Gaining Insight into Microbial Physiology in the Large Intestine: A Special Role for Stable Isotopes

Advances in Microbial Physiology

Volumn 53, Issue , 2007, Pages

  de Graaf, Albert A ^a,b   Venema, Koen ^a,c  

^a TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^b MAASTRICHT UNIVERSITY   (Netherlands)

^c TNO   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BUTYRIC ACID; PREBIOTIC AGENT; STABLE ISOTOPE;

BACTERIAL PHENOMENA AND FUNCTIONS; BIOMEDICINE; ECOSYSTEM; ENERGY BALANCE; GENOME; GENOMICS; IMMUNE SYSTEM; INNATE IMMUNITY; INTESTINE FLORA; LARGE INTESTINE; METABOLIC STRESS; METABOLOMICS; MICROBIAL METABOLISM; MICROORGANISM; NONHUMAN; OBESITY; PH; PROTEOMICS; REVIEW;

EID: 34547730755     PISSN: 00652911     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-2911(07)53002-X     Document Type: Review

References (344)

1. Ahmad M.S., Krishnan S., Ramakrishna B.S., Mathan M., Pulimood A.B., and Murthy S.N. Butyrate and glucose metabolism by colonocytes in experimental colitis in mice. Gut 46 (2000) 493-499
2. Amann R., and Ludwig W. Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol. Rev. 24 (2000) 555-565
3. Andoh A., Tsujikawa T., and Fujiyama Y. Role of dietary fiber and short-chain fatty acids in the colon. Curr. Pharm. Des. 9 (2003) 347-358
4. Antoniewicz M.R., Kelleher J.K., and Stephanopoulos G. Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab. Eng. 8 (2006) 324-337
5. Arai K., Lee K., Berthiaume F., Tompkins R.G., and Yarmush M.L. Intrahepatic amino acid and glucose metabolism in a d-galactosamine-induced rat liver failure model. Hepatology 34 (2001) 360-371
6. Aries V., and Hill M.J. Degradation of steroids by intestinal bacteria. I. Deconjugation of bile salts. Biochim. Biophys. Acta 202 (1970) 526-534
7. Ault-Riche D., Fraley C.D., Tzeng C.M., and Kornberg A. Novel assay reveals multiple pathways regulating stress-induced accumulations of inorganic polyphosphate in Escherichia coli. J. Bacteriol. 180 (1998) 1841-1847
8. Bacher A., Rieder C., Eichinger D., Fuchs G., Arigoni D., and Eisenreich W. Elucidation of biosynthetic pathways and metabolic flux patterns via retrobiosynthetic NMR analysis. FEMS Microbiol. Rev. 22 (1999) 567-598
9. Backhed F., Ding H., Wang T., Hooper L.V., Koh G.Y., Nagy A., Semenkovich C.F., and Gordon J.I. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl. Acad. Sci. USA 101 (2004) 15718-15723
10. Backhed F., Ley R.E., Sonnenburg J.L., Peterson D.A., and Gordon J.I. Host-bacterial mutualism in the human intestine. Science 307 (2005) 1915-1920
11. Badman M.K., and Flier J.S. The gut and energy balance: visceral allies in the obesity wars. Science 307 (2005) 1909-1914
12. Barabasi A.L., and Albert R. Emergence of scaling in random networks. Science 286 (1999) 509-512
13. Barbara G., Stanghellini V., De Giorgio R., Cremon C., Cottrell G.S., Santini D., Pasquinelli G., Morselli-Labate A.M., Grady E.F., Bunnett N.W., Collins S.M., and Corinaldesi R. Activated mast cells in proximity to colonic nerves correlate with abdominal pain in irritable bowel syndrome. Gastroenterology 26 (2004) 693-702
14. Barcelo A., Claustre J., Moro F., Chayvialle J.A., Cuber J.C., and Plaisancie P. Mucin secretion is modulated by luminal factors in the isolated vascularly perfused rat colon. Gut 46 (2000) 218-224
15. Barcenilla A., Pryde S.E., Martin J.C., Duncan S.H., Stewart C.S., Henderson C., and Flint H.J. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl. Environ. Microbiol. 66 (2000) 1654-1661
16. Baronofsky J.J., Schreurs W.J., and Kashket E.R. Uncoupling by acetic acid limits growth of and acetogenesis by Clostridium thermoaceticum. Appl. Environ. Microbiol. 48 (1984) 1134-1139
17. Barzaghi D., Isbister J.D., Lauer K.P., and Born T.L. Use of surface-enhanced laser desorption/ionization - time of flight to explore bacterial proteomes. Proteomics 4 (2004) 2624-2628
18. Baumgart D.C., and Dignass A.U. Intestinal barrier function. Curr. Opin. Clin. Nutr. Metab. Care 5 (2002) 685-694
19. Bederman I.R., Reszko A.E., Kasumov T., David F., Wasserman D.H., Kelleher J.K., and Brunengraber H. Zonation of labeling of lipogenic acetyl-CoA across the liver: implications for studies of lipogenesis by mass isotopomer analysis. J. Biol. Chem. 279 (2004) 43207-43216
20. Beecher C.W. The human metabolome. In: Harrigan G.G., and Goodacre R. (Eds). Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis (2003), Kluwer, Boston 311-319
21. Ben-Amor K., Heilig H., Smidt H., Vaughan E.E., Abee T., and de Vos W.M. Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis. Appl. Environ. Microbiol. 71 (2005) 4679-4689
22. Bergman E.N. Energy contributions of volatile fatty acids from the gastrointestinal tract in various species. Physiol. Rev. 70 (1990) 567-590
23. Bevins C.L. Paneth cell defensins: key effector molecules of innate immunity. Biochem. Soc. Trans. 34 (2006) 263-266
24. Binder S.R., Hixson C., and Glossenger J. Protein arrays and pattern recognition: new tools to assist in the identification and management of autoimmune disease. Autoimmun. Rev. 5 (2006) 234-241
25. Birkett A., Muir J., Phillips J., Jones G., and O'Dea K. Resistant starch lowers fecal concentrations of ammonia and phenols in humans. Am. J. Clin. Nutr. 63 (1996) 766-772
26. Blaut, M. (2003) The influence of food components on intestinal microbiota composition. In: Intestinal Microflora and Health. Inside Story: Diet, Intestinal Flora and Health, pp. 7-18.
27. Bocker U., Nebe T., Herweck F., Holt L., Panja A., Jobin C., Rossol S., Sartor R.B., and Singer M.V. Butyrate modulates intestinal epithelial cell-mediated neutrophil migration. Clin. Exp. Immunol. 131 (2003) 53-60
28. Boelens P.G., van Leeuwen P.A., Dejong C.H., and Deutz N.E. Intestinal renal metabolism of l-citrulline and l-arginine following enteral or parenteral infusion of l-alanyl-l-[2,15N]glutamine or l-[2,15N]glutamine in mice. Am. J. Physiol. Gastrointest. Liver Physiol. 289 (2005) G679-G685
29. Boren J., Lee W.N., Bassilian S., Centelles J.J., Lim S., Ahmed S., Boros L.G., and Cascante M. The stable isotope-based dynamic metabolic profile of butyrate-induced HT29 cell differentiation. J. Biol. Chem. 278 (2003) 28395-28402
30. Boros L.G. Metabolic targeted therapy of cancer: current tracer technologies and future drug design strategies in the old metabolic network. Metabolomics 1 (2005) 11-15
31. Boros L.G., Brackett D.J., and Harrigan G.G. Metabolic biomarker and kinase drug target discovery in cancer using stable isotope-based dynamic metabolic profiling (SIDMAP). Curr. Cancer Drug Targets 3 (2003) 445-453
32. Bourriaud C., Robins R.J., Martin L., Kozlowski F., Tenailleau E., Cherbut C., and Michel C. Lactate is mainly fermented to butyrate by human intestinal microfloras but inter-individual variation is evident. J. Appl. Microbiol. 99 (2005) 201-212
33. Bruins M.J., Soeters P.B., Lamers W.H., and Deutz N.E. l-Arginine supplementation in pigs decreases liver protein turnover and increases hindquarter protein turnover both during and after endotoxemia. Am. J. Clin. Nutr. 75 (2002) 1031-1044
34. Bruins M.J., Deutz N.E., and Soeters P.B. Aspects of organ protein, amino acid and glucose metabolism in a porcine model of hypermetabolic sepsis. Clin. Sci. (Lond.) 104 (2003) 127-141
35. Brune A., and Friedrich M. Microecology of the termite gut: structure and function on a microscale. Curr. Opin. Microbiol. 3 (2000) 263-269
36. Brydon W.G., McKay L.F., and Eastwood M.A. Intestinal gas formation and the use of breath measurements to monitor the influence of diet and disease. Dig. Dis. 4 (1986) 1-12
37. Burgard A.P., Nikolaev E.V., Schilling C.H., and Maranas C.D. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 14 (2004) 301-312
38. Busch R., Kim Y.K., Neese R.A., Schade-Serin V., Collins M., Awada M., Gardner J.L., Beysen C., Marino M.E., Misell L.M., and Hellerstein M.K. Measurement of protein turnover rates by heavy water labeling of nonessential amino acids. Biochim. Biophys. Acta 1760 (2006) 730-744
39. Butzner J.D., Parmar R., Bell C.J., and Dalal V. Butyrate enema therapy stimulates mucosal repair in experimental colitis in the rat. Gut 38 (1996) 568-573
40. Cakir T., Kirdar B., and Ulgen K.O. Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks. Biotechnol. Bioeng. 86 (2004) 251-260
