- Urbanczyk-Wochniak, E. et al. Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep. 4, 989–993 (2003).
CAS PubMed PubMed Central Google Scholar
- Nicholson, J. K., Holmes, E., Lindon, J. C. & Wilson, I. D. The challenges of modelling mammalian biocomplexity. Nature Biotechnol. 22, 1268–1274 (2004).
CAS Google Scholar
- Hood, L. & Galas, D. The digital code of DNA. Nature 421, 444–448 (2003).
PubMed Google Scholar
- Smith, L. L. Key challenges for toxicologists in the 21st Century. Trend. Pharm. Sci. 22, 281–285 (2001).
CAS Google Scholar
- Ungelman-Sundberg, M. Pharmacogenetics of cytochrome P450 & its application in drug therapy: the past, present and future. Trend. Pharm. Sci. 25, 193–200 (2004).
Google Scholar
- Nebert, D. W., Jorge-Nebert, L. & Vesell, E. S. Pharmacogenomics and 'individualized drug therapy': high expectations and disappointing achievements. Am. J. Pharmacogenomics 3, 361–370 (2003).
Google Scholar
- Nicholson, J. K., Connelly, J., Lindon, J. C. & Holmes, E. Metabonomics: a platform for studying drug toxicity and gene function. Nature Rev. Drug Disc. 1, 153–161 (2002).
CAS Google Scholar
- Lindon, J. C., Nicholson, J. K., Holmes, E. & Everett, J. R. Metabonomics: metabolic processes studied by NMR spectroscopy of biofluids. Concepts. Magn. Reson. 12, 289–320 (2000).
CAS Google Scholar
- Farthing, M. J. G. Bugs and the gut: an unstable marriage. Best Pract. Res. Clin. Gastroent. 18, 233–239 (2004).
Google Scholar
- Guarner, F. & Malagelada, J. R. Gut flora in health and disease. Lancet 361, 512–519 (2003).
Google Scholar
- Nicholls, A. W., Mortishire-Smith, R. J. & Nicholson, J. K. NMR spectroscopic-based metabonomic studies of urinary metabolite variation in acclimatizing germ-free rats. Chem. Res. Toxicol. 16, 1395–1404 (2003).
CAS Google Scholar
- Bull, T. J. et al. Detection and verification of Mycobacterium avium subsp. paratuberculosis in fresh ileocolonic mucosal biopsy specimens from individuals with and without Crohn's Disease. J. Clin. Microbiol. 41, 2915–2923 (2003).
CAS PubMed PubMed Central Google Scholar
- Lhoste, E. F. et al. The human colonic microflora influences the alterations of xenobiotic-metabolizing enzymes by catechins in male F344 rats. Food Chem. Toxicol. 41, 695–702 (2003).
CAS PubMed Google Scholar
- Xu, J. & Gordon, J. I. Honor thy symbionts. Proc. Natl Acad. Sci. USA 100, 10452–10459 (2003).
CAS PubMed Google Scholar
- Todar, K. The bacterial flora of humans. Todar's online textbook of bacteriology [online], <http://textbookofbacteriology.net> (2004).
Google Scholar
- Suau, A. et al. Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora. Syst. Appl. Microbiol. 24, 139–145 (2001).
CAS PubMed Google Scholar
- Suau, A. et al. Direct rDNA community analysis reveals a myriad of novel bacterial lineages within the human gut. Appl. Environ. Microbiol. 65, 4799–4807 (1999).
CAS PubMed PubMed Central Google Scholar
- Upreti, R. K., Shrivastava, R. & Chaturvedi, U. C. Gut microflora and toxic metals: chromium as a model. Indian J. Med. Res. 119, 49–59 (2004).
CAS PubMed Google Scholar
- Acheson, D. W. K. Mucosal immune responses. Best Pract. Res. Clin. Gastroent. 18, 387–404 (2004).
