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Chapter 16 : Commensal and Pathogenic Metabolism in the Gut

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Abstract:

Every mammal on the planet is colonized with ( ), as well as cold-blooded animals (e.g., fish) at an appropriately warm temperature ( ). We estimate there are 10 cells in the human population alone. is frequently the first bacterium to colonize human infants and is a lifelong colonizer of adults ( ). is arguably the best understood of all model organisms ( ). Yet the essence of how colonizes and/or causes disease is still not completely understood. Certainly, innate immunity, adaptive immunity, and bacterial cell-to-cell communication play important roles in modulating the populations of the 500–1000 different commensal species in the intestine ( ); however, these topics will not be a focus of this chapter. We have reviewed the mucus layer as habitat for to colonize the intestine, aspects of physiology that enable its success, and the model systems employed for colonization research ( ). Here, we focus on metabolism in the intestinal mucus layer. We discuss evidence that must obtain nutrients in the mucus layer to colonize, that it resides in the mucus layer as a member of mixed biofilms, and that each strain displays a unique nutritional program in the intestine. We also discuss evidence supporting the “Restaurant” hypothesis for commensal strains, i.e., that they colonize the intestine as sessile members of mixed biofilms obtaining the nutrients they need for growth locally, but compete for nutrients with invading pathogens planktonically.

Citation: Conway T, Cohen P. 2015. Commensal and Pathogenic Metabolism in the Gut, p 343-362. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0006-2014
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Figure 1

Nutrient flow in the intestine. The primary sources of carbohydrates in the large intestine are mucus, dietary fiber, and epithelial cell debris. Mucus and dietary fiber consist of complex polysaccharides. typically cannot degrade complex polysaccharides; that is the job of anaerobes. Hence, degradation of polysaccharides by anaerobes releases oligosaccharides, which are preferred by anaerobes, as well as mono- and disaccharides, which are preferred by . doi:10.1128/microbiolspec.MBP-0006-2014.f1

Citation: Conway T, Cohen P. 2015. Commensal and Pathogenic Metabolism in the Gut, p 343-362. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0006-2014
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References

/content/book/10.1128/9781555818883.chap16
1. Finegold SM,, Sutter VL,, Mathisen GE, . 1983. Normal indigenous intestinal microflora, p 331. In Hentges DJ (ed), Human intestinal microflora in health and disease. Academic Press, Inc, New York, NY. [CrossRef]
2. Huggins C,, Rast HV Jr . 1963. Incidence of coliform bacteria in the intestinal tract of Gambusia affinis holbrooki (Girard) and in their habitat water. J Bacteriol 85 : 489490.[PubMed]
3. Palmer C,, Bik EM,, Digiulio DB,, Relman DA,, Brown PO . 2007. Development of the human infant intestinal microbiota. PLoS Biol 5 : e177. doi:10.1371/journal.pbio.0050177 [CrossRef]
4. Riley M,, Abe T,, Arnaud MB,, Berlyn MK,, Blattner FR,, Chaudhuri RR,, Glasner JD,, Horiuchi T,, Keseler IM,, Kosuge T,, Mori H,, Perna NT,, Plunkett G III,, Rudd KE,, Serres MH,, Thomas GH,, Thomson NR,, Wishart D,, Wanner BL . 2006. Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res 34 : 19.[PubMed] [CrossRef]
5. Stecher B,, Berry D,, Loy A . 2013. Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle. FEMS Microbiol Rev 37 : 793829.[PubMed] [CrossRef]
6. Stecher B,, Hardt WD . 2011. Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol 14 : 8291.[PubMed] [CrossRef]
7. Clarke MB,, Sperandio V . 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 : G1105G1109.[PubMed] [CrossRef]
8. Cole AM,, Ganz T, . 2005. Defensins and other antimicrobial peptides: innate defense of mucosal surfaces, p 1734. In Nataro JP,, Cohen PS,, Mobley HLT,, Weiser JN (ed), Colonization of mucosal surfaces. ASM Press, Washington, DC. [CrossRef]
9. Kaper JB,, Sperandio V . 2005. Bacterial cell-to-cell signaling in the gastrointestinal tract. Infect Immun 73 : 31973209.[PubMed] [CrossRef]
10. Pasetti MF,, Salerno-Gonçalves R,, Sztein MB, . 2005. Mechanisms of adaptive immunity that prevent colonization of mucosal surfaces, p 3547. In Nataro JP,, Cohen PS,, Mobley HLT,, Weiser JN (ed), Colonization of mucosal surfaces. ASM Press, Washington, DC. [CrossRef]
11. Sansonetti PJ . 2004. War and peace at mucosal surfaces. Nat Rev Immunol 4 : 953964.[PubMed] [CrossRef]
12. Conway T,, Krogfelt KA,, Cohen PS, . 2004. Chapter 8.3.1.2, The life of commensal Escherichia coli in the mammalian intestine. In Kaper JB (ed), EcoSalPlus Cellular and molecular biology of E. coli Salmonella, and the Enterobacteriaceae:, 3 rd ed, (online). ASM Press, Washington, DC.
