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Chapter 1 : Glycolysis for Microbiome Generation

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Abstract:

There is no life without metabolism. There is nothing surprising about this statement; it is blatantly obvious and true for both host and bacteria, whether commensal or pathogen. What is surprising is the delayed general recognition that metabolism plays a, or perhaps, central role in pathogenesis, which is simply a manifestation of the need for certain “bad” bacteria to grow and divide on or in a host. Perhaps this delay is natural, as researchers tend to focus on particularities, in this case, cellular processes unique to pathogenesis. Another reason for this delay is likely the aversion of late 20th Century microbiologists, who came to science after the heyday of bacterial metabolic research and who were forced to memorize whole swaths of the metabolic chart, usually out of context and with little understanding of the intricate linkages between metabolic pathways and their connections to other cellular processes.

Citation: Wolfe A. 2015. Glycolysis for Microbiome Generation, p 1-16. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0014-2014
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Figure 1

Acetyl-coenzyme A (AcCoA) is the keystone molecule of central metabolism. Glucose is metabolized via the EMP pathway to AcCoA in an NAD-dependent manner. The AcCoA is interconverted with amino acids and fatty acids. It replenishes the NAD-dependent tricarboxylic acid (TCA) cycle. It is the substrate for most secondary metabolites and the acetyl donor for some lysine acetylations, such as the PAT-dependent acetylation of ACS (acCoA synthetase). Acetate dissimilation requires the Pta-AckA pathway. The enzyme PTA (phosphotransacetylase) converts AcCoA and inorganic phosphate (P) into coenzyme A (CoA) and the high-energy pathway intermediate AcP. AcP donates its phosphoryl group to certain two-component response regulators (RR). AcP also can donate its acetyl group to hundreds of proteins. The enzyme ACKA (acetate kinase) converts AcP and ADP to acetate and ATP. The acetate freely diffuses across the cell envelope into the environment. Acetate assimilation requires the high-affinity enzyme ACS. In a two-step process that involves an enzyme-bound intermediate (acAMP), Acs converts acetate, ATP, and CoA into AMP, pyrophosphate (PP), and acCoA. ACS activity is inhibited by acetylation of a conserved lysine catalyzed by the lysine acetyltransferase (PAT, also known as YfiQ and Pka). Reactivation is catalyzed by the NAD-dependent deacetylase CobB. Adapted from Hu et al., 2010. GAPDH, glyceraldehyde-3-phosphate dehydrogenase; PDH, pyruvate dehydrogenase.

Citation: Wolfe A. 2015. Glycolysis for Microbiome Generation, p 1-16. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0014-2014
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Figure 2

Three substrate-level phosphorylations. The first two examples are steps in the lower half of the EMP pathway. The third is a step in acetate fermentation.

Citation: Wolfe A. 2015. Glycolysis for Microbiome Generation, p 1-16. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0014-2014
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Figure 3

Glycolysis in and related bacteria. The Embden-Meyerhoff-Parnas (EMP), the Pentose Phosphate (PP), and Entner-Doudoroff (ED) pathways. The boxes highlight reactions unique to the PP and ED pathways. When glucose is metabolized by the EMP, the lower half of the pathway is repeated twice. In and related bacteria, glucose is transported and phosphorylated using PEP as the phosphoryl donor. Thus, one of the two PEP molecules generated by the EMP pathway is used to transport and phosphorylate another glucose molecule. For the PP pathway to function, two glucose molecules must be metabolized. Pentose sugars and sugar acids can be metabolized via the PP and ED pathways, respectively. PEP, phosphoenol pyruvate; PFK, phosphofructokinase; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; EDD, 6-phosphogluconate dehydratase; EDA, 2-keto 3-deoxy-D-gluconate 6-phosphate aldolase.

Citation: Wolfe A. 2015. Glycolysis for Microbiome Generation, p 1-16. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0014-2014
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Figure 4

Fermentation. A) General strategy, B) Homolactic acid fermentation, and C) Ethanol fermentation.

Citation: Wolfe A. 2015. Glycolysis for Microbiome Generation, p 1-16. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0014-2014
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Figure 5

A mixed-acid fermentation. Blue steps consume NAD, whereas red steps recycle NAD. Green compounds are excreted. GAP, glyceraldehyde 3-phosphate; PEP, phosphoenol pyruvate; HSCoA, coenzyme A; P, inorganic phosphate.

