COMMENSAL BACTERIA IN HEALTH AND DISEASE

4th Edition: Virulence Mechanisms of Bacterial Pathogens

Volumn , Issue , 2022, Pages 101-115

  Flint, Harry J ^a   Louis, Petra ^a   Scott, Karen P ^a   Duncan, Sylvia H ^a  

^a ROWETT RESEARCH INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85119908386     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1128/9781555815851.ch8     Document Type: Chapter

References (77)

1. Aminov, R. I., A. W. Walker, S. H. Duncan, H. J. M. Harmsen, G. W. Welling, and H. J. Flint. 2006. Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale. Appl. Environ. Microbiol. 72:6371-6376.
2. Anderson K. L., and A. A. Salyers. 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.
3. Barcenilla, A., S. E. Pryde, J. C. Martin, S. H. Duncan, C. S. Stewart, and H. J. Flint. 2000. Phylogenetic relationships of dominant butyrateproducing bacteria from the human gut. Appl. Environ. Microbiol. 66:1654-1661.
4. Belenguer, A., S. H. Duncan, G. Calder, G. Holtrop, P. Louis, G. E. Lobley, and H. J. Flint. 2006. Two routes of metabolic cross-feeding between bifidobacteria and butyrate-producing anaerobes from the human gut. Appl. Environ. Microbiol. 72:3593-3599.
5. Bobik, T. A., G. D. Havemann, R. J. Busch, D. S. Williams, and H. C. Aldrich. 1999. The propanediol utilization operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral bodies involved in coenzyme B12-dependent 1, 2-propanediol degradation. J. Bacteriol. 181:5967-5975.
6. Bourriaud, C., R. J. Robins, L. Martin, F. Kozlowski, E. Tenaileau, C. Cherbut, and C. Michel. 2005. Lactate is mainly fermented to butyrate by human intestinal microfloras but inter-individual variation is evident. J. Appl. Bacteriol. 99:201-212.
7. Bown, R. L., J. A. Gibson, G. E. Sladen, B. Hicks, and A. M. Dawson. 1974. Effects of lactulose and other laxatives on ileal and colonic pH as measured by a radiotelemetry device. Gut 15:999-1004.
8. Bry L., P. G. Falk, T. Midvedt, and J. I. Gordon. 1996. A model of host-microbial interactions in an open mammalian ecosystem. Science 273:1380-1383.
9. Campieri, M., and P. Gionchetti. 2001. Bacteria as the cause of ulcerative colitis. Gut 48:132-135.
10. Charrier, C., G. J. Duncan, M. D. Reid, G. J. Rucklidge, D. Henderson, P. Young, V. J. Russell, R. I. Aminov, H. J. Flint, and P. Louis. 2006. A novel class of CoA-transferase involved in short-chain fatty acid metabolism in butyrateproducing human colonic bacteria. Microbiology 152:179-185.
11. 2 and acetate transfers during xylan fermentation between a butyrate-producing xylanolytic species and hydrogenotrophic microorganisms from the human gut. FEMS Microbiol. Lett. 254:116-122.
12. Counotte, G. H. M., R. A. Prins, R. H. A. M. Jansen, and M. J. A. De Bie. 1981. Role of Megasphaera elsdenii in the fermentation of dllactate in the rumen of dairy cattle. Appl. Environ. Microbiol. 42:649-655.
13. Dabard, J., C. Bridonneau, C. Phillipe, P. Anglade, D. Molle, M. Nardi, M. Ladire, H. Griardin, F. Marcille, A. Gomez, and M. Fons. 2001. Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces. Appl. Environ. Microbiol. 67:4111-4118.
14. Derrien, M., E. E. Vaughan, C. M. Plugge, and W. M. de Vos. 2004. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin degrading bacterium. Int. J. Syst. Evol. Microbiol. 54:1469-1476.
15. Devillard, E., F. M. McIntosh, S. H. Duncan, and R. J. Wallace. 2007. Metabolism of linoleic acid by human gut bacteria: different routes for biosynthesis of conjugated linoleic acid. J. Bacteriol. 189:2566-2570.
16. Duchmann, R., E. May, M. Heike, P. Knolle, M. Neurath, and K.-H. Meyerzum Buschenfelde. 1999. T cell specificity and cross-reactivity towards enterobacteria, Bacteroides, Bifidobacterium and antigens from resident intestinal flora in humans. Gut 44:812-818.
17. Duncan, S. H., R. I. Aminov, K. P. Scott, P. Louis, T. B. Stanton, and H. J. Flint. 2006. Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov., and Roseburia inulinivorans sp. nov., based on isolates from human faeces. Int. J. Syst. Evol. Microbiol. 56:2437-2441.