13. Conway T,, Krogfelt KA,, Cohen PS, . 2007. Escherichia coli at the intestinal mucosal surface, p 175196. In Brogden KA,, Minion FC,, Cornick N,, Stanton TB,, Zhang Q,, Nolan LK,, Wannemuehler MJ (ed), Virulence mechanisms of bacterial pathogens, 4th ed. ASM Press, Washington, DC. [PubMed]
14. Laux DC,, Cohen PS,, Conway T, . 2005. Role of the mucus layer in bacterial colonization of the intestine, p 199212. In Nataro JP,, Mobley HLT,, Cohen PS (ed), Colonization of mucosal surfaces. ASM Press, Washington, DC. [CrossRef]
15. Wadolkowski EA,, Laux DC,, Cohen PS . 1988. Colonization of the streptomycin-treated mouse large intestine by a human fecal Escherichia coli strain: role of growth in mucus. Infect Immun 56 : 10301035.[PubMed]
16. Foster JW . 2004. Escherichia coli acid resistance: tales of an amateur acidophile. Nat Rev Microbiol 2 : 898907.[PubMed] [CrossRef]
17. Lin J,, Smith MP,, Chapin KC,, Baik HS,, Bennett GN,, Foster JW . 1996. Mechanisms of acid resistance in enterohemorrhagic Escherichia coli . Appl Environ Microbiol 62 : 30943100.[PubMed]
18. Freter R,, Brickner H,, Fekete J,, Vickerman MM,, Carey KE . 1983. Survival and implantation of Escherichia coli in the intestinal tract. Infect Immun 39 : 686703.[PubMed]
19. Moller AK,, Leatham MP,, Conway T,, Nuijten PJ,, de Haan LA,, Krogfelt KA,, Cohen PS . 2003. An Escherichia coli MG1655 lipopolysaccharide deep-rough core mutant grows and survives in mouse cecal mucus but fails to colonize the mouse large intestine. Infect Immun 71 : 21422152.[PubMed] [CrossRef]
20. McCormick BA,, Laux DC,, Cohen PS . 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 : 29572961.[PubMed]
21. McGuckin MA,, Lindén SK,, Sutton P,, Florin TH . 2011. Mucin dynamics and enteric pathogens. Nat Rev Microbiol 9 : 265278.[PubMed] [CrossRef]
22. Bergstrom KS,, Sham HP,, Zarepour M,, Vallance BA . 2012. Innate host responses to enteric bacterial pathogens: a balancing act between resistance and tolerance. Cell Microbiol 14 : 475484.[PubMed] [CrossRef]
23. Rang CU,, Licht TR,, Midtvedt T,, Conway PL,, Chao L,, Krogfelt KA,, Cohen PS,, 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 : 434436.[PubMed]
24. Poulsen LK,, Lan F,, Kristensen CS,, Hobolth P,, Molin S,, Krogfelt KA . 1994. Spatial distribution of Escherichia coli in the mouse large intestine inferred from rRNA in situ hybridization. Infect Immun 62 : 51915194.[PubMed]
25. Poulsen LK,, Licht TR,, Rang C,, Krogfelt KA,, Molin S . 1995. Physiological state of Escherichia coli BJ4 growing in the large intestines of streptomycin-treated mice. J Bacteriol 177 : 58405845.[PubMed]
26. Freter R, . 1992. Factors affecting the microecology of the gut, p 355376. In Fuller R (ed), Probiotics. The scientific basis. Chapman and Hall, London. [CrossRef]
27. Freter R, . 1983. Mechanisms that control the microflora in the large intestine, p 3354. In Hentges DJ (ed), Human intestinal microflora in health and disease. Academic Press, Inc., New York, NY. [CrossRef]
28. Freter R, . 1988. Mechanisms of bacterial colonization of the mucosal surfaces of the gut, p 4560. In Roth JA (ed), Virulence mechanisms of bacterial pathogens. American Society for Microbiology, Washington, DC.