CAS Google Scholar
- Hooper, L. V., Bry, L., Falk, P. G. & Gordon, J. I. Host–microbial symbiosis in the mammalian intestine: exploring an intestinal ecosystem. Bioessays 20, 336–343 (1998).
CAS Google Scholar
- Hallstrom, M., Eerola, E., Janas, M. & Tammela, O. Effects of mode of delivery and necrotizing enterocolitis on the intestinal microflora in preterm infants. Eur. J. Clin. Microbiol. Infect. Dis. 23, 463–470 (2004).
CAS PubMed Google Scholar
- Dai, D. & Walker, W. A. Protective nutrients and bacterial colonization in the immature human gut. Adv. Pediatr. 46, 353–382 (1999).
CAS PubMed Google Scholar
- Fanaro, S., Chierici, R., Guerrini, P & Vigi, V. Intestinal microflora in early infancy: composition and development. Acta Paediatr. Supp. 91, 48–55 (2003).
CAS Google Scholar
- Lederberg, J. & McCray, A. T. 'Ome sweet 'Omics – a genealogical treasury of words. Scientist 15, 8 (2001).
Google Scholar
- Illing, H. P. A. Techniques for microfloral and associated metabolic studies in relation to the absorption and enterohepatic circulation of drugs. Xenobiotica 11, 815–830 (1981).
CAS PubMed Google Scholar
- Boxenbaum, H. G., Bekersky, I., Jack, M. J. & Kaplan, S. A. Influence of gut microflora on bioavailability. Drug. Met. Rev. 9, 259–279 (1979).
CAS Google Scholar
- Nicholson, J. K. & Wilson, I. D. Understanding 'global' systems biology: metabonomics and the continuum of metabolism. Nature Rev. Drug Discov. 2, 668–676 (2003).
CAS Google Scholar
- Gilmore, M. S. & Ferretti, J. J. The thin line between gut commensal and pathogen. Science 299, 1999–2002 (2003).
CAS PubMed Google Scholar
- Hooper, L. V. & Gordon, J. L. Commensal host-bacterial relationships in the gut. Science 292, 1115–1118 (2001).
CAS Google Scholar
- Yoshida, K. et al. Urinary sulfur-containing metabolite produced by intestinal bacteria following oral administration of dimethylarsinic acid to rats. Chem. Res. Toxicol. 16, 1124–1129 (2003).
CAS PubMed Google Scholar
- Adlerberth, I. et al. Intestinal colonization of Enterobacteriaceae in Pakistani and Swedish hospital-delivered children. Acta Pediatr. Scand. 80, 602–610 (1991).
CAS Google Scholar
- Drasar, B. S., Montgomery, F. & Tomkins, A. M. Diet and faecal flora in three dietary groups in rural northern Nigeria. J. Hyg. 96, 59–65 (1986).
CAS PubMed Google Scholar
- Mathan, V. I., Wiederman, J., Dobkin, J. F. & Lindenbaum, J. Geographic differences in digoxin inactivation, a metabolic activity of the human anaerobic gut flora. Gut 30, 971–977 (1989).
CAS PubMed PubMed Central Google Scholar
- Kelly, D. et al. Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR–γ and ReIA. Nature Immunol. 5, 104–112 (2004).
CAS Google Scholar
- Koo, S. H. et al. PGC-1 promotes insulin resistance in liver through PPAR-α-dependent induction of TRB-3. Nature Med. 10, 530–534 (2004).
CAS PubMed Google Scholar
- Wellen, K. E. & Hotamisligil, G. S. Obesity-induced inflammatory changes in adipose tissue. J. Clin. Invest. 112, 1785–1788 (2003).
CAS PubMed PubMed Central Google Scholar
- Fekete, S. Recent findings and future perspectives of digestive physiology in rabbits: a review. Acta Vet. Hung. 37, 265–279 (1989).