Citation: Wolfe A. 2015. Glycolysis for Microbiome Generation, p 1-16. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0014-2014
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Figure 6

The heterolactic pathway. EC 4.1.29 is a phosphoketolase that cleaves a 5-carbon phosphosugar (xylulose 5-phosphate) into a 3-carbon phosphate (glyceraldehyde 3-phosphate) and a 2-carbon phosphate (acetyl phosphate). Note that all the NAD-consuming steps are balanced by NAD-producing steps. Because acetyl phosphate is used to recycle NAD, it is not used to generate ATP.

Citation: Wolfe A. 2015. Glycolysis for Microbiome Generation, p 1-16. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0014-2014
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Figure 7

The Bifidobacterium shunt. Xfp is a bifunctional phosphoketolase. One activity (EC 4.1.2.22) cleaves a 6-carbon phosphosugar (fructose 6-phosphate) into a 4-carbon phosphate (erythrose 4-phosphate) and a 2-carbon phosphate (acetyl phosphate). A second activity (EC 4.1.29) cleaves a 5-carbon phosphosugar (xylulose 5-phosphate) into a 3-carbon phosphate (glyceraldehyde 3-phosphate) and a 2-carbon phosphate (acetyl phosphate). Note that all the NAD-consuming steps are balanced by NAD-producing steps. Acetyl phosphate is used to generate ATP.

Citation: Wolfe A. 2015. Glycolysis for Microbiome Generation, p 1-16. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0014-2014
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References