41. Cassidy M.M., Lightfoot F.G., and Vahouny G.V. Morphological aspects of dietary fibers in the intestine. Adv. Lipid Res. 19 (1982) 203-229
42. Chadwick V.S., and Anderson R.P. The role of intestinal bacteria in etiology and maintenance of inflammatory bowel disease. In: Gibson G.R., and Macfarlane G.T. (Eds). Human Colonic Bacteria: Role in Nutrition, Physiology, and Pathology (1995), CRC Press, Boca Raton, FL 227-256
43. Champomier-Verges M.C., Maguin E., Mistou M.Y., Anglade P., and Chich J.F. Lactic acid bacteria and proteomics: current knowledge and perspectives. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 771 (2002) 329-342
44. Chapman M.A., Grahn M.F., Boyle M.A., Hutton M., Rogers J., and Williams N.S. Butyrate oxidation is impaired in the colonic mucosa of sufferers of quiescent ulcerative colitis. Gut 35 (1994) 73-76
45. Cherbut C., Michel C., and Lecannu G. The prebiotic characteristics of fructooligosaccharides are necessary for reduction of TNBS-induced colitis in rats. J. Nutr. 133 (2003) 21-27
46. Chin J. Intestinal microflora: negotiating health outcomes with the warring community within us. Asia Pac. J. Clin. Nutr. 13 (2004) S24-S25
47. Christensen B., and Nielsen J. Isotopomer analysis using GC-MS. Metab. Eng. 1 (1999) 282-290
48. 13C breath curves to determine site and extent of starch digestion and fermentation in infants. J. Pediatr. Gastroenterol. Nutr. 34 (2002) 158-164
49. Christl S.U., Eisner H.D., Scheppach W., and Kasper H. Effects of sodium hydrogen sulfide on cell proliferation of colonic mucosa. Gastroenterology 106 (1994) A664
50. Clinton S.K. Dietary protein and carcinogenesis. In: Rowland I.R. (Ed). Nutrition, Toxicity and Cancer (1992), CRC Press, Boca Raton, FL 455-479
51. Coeffier M., Claeyssens S., Hecketsweiler B., Lavoinne A., Ducrotte P., and Dechelotte P. Enteral glutamine stimulates protein synthesis and decreases ubiquitin mRNA level in human gut mucosa. Am. J. Physiol. Gastrointest. Liver Physiol. 285 (2003) G266-G273
52. Collins S.M. Peripheral mechanisms of symptom generation in irritable bowel syndrome. Can. J. Gastroenterol. 15 Suppl. B (2001) 14B-16B
53. Corfield A.P., Wagner S.A., Clamp J.R., Kriaris M.S., and Hoskins L.C. Mucin degradation in the human colon: production of sialidase, sialate O-acetylesterase, N-acetylneuraminate lyase, arylesterase, and glycosulfatase activities by strains of fecal bacteria. Infect. Immun. 60 (1992) 3971-3978
54. Csordas A. Butyrate, aspirin and colorectal cancer. Eur. J. Cancer Prev. 5 (1996) 221-231
55. Cummings J.H. Production and metabolism of short-chain fatty acids in humans. In: Roche A.F.A.F. (Ed). Short-Chain Fatty Acids: Metabolism and Clinical Importance. Report of the Tenth Ross Conference on Medical Research (1991), Ross Laboratories, Columbus, OH 11-17
56. Cummings J.H. Short chain fatty acids. In: Gibson G.R., and Macfarlane G.T. (Eds). Human Colonic Bacteria: Role in Nutrition, Physiology, and Pathology (1995), CRC Press, Boca Raton, FL 101-130
57. Cummings J.H., and Bingham S.A. Dietary fibre, fermentation and large bowel cancer. Cancer Surv. 6 (1987) 601-621
58. Cummings J.H., and Macfarlane G.T. The control and consequences of bacterial fermentation in the human colon. J. Appl. Bacteriol. 70 (1991) 443-459
59. Cummings J.H., and Macfarlane G.T. Role of intestinal bacteria in nutrient metabolism. JPEN J. Parenter. Enteral Nutr. 21 (1997) 357-365
60. Cummings J.H., Pomare E.W., Branch W.J., Naylor C.P., and Macfarlane G.T. Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut 28 (1987) 1221-1227
61. Daly K., and Shirazi-Beechey S.P. Microarray analysis of butyrate regulated genes in colonic epithelial cells. DNA Cell. Biol. 25 (2006) 49-62
62. D'Argenio G., Cosenza V., Delle Cave M., Iovino P., Delle Valle N., Lombardi G., and Mazzacca G. Butyrate enemas in experimental colitis and protection against large bowel cancer in a rat model. Gastroenterology 110 (1996) 1727-1734
63. Davis C.D., and Hord N.G. Nutritional "omics" technologies for elucidating the role(s) of bioactive food components in colon cancer prevention. J. Nutr. 135 (2005) 2694-2697
64. Davis S.R., Stacpoole P.W., Williamson J., Kick L.S., Quinlivan E.P., Coats B.S., Shane B., Bailey L.B., and Gregory III J.F. Tracer-derived total and folate-dependent homocysteine remethylation and synthesis rates in humans indicate that serine is the main one-carbon donor. Am. J. Physiol. Endocrinol. Metab. 286 (2004) E272-E279
65. De Boever P., Deplancke B., and Verstraete W. Fermentation by gut microbiota cultured in a simulator of the human intestinal microbial ecosystem is improved by supplementing a soygerm powder. J. Nutr. 130 (2000) 2599-2606
66. 13C labeling and NMR spectroscopy in metabolic flux analysis. In: Barbotin J.N., and Portais J.C. (Eds). NMR in Microbiology: Theory and Application (2000), Horizon Scientific Press, Norwich, UK
67. de Graaf A.A., Eggeling L., and Sahm H. Metabolic engineering for l-lysine production by Corynebacterium glutamicum. Adv. Biochem. Eng. Biotechnol. 73 (2001) 9-29
68. 4]tyrosine to assess the effects of pro- and prebiotics on the intestinal flora of healthy human volunteers. Br. J. Nutr. 92 (2004) 439-446
69. de Vos W.M. Advances in genomics for microbial food fermentations and safety. Curr. Opin. Biotechnol. 12 (2001) 493-498
70. Derrien M., Vaughan E.E., Plugge C.M., and de Vos W.M. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int. J. Syst. Evol. Microbiol. 54 (2004) 1469-1476
71. Des Rosiers C., Lloyd S., Comte B., and Chatham J.C. A critical perspective of the use of (13)C-isotopomer analysis by GCMS and NMR as applied to cardiac metabolism. Metab. Eng. 6 (2004) 44-58
72. Deutz N.E., Bruins M.J., and Soeters P.B. Infusion of soy and casein protein meals affects interorgan amino acid metabolism and urea kinetics differently in pigs. J. Nutr. 128 (1998) 2435-2445
73. Distrutti E., Sediari L., Mencarelli A., Renga B., Orlandi S., Antonelli E., Roviezzo F., Morelli A., Cirino G., Wallace J.L., and Fiorucci S. Evidence that hydrogen sulfide exerts antinociceptive effects in the gastrointestinal tract by activating KATP channels. J. Pharmacol. Exp. Ther. 316 (2006) 325-335
74. Dolnikowski G.G., Marsh J.B., Das S.K., and Welty F.K. Stable isotopes in obesity research. Mass Spectrom. Rev. 24 (2005) 311-327
75. Dumont M.G., and Murrell J.C. Stable isotope probing - linking microbial identity to function. Nat. Rev. Microbiol. 3 (2005) 499-504
76. Duncan S.H., Barcenilla A., Stewart C.S., Pryde S.E., and Flint H.J. Acetate utilization and butyryl coenzyme A (CoA):acetate-CoA transferase in butyrate-producing bacteria from the human large intestine. Appl. Environ. Microbiol. 68 (2002) 5186-5190
77. Duncan S.H., Louis P., and Flint H.J. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl. Environ. Microbiol. 70 (2004) 5810-5817
78. Dunkley T.P., Dupree P., Watson R.B., and Lilley K.S. The use of isotope-coded affinity tags (ICAT) to study organelle proteomes in Arabidopsis thaliana. Biochem. Soc. Trans. 32 (2004) 520-523
79. Edwards J.S., and Palsson B.O. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinform. 1 (2000) 1
80. Egert M., Wagner B., Lemke T., Brune A., and Friedrich M.W. Microbial community structure in midgut and hindgut of the humus-feeding larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae). Appl. Environ. Microbiol. 69 (2003) 6659-6668
81. Egert M., Marhan S., Wagner B., Scheu S., and Friedrich M.W. Molecular profiling of 16S rRNA genes reveals diet-related differences of microbial communities in soil, gut, and casts of Lumbricus terrestris L. (Oligochaeta: Lumbricidae). FEMS Microbiol. Ecol. 48 (2004) 187-197
82. Egert M., Stingl U., Bruun L.D., Pommerenke B., Brune A., and Friedrich M.W. Structure and topology of microbial communities in the major gut compartments of Melolontha melolontha larvae (Coleoptera: Scarabaeidae). Appl. Environ. Microbiol. 71 (2005) 4556-4566
83. Egert M., de Graaf A.A., Smidt H., de Vos W.M., and Venema K. Beyond diversity: functional microbiomics of the human colon. Trends Microbiol. 14 (2006) 86-91
84. Egert M., de Graaf A.A., Maathuis A., de Waard P., Plugge C.M., Smidt H., Deutz N.E.P., Dijkema C., de Vos W.M., and Venema K. Identification of glucose-fermenting bacteria present in an in vitro model of the human intestine by RNA-stable isotope probing. FEMS Microbiol. Ecol. 60 (2007) 126-135
