Understanding the role of gut microbiome–host metabolic signal disruption in health and disease

An obesity-associated gut microbiome with increased capacity for energy harvest

Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444 · see citing works

Human gut microbes associated with obesity

Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785 · see citing works

Enterotypes of the human gut microbiome

MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548 · see citing works

Metabolic Endotoxemia Initiates Obesity and Insulin Resistance

Cani, P. D., Amar, J., Iglesias, M. A., Poggi, M., Knauf, C., Bastelica, D., Neyrinck, A. M., Fava, F., Tuohy, K. M., Chabo, C., et al. (2007) · Diabetes · doi:10.2337/db06-1491 · Cited by 6,638 · see citing works

The gut microbiota as an environmental factor that regulates fat storage

Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245 · see citing works

Obesity alters gut microbial ecology

Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176 · see citing works

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

Wang, Z., Klipfell, E., Bennett, B. J., Koeth, R., Levison, B. S., DuGar, B., Feldstein, A. E., Britt, E. B., Fu, X., Chung, Y.-M., et al. (2011) · Nature · doi:10.1038/nature09922 · Cited by 5,597 · see citing works

Host-Bacterial Mutualism in the Human Intestine

Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277 · see citing works

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706625104 · Cited by 4,611 · see citing works

Interleukin-10-deficient mice develop chronic enterocolitis

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Gut microbiota in health and disease

Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010) · Physiological Reviews · doi:10.1152/physrev.00045.2009 · Cited by 4,182 · see citing works

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome

Turnbaugh, P. J., Bäckhed, F., Fulton, L., & Gordon, J. I. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.02.015 · Cited by 2,915 · see citing works

Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice

Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X., Kubo, C., & Koga, Y. (2004) · The Journal of Physiology · doi:10.1113/jphysiol.2004.063388 · Cited by 2,735 · see citing works

Mechanisms underlying the resistance to diet-induced obesity in germ-free mice

Bäckhed, F., Manchester, J. K., Semenkovich, C. F., & Gordon, J. I. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605374104 · Cited by 2,615 · see citing works

Innate immunity and intestinal microbiota in the development of Type 1 diabetes

Wen, L., Ley, R. E., Volchkov, P. Y., Stranges, P. B., Avanesyan, L., Stonebraker, A. C., Hu, C., Wong, F. S., Szot, G. L., Bluestone, J. A., et al. (2008) · Nature · doi:10.1038/nature07336 · Cited by 1,921 · see citing works

Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia

Cani, P. D., Neyrinck, A. M., Fava, F., Knauf, C., Burcelin, R., Tuohy, K. M., Gibson, G. R., & Delzenne, N. M. (2007) · Diabetologia · doi:10.1007/s00125-007-0791-0 · Cited by 1,770 · see citing works

Differential Adaptation of Human Gut Microbiota to Bariatric Surgery–Induced Weight Loss

Furet, J.-P., Kong, L.-C., Tap, J., Poitou, C., Basdevant, A., Bouillot, J.-L., Mariat, D., Corthier, G., Doré, J., Henegar, C., et al. (2010) · Diabetes · doi:10.2337/db10-0253 · Cited by 1,173 · see citing works

Symbiotic gut microbes modulate human metabolic phenotypes

Li, M., Wang, B., Zhang, M., Rantalainen, M., Wang, S., Zhou, H., Zhang, Y., Shen, J., Pang, X., Zhang, M., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712038105 · Cited by 1,144 · see citing works

Human metabolic phenotype diversity and its association with diet and blood pressure

Holmes, E., Loo, R. L., Stamler, J., Bictash, M., Yap, I. K. S., Chan, Q., Ebbels, T., De Iorio, M., Brown, I. J., Veselkov, K. A., et al. (2008) · Nature · doi:10.1038/nature06882 · Cited by 1,054 · see citing works

Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice

Dumas, M.-E., Barton, R. H., Toye, A., Cloarec, O., Blancher, C., Rothwell, A., Fearnside, J., Tatoud, R., Blanc, V., Lindon, J. C., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601056103 · Cited by 1,042 · see citing works

An African origin for the intimate association between humans and Helicobacter pylori

Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F., der Merwe, V., et al. (2007) · Nature · doi:10.1038/nature05562 · Cited by 977 · see citing works

Pharmaco-metabonomic phenotyping and personalized drug treatment

Andrew Clayton, T., Lindon, J. C., Cloarec, O., Antti, H., Charuel, C., Hanton, G., Provost, J.-P., Le Net, J.-L., Baker, D., Walley, R. J., et al. (2006) · Nature · doi:10.1038/nature04648 · Cited by 824 · see citing works

Bile acid biosynthesis

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Systemic gut microbial modulation of bile acid metabolism in host tissue compartments