/content/book/10.1128/9781555818883.chap1
1. Wolfe AJ,, Conley MP,, Berg HC . 1988. Acetyladenylate plays a role in controlling the direction of flagellar rotation. Proc Natl Acad Sci U S A 85( 18) : 6711 6715.[PubMed] [CrossRef]
2. Lipmann F . 1954. Development of the acetylation problem, a personal account. Science 120( 3126) : 855 865.[PubMed] [CrossRef]
3. Bentley R . 2000. From ‘reactive C2 units’ to acetyl coenzyme A: a long trail with an acetyl phosphate detour. Trends Biochem Sci 25( 6) : 302 305.[PubMed] [CrossRef]
4. Barak R,, Eisenbach M . 2001. Acetylation of the response regulator, CheY, is involved in bacterial chemotaxis. Mol Microbiol 40( 3) : 731 743.[PubMed] [CrossRef]
5. Barak R,, Prasad K,, Shainskaya A,, Wolfe AJ,, Eisenbach M . 2004. Acetylation of the chemotaxis response regulator cheY by acetyl-CoA synthetase purified from Escherichia coli . J Mol Biol 342( 2) : 383 401.[PubMed] [CrossRef]
6. Barak R,, Welch M,, Yanovsky A,, Oosawa K,, Eisenbach M . 1992. Acetyladenylate or its derivative acetylates the chemotaxis protein CheY in vitro and increases its activity at the flagellar switch. Biochemistry 31 : 10099 10107.[PubMed] [CrossRef]
7. Barak R,, Yan J,, Shainskaya A,, Eisenbach M . 2006. The chemotaxis response regulator CheY can catalyze its own acetylation. J Mol Biol 359( 2) : 251 265.[PubMed] [CrossRef]
8. Li R,, Gu J,, Chen Y-Y,, Xiao C-L,, Wang L-W,, Zhang Z-P,, Bi L-J,, Wei H-P,, Wang X-D,, Deng J-Y,, Zhang X-E . 2010. CobB regulates Escherichia coli chemotaxis by deacetylating the response regulator CheY. Mol Microbiol 76( 5) : 1162 1174.[PubMed] [CrossRef]
9. Liarzi O,, Barak R,, Bronner V,, Dines M,, Sagi Y,, Shainskaya A,, Eisenbach M . 2010. Acetylation represses the binding of CheY to its target proteins. Mol Microbiol 76( 4) : 932 943.[PubMed] [CrossRef]
10. Yan J,, Barak R,, Liarzi O,, Shainskaya A,, Eisenbach M . 2008. In vivo acetylation of heY, a response regulator in chemotaxis of Escherichia coli . JMol Biol 376( 5) : 1260 1271.[PubMed] [CrossRef]
11. Lukat GS,, McCleary WR,, Stock AM,, Stock JB . 1992. Phosphorylation of bacterial response regulator proteins by low molecular weight phospho-donors. Proc Natl Acad Sci U S A 89( 2) : 718 722.[PubMed] [CrossRef]
12. McCleary WR,, Stock JB . 1994. Acetyl phosphate and the activation of two-component response regulators. J Biol Chem 269( 50) : 31567 31572.[PubMed]
13. Barak R,, Abouhamad WN,, Eisenbach M . 1998. Both acetate kinase and acetyl coenzyme A synthetase are involved in acetate-stimulated change in the direction of flagellar rotation in Escherichia coli . J Bacteriol 180( 4) : 985 988.[PubMed]
14. Barak R,, Eisenbach M . 2004. Co-regulation of acetylation and phosphorylation of CheY, a response regulator in chemotaxis of Escherichia coli . J Mol Biol 342( 2) : 375 381.[PubMed] [CrossRef]
15. Li R,, Chen P,, Gu J,, Deng JY . 2013. Acetylation reduces the ability of CheY to undergo autophosphorylation. FEMS Microbiol Lett 347( 1) : 70 76.[PubMed] [CrossRef]
16. Ramakrishnan R,, Schuster M,, Bourret RB . 1998. Acetylation at Lys-92 enhances signaling by the chemotaxis response regulator protein CheY. Proc Natl Acad Sci U S A 95( 9) : 4918 4923.[PubMed] [CrossRef]
17. Fraiberg M,, Afanzar O,, Cassidy CK,, Gabashvili A,, Schulten K,, Levin Y,, Eisenbach M . 2015. CheY’s acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli . Mol Microbiol, in press. [PubMed] [CrossRef]
18. Danese PN,, Silhavy TJ . 1998. CpxP, a stress-combative member of the Cpx regulon. J Bacteriol 180( 4) : 831 839.[PubMed]