CAS PubMed Google Scholar
- Weimer, P. J. Manipulating ruminal fermentation: a microbial ecological perspective. J. Anim. Sci. 76, 3114–3122 (1998).
CAS PubMed Google Scholar
- Rowland, I. R. Factors affecting metabolic activity of the intestinal microflora. Drug Met. Rev. 19, 243–261 (1988).
CAS Google Scholar
- Caldwell, J. & Hawksworth, G. M. The demethylation of methamphetamine by intestinal microflora. J. Pharm. Pharmacol. 25, 422–4244 (1973).
CAS PubMed Google Scholar
- Woolley, J. L. Jr & Siegel, C. W. The role of dietary nitrate and nitrite in the reductive deamination of sulfadiazine by the rat, guinea pig and neonatal calf. Life Sci. 30, 2229–2234 (1982).
CAS PubMed Google Scholar
- Gardana, C., Simonetti, P., Canzi, E., Zanchi, R. & Pietta, P. Metabolism of stevioside and rebaudioside A from Stevia rebaudiana extracts by human microflora. J. Agric. Food. Chem. 51, 6618–6622 (2003).
CAS PubMed Google Scholar
- Chourasia, M. K. & Jain, S. K. Pharmaceutical approaches to colon targeted drug delivery systems. J. Pharm. Pharm. Sci. 6, 33–66 (2003).
CAS PubMed Google Scholar
- Bakke, J. E. & Gustafsson, J. A. Role of intestinal flora in metabolism of agrochemicals conjugated with glutathione. Xenobiotica 16, 1047–1056 ( 1986).
CAS PubMed Google Scholar
- Buhler, R. et al. Human alcohol dehydrogenase: structural differences between the β and γ subunits suggest parallel duplications in isoenzyme evolution and predominant expression of separate gene descendants in livers of different mammals. Proc. Natl Acad. Sci. USA 81, 6320–6324 (1984).
CAS PubMed Google Scholar
- Wostmann, B. S. The germ free animal in nutritional studies. Ann. Rev. Nutr. 1, 257–279 (1981).
CAS Google Scholar
- Ogawa, H. et al. Sodium butyrate inhibits angiogenesis of human intestinal microvascular endothelial cells through COX-2 inhibition. FEBS Lett. 554, 88–94 (2003).
CAS PubMed Google Scholar
- Gordon, J. I., Hooper, L. V., McNevin, M. S., Wong, M. & Bry, L. Epithelial cell growth and differentiation. III. Promoting diversity in the intestine: conversations between the microflora, epithelium and diffuse GALT. Am. J. Physiol. 273, G565–G570 (1997).
CAS PubMed Google Scholar
- Rawls, J. F., Samuel, B. S. & Gordon, J. I. Gnotobiotic zebrafish reveal evolutionary conserved responses to the gut microbiota. Proc. Natl Acad. Sci. USA 101, 4596–4601 (2004)
CAS PubMed Google Scholar
- Tabita, K., Sakaguchi, S., Kozaki, S. & Sakaguchi, G. Comparative studies on Clostridium botulinum type A strains associated with infant botulism in Japan and in California, USA. Jpn. J. Med. Sci. Biol. 43, 219–231 (1990).
CAS PubMed Google Scholar
- Danielson, P. B. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr. Drug Metab. 3, 561–597 (2002).
CAS PubMed Google Scholar
- Phipps, A. N., Stewart, J., Wright, B. & Wilson, I. D. Effect of diet on the urinary excretion of hippuric acid and other dietary-derived aromatics in rat. A complex interaction between diet, gut microflora and substrate specificity. Xenobiotica 28, 527–537 (1998).
CAS PubMed Google Scholar
- Williams, R. E., Eyton-Jones, H. W., Farnworth, M. J., Gallagher, R. & Provan, W. M. Effect of intestinal microflora on the urinary metabolic profile of rats: a 1H-nuclear magnetic resonance spectroscopy study. Xenobiotica 32, 783–794 (2002).