Swann, J. R., Want, E. J., Geier, F. M., Spagou, K., Wilson, I. D., Sidaway, J. E., Nicholson, J. K., & Holmes, E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006734107 · Cited by 726 · see citing works

A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism

Samuel, B. S., & Gordon, J. I. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602187103 · Cited by 674 · see citing works

New IBD genetics: common pathways with other diseases

Lees, C. W., Barrett, J. C., Parkes, M., & Satsangi, J. (2011) · Gut · doi:10.1136/gut.2009.199679 · Cited by 635 · see citing works

Rapid and Noninvasive Metabonomic Characterization of Inflammatory Bowel Disease

Marchesi, J. R., Holmes, E. C., Khan, F. M. A., Kochhar, S., Scanlan, P. D., Shanahan, F., Wilson, I. D., & Wang, Y. (2007) · Journal of Proteome Research · doi:10.1021/pr060470d · Cited by 632 · see citing works

CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease

Barnich, N., Carvalho, F. A., Glasser, A.-L., Darcha, C., Jantscheff, P., Allez, M., Peeters, H., Bommelaer, G., Desreumaux, P., Colombel, J., et al. (2007) · Journal of Clinical Investigation · doi:10.1172/jci30504 · Cited by 590 · see citing works

Energy intake is associated with endotoxemia in apparently healthy men

Amar, J., Burcelin, R., Ruidavets, J. B., Cani, P. D., Fauvel, J., Alessi, M., Chamontin, B., & Ferrières, J. (2008) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/87.5.1219 · Cited by 588 · see citing works

Chemometrics in metabolomics—A review in human disease diagnosis

Madsen, R., Lundstedt, T., & Trygg, J. (2009) · Analytica Chimica Acta · doi:10.1016/j.aca.2009.11.042 · Cited by 559 · see citing works

Metabolic Footprint of Diabetes: A Multiplatform Metabolomics Study in an Epidemiological Setting

Suhre, K., Meisinger, C., Döring, A., Altmaier, E., Belcredi, P., Gieger, C., Chang, D., Milburn, M. V., Gall, W. E., Weinberger, K. M., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013953 · Cited by 551 · see citing works

Enumeration of human colonic bacteria producing phenolic and indolic compounds: effects of pH, carbohydrate availability and retention time on dissimilatory aromatic amino acid metabolism

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Metabolic surgery profoundly influences gut microbial–host metabolic cross-talk

Li, J. V., Ashrafian, H., Bueter, M., Kinross, J. K., Sands, C. J., le Roux, C. W., Bloom, S. R., Darzi, A. W., Athanasiou, T., Marchesi, J. R., et al. (2011) · Gut · doi:10.1136/gut.2010.234708 · Cited by 444 · see citing works

Modulation of the Intestinal Microbiota Alters Colitis-Associated Colorectal Cancer Susceptibility

Uronis, J. M., Mühlbauer, M., Herfarth, H. H., Rubinas, T. C., Jones, G. S., & Jobin, C. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006026 · Cited by 425 · see citing works

Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model

Martin, F. J., Wang, Y., Sprenger, N., Yap, I. K. S., Lundstedt, T., Lek, P., Rezzi, S., Ramadan, Z., van Bladeren, P., Fay, L. B., et al. (2008) · Molecular Systems Biology · doi:10.1038/msb4100190 · Cited by 421 · see citing works

The end products of the metabolism of aromatic amino acids by Clostridia

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Phylogeny of the Defined Murine Microbiota: Altered Schaedler Flora

Dewhirst, F. E., Chien, C., Paster, B. J., Ericson, R. L., Orcutt, R. P., Schauer, D. B., & Fox, J. G. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.8.3287-3292.1999 · Cited by 366 · see citing works

Diet-Induced Metabolic Improvements in a Hamster Model of Hypercholesterolemia Are Strongly Linked to Alterations of the Gut Microbiota

Martínez, I., Wallace, G., Zhang, C., Legge, R. M., Benson, A. K., Carr, T. P., Moriyama, E. N., & Walter, J. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00380-09 · Cited by 355 · see citing works

HELICOBACTER PYLORI AND GASTRIC CANCER

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Statistical Heterospectroscopy, an Approach to the Integrated Analysis of NMR and UPLC-MS Data Sets: Application in Metabonomic Toxicology Studies

Crockford, D. J., Holmes, E. C., Lindon, J. C., Plumb, R. S., Zirah, S., Bruce, S. J., Rainville, P. D., Stumpf, C. L., & Nicholson, J. K. (2005) · Analytical Chemistry · doi:10.1021/ac051444m · Cited by 341 · see citing works