19. Fredericks CE,, Shibata S,, Aizawa S-I,, Reimann SA,, Wolfe AJ . 2006. Acetyl phosphate-sensitive regulation of flagellar biogenesis and capsular biosynthesis depends on the Rcs phosphorelay. Mol Microbiol 61( 3) : 734 747.[PubMed] [CrossRef]
20. Hu LI,, Chi BK,, Kuhn ML,, Filippova EV,, Walker-Peddakotla AJ,, Basell K,, Becher D,, Anderson WF,, Antelmann H,, Wolfe AJ . 2013. Acetylation of the response regulator RcsB controls transcription from a small RNA promoter. J Bacteriol 195( 18) : 4174 4186.[PubMed] [CrossRef]
21. Lima BP,, Antelmann H,, Gronau K,, Chi BK,, Becher D,, Brinsmade SR,, Wolfe AJ . 2011. Involvement of protein acetylation in glucose-induced transcription of a stress-responsive promoter. Mol Microbiol 81 : 1190 1204.[PubMed] [CrossRef]
22. Lima BP,, Thanh Huyen TT,, Bassell K,, Becher D,, Antelmann H,, Wolfe AJ . 2012. Inhibition of acetyl phosphate-dependent transcription by an acetylatable lysine on RNA polymerase. J Biol Chem 287( 38) : 32147 32160.[PubMed] [CrossRef]
23. Feng J,, Atkinson MR,, McCleary W,, Stock JB,, Wanner BL,, Ninfa AJ . 1992. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli . J Bacteriol 174( 19) : 6061 6070.[PubMed]
24. Mitra A,, Fay PA,, Vendura KW,, Alla Z,, Carroll RK,, Shaw LN,, Riordan JT . 2014. Sigma(N)-dependent control of acid resistance and the locus of enterocyte effacement in enterohemorrhagic Escherichia coli is activated by acetyl phosphate in a manner requiring flagellar regulator FlhDC and the sigma(S) antagonist FliZ. Microbiologyopen 3( 4) : 497 512.[PubMed] [CrossRef]
25. Boll JM,, Hendrixson DR . 2011. A specificity determinant for phosphorylation in a response regulator prevents in vivo cross-talk and modification by acetyl phosphate. Proc Natl Acad Sci U S A 108( 50) : 20160 20165.[PubMed] [CrossRef]
26. Xu H,, Caimano MJ,, Lin T,, He M,, Radolf JD,, Norris SJ,, Gherardini F,, Wolfe AJ,, Yang XF . 2010. Role of acetyl-phosphate in activation of the Rrp2-RpoN-RpoS pathway in Borrelia burgdorferi . PLoS Pathog 6( 9) : e1001104. [PubMed] [CrossRef]
27. Liu J,, Obi IR,, Thanikkal EJ,, Kieselbach T,, Francis MS . 2011. Phosphorylated CpxR restricts production of the RovA global regulator in Yersinia pseudotuberculosis . PLoS One 6( 8) : e23314. [PubMed] [CrossRef]
28. Shin S,, Park C . 1995. Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR. J Bacteriol 177( 16) : 4696 4702.[PubMed]
29. Bouche S,, Klauck E,, Fischer D,, Lucassen M,, Jung K,, Hengge-Aronis R . 1998. Regulation of RssB-dependent proteolysis in Escherichia coli: a role for acetyl phosphate in a response regulator-controlled process. Mol Microbiol 27( 4) : 787 795.[PubMed] [CrossRef]
30. Gueriri I,, Bay S,, Dubrac S,, Cyncynatus C,, Msadek T . 2008. The Pta-AckA pathway controlling acetyl phosphate levels and the phosphorylation state of the DegU orphan response regulator both play a role in regulating Listeria monocytogenes motility and chemotaxis. Mol Microbiol 70( 6) : 1342 1357.[PubMed] [CrossRef]
31. Lawhon SD,, Maurer R,, Suyemoto M,, Altier C . 2002. Intestinal short-chain fatty acids alter Salmonella typhimurium invasion gene expression and virulence through BarA/SirA. Mol Microbiol 46( 5) : 1451 1464.[PubMed] [CrossRef]
32. Bang IS,, Kim BH,, Foster JW,, Park YK . 2000. OmpR regulates the stationary-phase acid tolerance response of Salmonella enterica serovar typhimurium. J Bacteriol 182( 8) : 2245 2252.[PubMed] [CrossRef]
33. Heyde M,, Laloi P,, Portalier R . 2000. Involvement of carbon source and acetyl phosphate in the external-pH-dependent expression of porin genes in Escherichia coli . J Bacteriol 182( 1) : 198 202.[PubMed] [CrossRef]