18. Duncan, S. H., H. J. Flint, and C. S. Stewart. 1998. Inhibitory activity of gut bacteria against Escherichia coli O157 mediated by dietary plant metabolites. FEMS Microbiol. Lett. 164:283-288.
19. Duncan, S. H., G. L. Hold, A. Barcenilla, C. S. Stewart, and H. J. Flint. 2002. Roseburia intestinalis sp. nov., a novel saccharolytic, butyrateproducing bacterium from human faeces. Int. J. Syst. Evol. Microbiol. 52:1-6.
20. Duncan, S. H., G. Holtrop, G. E. Lobley, G. Calder, C. S. Stewart, and H. J. Flint. 2004. Contribution of acetate to butyrate formation by human faecal bacteria. Br. J. Nutr. 91:915-923.
21. Duncan, S. H., P. Louis, and H. J. Flint. 2004. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl. Environ. Microbiol. 70:5810-5817.
22. Duncan, S. H. 2001. Effects of rumen and gut microorganisms and their metabolites on the growth and survival of Escherichia coli O157. Ph.D. thesis. University of Aberdeen, Aberdeen, United Kingdom.
23. Eckburg, P. B., E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson, and D. A. Relman. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638.
24. Finegold, S. M., V. L. Sutter, and G. E. Mathison. 1983. Normal indigenous flora, p. 3-31. In D. J. Hentges (ed.), Human Intestinal Microbiology in Health and Disease. Academic Press, New York, NY.
25. Flint, H. J. 2006. The significance of prokaryote diversity in the human gastrointestinal tract, p. 65-90. In N. A. Logan, H. M. Lappin-Scott, and P. C. F. Oyston (ed.), Society for General Micro biology Symposia, vol. 66. Prokaryotic Diversity: Mechanisms and Significance. Cambridge Uniersity Press, Cambridge, United Kingdom.
26. Florin, T. H. F., G. Zhu, K. M. Kirk, and N. G. Martin. 2000. Shared and unique environmental factors determine the ecology of methanogens in humans and rats. Am. J. Gastroenterol. 95:2872-2879.
27. Furrie, E., S. Macfarlane, A. Kennedy, J. H. Cummings, S. V. Walsh, D. O’Neil, and G. T. Macfarlane. 2005. Synbiotic therapy (Bifidobacterium longum/Synergy 1) initiates resolution of inflammation in patients with active ulcerative colitis: a randomised controlled pilot trial. Gut 54:242-249.
28. Gibson, G. R., and M. B. Roberfroid. 1995. Dietary modulation of the human colonic microbiota-introducing the concept of prebiotics. J. Nutr. 125:1401-1412.
29. Gill, C. I. R., and I. R. Rowland. 2002. Diet and cancer: assessing the risk. Br. J. Nutr. 88(Suppl.1):S73-S87.
30. Harmsen, H. J. M., G. C. Raangs, T. He, J. E. Degener, and G. W. Welling. 2002. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl. Environ. Microbiol. 68:2982-2990.
31. Hold, G. L., S. E. Pryde, V. J. Russell, E. Furrie, and H. J. Flint. 2002. Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol. Ecol. 39:33-39.
32. Hold, G. L., A. Schwiertz, R. I. Aminov, M. Blaut, and H. J. Flint. 2003. Oligonucleotide probes that detect quantitatively significant groups of butyrate producing bacteria in human feces. Appl. Environ. Microbiol. 69:4320-4324.
33. Hooper, L. V., and J. I. Gordon. 2001. Commensal host-bacterial relationships in the gut. Science 292:1115-1118.
34. Hoskins, L. C. 1993. Mucin degradation in the human gastrointestinal tract and its significance to enteric microbial ecology. Eur. J. Gastroenterol. Hepatol. 5:205-213.
35. Jordan, S. L., J. Glover, L. Malcolm, F. M. Thomson-Carter, I. R. Booth, and S. F. Park. 1999. Augmentation of killing of Escherichia coli O157 by combinations of lactate, ethanol, and low pH conditions. Appl. Environ. Microbiol. 65:1308-1311.
36. Kalmakoff, M. L., D. Lu, M. F. Whitford, and R. M. Teather. 1999. Evidence for production of a new lantibiotic (butyrivibriocin OR79A) by the ruminal anaerobe Butyrivibrio fibrisolvens OR79: characterization of the structural gene encoding butyrivibriocin OR79A. Appl. Environ. Microbiol. 65:2128-2135.