CAS PubMed Google Scholar
- Park, B. K., Kitteringham, N. R., Powell, H. & Pirmohamed, M. Advances in molecular toxicology — towards understanding idiosyncratic drug toxicity. Toxicology 153, 39–60 (2000).
CAS PubMed Google Scholar
- Ingelman-Sundberg, M. Polymorphism of cytochrome P450 and xenobiotic toxicity. Toxicology 181, 447–452 (2002).
PubMed Google Scholar
- Lindon, J. C et al. Contemporary issues in toxicology the role of metabonomics in toxicology and its evaluation by the COMET project. Toxicol. Appl. Pharmacol. 187, 137–146 (2003).
CAS PubMed Google Scholar
- Ebbels, T. M. D. et al. Toxicity classification from metabonomic data using a density superposition approach: 'CLOUDS'. Anal. Chim. Acta 490, 109–122 (2003).
CAS Google Scholar
- Akao, T, et al. Baicalin, the predominant flavone glucuronide of Scutellariae radix, is absorbed from the rat gastrointestinal tract as the aglycone and restored to its original form. J. Pharm. Pharmacol. 52, 1563–1568 (2000).
CAS PubMed Google Scholar
- Bowey, E., Adlercreutz, H. & Rowland, I. Metabolism of isoflavones and lignans by the gut microflora: a study in germ-free and human flora associated rats. Food Chem. Toxicol. 41, 631–636 (2003).
CAS PubMed Google Scholar
- Turner, N. J., Thomson, B. M. & Shaw, I. C. Bioactive isoflavones in functional foods: the importance of gut microflora and bioavailability. Nutr. Rev. 61, 204–213 (2003).
PubMed Google Scholar
- Gonthier, M. P. et al. Microbial aromatic metabolites formed in the gut account for a major fraction of the polyphenols excreted in urine of rats fed red wine polyphenols. J. Nutr. 133, 461–467 (2003).
CAS PubMed Google Scholar
- Solanky, K. S. et al. Application of biofluid 1H nuclear magnetic resonance-based metabonomic techniques for the analysis of the biochemical effects of dietary isoflavones on human plasma profile. Anal. Biochem. 323, 197–204 (2003).
CAS PubMed Google Scholar
- Solanky, K. S. et al. NMR-based metabonomic studies on the biochemical effects of epicatechin in the rat. J. Agric. Food Chem. 51, 4139–4145 (2003).
CAS PubMed Google Scholar
- Beale, B. Probiotics: their tiny worlds are under scrutiny. Scientist 16, 20–22 (2002).
Google Scholar
- Wang, Y. et al. NMR-based metabonomic strategy for the detection of the metabolic effects of chamomile (Matricaria recutita L.) ingestion. J. Agric. Food Chem. 53, 191–196 (2005).
CAS PubMed Google Scholar
- Peppercorn, M. A. & Goldman, P. Caffeic acid metabolism by bacteria of the human gastrointestinal tract. J. Bacteriol. 108, 996–1000 (1971).
CAS PubMed PubMed Central Google Scholar
- Sullivan, A., Edlund, C. & Nord, C. E. Effect of antimicrobial agents on the ecological balance of human microflora. Scand. J. Infect. Dis. 33, 899–903 (2001).
Google Scholar
- Lode, H., Von der Hoh, N., Ziege, S., Borner, K. & Nord, C. E. Ecological effects of linezolid versus amoxicillin/clavulanic acid on the normal intestinal microflora. J. Antimicrobiol. Chemother. 46, 741–749 (2000).
Google Scholar
- Brindle, J. T. et al. Rapid and non-invasive diagnosis of the presence of coronary heart disease using 1H NMR-based metabonomics. Nature Med. 8, 1439–1444 (2002).