29. van der Waaij D,, Berghuis-de Vries JM,, Lekkerkerk-k-v . 1971. Colonization resistance of the digestive tract in conventional and antibiotic-treated mice. J Hyg (Lond) 69 : 405411.[CrossRef]
30. Apperloo-Renkema HZ,, Van der Waaij BD,, Van der Waaij D . 1990. Determination of colonization resistance of the digestive tract by biotyping of Enterobacteriaceae. Epidemiol Infect 105 : 355361.[PubMed] [CrossRef]
31. Leatham MP,, Banerjee S,, Autieri SM,, Mercado-Lubo R,, Conway T,, Cohen PS . 2009. Precolonized human commensal Escherichia coli strains serve as a barrier to E. coli O157:H7 growth in the streptomycin-treated mouse intestine. Infect Immun 77 : 28762886.[PubMed] [CrossRef]
32. Stecher B,, Barthel M,, Schlumberger MC,, Haberli L,, Rabsch W,, Kremer M,, Hardt WD . 2008. Motility allows S. Typhimurium to benefit from the mucosal defence. Cell Microbiol 10 : 11661180.[PubMed] [CrossRef]
33. Stecher B,, Hapfelmeier S,, Müller C,, Kremer M,, Stallmach T,, Hardt WD . 2004. Flagella and chemotaxis are required for efficient induction of Salmonella enterica serovar Typhimurium colitis in streptomycin-pretreated mice. Infect Immun 72 : 41384150.[PubMed] [CrossRef]
34. Stecher B,, Robbiani R,, Walker AW,, Westendorf AM,, Barthel M,, Kremer M,, Chaffron S,, Macpherson AJ,, Buer J,, Parkhill J,, Dougan G,, von Mering C,, Hardt WD . 2007. Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol 5 : 21772189. doi:10.1371/journal.pbio.0050244 [CrossRef]
35. Maltby R,, Leatham-Jensen MP,, Gibson T,, Cohen PS,, Conway T . 2013. Nutritional basis for colonization resistance by human commensal Escherichia coli strains HS and Nissle 1917 against E. coli O157:H7 in the mouse intestine. PLoS One 8 : e53957. doi:10.1371/journal.pone.0053957 [CrossRef]
36. Fabich AJ,, Jones SA,, Chowdhury FZ,, Cernosek A,, Anderson A,, Smalley D,, McHargue JW,, Hightower GA,, Smith JT,, Autieri SM,, Leatham MP,, Lins JJ,, Allen RL,, Laux DC,, Cohen PS,, Conway T . 2008. Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine. Infect Immun 76 : 11431152.[PubMed] [CrossRef]
37. Stecher B,, Hardt WD . 2008. The role of microbiota in infectious disease. Trends Microbiol 16 : 107114.[PubMed] [CrossRef]
38. Cook H,, Ussery DW . 2013. Sigma factors in a thousand E. coli genomes. Environ Microbiol 15 : 31213129.[PubMed] [CrossRef]
39. Chang DE,, Smalley DJ,, Tucker DL,, Leatham MP,, Norris WE,, Stevenson SJ,, Anderson AB,, Grissom JE,, Laux DC,, Cohen PS,, Conway T . 2004. Carbon nutrition of Escherichia coli in the mouse intestine. Proc Natl Acad Sci U S A 101 : 74277432.[PubMed] [CrossRef]
40. Bowden SD,, Rowley G,, Hinton JC,, Thompson A . 2009. Glucose and glycolysis are required for the successful infection of macrophages and mice by Salmonella enterica serovar typhimurium. Infect Immun 77 : 31173126.[PubMed] [CrossRef]
41. Njoroge JW,, Nguyen Y,, Curtis MM,, Moreira CG,, Sperandio V . 2012. Virulence meets metabolism: Cra and KdpE gene regulation in enterohemorrhagic Escherichia coli . MBio 3 : e00280-00212. doi:10.1128/mBio.00280-12 [PubMed] [CrossRef]
42. Waligora EA,, Fisher CR,, Hanovice NJ,, Rodou A,, Wyckoff EE,, Payne SM . 2014. Role of intracellular carbon metabolism pathways in Shigella flexneri virulence. Infect Immun 82 : 27462755.[PubMed] [CrossRef]