37. Kazimierczak, K. A., H. J. Flint, and K. P. Scott. 2006. Comparative analysis of sequences flanking tet(W) resistance genes in multiple species of gut bacteria. Antimicrob. Agents Chemother. 50:2632-2639.
38. Larue, R., Z. Yu, V. A. Parisi, A. R. Egan, and M. Morrison. 2005. Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ. Microbiol. 7:530-543.
39. Lin, C. Z., and D. A. Stahl. 1995. Taxonspecific probes for the cellulolytic genus Fibrobacter reveal abundant and novel equine-associated populations. Appl. Environ. Microbiol. 61:1348-1351.
40. Louis, P., S. H. Duncan, S. I. McCrae, J. Millar, M. S. Jackson, and H. J. Flint. 2004. Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. J. Bacteriol. 186:2099-2106.
41. Macfarlane, G. T., and G. R. Gibson. 1995. Carbohydrate fermentation, energy transduction and gas metabolism in the human large intestine, p. 269-318. In R. I. Mackie and B. A. White (ed.), Gastrointestinal Microbiology, vol. 1. Chapman and Hall, New York, NY.
42. Malinen, E., T. Rintilla, K. Kajander, J. Matto, A. Kassinen, L. Krogius, M. Saarela, R. Korpela, and A. Palva. 2005. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real time PCR. Am. J. Gastroenterol. 100:373-382.
43. Mangin, I., R. Bonnet, P. Seksik, L. Rigottier-Gois, M. Sutren, Y. Bouhnik, C. Neut, M. D. Collins, J.-F. Colombel, P. Marteau, and J. Doré. 2004. Molecular inventory of faecal microflora in patients with Crohn’s disease. FEMS Microbiol. Ecol. 50:25-36.
44. Manichanh, C., L. Rigottier-Gois, E. Bonnaud, K. Gloux, E. Pelletier, L. Frangeul, R. Nalin, C. Jarrin, P. Chardon, P. Marteau, J. Roca, and J. Dore. 2005. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55:205-211.
45. Martin, H. M., and J. M. Rhodes. 2000. Bacteria and inflammatory bowel disease. Curr. Opin. Infect. Dis. 13:503-509.
46. McIntyre, A., P. R. Gibson, and G. P. Young. 1993. Butyrate production from dietary fiber and protection against large bowel cancer in a rat model. Gut 34:386-391.
47. 14). Anaerobe 3:373-381.
48. Moore, W. E. C., and L. H. Moore. 1995. Intestinal floras of populations that have a high risk of colon cancer. Appl. Environ. Microbiol. 61:3202-3207.
49. Mueller, S., K. Saunier, C. Hanisch, E. Norin, L. Alm, T. Midvedt, A. Cresci, S. Silvi, C. Orpianesi, M. C. Verdenelli, T. Calvel, C. Koebnick, H.-J. F. Zunft, J. Dore, and M. Blaut. 2006. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl. Environ. Microbiol. 72:1027-1033.
50. Pryde, S. E., S. H. Duncan, G. L. Hold, C. S. Stewart, and H. J. Flint. 2002. The microbiology of butyrate formation in the human colon. FEMS Microbiol. Lett. 217:133-139.
51. Ramsay, A. G., K. P. Scott, J. C. Martin, M. T. Rincon, and H. J. Flint. 2006. Cell-associated α amylases of butyrate-producing Firmicute bacteria from the human colon. Microbiology 152:3281-3290.
52. Reeves, A. R., G. R. Wang, and A. A Salyers. 1997. Characterization of four outer membrane proteins that play a role in utilization of starch by. Bacteroides thetaiotaomicron. J. Bacteriol. 179:643-649.
53. Rincon, M. T., T. Cepelnik, J. C. Martin, R. Lamed, E. A. Bayer, and H. J. Flint. 2005. Unconventional mode of attachment of the Ruminococcus flavefaciens cellulosome to the bacterial cell wall. J. Bacteriol. 187:7569-7578.
54. Robert, C., and A. Bernalier-Donadille. 2003. The cellulolytic microflora of the human colon: evidence of microcrystalline cellulose-degrading bacteria in methane excreting subjects. FEMS Microbiol. Ecol. 46:81-89.
55. Roe, A. J., C. O’Byrne, D. McLaggan, and I. R. Booth. 2002. Inhibition of Escherichia coli growth by acetic acid: a problem with methionine biosynthesis and homocysteine toxicity. Microbiology 148:2215-2222.
