.-C., Desiere, F., Bork, P., Delley, M., Pridmore, R. D. and Arigoni, F. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Nat. Acad. Sci. (USA) 99: 14422-14427.
184. Schneider, D., Duperchy, E., Coursange, E., Lenski, R. E. and Blot, M. 2000. Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements. Genetics 156: 477-488.
185. Sebald, M. 1994. Genetic basis for antibiotic resistance in anaerobes. Clin. Infect. Dis. 18(Suppl. 4): S297-S304.
186. Shapiro, J. A. 1997. Multicellularity: the rule not the exception. Pages 14-49 in J. A. Shapiro and M. Dworkin, eds. Bacteria as multicellular organisms. Oxford University Press, New York, NY.
187. Shih, P.-C. and Huang, C.-T. 2002. Effects of quorum sensing deficiency on Pseudomonas aeruginosa biofilm formation and antibiotic resistance. J. Antimicrob. Chemother. 49: 309-314.
188. 14. Appl. Environ. Microbiol. 57: 2114-2120.
189. Shoemaker, N. B., Vlamakis, H., Hayes, K. and Salyers, A. A. 2001. Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon. Appl. Environ. Microbiol. 67: 561-568.
190. Smith, H. W. 1965. Development of the flora of the alimentary tract in young animals. J. Pathol. Bacteriol. 90: 495-513.
191. Spoering, A. L. and Lewis, K. 2001. Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials. J. Bacteriol. 183: 6746-6751.
192. Stackebrandt, E. and Embley, T. M. 2000. Diversity of uncultured microorganisms in the environment. Pages 57-75 in R. R. Colwell and D. J. Grimes, eds. Nonculturable microorganisms in the environment. ASM Press, Washington DC.
193. Stewart, P. S. 1998. A review of experimental measurements of effective diffusive permeabilities and effective diffusion coefficients in biofilms. Biotechnol. Bioeng. 59: 261-272.
194. Stewart, P. S. 2002. Mechanisms of antibiotic resistance in bacterial biofilms. Int. J. Med. Microbiol. 292: 107-113.
195. Stoodley, P., deBeer, D. and Lewandowski, Z. 1994. Liquid flow in biofilm systems. Appl. Environ. Microbiol. 60: 2711-2716.
196. Stoodley, P., Lewandowski, Z., Boyle, J. D. and Lappin-Scott, H. M. 1999. The formation of migratory ripples in a mixed species bacterial biofilm growing in turbulent flow. Environ. Microbiol. 1: 447-455.
197. Stouthamer, A. H. 1973. A theoretical study on the amount of ATP required for synthesis of microbial cell material. Anton. van Leeuwen. 39: 545-565.
198. Suau, A., Bonnet, R., Sutren, M., Godon, J.-J., Gibson, G. R., Collins, M. D. and Doré, J. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65: 4799-4807.
199. Suci, P. A., Mittelman, M. W., Yu, F. P. and Geesey, G. G. 1994. Investigation of ciprofloxacin penetration into Pseudomonas aeruginosa biofilms. Antimicrob. Ag. Chemother. 38: 2125-2133.
200. Surette, M. G. and Bassler, B. L. 1998. Quorum sensing in Escherichia coli and Salmonella typhimurium. Proc. Natl. Acad. Sci. 95: 7046-7050.
201. Sutherland, I. W. 2001. Biofilm exopolysaccarides: a strong and sticky framework. Microbiology 147: 3-9.
202. Sutton, J. D., Hart, I. C., Broster, W. H., Elliott, R. J. and Schuller, E. 1986. Feeding frequency for lactating cows: effects on rumen fermentation and blood metabolites and hormones. Br. J. Nutr. 56: 181-192.
203. Tait, K. and Sutherland, I. W. 2002. Antagonistic interactions amongst bacteriocin-producing enteric bacteria in dual species biofilms. J. Appl. Microbiol. 93: 345-352.
204. Takeoka, K., Ichimiya, T., Yamasaki, T. and Nasu, M. 1998. The in vitro effect of macrolides on the interaction of human polymorphonuclear leukocytes with Pseudomonas aeruginosa in biofilm. Chemotherapy 44: 190-197.
205. Tajima, K., Aminov, R. I., Nagamine, T., Ogata, K., Nakamura, M., Matsui, H. and Benno, Y. 1999. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29: 159-169.
206. Tisa, L. S. and Rosen, B. P. 1990. Transport systems encoded by bacterial plasmids. J. Bioenerg. Biomembr. 22: 493-507.
207. Tolker-Nielsen, T., Brinch, U. C., Ragas, P. C., Andersen, J. B., Jacobsen, C. S. and Molin, S. 2000. Development and dynamics of Pseudomonas sp. biofilms. J. Bacteriol. 182: 6482-6489.