43. Sweeney NJ,, Laux DC,, Cohen PS . 1996. Escherichia coli F-18 and E. coli K-12 eda mutants do not colonize the streptomycin-treated mouse large intestine. Infect Immun 64 : 35043511.[PubMed]
44. Peekhaus N,, Conway T . 1998. What’s for dinner?: Entner-Doudoroff metabolism in Escherichia coli . J Bacteriol 180 : 34953502.[PubMed]
45. Conway T . 1992. The Entner-Doudoroff pathway: history, physiology and molecular biology. FEMS Microbiol Rev 9 : 127.[PubMed] [CrossRef]
46. Eriksson S,, Lucchini S,, Thompson A,, Rhen M,, Hinton JC . 2003. Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica . Mol Microbiol 47 : 103118.[PubMed] [CrossRef]
47. Patra T,, Koley H,, Ramamurthy T,, Ghose AC,, Nandy RK . 2012. The Entner-Doudoroff pathway is obligatory for gluconate utilization and contributes to the pathogenicity of Vibrio cholerae . J Bacteriol 194 : 33773385.[PubMed] [CrossRef]
48. Zhao J,, Baba T,, Mori H,, Shimizu K . 2004. Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities. Appl Microbiol Biotechnol 64 : 9198.[PubMed] [CrossRef]
49. Steinsiek S,, Frixel S,, Stagge S,, SUMO, Bettenbrock K . 2011. Characterization of E. coli MG1655 and frdA and sdhC mutants at various aerobiosis levels. J Biotechnol 154 : 3545.[PubMed] [CrossRef]
50. Tchawa Yimga M,, Leatham MP,, Allen JH,, Laux DC,, Conway T,, Cohen PS . 2006. Role of gluconeogenesis and the tricarboxylic acid cycle in the virulence of Salmonella enterica serovar Typhimurium in BALB/c mice. Infect Immun 74 : 11301140.[PubMed] [CrossRef]
51. Fang FC,, Libby SJ,, Castor ME,, Fung AM . 2005. Isocitrate lyase (AceA) is required for Salmonella persistence but not for acute lethal infection in mice. Infect Immun 73 : 25472549.[PubMed] [CrossRef]
52. Spector MP,, DiRusso CC,, Pallen MJ,, Garcia del Portillo F,, Dougan G,, Finlay BB . 1999. The medium-/long-chain fatty acyl-CoA dehydrogenase (fadF) gene of Salmonella typhimurium is a phase 1 starvation-stress response (SSR) locus. Microbiology 145(Pt 1): 1531.[PubMed] [CrossRef]
53. Dahal N,, Abdelhamed H,, Lu J,, Karsi A,, Lawrence ML . 2013. Tricarboxylic acid cycle and one-carbon metabolism pathways are important in Edwardsiella ictaluri virulence. PLoS One 8 : e65973. doi:10.1371/journal.pone.0065973 [CrossRef]
54. Miranda RL,, Conway T,, Leatham MP,, Chang DE,, Norris WE,, Allen JH,, Stevenson SJ,, Laux DC,, Cohen PS . 2004. Glycolytic and gluconeogenic growth of Escherichia coli O157:H7 (EDL933) and E. coli K-12 (MG1655) in the mouse intestine. Infect Immun 72 : 16661676.[PubMed] [CrossRef]
55. Schinner SA,, Mokszycki ME,, Adediran J,, Leatham-Jensen M,, Conway T,, Cohen PS . 2015. Escherichia coli EDL933 Requires Gluconeogenic Nutrients To Successfully Colonize the Intestines of Streptomycin-Treated Mice Precolonized with E. coli Nissle 1917. Infect Immun 83 : 19831991. [PubMed] [CrossRef]
56. Lin ECC, . 1996. Sugars, polyols, and carboxylates, p 307342. In Neidhardt FC,, Curtiss R III,, Ingraham JL,, Lin ECC,, Low KB,, Magasanik B,, Reznikoff WS,, Riley M,, Schaechter M,, Umbarger HE (ed), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, DC.