34. Matsubara M,, Mizuno T . 1999. EnvZ-independent phosphotransfer signaling pathway of the OmpR-mediated osmoregulatory expression of OmpC and OmpF in Escherichia coli . Biosci Biotechnol Biochem 63( 2) : 408 414.[PubMed] [CrossRef]
35. Pruss BM . 1998. Acetyl phosphate and the phosphorylation of OmpR are involved in the regulation of the cell division rate in Escherichia coli . Arch Microbiol 170( 3) : 141 146.[PubMed] [CrossRef]
36. Wolfe AJ . 2005. The acetate switch. Microbiol Mol Biol Rev 69( 1) : 12 50.[PubMed] [CrossRef]
37. Wolfe AJ . 2010. Physiologically relevant small phosphodonors link metabolism to signal transduction. Curr Opin Microbiol 13( 2) : 204 209.[PubMed] [CrossRef]
38. Starai VJ,, Escalante-Semerena JC . 2004. Identification of the protein acetyltransferase (Pat) enzyme that acetylates acetyl-CoA synthetase in Salmonella enterica . J Mol Biol 340( 5) : 1005 1012.[PubMed] [CrossRef]
39. Starai VJ,, Celic I,, Cole RN,, Boeke JD,, Escalante-Semerena JC . 2002. Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine. Science 298( 5602) : 2390 2392.[PubMed] [CrossRef]
40. Blander G,, Guarente L . 2004. The SIR2 family of protein deacetylases. Ann Rev Biochem 73( 1) : 417 435.[PubMed] [CrossRef]
41. Greiss S,, Gartner A . 2009. Sirtuin/Sir2 phylogeny, evolutionary considerations and structural conservation. Mol Cells 28( 5) : 407 415.[PubMed] [CrossRef]
42. Yang XJ,, Seto E . 2008. The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9( 3) : 206 218.[PubMed] [CrossRef]
43. Vetting MW,, LP SdC,, Yu M,, Hegde SS,, Magnet S,, Roderick SL,, Blanchard JS . 2005. Structure and functions of the GNAT superfamily of acetyltransferases. Arch Biochem Biophys 433( 1) : 212 226.[PubMed] [CrossRef]
44. Hildmann C,, Riester D,, Schwienhorst A . 2007. Histone deacetylases: an important class of cellular regulators with a variety of functions, p 487 497. In Applied microbiology and biotechnology, vol. 75. Springer, Berlin/Heidelberg. [CrossRef]
45. Kuhn ML,, Zemaitaitis B,, Hu LI,, Sahu A,, Sorensen D,, Minasov G,, Lima BP,, Scholle M,, Mrksich M,, Anderson WF,, Gibson BW,, Schilling B,, Wolfe AJ . 2014. Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation. PLoS One 9( 4) : e94816. [PubMed] [CrossRef]
46. Weinert Brian T,, Iesmantavicius V,, Wagner Sebastian A,, Scholz C,, Gummesson B,, Beli P,, Nystrom T,, Choudhary C . 2013. Acetyl-phosphate is a critical determinant of lysine acetylation in E. coli . Mol Cells 51( 2) : 265 272.[PubMed] [CrossRef]
47. Beckham KS,, Connolly JP,, Ritchie JM,, Wang D,, Gawthorne JA,, Tahoun A,, Gally DL,, Burgess K,, Burchmore RJ,, Smith BO,, Beatson SA,, Byron O,, Wolfe AJ,, Douce GR,, Roe AJ . 2014. The metabolic enzyme AdhE controls the virulence of Escherichia coli O157:H7. Mol Microbiol 93( 1) : 199 211.[PubMed] [CrossRef]
48. Witchell TD,, Eshghi A,, Nally JE,, Hof R,, Boulanger MJ,, Wunder EA Jr,, Ko AI,, Haake DA,, Cameron CE . 2014. Post-translational modification of LipL32 during Leptospira interrogans infection. PLoS Negl Trop Dis 8( 10) : e3280. [PubMed] [CrossRef]
49. Ding T,, Schloss PD . 2014. Dynamics and associations of microbial community types across the human body. Nature 509( 7500) : 357 360.[PubMed] [CrossRef]
50. Kraal L,, Abubucker S,, Kota K,, Fischbach MA,, Mitreva M . 2014. The prevalence of species and strains in the human microbiome: a resource for experimental efforts. PLoS One 9( 5) : e97279. [PubMed] [CrossRef]
51. Aagaard K,, Petrosino J,, Keitel W,, Watson M,, Katancik J,, Garcia N,, Patel S,, Cutting M,, Madden T,, Hamilton H,, Harris E,, Gevers D,, Simone G,, McInnes P,, Versalovic J . 2013. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J 27( 3) : 1012 1022.[PubMed] [CrossRef]