208. Top, E., Mergeay, M., Springael, D. and Verstraete, W. 1990. Gene escape model: transfer of heavy metal resistance genes from Escherichia coli to Alcaligenes eutrophus on agar plates and in soil samples. Appl. Environ. Microbiol. 56: 2471-2479.
209. Valentine, P. J. and Salyers, A. A. 1992. Use of inducible disaccharidases to assess the importance of different carbohydrate sources for Bacteroides ovatus growing in the intestinal tracts of germfree mice. Appl. Environ. Microbiol. 58: 2698-2700.
210. van der Wielen, P. W. J. J., Biesterveld, S., Notermans, S., Hofstra, H., Urlings, A. P. and van Knapen, F. 2000. Role of volatile fatty acids in development of the cecal microflora in broiler chickens during growth. Appl. Environ. Microbiol. 66: 2536-2540.
211. van Kessel, J. S. and Russell, J. B. 1996. The effect of amino acid nitrogen on the energetics of ruminal bacteria and its impact on energy spilling. J. Dairy Sci. 79: 1237-1243.
212. Vercellotti, J. R., Salyers, A. A. and Wilkins, T. D. 1978. Complex carbohydrate breakdown in the human colon. Am. J. Clin. Nutr. 31: S86-S89.
213. Victoria, J. M. A., Callow, M. E., Macaskie, L. E. and Paterson-Beedle, M. 2002. Effect of nutrient limitation on biofilm formation and phosphatase activity of a Citrobacter sp. Microbiology 148: 277-288.
214. Vroom, J. M., de Grauw, K. J., Gerritsen, H. C., Bradshaw, D. J., Marsh, P. D., Watson, G. K., Birmingham, J. J. and Allison, C. 1999. Depth penetration and detection of pH gradients in biofilms by two-proton excitation microscopy. Appl. Environ. Microbiol. 65: 3502-3511.
215. Wadolkowski, E. A., Laux, D. C. and Cohen, P. S. 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.
216. Watnick, P. I. and Kolter, R. 1999. Steps in the development of a Vibrio cholerae biofilm. Mol. Microbiol. 34: 586-595.
217. Watnick, P. I. and Kolter, R. 2000. Biofilm, city of microbes. J. Bacteriol. 182: 2675-2679.
218. Watson, W. T., Minoque, T. D., Val, D. L., von Bodman, S. B. and Churchill, M. E. 2002. Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing. Mol. Cell 9: 685-694.
219. Weichart, D. and Kjelleberg, S. 1996. Stress resistance and recovery potential of culturable and viable but nonculturable cells of Vibrio vulnificus. Microbiology 142: 845-853.
220. Whitehead, N. A., Barnard, A. M. L., Slater, H., Simpson, N. J. L. and Salmond, G. P. C. 2001. Quorum-sensing in gram-negative bacteria. FEMS Microbiol. Rev. 25: 365-404.
221. Whitesides, M. D. and Oliver, J. D. 1997. Resuscitation of Vibrio vulnificus from the viable but nonculturable state. Appl. Environ. Microbiol. 63: 1002-1005.
222. Wimpenny, J. W. T. and Colasanti, R. 1997. A unifying hypothesis for the structure of microbial biofilms based on cellular automation models. FEMS Micorbiol. Ecol. 22: 1-16.
223. Wolfaardt, G. M., Lawrence, J. R., Robarts, R. D., Caldwell, S. J. and Caldwell, D. E. 1994. Multicelluar organization in a degradative biofilm community. Appl. Environ. Microbiol. 60: 434-446.
224. Yildirim, Z., Winters, D. K. and Johnson, M. G. 1999. Purification, amino acid sequence and mode of action of bifidocin B produced by Bifidobacterium bifidum NCFB 1454. J. Appl. Microbiol. 86: 45-54.
225. Yoshida, A. and Kuramitsu, H. K. 2002. Multiple Streptococcus mutans genes are involved in biofilm formation. Appl. Environ. Microbiol. 68: 6283-6291.
226. Yung-Hua, L., Lau, P. C., Lee, J. H., Ellen, R. P. and Cvitkovithch, D. G. 2001. Natural genetic transformation of Streptococcus mutans growing in biofilms. J. Bacteriol. 183: 897-908.
227. Zheng, Z. and Stewart, P. S. 2002. Penetration of rifampin through Staphylococcus epidermidis biofilms. Antimicrobiol. Ag. Chemother. 46: 900-903.
228. Zoetendal, E. G., van Wright, A., Vilpponen-Salmela, T., Ben-Amor, K., Akkermans, A. D. and de Vos, W. M. 2002. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl. Environ. Microbiol. 68: 3401-3407.