57. Reitzer L, . 2005. Chapter 3.4.7 Catabolism of Amino Acids and Related Compounds. In Böck A,, Curtiss R III,, Kaper JB,, Karp PD,, Neidhardt FC,, Nyström T,, Slauch JM,, Squires CL,, Usery D (ed), EcoSal–Escherichia coli and Salmonella: cellular and molecular biology, 3 rd ed (online). ASM Press, Washington, DC.
58. Monk JM,, Charusanti P,, Aziz RK,, Lerman JA,, Premyodhin N,, Orth JD,, Feist AM,, Palsson . 2013. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A 110 : 2033820343.[PubMed] [CrossRef]
59. Autieri SM,, Lins JJ,, Leatham MP,, Laux DC,, Conway T,, Cohen PS . 2007. L-fucose stimulates utilization of D-ribose by Escherichia coli MG1655 ΔfucAO and E. coli Nissle 1917 ΔfucAO mutants in the mouse intestine and in M9 minimal medium. Infect Immun 75 : 54655475.[PubMed] [CrossRef]
60. Jones SA,, Jorgensen M,, Chowdhury FZ,, Rodgers R,, Hartline J,, Leatham MP,, Struve C,, Krogfelt KA,, Cohen PS,, Conway T . 2008. Glycogen and maltose utilization by Escherichia coli O157:H7 in the mouse intestine. Infect Immun 76 : 25312540.[PubMed] [CrossRef]
61. Leatham-Jensen MP,, Frimodt-Møller J,, Adediran J,, Mokszycki ME,, Banner ME,, Caughron JE,, Krogfelt KA,, Conway T,, Cohen PS . 2012. The streptomycin-treated mouse intestine selects Escherichia coli envZ missense mutants that interact with dense and diverse intestinal microbiota. Infect Immun 80 : 17161727.[PubMed] [CrossRef]
62. Atuma C,, Strugala V,, Allen A,, Holm L . 2001. The adherent gastrointestinal mucus gel layer: thickness and physical state in vivo . Am J Physiol Gastrointest Liver Physiol 280 : G922G929.[PubMed]
63. Allen A, . 1984. The structure and function of gastrointestinal mucus, p 311. In Boedeker EC (ed), Attachment of organisms to the gut mucosa, vol II. CRC Press, Boca Raton, FL.
64. Kim YS,, Morita A,, Miura S,, Siddiqui B, . 1984. Structure of glycoconjugates of intestinal mucosal membranes, p 99109. In Boedeker EC (ed), Attachment of organisms to the gut mucosa, vol II. CRC Press, Boca Raton, FL.
65. Slomiany BL,, Slomiany A, . 1984. Lipid and mucus secretions of the alimentary tract, p 2431. In Boedeker EC (ed), Attachment of organisms to the gut mucosa, vol II. CRC Press, Boca Raton, FL.
66. Johansson ME,, Gustafsson JK,, Holmén-Larsson J,, Jabbar KS,, Xia L,, Xu H,, Ghishan FK,, Carvalho FA,, Gewirtz AT,, Sjövall H,, Hansson GC . 2014. Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis. Gut 63 : 281291.[PubMed]
67. Johansson ME,, Larsson JM,, Hansson GC . 2011. The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc Natl Acad Sci U S A 108(Suppl 1): 46594665.[PubMed] [CrossRef]
68. Hoskins LC, . 1984. Mucin degradation by enteric bacteria: ecological aspects and implications for bacterial attachment to gut mucosa, p 5165. In Boedeker EC (ed), Attachment of organisms to the gut mucosa, vol II. CRC Press, Boca Raton, FL.
69. Neutra MR, . 1984. The mechanism of intestinal mucous secretion, p 3341. In Boedeker EC (ed), Attachment of organisms to the gut mucosa, vol II. CRC Press, Boca Raton, FL.