85. Ekberg K., Landau B.R., Wajngot A., Chandramouli V., Efendic S., Brunengraber H., and Wahren J. Contributions by kidney and liver to glucose production in the postabsorptive state and after 60 h of fasting. Diabetes 48 (1999) 292-298
86. Elson C.O., Cong Y., McCracken V.J., Dimmitt R.A., Lorenz R.G., and Weaver C.T. Experimental models of inflammatory bowel disease reveal innate, adaptive, and regulatory mechanisms of host dialogue with the microbiota. Immunol. Rev. 206 (2005) 260-276
87. Engelen M.P., Deutz N.E., Wouters E.F., and Schols A.M. Enhanced levels of whole-body protein turnover in patients with chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med 162 (2000) 1488-1492
88. Engelen M.P., Rutten E.P., De Castro C.L., Wouters E.F., Schols A.M., and Deutz N.E. Altered interorgan response to feeding in patients with chronic obstructive pulmonary disease. Am. J. Clin. Nutr. 82 (2005) 366-372
89. Falk P.G., Hooper L.V., Midtvedt T., and Gordon J.I. Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology. Microbiol. Mol. Biol. Rev. 62 (1998) 1157-1170
90. Faure M., Moennoz D., Montigon F., Fay L.B., Breuille D., Finot P.A., Ballevre O., and Boza J. Development of a rapid and convenient method to purify mucins and determine their in vivo synthesis rate in rats. Anal. Biochem. 307 (2002) 244-251
91. Faure M., Moennoz D., Montigon F., Mettraux C., Breuille D., and Ballevre O. Dietary threonine restriction specifically reduces intestinal mucin synthesis in rats. J. Nutr. 135 (2005) 486-491
92. Ferchaud-Roucher V., Pouteau E., Piloquet H., Zair Y., and Krempf M. Colonic fermentation from lactulose inhibits lipolysis in overweight subjects. Am. J. Physiol. Endocrinol. Metab. 289 (2005) E716-E720
93. Fernandez-Banares F., Hinojosa J., Sanchez-Lombrana J.L., Navarro E., Martinez-Salmeron J.F., Garcia-Puges A., Gonzalez-Huix F., Riera J., Gonzalez-Lara V., Dominguez-Abascal F., Gine J.J., Moles J., Gomollon F., and Gassull M.A. Randomized clinical trial of Plantago ovata seeds (dietary fiber) as compared with mesalamine in maintaining remission in ulcerative colitis. Spanish Group for the Study of Crohn's Disease and Ulcerative Colitis (GETECCU). Am. J. Gastroenterol. 94 (1999) 427-433
94. Ferrer M., Golyshina O.V., Chernikova T.N., Khachane A.N., Reyes-Duarte D., Santos V.A., Strompl C., Elborough K., Jarvis G., Neef A., Yakimov M.M., Timmis K.N., and Golyshin P.N. Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ. Microbiol. 7 (2005) 1996-2010
95. Finegold S.M., Sutter V.L., and Mathisen G.E. Normal indigenous intestinal flora. In: Hentges D.J. (Ed). Human Intestinal Microflora in Health and Disease (1983), Academic Press Inc., New York, NY 3-31
96. Finnie I.A., Dwarakanath A.D., Taylor B.A., and Rhodes J.M. Colonic mucin synthesis is increased by sodium butyrate. Gut 36 (1995) 93-99
97. Fischer E., and Sauer U. Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat. Genet. 37 (2005) 636-640
98. Freitas M., Cayuela C., Antoine J.M., Piller F., Sapin C., and Trugnan G. A heat labile soluble factor from Bacteroides thetaiotaomicron VPI-5482 specifically increases the galactosylation pattern of HT29-MTX cells. Cell. Microbiol. 3 (2001) 289-300
99. Freitas M., Tavan E., Cayuela C., Diop L., Sapin C., and Trugnan G. Host-pathogens cross-talk. Indigenous bacteria and probiotics also play the game. Biol. Cell 95 (2003) 503-506
100. Fusunyan R.D., Quinn J.J., Ohno Y., MacDermott R.P., and Sanderson I.R. Butyrate enhances interleukin (IL)-8 secretion by intestinal epithelial cells in response to IL-1beta and lipopolysaccharide. Pediatr. Res. 43 (1998) 84-90
101. Fusunyan R.D., Quinn J.J., Fujimoto M., MacDermott R.P., and Sanderson I.R. Butyrate switches the pattern of chemokine secretion by intestinal epithelial cells through histone acetylation. Mol. Med. 5 (1999) 631-640
102. Gamet L., Daviaud D., Denis-Pouxviel C., Remesy C., and Murat J.C. Effects of short-chain fatty acids on growth and differentiation of the human colon-cancer cell line HT29. Int. J. Cancer 52 (1992) 286-289
103. Ganessunker D., Gaskins H.R., Zuckermann F.A., and Donovan S.M. Total parenteral nutrition alters molecular and cellular indices of intestinal inflammation in neonatal piglets. JPEN J. Parenter. Enteral Nutr. 23 (1999) 337-344
104. Gao K., Xu A., Krul C., Venema K., Liu Y., Niu Y., Lu J., Bensoussan L., Seeram N.P., Heber D., and Henning S.M. Of the major phenolic acids formed during human microbial fermentation of tea, citrus, and soy flavonoid supplements, only 3,4-dihydroxyphenylacetic acid has antiproliferative activity. J. Nutr. 136 (2006) 52-57
105. Geboes K.P., De Preter V., Luypaerts A., Bammens B., Evenepoel P., Ghoos Y., Rutgeerts P., and Verbeke K. Validation of lactose[15N,15N]ureide as a tool to study colonic nitrogen metabolism. Am. J. Physiol. Gastrointest. Liver Physiol. 288 (2005) G994-G999
106. Gharat L., Taneja R., Weerapreeyakul N., Rege B., Polli J., and Chikhale P.J. Targeted drug delivery systems. 6: Intracellular bioreductive activation, uptake and transport of an anticancer drug delivery system across intestinal Caco-2 cell monolayers. Int. J. Pharm. 219 (2001) 1-10
107. Gibson G.R., Rastall R.A., and Roberfroid M.B. Prebiotics. In: Gibson G.R., and Roberfroid M.B. (Eds). The Colonic Microbiota: Nutrition and Health (1999), Kluwer Academic Publishers, Dordrecht 101-124
108. Gibson G.R., and Roberfroid M.B. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J. Nutr. 125 (1995) 1401-1412
109. Gibson P., and Rosella O. Interleukin 8 secretion by colonic crypt cells in vitro: response to injury suppressed by butyrate and enhanced in inflammatory bowel disease. Gut 37 (1995) 536-543
110. Gibson, P.R. (2000) The intracellular target of butyrate's actions: HDAC or HDON'T? Gut 46, 447-448.
111. Gibson P.R., Moeller I., Kagelari O., Folino M., and Young G.P. Contrasting effects of butyrate on the expression of phenotypic markers of differentiation in neoplastic and non-neoplastic colonic epithelial cells in vitro. J. Gastroenterol. Hepatol. 7 (1992) 165-172
112. Gibson P.R., Ourania R., Wilson A.J., Mariadason J.M., Rickard K., Byron K., and Barkla D.H. Colonic epithelial cell activation and the paradoxical effect of butyrate. Carcinogenesis 20 (1999) 539-544
113. Gill S.R., Pop M., Deboy R.T., Eckburg P.B., Turnbaugh P.J., Samuel B.S., Gordon J.I., Relman D.A., Fraser-Liggett C.M., and Nelson K.E. Metagenomic analysis of the human distal gut microbiome. Science 312 (2006) 1355-1359
114. Goodacre R., and Kell D.B. Evolutionary computation for the interpretation of metabolomic data. In: Harrigan G.G., and Goodacre R. (Eds). Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis (2003), Kluwer, Boston 239-256
115. Grundy, D. (2004) What activates visceral afferents? Gut 53 (Suppl. 2), ii5-8.
116. Grundy D., and Schemann M. Enteric nervous system. Curr. Opin. Gastroenterol. 21 (2005) 176-182
117. Gupta N., Martin P.M., Prasad P.D., and Ganapathy V. SLC5A8 (SMCT1)-mediated transport of butyrate forms the basis for the tumor suppressive function of the transporter. Life Sci. 78 (2006) 2419-2425
118. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 (1999) 994-999
119. Handelsman J. Sorting out metagenomes. Nat. Biotechnol. 23 (2005) 38-39
120. Harig J.M., Soergel K.H., Komorowski R.A., and Wood C.M. Treatment of diversion colitis with short-chain-fatty acid irrigation. N. Engl. J. Med. 320 (1989) 23-28
121. Harmsen H.J., Raangs G.C., He T., Degener J.E., and Welling G.W. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl. Environ. Microbiol. 68 (2002) 2982-2990
122. Heilig H.G., Zoetendal E.G., Vaughan E.E., Marteau P., Akkermans A.D., and de Vos W.M. Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl. Environ. Microbiol. 68 (2002) 114-123
123. Hellerstein M.K. New stable isotope-mass spectrometric techniques for measuring fluxes through intact metabolic pathways in mammalian systems: introduction of moving pictures into functional genomics and biochemical phenotyping. Metab. Eng. 6 (2004) 85-100
124. Hellerstein M.K., and Neese R.A. Mass isotopomer distribution analysis at eight years: theoretical, analytic, and experimental considerations. Am. J. Physiol. 276 (1999) E1146-E1170
125. Hill, M.J. (1995) The metabolic activity of gut bacteria. In: Role of Gut Bacteria in Human Toxicology and Pharmacology (M.J. Hill, ed.), Vols. 19-25. Taylor & Francis Ltd, London.