52. Tojo R,, Suarez A,, Clemente MG,, de Los Reyes-Gavilan CG,, Margolles A,, Gueimonde M,, Ruas-Madiedo P . 2014. Intestinal microbiota in health and disease: Role of bifidobacteria in gut homeostasis. World J Gastroenterol 20( 41) : 15163 15176.[PubMed] [CrossRef]
53. Turroni F,, Ventura M,, Butto LF,, Duranti S,, O’Toole PW,, Motherway MO,, van Sinderen D . 2014. Molecular dialogue between the human gut microbiota and the host: a Lactobacillus and Bifidobacterium perspective. Cell Mol Life Sci 71( 2) : 183 203.[PubMed] [CrossRef]
54. Shreiner AB,, Kao JY,, Young VB . 2015. The gut microbiome in health and in disease. Curr Opin Gastroenterol 31 : 69 75.[PubMed] [CrossRef]
55. Ravel J,, Gajer P,, Abdo Z,, Schneider GM,, Koenig SS,, McCulle SL,, Karlebach S,, Gorle R,, Russell J,, Tacket CO,, Brotman RM,, Davis CC,, Ault K,, Peralta L,, Forney LJ . 2011. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A 108( Suppl 1) : 4680 4687.[PubMed] [CrossRef]
56. Ravel J,, Brotman RM,, Gajer P,, Ma B,, Nandy M,, Fadrosh DW,, Sakamoto J,, Koenig SS,, Fu L,, Zhou X,, Hickey RJ,, Schwebke JR,, Forney LJ . 2013. Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. Microbiome 1( 1) : 29. [PubMed] [CrossRef]
57. Gajer P,, Brotman RM,, Bai G,, Sakamoto J,, Schutte UM,, Zhong X,, Koenig SS,, Fu L,, Ma ZS,, Zhou X,, Abdo Z,, Forney LJ,, Ravel J . 2012. Temporal dynamics of the human vaginal microbiota. Sci Transl Med 4( 132) : 132ra152. [PubMed] [CrossRef]
58. Hickey RJ,, Zhou X,, Pierson JD,, Ravel J,, Forney LJ . 2012. Understanding vaginal microbiome complexity from an ecological perspective. Transl Res 160( 4) : 267 282.[PubMed] [CrossRef]
59. Ma B,, Forney LJ,, Ravel J . 2012. Vaginal microbiome: rethinking health and disease. Annu Rev Microbiol 66 : 371 389.[PubMed] [CrossRef]
60. Fouts DE,, Pieper R,, Szpakowski S,, Pohl H,, Knoblach S,, Suh MJ,, Huang ST,, Ljungberg I,, Sprague BM,, Lucas SK,, Torralba M,, Nelson KE,, Groah SL . 2012. Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury. J Transl Med 10 : 174. [PubMed] [CrossRef]
61. Hilt EE,, McKinley K,, Pearce MM,, Rosenfeld AB,, Zilliox MJ,, Mueller ER,, Brubaker L,, Gai X,, Wolfe AJ,, Schreckenberger PC . 2014. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol 52( 3) : 871 876.[PubMed] [CrossRef]
62. Khasriya R,, Sathiananthamoorthy S,, Ismail S,, Kelsey M,, Wilson M,, Rohn JL,, Malone-Lee J . 2013. Spectrum of bacterial colonization associated with urothelial cells from patients with chronic lower urinary tract symptoms. J Clin Microbiol 51( 7) : 2054 2062.[PubMed] [CrossRef]
63. Pearce MM,, Hilt EE,, Rosenfeld AB,, Zilliox MJ,, Thomas-White K,, Fok C,, Kliethermes S,, Schreckenberger PC,, Brubaker L,, Gai X,, Wolfe AJ . 2014. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. MBio 5( 4) : e01283–01214.[PubMed] [CrossRef]
64. Wolfe AJ,, Toh E,, Shibata N,, Rong R,, Kenton K,, Fitzgerald M,, Mueller ER,, Schreckenberger P,, Dong Q,, Nelson DE,, Brubaker L . 2012. Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol 50( 4) : 1376 1383.[PubMed] [CrossRef]
65. Mayer C,, Boos W . 2005. Hexose/pentose and hexitol/pentitol metabolism. In EcoSal Plus 2005.
66. Romeo T,, Snoep J . 2005. Glycolysis and flux control. In EcoSal Plus 2005.
67. Peekhaus N,, Conway T . 1998. What’s for dinner? Entner-Doudoroff metabolism in Escherichia coli . J Bacteriol 180( 14) : 3495 3502.[PubMed]
68. Lessie TG,, Phibbs PVJ . 1984. Alternative pathways of carbohydrate utilization in pseudomonads. Annu Rev Microbiol 38 : 359 388.[PubMed] [CrossRef]
69. Conway T . 1992. The Entner-Doudoroff pathway: history, physiology and molecular biology. FEMS Microbiol Rev 9( 1) : 1 27.[PubMed] [CrossRef]