70. Johansson ME,, Phillipson M,, Petersson J,, Velcich A,, Holm L,, Hansson GC . 2008. The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci U S A 105 : 1506415069.[PubMed] [CrossRef]
71. Holmén Larsson JM,, Thomsson KA,, Rodriguez-Piñeiro AM,, Karlsson H,, Hansson GC . 2013. Studies of mucus in mouse stomach, small intestine, and colon. III. Gastrointestinal Muc5ac and Muc2 mucin O-glycan patterns reveal a regiospecific distribution. Am J Physiol Gastrointest Liver Physiol 305 : G357G363.[PubMed] [CrossRef]
72. Hoskins LC,, Agustines M,, McKee WB,, Boulding ET,, Kriaris M,, Niedermeyer G . 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 Invest 75 : 944953.[PubMed] [CrossRef]
73. Moore WE,, Holdeman LV . 1974. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl Microbiol 27 : 961979.[PubMed]
74. Comstock LE,, Coyne MJ . 2003. Bacteroides thetaiotaomicron: a dynamic, niche-adapted human symbiont. Bioessays 25 : 926929.[PubMed] [CrossRef]
75. Goodman AL,, McNulty NP,, Zhao Y,, Leip D,, Mitra RD,, Lozupone CA,, Knight R,, Gordon JI . 2009. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6 : 279289.[PubMed] [CrossRef]
76. Martens EC,, Chiang HC,, Gordon JI . 2008. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4 : 447457.[PubMed] [CrossRef]
77. Ng KM,, Ferreyra JA,, Higginbottom SK,, Lynch JB,, Kashyap PC,, Gopinath S,, Naidu N,, Choudhury B,, Weimer BC,, Monack DM,, Sonnenburg JL . 2013. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502 : 9699.[PubMed] [CrossRef]
78. Salyers AA,, Pajeau M . 1989. Competitiveness of different polysaccharide utilization mutants of Bacteroides thetaiotaomicron in the intestinal tracts of germfree mice. Appl Environ Microbiol 55 : 25722578.[PubMed]
79. Mahowald MA,, Rey FE,, Seedorf H,, Turnbaugh PJ,, Fulton RS,, Wollam A,, Shah N,, Wang C,, Magrini V,, Wilson RK,, Cantarel BL,, Coutinho PM,, Henrissat B,, Crock LW,, Russell A,, Verberkmoes NC,, Hettich RL,, Gordon JI . 2009. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A 106 : 58595864.[PubMed] [CrossRef]
80. Tilman D . 1982. Resource competition and community structure. Monogr Popul Biol 17 : 1296.[PubMed]
81. Lendenmann U,, Snozzi M,, Egli T . 1996. Kinetics of the simultaneous utilization of sugar mixtures by Escherichia coli in continuous culture. Appl Environ Microbiol 62 : 14931499.[PubMed]
82. Ihssen J,, Egli T . 2005. Global physiological analysis of carbon- and energy-limited growing Escherichia coli confirms a high degree of catabolic flexibility and preparedness for mixed substrate utilization. Environ Microbiol 7 : 15681581.[PubMed] [CrossRef]
83. Liu M,, Durfee T,, Cabrera JE,, Zhao K,, Jin DJ,, Blattner FR . 2005. Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli . J Biol Chem 280 : 1592115927.[PubMed] [CrossRef]
84. Ferenci T . 2001. Hungry bacteria–definition and properties of a nutritional state. Environ Microbiol 3 : 605611.[PubMed] [CrossRef]
85. Sartor RB . 2005. Probiotic therapy of intestinal inflammation and infections. Curr Opin Gastroenterol 21 : 4450.[PubMed]
86. Grozdanov L,, Raasch C,, Schulze J,, Sonnenborn U,, Gottschalk G,, Hacker J,, Dobrindt U . 2004. Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. J Bacteriol 186 : 54325441.[PubMed] [CrossRef]
87. Sun J,, Gunzer F,, Westendorf AM,, Buer J,, Scharfe M,, Jarek M,, Gössling F,, Blöcker H,, Zeng AP . 2005. Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data. J Biotechnol 117 : 147161.[PubMed] [CrossRef]
88. Alteri CJ,, Smith SN,, Mobley HL . 2009. Fitness of Escherichia coli during urinary tract infection requires gluconeogenesis and the TCA cycle. PLoS Pathog 5 : e1000448. doi:10.1371/journal.ppat.1000448 [PubMed] [CrossRef]
89. Fabich AJ,, Leatham MP,, Grissom JE,, Wiley G,, Lai H,, Najar F,, Roe BA,, Cohen PS,, Conway T . 2011. Genotype and phenotypes of an intestine-adapted Escherichia coli K-12 mutant selected by animal passage for superior colonization. Infect Immun 79 : 24302439.[PubMed] [CrossRef]
90. Adediran J,, Leatham-Jensen MP,, Mokszycki ME,, Frimodt-Møller J,, Krogfelt KA,, Kazmierczak K,, Kenney LJ,, Conway T,, Cohen PS . 2014. An Escherichia coli Nissle 1917 missense mutant colonizes the streptomycin-treated mouse intestine better than the wild type but is not a better probiotic. Infect Immun 82 : 670682.[PubMed] [CrossRef]
91. Bohnhoff M,, Drake BL,, Miller CP . 1954. Effect of streptomycin on susceptibility of intestinal tract to experimental Salmonella infection. Proc Soc Exp Biol Med 86 : 132137.[PubMed] [CrossRef]
92. Hentges DJ,, Que JU,, Casey SW,, Stein AJ . 1984. The influence of streptomycin on colonization resistance in mice. Microecol Ther 14 : 5362.