126. Hill M.J., Ellwood D.C., and Watson J.H.P. Sulfate-reducing bacteria (SRB). In: Hill M.J. (Ed). Role of Gut Bacteria in Human Toxicology and Pharmacology (1995), Taylor & Francis Ltd, London 187-193
127. Holzhutter H.G. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur. J. Biochem. 271 (2004) 2905-2922
128. Hooper L.V., Xu J., Falk P.G., Midtvedt T., and Gordon J.I. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc. Natl. Acad. Sci. USA 96 (1999) 9833-9838
129. Hooper L.V., Wong M.H., Thelin A., Hansson L., Falk P.G., and Gordon J.I. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291 (2001) 881-884
130. Hooper L.V., Midtvedt T., and Gordon J.I. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu. Rev. Nutr. 22 (2002) 283-307
131. Hope M.E., Hold G.L., Kain R., and El-Omar E.M. Sporadic colorectal cancer - role of the commensal microbiota. FEMS Microbiol. Lett. 244 (2005) 1-7
132. Hoskins L.C., Agustines M., McKee W.B., Boulding E.T., Kriaris M., and Niedermeyer G. 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 (1985) 944-953
133. Hove H., Rye Clausen M., and Brobech Mortensen P. Lactate and pH in faeces from patients with colonic adenomas or cancer. Gut 34 (1993) 625-629
134. Hugenholtz P., Goebel B.M., and Pace N.R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180 (1998) 4765-4774
135. Hughes R., Magee E.A., and Bingham S. Protein degradation in the large intestine: relevance to colorectal cancer. Curr. Issues. Intest. Microbiol. 1 (2000) 51-58
136. Humblot C., Combourieu B., Vaisanen M.L., Furet J.P., Delort A.M., and Rabot S. 1H nuclear magnetic resonance spectroscopy-based studies of the metabolism of food-borne carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline by human intestinal microbiota. Appl. Environ. Microbiol. 71 (2005) 5116-5123
137. Hwang E.S., and Lee H.J. Allyl isothiocyanate and its N-acetylcysteine conjugate suppress metastasis via inhibition of invasion, migration, and matrix metalloproteinase-2/-9 activities in SK-Hep 1 human hepatoma cells. Exp. Biol. Med. (Maywood) 231 (2006) 421-430
138. Hyman M.A. Systems biology: the gut-brain-fat cell connection and obesity. Altern. Ther. Health Med. 12 (2006) 10-16
139. Inan M.S., Rasoulpour R.J., Yin L., Hubbard A.K., Rosenberg D.W., and Giardina C. The luminal short-chain fatty acid butyrate modulates NF-kappaB activity in a human colonic epithelial cell line. Gastroenterology 118 (2000) 724-734
140. Isermann N., and Wiechert W. Metabolic isotopomer labeling systems, Part II: structural flux identifiability analysis. Math. Biosci. 183 (2003) 175-214
141. Issaq H.J., Veenstra T.D., Conrads T.P., and Felschow D. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem. Biophys. Res. Commun. 292 (2002) 587-592
142. Jansson K., Strand I., Redler B., Magnuson A., Ungerstedt U., and Norgren L. Results of intraperitoneal microdialysis depend on the location of the catheter. Scand. J. Clin. Lab. Invest. 64 (2004) 63-70
143. Jensen B.B., and Jorgensen H. Effect of dietary fiber on microbial activity and microbial gas production in various regions of the gastrointestinal tract of pigs. Appl. Environ. Microbiol. 60 (1994) 1897-1904
144. Jorgensen J., and Mortensen P.B. Utilization of short-chain fatty acids by colonic mucosal tissue strips. A new method of assessing colonic mucosal metabolism. Scand. J. Gastroenterol. 35 (2000) 659-666
145. Jorgensen J., and Mortensen P.B. Substrate utilization by intestinal mucosal tissue strips from patients with inflammatory bowel disease. Am. J. Physiol. Gastrointest. Liver Physiol. 281 (2001) G405-G411
146. Ju H.R., Wu H.Y., Nishizono S., Sakono M., Ikeda I., Sugano M., and Imaizumi K. Effects of dietary fats and curcumin on IgE-mediated degranulation of intestinal mast cells in brown Norway rats. Biosci. Biotechnol. Biochem. 60 (1996) 1856-1860
147. Juste C. Dietary fatty acids, intestinal microbiota and cancer. Bull. Cancer 92 (2005) 708-721
148. Kanauchi O., Andoh A., Iwanaga T., Fujiyama Y., Mitsuyama K., Toyonaga A., and Bamba T. Germinated barley foodstuffs attenuate colonic mucosal damage and mucosal nuclear factor kappa B activity in a spontaneous colitis model. J. Gastroenterol. Hepatol. 14 (1999) 1173-1179
149. Kato S., Haruta S., Cui Z.J., Ishii M., and Igarashi Y. Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl. Environ. Microbiol. 71 (2005) 7099-7106
150. Kelleher J.K. Probing metabolic pathways with isotopic tracers: insights from mammalian metabolic physiology. Metab. Eng. 6 (2004) 1-5
151. Kerr B., Riley M.A., Feldman M.W., and Bohannan B.J. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418 (2002) 171-174
152. Kien C.L., Murray R.D., Ailabouni A., Powers P., Kepner J., Powers L., and Brunengraber H. Stable isotope model for assessing production of short chain fatty acids from colon-derived sugar: application in pigs. J. Nutr. 126 (1996) 3069-3076
153. Kien C.L., Chang J.C., and Cooper J.R. Butyric acid is synthesized by piglets. J. Nutr. 130 (2000) 234-237
154. Kien C.L., Chang J.C., and Cooper J.R. Quantitation of colonic luminal synthesis of butyric acid in piglets. J. Pediatr. Gastroenterol. Nutr. 35 (2002) 324-328
155. Kirkup B.C., and Riley M.A. Antibiotic-mediated antagonism leads to a bacterial game of rock-paper-scissors in vivo. Nature 428 (2004) 412-414
156. Kitayama T., Kinoshita A., Sugimoto M., Nakayama Y., and Tomita M. A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles. Theor. Biol. Med. Model. 3 (2006) 24
157. 13C starch meal. Am. J. Clin. Nutr. 80 (2004) 881-886
158. Kriengsinyos W., Wykes L.J., Ball R.O., and Pencharz P.B. Oral and intravenous tracer protocols of the indicator amino acid oxidation method provide the same estimate of the lysine requirement in healthy men. J. Nutr. 132 (2002) 2251-2257
159. Kromer J.O., Sorgenfrei O., Klopprogge K., Heinzle E., and Wittmann C. In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. J. Bacteriol. 186 (2004) 1769-1784
160. Kruh J., Defer N., and Tichonicky L. Molecular and cellular effects of sodium butyrate. In: Roche A.F. (Ed). Short-Chain Fatty Acids: Metabolism and Clinical Importance. Report of the Tenth Ross Conference on Medical Research (1991), Ross Laboratories, Columbus, OH 45-50
161. Krul C., Humblot C., Philippe C., Vermeulen M., van Nuenen M., Havenaar R., and Rabot S. Metabolism of sinigrin (2-propenyl glucosinolate) by the human colonic microflora in a dynamic in vitro large-intestinal model. Carcinogenesis 23 (2002) 1009-1016
162. Kurpad A.V., and Young V.R. What is apparent is not always real: lessons from lysine requirement studies in adult humans. J. Nutr. 133 (2003) 1227-1230
163. Labayen I., Diez N., Parra M.D., Gonzalez A., and Martinez J.A. Time-course changes in macronutrient metabolism induced by a nutritionally balanced low-calorie diet in obese women. Int. J. Food Sci. Nutr. 55 (2004) 27-35
164. Larauche M., Bueno L., and Fioramonti J. Effect of dietary nitric oxide on gastric mucosal mast cells in absence or presence of an experimental gastritis in rats. Life Sci. 73 (2003) 1505-1516
165. Lau T., Owen W., Yu Y.M., Noviski N., Lyons J., Zurakowski D., Tsay R., Ajami A., Young V.R., and Castillo L. Arginine, citrulline, and nitric oxide metabolism in end-stage renal disease patients. J. Clin. Invest. 105 (2000) 1217-1225
166. Lee K., Berthiaume F., Stephanopoulos G.N., and Yarmush M.L. Profiling of dynamic changes in hypermetabolic livers. Biotechnol. Bioeng. 83 (2003) 400-415
167. Lee S.Y., Lee D.Y., and Kim T.Y. Systems biotechnology for strain improvement. Trends Biotechnol. 23 (2005) 349-358
168. Lemke T., Stingl U., Egert M., Friedrich M.W., and Brune A. Physicochemical conditions and microbial activities in the highly alkaline gut of the humus-feeding larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae). Appl. Environ. Microbiol. 69 (2003) 6650-6658