70. Crabtree H . 1928. The carbohydrate metabolism of certain pathological overgrowths. Biochem J 22 : 1289 1298.[PubMed]
71. Warburg O,, Wind F,, Negelein E . 1927. The metabolism of tumors in the body. J Gen Physiol 8 : 519 530.[PubMed] [CrossRef]
72. Greiner EF,, Guppy M,, Brand K . 1994. Glucose is essential for proliferation and the glycolytic enzyme induction that provokes a transition to glycolytic energy production. J Biol Chem 269( 50) : 31484 31490.[PubMed]
73. Warburg O . 1956. On the origin of cancer cells. Science 123( 3191) : 309 314.[PubMed] [CrossRef]
74. Mustea I,, Muresian T . 1967. Crabtree effect in some bacterial cultures. Cancer Res 20 : 1499 1501.[PubMed] [CrossRef]
75. Doelle HW,, Ewings KN,, Hollywood NW . 1982. Regulation of glucose metabolism in bacterial systems. Adv Biochem Eng 23 : 1 35.[CrossRef]
76. Luli GW,, Strohl WR . 1990. Comparison of growth, acetate production, and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations. Appl Environ Microbiol 56( 4) : 1004 1011.[PubMed]
77. Holms H . 1990. Flux analysis and control of the central metabolic pathways in Escherichia coli . FEMS Microbiol Rev 1996, 19( 2) : 85 116.[PubMed] [CrossRef]
78. Holms WH . 1986. The central metabolic pathways of Escherichia coli: relationship between flux and control at a branch point, efficiency of conversion to biomass, and excretion of acetate. Curr Top Cell Regul 28 : 69 105.[PubMed] [CrossRef]
79. Krebs HA . 1972. The Pasteur effect and the relations between respiration and fermentation. Essays Biochem 8 : 1 34.[PubMed]
80. Diaz-Ruiz R,, Averet N,, Araiza D,, Pinson B,, Uribe-Carvajal S,, Devin A,, Rigoulet M . 2008. Mitochondrial oxidative phosphorylation is regulated by fructose 1,6-bisphosphate. A possible role in Crabtree effect induction? J Biol Chem 283( 40) : 26948 26955.[PubMed] [CrossRef]
81. Diaz-Ruiz R,, Rigoulet M,, Devin A . 2011. The Warburg and Crabtree effects: On the origin of cancer cell energy metabolism and of yeast glucose repression. Biochim Biophys Acta 1807( 6) : 568 576.[PubMed] [CrossRef]
82. Cocaign-Bousquet M,, Garrigues C,, Loubiere P,, Lindley ND . 1996. Physiology of pyruvate metabolism in Lactococcus lactis . Antonie Van Leeuwenhoek 70( 2–4) : 253 267.[PubMed] [CrossRef]
83. Melchiorsen CR,, Jensen NB,, Christensen B,, Vaever Jokumsen K,, Villadsen J . 2001. Dynamics of pyruvate metabolism in Lactococcus lactis . Biotechnol Bioeng 74( 4) : 271 279.[PubMed] [CrossRef]
84. Pessione E . 2012. Lactic acid bacteria contribution to gut microbiota complexity: lights and shadows. Front Cell Infect Microbiol 2 : 86. [PubMed] [CrossRef]
85. Dashko S,, Zhou N,, Compagno C,, Piskur J . 2014. Why, when, and how did yeast evolve alcoholic fermentation? FEMS Yeast Res 14( 6) : 826 832.[PubMed] [CrossRef]
86. Bock A,, Sawers G, . 1996. Fermentation, p 262 282. In Neidhardt FC,, Curtiss R III,, Ingraham JL,, Lin ECC,, Low KB,, Magasanik B,, Reznikoff WS,, Riley M,, Schaechter M,, E UH (ed), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, D.C.
87. van Hoek MJ,, Merks RM . 2012. Redox balance is key to explaining full vs. partial switching to low-yield metabolism. BMC Syst Biol 6 : 22. [PubMed] [CrossRef]
88. Xiao Z,, Xu P . 2007. Acetoin metabolism in bacteria. Crit Rev Microbiol 33( 2) : 127 140.[PubMed] [CrossRef]
89. Biebl H,, Menzel K,, Zeng AP,, Deckwer WD . 1999. Microbial production of 1,3-propanediol. Appl Microbiol Biotechnol 52( 3) : 289 297.[PubMed] [CrossRef]
90. Macfarlane GT,, Macfarlane S . 2012. Bacteria, colonic fermentation, and gastrointestinal health. J AOAC Int 95( 1) : 50 60.[PubMed] [CrossRef]