93. Sonnenburg JL,, Chen CT,, Gordon JI . 2006. Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol 4 : e413. doi:10.1371/journal.pbio.0040413 [PubMed] [CrossRef]
94. Samuel BS,, Gordon JI . 2006. A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A 103 : 1001110016.[PubMed] [CrossRef]
95. Winter SE,, Winter MG,, Xavier MN,, Thiennimitr P,, Poon V,, Keestra AM,, Laughlin RC,, Gomez G,, Wu J,, Lawhon SD,, Popova IE,, Parikh SJ,, Adams LG,, Tsolis RM,, Stewart VJ,, Bäumler AJ . 2013. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science 339 : 708711.[PubMed] [CrossRef]
96. Meador JP,, Caldwell ME,, Cohen PS,, Conway T . 2014. Escherichia coli pathotypes occupy distinct niches in the mouse intestine. Infect Immun 82 : 19311938.[PubMed] [CrossRef]
97. Gauger EJ,, Leatham MP,, Mercado-Lubo R,, Laux DC,, Conway T,, Cohen PS . 2007. Role of motility and the flhDC Operon in Escherichia coli MG1655 colonization of the mouse intestine. Infect Immun 75 : 33153324.[PubMed] [CrossRef]
98. Leatham MP,, Stevenson SJ,, Gauger EJ,, Krogfelt KA,, Lins JJ,, Haddock TL,, Autieri SM,, Conway T,, Cohen PS . 2005. Mouse intestine selects nonmotile flhDC mutants of Escherichia coli MG1655 with increased colonizing ability and better utilization of carbon sources. Infect Immun 73 : 80398049.[PubMed] [CrossRef]
99. Bartlett DH,, Frantz BB,, Matsumura P . 1988. Flagellar transcriptional activators FlbB and FlaI: gene sequences and 5′ consensus sequences of operons under FlbB and FlaI control. J Bacteriol 170 : 15751581.[PubMed]
100. Prüss BM,, Campbell JW,, Van Dyk TK,, Zhu C,, Kogan Y,, Matsumura P . 2003. FlhD/FlhC is a regulator of anaerobic respiration and the Entner-Doudoroff pathway through induction of the methyl-accepting chemotaxis protein Aer. J Bacteriol 185 : 534543.[PubMed] [CrossRef]
101. De Paepe M,, Gaboriau-Routhiau V,, Rainteau D,, Rakotobe S,, Taddei F,, Cerf-Bensussan N . 2011. Trade-off between bile resistance and nutritional competence drives Escherichia coli diversification in the mouse gut. PLoS Genet 7 : e1002107. doi:10.1371/journal.pgen.1002107 [PubMed] [CrossRef]
102. Giraud A,, Arous S,, Paepe MD,, Gaboriau-Routhiau V,, Bambou JC,, Rakotobe S,, Lindner AB,, Taddei F,, Cerf-Bensussan N . 2008. Dissecting the genetic components of adaptation of Escherichia coli to the mouse gut. PLoS Genet 4 : e2. doi:10.1371/journal.pgen.0040002 [PubMed] [CrossRef]
103. Egger LA,, Park H,, Inouye M . 1997. Signal transduction via the histidyl-aspartyl phosphorelay. Genes Cells 2 : 167184.[PubMed] [CrossRef]
104. Walthers D,, Go A,, Kenney LJ, . 2004. Regulation of porin gene expression by the two-component regulatory system EnvZ/OmpR. In Benz R (ed), Bacterial and eukaryotic porins. Structure, function, mechanism. Wiley-VCH, Germany. [CrossRef]
105. Pratt LA,, Kolter R . 1998. Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili. Mol Microbiol 30 : 285293.[PubMed] [CrossRef]
106. Licht TR,, Christensen BB,, Krogfelt KA,, Molin S . 1999. Plasmid transfer in the animal intestine and other dynamic bacterial populations: the role of community structure and environment. Microbiology 145(Pt 9): 26152622.[PubMed]