169. 13C-NMR study of propionate metabolism by sludges from bioreactors treating sulfate and sulfide rich wastewater. Biodegradation 9 (1998) 179-186
170. Levine J., Ellis C.J., Furne J.K., Springfield J., and Levitt M.D. Fecal hydrogen sulfide production in ulcerative colitis. Am. J. Gastroenterol. 93 (1998) 83-87
171. Levitt M.D., Gibson G.R., and Christl S.U. Gas metabolism in the large intestine. In: Gibson G.R., and Macfarlane G.T. (Eds). Human Colonic Bacteria: Role in Nutrition, Physiology, and Disease (1995), CRC Press, Boca Raton, FL 131-154
172. Levy R.D., Segal I., Hassan H., and Saadia R. Stool weight and faecal pH in two South African populations with a dissimilar colon cancer risk. S. Afr. J. Surg. 32 (1994) 127-128 discussion 128-129
173. Lichtenberger L.M. The hydrophobic barrier properties of gastrointestinal mucus. Annu. Rev. Physiol. 57 (1995) 565-583
174. Lien K.A., Sauer W.C., and Dugan M.E. Evaluation of the 15N-isotope dilution technique for determining the recovery of endogenous protein in ileal digesta of pigs: effect of the pattern of blood sampling, precursor pools, and isotope dilution technique. J. Anim. Sci. 75 (1997) 159-169
175. Luiking Y.C., and Deutz N.E. Isotopic investigation of nitric oxide metabolism in disease. Curr. Opin. Clin. Nutr. Metab. Care 6 (2003) 103-108
176. Ma T.Y., Iwamoto G.K., Hoa N.T., Akotia V., Pedram A., Boivin M.A., and Said H.M. TNF-alpha-induced increase in intestinal epithelial tight junction permeability requires NF-kappa B activation. Am. J. Physiol. Gastrointest. Liver Physiol. 286 (2004) G367-G376
177. Macfarlane G.T., and Cummings J.H. The colonic flora, fermentation and large bowel digestive function. In: Phillips S.F., Pemberton J.H., and Shorter R.G. (Eds). The Large Intestine: Physiology, Pathophysiology, and Disease (1991), Raven Press, New York 51-92
178. Macfarlane G.T., and Englyst H.N. Starch utilization by the human large intestinal microflora. J. Appl. Bacteriol. 60 (1986) 195-201
179. Macfarlane G.T., Gibson G.R., and Cummings J.H. Comparison of fermentation reactions in different regions of the human colon. J. Appl. Bacteriol. 72 (1992) 57-64
180. Macfarlane, G.T., Gibson, G.R. and Cummings, J.H. (1992b). In vivo and in vitro studies on formation of phenols and phenolic acids by human colonic bacteria. Growth Development Nutrition A565.
181. Macfarlane S., and Macfarlane G.T. Proteolysis and amino acid fermentation. In: Gibson G.R., and Macfarlane G.T. (Eds). Human Colonic Bacteria: Role in Nutrition, Physiology, and Pathology (1995), CRC Press, Boca Raton, FL 75-100
182. Macfarlane S., and Macfarlane G.T. Regulation of short-chain fatty acid production. Proc. Nutr. Soc. 62 (2003) 67-72
183. MacGregor B.J., Bruchert V., Fleischer S., and Amann R. Isolation of small-subunit rRNA for stable isotopic characterization. Environ. Microbiol. 4 (2002) 451-464
184. Magee E.A., Richardson C.J., Hughes R., and Cummings J.H. Contribution of dietary protein to sulfide production in the large intestine: an in vitro and a controlled feeding study in humans. Am. J. Clin. Nutr. 72 (2000) 1488-1494
185. Manefield M., Whiteley A.S., Griffiths R.I., and Bailey M.J. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl. Environ. Microbiol. 68 (2002) 5367-5373
186. Manefield, M., Whiteley, A.S. and Bailey, M.J. (2004) What can stable isotope probing do for bioremediation? Int. Biodeterior. Biodegrad. 54, 163-166.
187. Manichanh C., Rigottier-Gois L., Bonnaud E., Gloux K., Pelletier E., Frangeul L., Nalin R., Jarrin C., Chardon P., Marteau P., Roca J., and Dore J. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55 (2006) 205-211
188. Mariadason J.M., Corner G.A., and Augenlicht L.H. Genetic reprogramming in pathways of colonic cell maturation induced by short chain fatty acids: comparison with trichostatin A, sulindac, and curcumin and implications for chemoprevention of colon cancer. Cancer Res. 60 (2000) 4561-4572
189. Maskarinec G., Takata Y., Pagano I., Carlin L., Goodman M.T., Le Marchand L., Nomura A.M., Wilkens L.R., and Kolonel L.N. Trends and dietary determinants of overweight and obesity in a multiethnic population. Obesity (Silver Spring) 14 (2006) 717-726
190. Matthews D.E., Marano M.A., and Campbell R.G. Splanchnic bed utilization of leucine and phenylalanine in humans. Am. J. Physiol. 264 (1993) E109-E118
191. McBain A.J., and Macfarlane G.T. Investigations of bifidobacterial ecology and oligosaccharide metabolism in a three-stage compound continuous culture system. Scand. J. Gastroenterol. Suppl. 222 (1997) 32-40
192. McBain A.J., and Macfarlane G.T. Ecological and physiological studies on large intestinal bacteria in relation to production of hydrolytic and reductive enzymes involved in formation of genotoxic metabolites. J. Med. Microbiol. 47 (1998) 407-416
193. McCabe B.J., and Previs S.F. Using isotope tracers to study metabolism: application in mouse models. Metab. Eng. 6 (2004) 25-35
194. McGarr S.E., Ridlon J.M., and Hylemon P.B. Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature. J. Clin. Gastroenterol. 39 (2005) 98-109
195. McIntosh T.S., Davis H.M., and Matthews D.E. A liquid chromatography-mass spectrometry method to measure stable isotopic tracer enrichments of glycerol and glucose in human serum. Anal. Biochem. 300 (2002) 163-169
196. McIntyre A., Gibson P.R., and Young G.P. Butyrate production from dietary fibre and protection against large bowel cancer in a rat model. Gut 34 (1993) 386-391
197. Metges C.C. Contribution of microbial amino acids to amino acid homeostasis of the host. J. Nutr. 130 (2000) 1857S-1864S
198. Minekus M., Smeets-Peeters M., Bernalier A., Marol-Bonnin S., Havenaar R., Marteau P., Alric M., Fonty G., and Huis in't Veld J.H. A computer-controlled system to simulate conditions of the large intestine with peristaltic mixing, water absorption and absorption of fermentation products. Appl. Microbiol. Biotechnol. 53 (1999) 108-114
199. Mizoguchi E. Chitinase 3-like-1 exacerbates intestinal inflammation by enhancing bacterial adhesion and invasion in colonic epithelial cells. Gastroenterology 130 (2006) 398-411
200. Mizota T. Lactulose as a growth promoting factor for Bifidobacterium and its physiological aspects. Bull. Intern. Dairy Fed. 313 (1996) 43-48
201. Mollney M., Wiechert W., Kownatzki D., and de Graaf A.A. Bidirectional reaction steps in metabolic networks: IV. Optimal design of isotopomer labeling experiments. Biotechnol. Bioeng. 66 (1999) 86-103
202. Moran B.J., and Jackson A.A. Metabolism of 15N-labeled urea in the functioning and defunctioned human colon. Clin. Sci. (Lond.) 79 (1990) 253-258
203. Moreau N.M., Champ M.M., Goupry S.M., Le Bizec B.J., Krempf M., Nguyen P.G., Dumon H.J., and Martin L.J. Resistant starch modulates in vivo colonic butyrate uptake and its oxidation in rats with dextran sulfate sodium-induced colitis. J. Nutr. 134 (2004) 493-500
204. Morita T., Tanabe H., Takahashi K., and Sugiyama K. Ingestion of resistant starch protects endotoxin influx from the intestinal tract and reduces d-galactosamine-induced liver injury in rats. J. Gastroenterol. Hepatol. 19 (2004) 303-313
205. Morrison D.J., Cooper K., Waldron S., Slater C., Weaver L.T., and Preston T. A streamlined approach to the analysis of volatile fatty acids and its application to the measurement of whole-body flux. Rapid Commun. Mass Spectrom. 18 (2004) 2593-2600
206. Morrison, D.J., Mackay, W.G., Edwards, C.A., Preston, T., Dodson, B. and Weaver, L.T. (2006) Butyrate production from oligofructose fermentation by the human faecal flora: what is the contribution of extracellular acetate and lactate? Br. J. Nutr. 96, 570-577.