56. Romling, U. 2002. Molecular biology of cellulose production in bacteria. Res. Microbiol. 153:205-212.
57. Saarela, M., G. Mogensen, R. Fonden, J. Matto, and T. Mattila-Sandholm. 2000. Probiotic bacteria: safety, functional properties and technological properties. J. Biotechnol. 84:197-215.
58. Salyers, A. A., S. E. H. West, J. R. Vercellotti, and T. D. Wilkins. 1977. Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon. Appl. Environ. Microbiol. 34:529-533.
59. Salyers, A. A., J. R. Vercellotti, S. E. H. West, and T. D. Wilkins. 1977. Fermentation of mucins and plant polysaccharides by strains of Bacteroides from the human colon. Appl. Environ. Microbiol. 33:319-322.
60. Schell, M. A., M. Karmirantzou, B. Snel, D. Vilanova, B. Berger, G. Pessi, M.-C. Zwaheln, F. Desiere, P. Bork, M. Delley, R. D. Pridmore, and F. Arigoni. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA 99:14422-14427.
61. Scott, K. P., J. C. Martin, G. Campbell, C.-D. Mayer, and H. J. Flint. 2006. Whole genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium. Roseburia inulinivorans. J. Bacteriol. 188:4340-4349.
62. Sijpestein, A. K. 1951. On Ruminococcus flavefaciens, a cellulose-decomposing bacterium from the rumen of sheep and cattle. J. Gen. Microbiol. 5:869-879.
63. Simmering, R., H. Pforte, G. Jacobasch, and M. Blaut. 2002. The growth of the flavonoiddegrading intestinal bacterium, Eubacterium ramulus, is stimulated by dietary flavonoids. FEMS Microbiol. Ecol. 40:243-248.
64. Stanton, T. B., and D. C. Savage. 1983. Roseburia cecicola gen. nov., sp. nov., a motile, obligately anaerobic bacterium from a mouse cecum. Int. J. Syst. Bacteriol. 33:618-627.
65. Stanton, T. B., J. S. McDowell, and M. A. Rasmussen. 2004. Diverse tetracyline resistance genotypes of Megasphaera elsdenii strains selectively cultured from swine feces. Appl. Environ. Microbiol. 70:3754-3757.
66. Suau, A., R. Bonnet, M. Sutren, J. J. Godon, G. R. Gibson, M. D. Collins, and J. Dore. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 24:4799-4807.
67. Swidsinski, A., J. Weber, V. Loening-Baucke, L. P. Hale, and H. Lochs. 2005. Spatial organisation and composition of the mucosal flora in patients with inflammatory bowel disease. J. Clin. Microbiol. 43:3380-3389.
68. Tajima, K., R. I. Aminov, T. Nagamine, K. Ogata, M. Nakamura, H. Matsui, and Y. Benno. 1999. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29:159-169.
69. Topping, D. L., and P. M. Clifton. 2001. Short chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol. Rev. 81:1031-1064.
70. Vernia, P., R. Caprilli, G. Latella, F. Barbetti, F. M. Magliocca, and M. Cittadini. 1988. Fecal lactate and ulcerative colitis. Gastroenterology 95:1564-1568.
71. Walker, A. W. 2006. Influence of substrate and environmental factors on human gut microbial ecology and metabolism. Ph.D. thesis. University of Aberdeen, Aberdeen, United Kingdom.
72. Walker, A. W., S. H. Duncan, E. C. McWilliam Leitch, M. W. Child, and H. J. Flint. 2005. pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl. Environ. Microbiol. 71:3692-3700.
73. Wells, J. E., and P. B. Hylemon. 2000. Identification and characterization of a bile acid 7α-dehydroxylation operon in Clostridium sp. strain TO-931, a highly active 7α-dehydroxylating strain isolated from human feces. Appl. Environ. Microbiol. 66:1107-1113.
74. Wolin, M. J. 1969. Volatile fatty acids and the inhibition of Escherichia coli growth by rumen fluid. Appl. Microbiol. 17:83-87.
75. Xu, J., M. K. Bjursell, J. Himrod, S. Deng, L. K. Carmichael, H. C. Chiang, L. V. Hooper, and J. I. Gordon. 2003. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299:2074-2076.
76. Zoetendal, E. G., A. D. L. Akkermans, W. M. Akkermans-van-Vliet, J. A. G. M. de Vissar, and W. M. de Vos. 2001. The host genotype affects the bacterial community in the human gastrointestinal tract. Microbiol. Health Dis. 13:129-134.
77. Zoetendal, E. G., E. E. Vaughan, and W. M. de Vos. 2006. A microbial world within us. Mol. Microbiol. 59:1639-1650.