107. Macfarlane S . 2008. Microbial biofilm communities in the gastrointestinal tract. J Clin Gastroenterol 42(Suppl 3 Pt 1): S142S143.[PubMed] [CrossRef]
108. Macfarlane S,, Bahrami B,, Macfarlane GT . 2011. Mucosal biofilm communities in the human intestinal tract. Adv Appl Microbiol 75 : 111143.[PubMed] [CrossRef]
109. Palestrant D,, Holzknecht ZE,, Collins BH,, Parker W,, Miller SE,, Bollinger RR . 2004. Microbial biofilms in the gut: visualization by electron microscopy and by acridine orange staining. Ultrastruct Pathol 28 : 2327.[PubMed] [CrossRef]
110. Swidsinski A,, Weber J,, Loening-Baucke V,, Hale LP,, Lochs H . 2005. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol 43 : 33803389.[PubMed] [CrossRef]
111. Macfarlane S,, Woodmansey EJ,, Macfarlane GT . 2005. Colonization of mucin by human intestinal bacteria and establishment of biofilm communities in a two-stage continuous culture system. Appl Environ Microbiol 71 : 74837492.[PubMed] [CrossRef]
112. Zoetendal EG,, von Wright A,, Vilpponen-Salmela T,, Ben-Amor K,, Akkermans AD,, de Vos WM . 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 : 34013407.[PubMed] [CrossRef]
113. Fong JC,, Syed KA,, Klose KE,, Yildiz FH . 2010. Role of Vibrio polysaccharide (vps) genes in VPS production, biofilm formation and Vibrio cholerae pathogenesis. Microbiology 156 : 27572769.[PubMed] [CrossRef]
114. Henrissat B,, Davies G . 1997. Structural and sequence-based classification of glycoside hydrolases. Curr Opin Struct Biol 7 : 637644.[PubMed] [CrossRef]
115. Franklin DP,, Laux DC,, Williams TJ,, Falk MC,, Cohen PS . 1990. Growth of Salmonella typhimurium SL5319 and Escherichia coli F-18 in mouse cecal mucus: role of peptides and iron. FEMS Microbiol Lett 74 : 229240.[CrossRef]
116. Licht TR,, Tolker-Nielsen T,, Holmstrøm K,, Krogfelt KA,, Molin S . 1999. Inhibition of Escherichia coli precursor-16S rRNA processing by mouse intestinal contents. Environ Microbiol 1 : 2332.[PubMed] [CrossRef]
117. Newman JV,, Kolter R,, Laux DC,, Cohen PS . 1994. Role of leuX in Escherichia coli colonization of the streptomycin-treated mouse large intestine. Microb Pathog 17 : 301311.[PubMed] [CrossRef]
118. Sweeney NJ,, Klemm P,, McCormick BA,, Moller-Nielsen E,, Utley M,, Schembri MA,, Laux DC,, Cohen PS . 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 : 34973503.[PubMed]
119. McCormick BA,, Stocker BA,, Laux DC,, Cohen PS . 1988. Roles of motility, chemotaxis, and penetration through and growth in intestinal mucus in the ability of an avirulent strain of Salmonella typhimurium to colonize the large intestine of streptomycin-treated mice. Infect Immun 56 : 22092217.[PubMed]

Tables

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TABLE 1

Central metabolism mutants tested for colonization defects in the mouse intestine

Citation: Conway T, Cohen P. 2015. Commensal and Pathogenic Metabolism in the Gut, p 343-362. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0006-2014
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TABLE 2

Sugar utilization in the intestine by strains

Citation: Conway T, Cohen P. 2015. Commensal and Pathogenic Metabolism in the Gut, p 343-362. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0006-2014

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