207. Mortensen P.B., and Clausen M.R. Short-chain fatty acids in the human colon: relation to gastrointestinal health and disease. Scand. J. Gastroenterol. Suppl. 216 (1996) 132-148
208. Nusrat A., Parkos C.A., Verkade P., Foley C.S., Liang T.W., Innis-Whitehouse W., Eastburn K.K., and Madara J.L. Tight junctions are membrane microdomains. J. Cell Sci. 113 Pt 10 (2000) 1771-1781
209. O'Hara A.M., O'Regan P., Fanning A., O'Mahony C., Macsharry J., Lyons A., Bienenstock J., O'Mahony L., and Shanahan F. Functional modulation of human intestinal epithelial cell responses by Bifidobacterium infantis and Lactobacillus salivarius. Immunology 118 (2006) 202-215
210. Ohge H., Furne J.K., Springfield J., Rothenberger D.A., Madoff R.D., and Levitt M.D. Association between fecal hydrogen sulfide production and pouchitis. Dis. Colon Rectum 48 (2005) 469-475
211. Okamoto T., Sasaki M., Tsujikawa T., Fujiyama Y., Bamba T., and Kusunoki M. Preventive efficacy of butyrate enemas and oral administration of Clostridium butyricum M588 in dextran sodium sulfate-induced colitis in rats. J. Gastroenterol. 35 (2000) 341-346
212. O'Keefe S.J., Kidd M., Espitalier-Noel G., and Owira P. Rarity of colon cancer in Africans is associated with low animal product consumption, not fiber. Am. J. Gastroenterol. 94 (1999) 1373-1380
213. Olde Damink S.W., Jalan R., Redhead D.N., Hayes P.C., Deutz N.E., and Soeters P.B. Interorgan ammonia and amino acid metabolism in metabolically stable patients with cirrhosis and a TIPSS. Hepatology 36 (2002) 1163-1171
214. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., and Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 1 (2002) 376-386
215. Oo C., Snell P., Barrett J., Dorr A., Liu B., and Wilding I. Pharmacokinetics and delivery of the anti-influenza prodrug oseltamivir to the small intestine and colon using site-specific delivery capsules. Int. J. Pharm. 257 (2003) 297-299
216. O'Sullivan M., Clayton N., Breslin N.P., Harman I., Bountra C., McLaren A., and O'Morain C.A. Increased mast cells in the irritable bowel syndrome. Neurogastroenterol. Motil. 12 (2000) 449-457
217. Paulo P.L., Stams A.J., Field J.A., Dijkema C., van Lier J.B., and Lettinga G. Pathways of methanol conversion in a thermophilic anaerobic (55 degrees C) sludge consortium. Appl. Microbiol. Biotechnol. 63 (2003) 307-314
218. Petersen S., de Graaf A.A., Eggeling L., Mollney M., Wiechert W., and Sahm H. In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum. J. Biol. Chem. 275 (2000) 35932-35941
219. Petersen S., Mack C., de Graaf A.A., Riedel C., Eikmanns B.J., and Sahm H. Metabolic consequences of altered phosphoenolpyruvate carboxykinase activity in Corynebacterium glutamicum reveal anaplerotic regulation mechanisms in vivo. Metab. Eng. 3 (2001) 344-361
220. Petersen S., von Lieres E., de Graaf A.A., Sahm H., and Wiechert W. A multi-scale approach for the predictive modeling of metabolic regulation. In: Kholodenko B.N., and Westerhoff H.V. (Eds). Metabolic Engineering in the Post-Genomic Era (2003), Horizon Scientific Press, London Chapter 10
221. Pfeiffer T., and Schuster S. Game-theoretical approaches to studying the evolution of biochemical systems. Trends Biochem. Sci. 30 (2005) 20-25
222. Pfeiffer T., Schuster S., and Bonhoeffer S. Cooperation and competition in the evolution of ATP-producing pathways. Science 292 (2001) 504-507
223. Pouteau E., Nguyen P., Ballevre O., and Krempf M. Production rates and metabolism of short-chain fatty acids in the colon and whole body using stable isotopes. Proc. Nutr. Soc. 62 (2003) 87-93
224. Pouteau E., Frenais R., Dumon H., Noah L., Martin L., and Nguyen P. Colonic fermentation of inulin increases whole-body acetate turnover in dogs. J. Nutr. 135 (2005) 2845-2851
225. Pretzer G., Snel J., Molenaar D., Wiersma A., Bron P.A., Lambert J., de Vos W.M., van der Meer R., Smits M.A., and Kleerebezem M. Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum. J. Bacteriol. 187 (2005) 6128-6136
226. Previs S.F., and Brunengraber H. Methods for measuring gluconeogenesis in vivo. Curr. Opin. Clin. Nutr. Metab. Care 1 (1998) 461-465
227. Priebe M.G., Wachters-Hagedoorn R.E., Stellaard F., Heiner A.M., Elzinga H., and Vonk R.J. Oro-cecal transit time: influence of a subsequent meal. Eur. J. Clin. Invest. 34 (2004) 417-421
228. Radajewski S., Ineson P., Parekh N.R., and Murrell J.C. Stable-isotope probing as a tool in microbial ecology. Nature 403 (2000) 646-649
229. 2]taurine in healthy adult humans. Am. J. Physiol. Endocrinol. Metab. 287 (2004) E255-E262
230. Ram R.J., Verberkmoes N.C., Thelen M.P., Tyson G.W., Baker B.J., Blake II R.C., Shah M., Hettich R.L., and Banfield J.F. Community proteomics of a natural microbial biofilm. Science 308 (2005) 1915-1920
231. Ramachandran N., Larson D.N., Stark P.R., Hainsworth E., and LaBaer J. Emerging tools for real-time label-free detection of interactions on functional protein microarrays. FEBS J. 272 (2005) 5412-5425
232. Ramakrishna R., Edwards J.S., McCulloch A., and Palsson B.O. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am. J. Physiol. Regul. Integr. Comp. Physiol. 280 (2001) R695-R704
233. Ratcliffe R.G., and Shachar-Hill Y. Measuring multiple fluxes through plant metabolic networks. Plant J. 45 (2006) 490-511
234. Ratner, S., Rittenberg, D., Keston, A.S. and Schoenheimer, R. (1987) J. Biol. Chem. 134, June 1940: Studies in protein metabolism. XIV. The chemical interaction of dietary glycine and body proteins in rats. By Ratner, S., Rittenberg, D., Keston, A.S. and Schoenheimer, R. Nutr. Rev. 45, 310-312.
235. Reed J.L., and Palsson B.O. Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol. 185 (2003) 2692-2699
236. Relman D.A., and Falkow S. The meaning and impact of the human genome sequence for microbiology. Trends Microbiol. 9 (2001) 206-208
237. Rerat A.A. Intestinal absorption of end products from digestion of carbohydrates and proteins in the pig. Arch. Tierernahr. 35 (1985) 461-480
238. Rhee S.H., Im E., Riegler M., Kokkotou E., O'Brien M., and Pothoulakis C. Pathophysiological role of Toll-like receptor 5 engagement by bacterial flagellin in colonic inflammation. Proc. Natl. Acad. Sci. USA 102 (2005) 13610-13615
239. Rigottier-Gois L., Le Bourhis A.-G., Gramet G., Rochet V., and Doré J. Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes. FEMS Microbiol. Ecol. 43 (2003) 237-245
240. Roediger W.E. Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man. Gut 21 (1980) 793-798
241. Roediger W.E. Utilization of nutrients by isolated epithelial cells of the rat colon. Gastroenterology 83 (1982) 424-429
242. Roediger, W.E., Duncan, A., Kapaniris, O. and Millard, S. (1993) Sulphide impairment of substrate oxidation in rat colonocytes: a biochemical basis for ulcerative colitis? Clin. Sci. (Lond.) 85, 623-627.