91. Puertollano E,, Kolida S,, Yaqoob P . 2014. Biological significance of short-chain fatty acid metabolism by the intestinal microbiome. Curr Opin Clin Nutr Metab Care 17( 2) : 139 144.[PubMed] [CrossRef]
92. Zaunmuller T,, Eichert M,, Richter H,, Unden G . 2006. Variations in the energy metabolism of biotechnologically relevant heterofermentative lactic acid bacteria during growth on sugars and organic acids. Appl Microbiol Biotechnol 72( 3) : 421 429.[PubMed] [CrossRef]
93. Yin X,, Chambers JR,, Barlow K,, Park AS,, Wheatcroft R . 2005. The gene encoding xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (xfp) is conserved among Bifidobacterium species within a more variable region of the genome and both are useful for strain identification. FEMS Microbiol Lett 246( 2) : 251 257.[PubMed] [CrossRef]
94. Sgorbati B,, Lenaz G,, Casalicchio F . 1976. Purification and properties of two fructose-6-phosphate phosphoketolases in Bifidobacterium . Antonie Van Leeuwenhoek 42( 1–2) : 49 57.[PubMed] [CrossRef]
95. Grill JP,, Crociani J,, Ballongue J . 1995. Characterization of fructose 6 phosphate phosphoketolases purified from Bifidobacterium species. Curr Microbiol 31( 1) : 49 54.[PubMed] [CrossRef]
96. Heath EC,, Hurwitz J,, Horecker BL,, Ginsburg A . 1958. Pentose fermentation by Lactobacillus plantarum. I. The cleavage of xylulose 5-phosphate by phosphoketolase. J Biol Chem 231( 2) : 1009 1029.[PubMed]
97. Lee JM,, Jeong DW,, Koo OK,, Kim MJ,, Lee JH,, Chang HC,, Kim JH,, Lee HJ . 2005. Cloning and characterization of the gene encoding phosphoketolase in Leuconostoc mesenteroides isolated from kimchi. Biotechnol Lett 27( 12) : 853 858.[PubMed] [CrossRef]
98. Posthuma CC,, Bader R,, Engelmann R,, Postma PW,, Hengstenberg W,, Pouwels PH . 2002. Expression of the xylulose 5-phosphate phosphoketolase gene, xpkA, from Lactobacillus pentosus MD363 is induced by sugars that are fermented via the phosphoketolase pathway and is repressed by glucose mediated by CcpA and the mannose phosphoenolpyruvate phosphotransferase system. Appl Environ Microbiol 68( 2) : 831 837.[PubMed] [CrossRef]
99. Macfarlane S,, McBain AJ,, Macfarlane GT . 1997. Consequences of biofilm and sessile growth in the large intestine. Adv Dent Res 11( 1) : 59 68.[PubMed] [CrossRef]
100. McNeil NI . 1984. The contribution of the large intestine to energy supplies in man. Am J Clin Nutr 39( 2) : 338 342.[PubMed]
101. Mortensen PB,, Clausen MR . 1996. Short-chain fatty acids in the human colon: relation to gastrointestinal health and disease. Scand J Gastroenterol Suppl 216 : 132 148.[PubMed] [CrossRef]
102. Topping DL,, Clifton PM . 2001. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol Rev 81( 3) : 1031 1064.[PubMed]
103. 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( 5) : 1030 1035.[PubMed]
104. Batt RM,, Rutgers HC,, Sancak AA . 1996. Enteric bacteria: friend or foe? J Small Anim Pract 37( 6) : 261 267.[PubMed] [CrossRef]
105. Wong JM,, de Souza R,, Kendall CW,, Emam A,, Jenkins DJ . 2006. Colonic health: fermentation and short chain fatty acids. J Clin Gastroenterol 40( 3) : 235 243.[PubMed] [CrossRef]
106. Tan J,, McKenzie C,, Potamitis M,, Thorburn AN,, Mackay CR,, Macia L . 2014. The role of short-chain fatty acids in health and disease. Adv Immunol 121 : 91 119.[CrossRef]
107. Russell WR,, Hoyles L,, Flint HJ,, Dumas ME . 2013. Colonic bacterial metabolites and human health. Curr Opin Microbiol 16( 3) : 246 254.[PubMed] [CrossRef]
108. Hu LI,, Lima BP,, Wolfe AJ . 2010. Bacterial protein acetylation: the dawning of a new age. Mol Microbiol 77 : 15 21.[PubMed] [CrossRef]

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