CAS PubMed Google Scholar
- 't Hart, B. A. et al. 1H-NMR spectroscopy combined with pattern recognition analysis reveals characteristic chemical patterns in urines of MS patients and non-human primates with MS-like disease. J. Neurol. Sci. 212, 21–30 (2003).
CAS PubMed Google Scholar
- Wang, Y. et al. Metabonomic investigations in mice infected with Schistosoma mansoni: an approach for biomarker identification. Proc. Natl Acad. Sci. USA 101, 12676–12681 (2004).
CAS PubMed Google Scholar
- Fiehn, O. et al. Metabolite profiling for plant functional genomics. Nature Biotech. 18, 1157–1161 (2000).
CAS Google Scholar
- Hall, R. et al. Plant metabolomics: the missing link in functional genomics strategies. Plant Cell 14, 1437–1440 (2002).
CAS PubMed PubMed Central Google Scholar
- Kell, D. B. Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7, 296–307 (2004).
CAS PubMed Google Scholar
- Jonsson, P. et al. A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS. Anal. Chem. 76, 1738–1745 (2004).
CAS PubMed Google Scholar
- Clish, C. B. et al. Integrative biological analysis of the APOE*3-leiden transgenic mouse. OMICS 8, 3–13 (2004).
CAS PubMed Google Scholar
- Pham-Tuan, H., Kaskavelis, L., Daykin, C. A. & Janssen, H. G. Method development in high-performance liquid chromatography for high-throughput profiling and metabonomic studies of biofluid samples. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 789, 283–301 (2003).
CAS PubMed Google Scholar
- Plumb, R. S. et al. Metabonomics: the use of electrospray mass spectrometry coupled to reversed-phase liquid chromatography shows potential for the screening of rat urine in drug development. Rapid Commun. Mass Spectrom. 16, 1991–1996 (2002).
CAS PubMed Google Scholar
- Buchholz, A., Hurlebaus, J., Wandrey, C. & Takors, R. Metabolomics: quantification of intracellular metabolite dynamics. Biomol. Eng. 19, 5–15 (2002).
CAS PubMed Google Scholar
- Nicholson, J. K. et al. High-performance liquid chromatography coupled to inductively coupled plasma mass spectrometry (HPLC-ICP-MS) and orthogonal acceleration time-of-flight mass spectrometry (o/a-TOF-MS) for the simultaneous analysis and identification of the metabolites of 2-bromo-4-trifluoromethylacetaniline in rat urine. Anal. Chem. 73, 1491–1494 (2001).
CAS PubMed Google Scholar
- Plumb, R. et al. Ultra-performance liquid chromatography coupled to quadrupole-orthogonal time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 18, 2331–2337 (2004).
CAS PubMed Google Scholar
- Cloarec, O. et al. Statistical total correlation spectroscopy (STOCSY); an exploratory approach for latent biomarker identification from metabolic 1H NMR datasets. Anal. Chem. 77, 1282–1289 (2005).
CAS Google Scholar
- Goodacre, R. et al. Rapid identification using pyrolysis mass spectrometry and artificial neural networks of Propionibacterium acnes isolated from dogs. J. Appl. Bacteriol. 76, 124–134 (1994).
CAS PubMed Google Scholar
- Davey, H. M., Jones, A., Shaw, A. D. & Kell, D. B. Variable selection and multivariate methods for the identification of microorganisms by flow cytometry. Cytometry 35, 162–168 (1999).
CAS PubMed Google Scholar
- Bolte, E. R. Autism and Clostridium tetani. Med. Hypotheses 51, 133–144 (1998).
CAS PubMed Google Scholar
- Shaw, W. in Biological treatments for autism and PDD. 2nd edn 25–26 (The Great Plains Publishing Company, Winfield, Kansas, 2002).
Google Scholar
- Martirosian, G. Anaerobic intestinal microflora in pathogenesis of autism. Postepy. Hig. Med. Dosw. 58, 349–351 (2004).
Google Scholar