Recursive Segment-Wise Peak Alignment of Biological 1 H NMR Spectra for Improved Metabolic Biomarker Recovery

Veselkov, K., Lindon, J. C., Ebbels, T. M. D., Crockford, D. J., Volynkin, V., Holmes, E. C., Davies, D. B., & Nicholson, J. K. (2008) · Analytical Chemistry · doi:10.1021/ac8011544 · Cited by 338 · see citing works

Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes

Claus, S. P., Tsang, T. M., Wang, Y., Cloarec, O., Skordi, E., Martin, F., Rezzi, S., Ross, A., Kochhar, S., Holmes, E., et al. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.56 · Cited by 334 · see citing works

Urinary Metabolic Phenotyping Differentiates Children with Autism from Their Unaffected Siblings and Age-Matched Controls

Yap, I. K. S., Angley, M. T., Veselkov, K., Holmes, E. C., Lindon, J. C., & Nicholson, J. K. (2010) · Journal of Proteome Research · doi:10.1021/pr901188e · Cited by 316 · see citing works

Dietary intake patterns are reflected in metabolomic profiles: potential role in dietary assessment studies

O'Sullivan, A., Gibney, M. J., & Brennan, L. (2011) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.110.000950 · Cited by 297 · see citing works

Lactobacillus johnsonii N6.2 Mitigates the Development of Type 1 Diabetes in BB-DP Rats

Valladares, R. B., Sankar, D., Li, N., Williams, E., Lai, K.-K., Abdelgeliel, A. S., González, C. F., Wasserfall, C. H., Larkin, J., Schatz, D., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010507 · Cited by 280 · see citing works

Top-Down Systems Biology Modeling of Host Metabotype−Microbiome Associations in Obese Rodents

Waldram, A., Holmes, E. C., Wang, Y., Rantalainen, M., Wilson, I. D., Tuohy, K. M., McCartney, A. L., Gibson, G. R., & Nicholson, J. K. (2009) · Journal of Proteome Research · doi:10.1021/pr8009885 · Cited by 266 · see citing works

Culture‐independent analysis of the gut microbiota in colorectal cancer and polyposis

Scanlan, P. D., Shanahan, F., Clune, Y., Collins, J. K., O'Sullivan, G. C., O'Riordan, M., Holmes, E., Wang, Y., & Marchesi, J. R. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01503.x · Cited by 245 · see citing works

The Blood Pressure-Lowering Effect and Safety of Chlorogenic Acid from Green Coffee Bean Extract in Essential Hypertension

Watanabe, T., Arai, Y., Mitsui, Y., Kusaura, T., Okawa, W., Kajihara, Y., & Saito, I. (2006) · Clinical and Experimental Hypertension · doi:10.1080/10641960600798655 · Cited by 242 · see citing works

Gut microbiome-derived metabolites characterize a peculiar obese urinary metabotype

Calvani, R., Miccheli, A., Capuani, G., Tomassini Miccheli, A., Puccetti, C., Delfini, M., Iaconelli, A., Nanni, G., & Mingrone, G. (2010) · International Journal of Obesity · doi:10.1038/ijo.2010.44 · Cited by 241 · see citing works

Urine Metabolite Analysis Offers Potential Early Diagnosis of Ovarian and Breast Cancers

Slupsky, C. M., Steed, H. L., Wells, T. H., Dabbs, K., Schepansky, A., Capstick, V. A., Faught, W., & Sawyer, M. B. (2010) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-10-1434 · Cited by 241 · see citing works

Gut microbes define liver cancer risk in mice exposed to chemical and viral transgenic hepatocarcinogens

Fox, J. G., Feng, Y., Theve, E. J., Raczynski, A. R., Fiala, J. L. A., Doernte, A. L., Williams, M. V., McFaline‐Figueroa, J. L., Essigmann, J. M., Schauer, D. B., et al. (2009) · Gut · doi:10.1136/gut.2009.183749 · Cited by 238 · see citing works

The Microbe-Derived Short Chain Fatty Acid Butyrate Targets miRNA-Dependent p21 Gene Expression in Human Colon Cancer

Hu, S., Dong, T. S., Dalal, S. R., Wu, F., Bissonnette, M., Kwon, J. H., & Chang, E. B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016221 · Cited by 231 · see citing works

Metabonomic and Microbiological Analysis of the Dynamic Effect of Vancomycin-Induced Gut Microbiota Modification in the Mouse

Yap, I. K. S., Li, J. V., Saric, J., Martin, F., Davies, H., Wang, Y., Wilson, I. D., Nicholson, J. K., Utzinger, J., Marchesi, J. R., et al. (2008) · Journal of Proteome Research · doi:10.1021/pr700864x · Cited by 231 · see citing works