243. Roediger W.E., Moore J., and Babidge W. Colonic sulfide in pathogenesis and treatment of ulcerative colitis. Dig. Dis. Sci. 42 (1997) 1571-1579
244. Roller M., Rechkemmer G., and Watzl B. Prebiotic inulin enriched with oligofructose in combination with the probiotics Lactobacillus rhamnosus and Bifidobacterium lactis modulates intestinal immune functions in rats. J. Nutr. 134 (2004) 153-156
245. Rooyackers O., Thorell A., Nygren J., and Ljungqvist O. Microdialysis methods for measuring human metabolism. Curr. Opin. Clin. Nutr. Metab. Care 7 (2004) 515-521
246. Rowland I.R. Toxicology of the colon: role of the intestinal microflora. In: Gibson G.R., and Macfarlane G.T. (Eds). Human Colonic Bacteria: Role in Nutrition, Physiology, and Pathology (1995), CRC Press, Boca Raton, FL 155-174
247. Rydzynski K., and Dalen H. Effect of sodium butyrate treatment on the granule morphology, histamine level and elemental content of the bone marrow-derived mast cell. Folia Histochem. Cytobiol. 32 (1994) 11-15
248. Saemann M.D., Bohmig G.A., Osterreicher C.H., Burtscher H., Parolini O., Diakos C., Stockl J., Horl W.H., and Zlabinger G.J. Anti-inflammatory effects of sodium butyrate on human monocytes: potent inhibition of IL-12 and up-regulation of IL-10 production. FASEB J. 14 (2000) 2380-2382
249. Saemann M.D., Bohmig G.A., and Zlabinger G.J. Short-chain fatty acids: bacterial mediators of a balanced host-microbial relationship in the human gut. Wien Klein. Wochenschr. 114 (2002) 289-300
250. Sahm H., Eggeling L., and de Graaf A.A. Pathway analysis and metabolic engineering in Corynebacterium glutamicum. Biol. Chem. 381 (2000) 899-910
251. Salyers A.A., Vercellotti J.R., West S.E., and Wilkins T.D. Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon. Appl. Environ. Microbiol. 33 (1977) 319-322
252. Sanchez B., Champomier-Verges M.C., Anglade P., Baraige F., de Los Reyes-Gavilan C.G., Margolles A., and Zagorec M. Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809. J. Bacteriol. 187 (2005) 5799-5808
253. Sanford K., Soucaille P., Whited G., and Chotani G. Genomics to fluxomics and physiomics - pathway engineering. Curr. Opin. Microbiol. 5 (2002) 318-322
254. Satokari R.M., Vaughan E.E., Akkermans A.D., Saarela M., and de Vos W.M. Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 67 (2001) 504-513
255. Scheppach W. Effects of short chain fatty acids on gut morphology and function. Gut 35 (1994) S35-S38
256. Scheppach W., Pomare E.W., Elia M., and Cummings J.H. The contribution of the large intestine to blood acetate in man. Clin. Sci. (Lond.) 80 (1991) 177-182
257. Scheppach W., Sommer H., Kirchner T., Paganelli G.M., Bartram P., Christl S., Richter F., Dusel G., and Kasper H. Effect of butyrate enemas on the colonic mucosa in distal ulcerative colitis. Gastroenterology 103 (1992) 51-56
258. Schilling C.H., Letscher D., and Palsson B.O. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203 (2000) 229-248
259. Schuster S., Dandekar T., and Fell D.A. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17 (1999) 53-60
260. Schuster S., Hilgetag C., Woods J.H., and Fell D.A. Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. J. Math. Biol. 45 (2002) 153-181
261. Segre D., Vitkup D., and Church G.M. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99 (2002) 15112-15117
262. Sekirov I., and Finlay B.B. Human and microbe: united we stand. Nat. Med. 12 (2006) 736-737
263. Selivanov V.A., Meshalkina L.E., Solovjeva O.N., Kuchel P.W., Ramos-Montoya A., Kochetov G.A., Lee P.W., and Cascante M. Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells. Bioinformatics 21 (2005) 3558-3564
264. Serra J., Azpiroz F., and Malagelada J.-R. Impaired transit and tolerance of intestinal gas in the irritable bowel syndrome. Gut 48 (2001) 14-19
265. Shlomi T., Berkman O., and Ruppin E. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc. Natl. Acad. Sci. USA 102 (2005) 7695-7700
266. Shu Y.Z., Kingston D.G., Van Tassell R.L., and Wilkins T.D. Metabolism of levamisole, an anti-colon cancer drug, by human intestinal bacteria. Xenobiotica 21 (1991) 737-750
267. 13C NMR of intermediary metabolism: implications for systemic physiology. Annu. Rev. Physiol. 63 (2001) 15-48
268. Siddiqui A.A., and Miner Jr. P.B. The role of mast cells in common gastrointestinal diseases. Curr. Allergy Asthma Rep. 4 (2004) 47-54
269. Singh B., Halestrap A.P., and Paraskeva C. Butyrate can act as a stimulator of growth or inducer of apoptosis in human colonic epithelial cell lines depending on the presence of alternative energy sources. Carcinogenesis 18 (1997) 1265-1270
270. Slater C., Preston T., and Weaver L.T. Advantages of deuterium-labeled mixed triacylglycerol in studies of intraluminal fat digestion. Rapid Commun. Mass Spectrom. 20 (2006) 75-80
271. Smid E.J., Molenaar D., Hugenholtz J., de Vos W.M., and Teusink B. Functional ingredient production: application of global metabolic models. Curr. Opin. Biotechnol. 16 (2005) 190-197
272. Smith E.A., and Macfarlane G.T. Enumeration of human colonic bacteria producing phenolic and indolic compounds: effects of pH, carbohydrate availability and retention time on dissimilatory aromatic amino acid metabolism. J. Appl. Bacteriol. 81 (1996) 288-302
273. Smith E.A., and MacFarlane G.T. Formation of phenolic and indolic compounds by anaerobic bacteria in the human large intestine. Microb. Ecol. 33 (1997) 180-188
274. Stappenbeck T.S., Hooper L.V., Manchester J.K., Wong M.H., and Gordon J.I. Laser capture microdissection of mouse intestine: characterizing mRNA and protein expression, and profiling intermediary metabolism in specified cell populations. Methods Enzymol. 356 (2002) 167-196
275. Stellaard F. Use of dual isotope tracers in biomedical research. Isotopes Environ. Health Stud. 41 (2005) 275-286
276. Stellaard, F. and Elzinga, H. (2005) Analytical techniques in biomedical stable isotope applications: (isotope ratio) mass spectrometry or infrared spectrometry? Isotopes Environ. Health Stud. 41, 345-361.
277. Stephanopoulos G., and Vallino J.J. Network rigidity and metabolic engineering in metabolite overproduction. Science 252 (1991) 1675-1681
278. Stewart C.S., Duncan S.H., and Cave D.R. Oxalobacter formigenes and its role in oxalate metabolism in the human gut. FEMS Microbiol. Lett. 230 (2004) 1-7
279. Suarez F.L. An understanding of excessive intestinal gas. Curr. Gastroenterol. Rep. 2 (2000) 413-419
280. Suarez F.L., Furne J.K., Springfield J.R., and Levitt M.D. Identification of gases responsible for the odor of human flatus and evaluation of a device purported to reduce this odor. Gut 43 (1998) 100-104
281. Suau A., Bonnet R., Sutren M., Godon J.J., Gibson G.R., Collins M.D., and Dore J. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65 (1999) 4799-4807
282. Suter P.M. Carbohydrates and dietary fiber. Handb Exp Pharmacol. 170 (2005) 231-261
283. Sweetlove L.J., and Fernie A.R. Regulation of metabolic networks: understanding metabolic complexity in the systems biology era. New Phytol. 168 (2005) 9-24
284. Szentkuti L., Riedesel H., Enss M.L., Gaertner K., and Von Engelhardt W. Pre-epithelial mucus layer in the colon of conventional and germ-free rats. Histochem. J. 22 (1990) 491-497
285. 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. Eur. J. Biochem. 232 (1995) 433-448
286. Te Biesebeke R., Boesten R., Klaassens E.S., Booijink C.C., de Vries M.C., Derrien M., Cohen D.P., Schuren F., Vaughan E.E., Kleerebezem M., and De Vos W.M. Microbial functionality in the human gastrointestinal tract. Microbes Environ. 19 (2004) 276-280
287. Ten Have G.A., Bost M.C., Suyk-Wierts J.C., van den Bogaard A.E., and Deutz N.E. Simultaneous measurement of metabolic flux in portally-drained viscera, liver, spleen, kidney and hindquarter in the conscious pig. Lab. Anim. 30 (1996) 347-358
288. Terada A., Hara A., Kataoka M., and Mitsuoka T. Effect of lactulose on the composition and metabolic activity of the human faecal flora. Microb. Ecol. Health Dis. 5 (1991) 43-50
289. Teusink B., Voshol P.J., Dahlmans V.E., Rensen P.C., Pijl H., Romijn J.A., and Havekes L.M. Contribution of fatty acids released from lipolysis of plasma triglycerides to total plasma fatty acid flux and tissue-specific fatty acid uptake. Diabetes 52 (2003) 614-620
290. Topping D.L., and Clifton P.M. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol. Rev. 81 (2001) 1031-1064
291. Torrallardona D., Harris C.I., and Fuller M.F. Pigs' gastrointestinal microflora provide them with essential amino acids. J. Nutr. 133 (2003) 1127-1131
292. Tuleu C., Basit A.W., Waddington W.A., Ell P.J., and Newton J.M. Colonic delivery of 4-aminosalicylic acid using amylose-ethylcellulose-coated hydroxypropylmethylcellulose capsules. Aliment. Pharmacol. Ther. 16 (2002) 1771-1779
293. Uchiyama T., Abe T., Ikemura T., and Watanabe K. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat. Biotechnol. 23 (2005) 88-93
294. Vaidyanathan S., and Goodacre R. Metabolome and proteome profiling for microbial characterization. In: Harrigan G.G., and Goodacre R. (Eds). Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis (2003), Kluwer, Boston 9-38
295. van de Kerkhof E.G., de Graaf I.A., de Jager M.H., Meijer D.K., and Groothuis G.M. Characterization of rat small intestinal and colon precision-cut slices as an in vitro system for drug metabolism and induction studies. Drug Metab. Dispos. 33 (2005) 1613-1620
296. van der Greef J., Stroobant P., and van der Heijden R. The role of analytical sciences in medical systems biology. Curr. Opin. Chem. Biol. 8 (2004) 559-565
297. van der Werf M.J., Jellema R.H., and Hankemeier T. Microbial metabolomics: replacing trial-and-error by the unbiased selection and ranking of targets. J. Ind. Microbiol. Biotechnol. 32 (2005) 234-252
298. van Eijk H.M., and Deutz N.E. The liquid chromatography mass spectrometry approach to measure amino acid isotope ratios. Curr. Opin. Clin. Nutr. Metab. Care 7 (2004) 557-563
299. van Nuenen M.H.M.C., Meyer P.D., and Venema K. The effect of various inulins and Clostridium difficile on the metabolic activity of the human colonic microbiota in vitro. Microb. Ecol. Health Dis. 15 (2003) 137-144
300. van Nuenen M.H., de Ligt R.A., Doornbos R.P., van der Woude J.C., Kuipers E.J., and Venema K. The influence of microbial metabolites on human intestinal epithelial cells and macrophages in vitro. FEMS Immunol. Med. Microbiol. 45 (2005) 183-189
301. Velazquez O.C., Lederer H.M., and Rombeau J.L. Butyrate and the colonocyte. Production, absorption, metabolism, and therapeutic implications. Adv. Exp. Med. Biol. 427 (1997) 123-134
302. Venema K., van Nuenen M.H.M.C., Pool W., van den Heuvel E.G., and van der Vossen J.M.B.M. The effect of lactulose on the composition of the intestinal microbiota and short-chain fatty acid production in human volunteers and a computer-controlled model of the proximal large intestine. Microb. Ecol. Health Dis. 15 (2003) 94-105
303. Venema K., Minekus M., and Havenaar R. Advanced in vitro models of the gastro-intestinal tract: novel tools to study functionallity of dietary fibres. In: Asp N.-G., Miller Jones J., Schaafsma G., and van der Kamp J.W. (Eds). Dietary Fibre. Bio-active Carbohydrates for Food and Feed (2004), Wageningen Academic Publishers, Wageningen 99-112
304. Venema K., Vermunt S.H., and Brink E.J. d-Tagatose increases butyrate production by the colonic microbiota in healthy men and women. Microb. Ecol. Health Dis. 17 (2005) 47-57
305. Verne G.N. The public awareness of the prevalence and impact of irritable bowel syndrome in the United States: perception versus reality. J. Clin. Gastroenterol. 38 (2004) 419-424
306. Vicente M.F., Basilio A., Cabello A., and Pelaez F. Microbial natural products as a source of antifungals. Clin. Microbiol. Infect. 9 (2003) 15-32
307. Vitali B., Wasinger V., Brigidi P., and Guilhaus M. A proteomic view of Bifidobacterium infantis generated by multi-dimensional chromatography coupled with tandem mass spectrometry. Proteomics 5 (2005) 1859-1867
308. Vollmer M., Nagele E., and Horth P. Differential proteome analysis: two-dimensional nano-LC/MS of E. coli proteome grown on different carbon sources. J. Biomol. Tech. 14 (2003) 128-135
309. Wahl S.A., Dauner M., and Wiechert W. New tools for mass isotopomer data evaluation in (13)C flux analysis: mass isotope correction, data consistency checking, and precursor relationships. Biotechnol. Bioeng. 85 (2004) 259-268
310. Walker A.W., Duncan S.H., McWilliam Leitch E.C., Child M.W., and Flint H.J. 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 (2005) 3692-3700
311. Walter J., Mangold M., and Tannock G.W. Construction, analysis, and beta-glucanase screening of a bacterial artificial chromosome library from the large-bowel microbiota of mice. Appl. Environ. Microbiol. 71 (2005) 2347-2354
312. Wiback S.J., Mahadevan R., and Palsson B.O. Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum. Biotechnol. Bioeng. 86 (2004) 317-331
313. 13C metabolic flux analysis. Metab. Eng. 3 (2001) 195-206
314. 13C metabolic flux analysis. Genet. Eng. (NY) 24 (2002) 215-238
315. 13C labeling experiments. Adv. Biochem. Eng. Biotechnol. 54 (1996) 109-154
316. Wiechert W., and De Graaf A.A. Bidirectional reaction steps in metabolic networks. I: Modeling and simulation of carbon isotope labeling experiments. Biotechnol. Bioeng. 55 (1997) 101-117
317. Wiechert W., and Noh K. From stationary to instationary metabolic flux analysis. Adv. Biochem. Eng. Biotechnol. 92 (2005) 145-172
318. Wiechert W., and Wurzel M. Metabolic isotopomer labeling systems. Part I: global dynamic behavior. Math. Biosci. 169 (2001) 173-205
319. Wiechert W., Siefke C., De Graaf A.A., and Marx A. Bidirectional reaction steps in metabolic networks. II: Flux estimation and statistical analysis. Biotechnol. Bioeng. 55 (1997) 118-135
320. Wiechert W., Mollney M., Isermann N., Wurzel M., and de Graaf A.A. Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems. Biotechnol. Bioeng. 66 (1999) 69-85
321. 13C metabolic flux analysis. Metab. Eng. 3 (2001) 265-283
322. Wilmes P., and Bond P.L. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol. 14 (2006) 92-97
323. Wilson D.C., Rafii M., Ball R.O., and Pencharz P.B. Threonine requirement of young men determined by indicator amino acid oxidation with use of l-[1-(13)C]phenylalanine. Am. J. Clin. Nutr. 71 (2000) 757-764
324. Wilson K.H., and Blitchington R.B. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62 (1996) 2273-2278
325. 13C]acetate into plasma lipids in humans. Am. J. Clin. Nutr. 61 (1995) 1241-1247
326. Wolfe R.R. Radioactive and Stable Isotope Tracers in Biomedicine: Principles and Practice of Kinetic Analysis (1992), Academic Press, Inc., New York
327. 13C-glucose: a signature for Bifidobacterium fermentation in the intestinal tract. J. Nutr. 128 (1998) 91-96
328. Wolin M.J., Miller T.L., Yerry S., Zhang Y., Bank S., and Weaver G.A. Changes of fermentation pathways of fecal microbial communities associated with a drug treatment that increases dietary starch in the human colon. Appl. Environ. Microbiol. 65 (1999) 2807-2812
329. Wright A., Wait R., Begum S., Crossett B., Nagy J., Brown K., and Fairweather N. Proteomic analysis of cell surface proteins from Clostridium difficile. Proteomics 5 (2005) 2443-2452
330. Wu G.D., Huang N., Wen X., Keilbaugh S.A., and Yang H. High-level expression of I kappa B-beta in the surface epithelium of the colon: in vitro evidence for an immunomodulatory role. J. Leukoc. Biol. 66 (1999) 1049-1056
331. Wunsche J., Bock H.D., Hennig U., Kreienbring F., and Borgmann E. Protein digestibility and absorption of amino acids in various segments of the digestive tract of pigs. 2. Protein and amino acid balances at the end of the small intestine and of the whole digestive tract (apparent and true protein and amino acid digestibility). Arch. Tierernahr. 29 (1979) 221-234
332. Yanagisawa N., Geironson L., Al-Soud W.A., and Ljungh S. Expression of matrix metalloprotease-2, -7 and -9 on human colon, liver and bile duct cell lines by enteric and gastric Helicobacter species. FEMS Immunol. Med. Microbiol. 44 (2005) 197-204
333. Yokoyama T., Banta S., Berthiaume F., Nagrath D., Tompkins R.G., and Yarmush M.L. Evolution of intrahepatic carbon, nitrogen, and energy metabolism in a d-galactosamine-induced rat liver failure model. Metab. Eng. 7 (2005) 88-103
334. Young G.P., and Gibson P. Butyrate and the colorectal cancer cell. In: Binder H.J., Cummings J., and Soergel K.H. (Eds). Short-Chain Fatty Acids (1994), Kluwer, Boston 148-160
335. Ytrebo L.M., Sen S., Rose C., Ten Have G.A., Davies N.A., Hodges S., Nedredal G.I., Romero-Gomez M., Williams R., Revhaug A., Jalan R., and Deutz N.E. Interorgan ammonia, glutamate, and glutamine trafficking in pigs with acute liver failure. Am. J. Physiol. Gastrointest. Liver Physiol. 291 (2006) G373-G381
336. Yuan J., Zhu L., Liu X., Li T., Zhang Y., Ying T., Wang B., Wang J., Dong H., Feng E., Li Q., Wang H., Wei K., Zhang X., Huang C., Huang P., Huang L., and Zeng M. A proteome reference map and proteomic analysis of Bifidobacterium longum NCC2705. Mol. Cell Proteomics 5 (2006) 1105-1118
337. Yugi K., Nakayama Y., Kinoshita A., and Tomita M. Hybrid dynamic/static method for large-scale simulation of metabolism. Theor. Biol. Med. Model. 2 (2005) 42
338. 13C]phenylalanine. Am. J. Physiol. 264 (1993) E677-E685
339. Zhang X.J., Chinkes D.L., and Wolfe R.R. Measurement of muscle protein fractional synthesis and breakdown rates from a pulse tracer injection. Am. J. Physiol. Endocrinol. Metab. 283 (2002) E753-E764
340. Zhong S.S., Zhang Z.S., Wang J.D., Lai Z.S., Wang Q.Y., Pan L.J., and Ren Y.X. Competitive inhibition of adherence of enterotoxigenic Escherichia coli, enteropathogenic Escherichia coli and Clostridium difficile to intestinal epithelial cell line Lovo by purified adhesin of Bifidobacterium adolescentis 1027. World J. Gastroenterol. 10 (2004) 1630-1633
341. Zoetendal E.G., Akkermans A.D., and De Vos W.M. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64 (1998) 3854-3859
342. Zoetendal E.G., Cheng B., Koike S., and Mackie R.I. Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function. Curr. Issues Intest. Microbiol. 5 (2004) 31-47
343. Zoetendal E.G., Collier C.T., Koike S., Mackie R.I., and Gaskins H.R. Molecular ecological analysis of the gastrointestinal microbiota: a review. J. Nutr. 134 (2004) 465-472
344. Zoetendal E.G., Vaughan E.E., and De Vos W.M. A microbial world within us. Mol. Microbiol. 59 (2006) 1639-1650