Metabolic Signatures of Lung Cancer in Biofluids: NMR-Based Metabonomics of Urine

Carrola, J., Rocha, C., Barros, A. S., Gil, A. M., Goodfellow, B. J., Carreira, I. M., Bernardo, J., Gomes, A., de Sousa, V. M. L., Carvalho, L., et al. (2010) · Journal of Proteome Research · doi:10.1021/pr100899x · Cited by 225 · see citing works

Urinary Metabonomic Study on Colorectal Cancer

Qiu, Y., Cai, G., Su, M., Chen, T., Liu, Y., Xu, Y., Ni, Y., Zhao, A., Cai, S., Xu, L. X., et al. (2010) · Journal of Proteome Research · doi:10.1021/pr901081y · Cited by 223 · see citing works

NMR Spectroscopic-Based Metabonomic Studies of Urinary Metabolite Variation in Acclimatizing Germ-Free Rats

Nicholls, A. W., Mortishire‐Smith, R. J., & Nicholson, J. K. (2003) · Chemical Research in Toxicology · doi:10.1021/tx0340293 · Cited by 215 · see citing works

Helicobacter Infection Is Required for Inflammation and Colon Cancer in Smad3-Deficient Mice

Maggio‐Price, L., Treuting, P. M., Zeng, W., Tsang, M., Bielefeldt‐Ohmann, H., & Iritani, B. M. (2006) · Cancer Research · doi:10.1158/0008-5472.can-05-2448 · Cited by 209 · see citing works

Human faecal microbiota display variable patterns of glycerol metabolism

Weirdt, R. D., Possemiers, S., Vermeulen, G., Moerdijk-Poortvliet, T. C. W., Boschker, H. T. S., Verstraete, W., & de Wiele, T. V. (2010) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2010.00974.x · Cited by 207 · see citing works

Elimination of colon cancer in germ-free transforming growth factor beta 1-deficient mice.

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Metabolite profiling of fecal water extracts from human colorectal cancer

Monleón, D., Morales, J. M., Barrasa, A., López, J. A., Vázquez, C., & Celda, B. (2009) · NMR in Biomedicine · doi:10.1002/nbm.1345 · Cited by 186 · see citing works

Innate Immune Inflammatory Response against Enteric Bacteria Helicobacter hepaticus Induces Mammary Adenocarcinoma in Mice

Rao, V. P., Poutahidis, T., Ge, Z., Nambiar, P. R., Boussahmain, C., Wang, Y. Y., Horwitz, B. H., Fox, J. G., & Erdman, S. E. (2006) · Cancer Research · doi:10.1158/0008-5472.can-06-0558 · Cited by 185 · see citing works

Nitric oxide and TNF-α trigger colonic inflammation and carcinogenesis in Helicobacter hepaticus -infected, Rag2 -deficient mice

Erdman, S. E., Rao, V. P., Poutahidis, T., Rogers, A. B., Taylor, C. L., Jackson, E. A., Ge, Z., Lee, C. W., Schauer, D. B., Wogan, G. N., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812347106 · Cited by 183 · see citing works

Characterization of Inflammatory Bowel Disease With Urinary Metabolic Profiling

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Why Do African Americans Get More Colon Cancer than Native Africans?

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Urine Metabolomic Analysis Identifies Potential Biomarkers and Pathogenic Pathways in Kidney Cancer

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Intestinal neoplasia in the ApcMin mouse: independence from the microbial and natural killer (beige locus) status.

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Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification

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Correlative and quantitative 1H NMR-based metabolomics reveals specific metabolic pathway disturbances in diabetic rats

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Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models

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Role of dietary sulphate in the regulation of methanogenesis in the human large intestine.

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Urinary metabonomic study on biochemical changes in chronic unpredictable mild stress model of depression

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Helicobacter pylori and gastric cancer

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Purification and Structural Characterization of 3-Hydroxypropionaldehyde and Its Derivatives

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Metabonomic Studies on the Physiological Effects of Acute and Chronic Psychological Stress in Sprague−Dawley Rats

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Metabolite Profiling Identifies Candidate Markers Reflecting the Clinical Adaptations Associated with Roux-en-Y Gastric Bypass Surgery

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Metabolic profiling reveals key metabolic features of renal cell carcinoma

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GCMS-based metabolomic study in mice with colitis induced by dextran sulfate sodium

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Lipid Metabolism in Anaerobic Ecosystems

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Fermentation potential of the gut microbiome: implications for energy homeostasis and weight management

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Production of Skatole and para -Cresol by a Rumen Lactobacillus sp

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Phylometabonomic Patterns of Adaptation to High Fat Diet Feeding in Inbred Mice

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