Microbiome and Diseases: Metabolic Disorders

  • Thomas ClavelEmail author
  • Josef Ecker


Following the work of pioneers at the beginning of the twentieth century and later in the 1960s, there is nowadays a renewed interest for the impact of gut microbial communities on host metabolism. Nonetheless, we still ignore the real contribution of the intestinal microbiota to our energy homeostasis. The obesity pandemic is due to unbalanced energy intake (too high) vs. expenditure (too low) and not to the colonization of our intestine by unfavorable microbes. Nonetheless, gut microorganisms and in particular bacteria can metabolize a variety of dietary compounds, thereby releasing bioactive molecules that can influence metabolic functions of the host. Intestinal bacteria can also influence immune responses, which are known to play a role in the development of chronic metabolic disorders. Moreover, the approach of transferring gut microbial communities via fecal transplantation to germfree animals or human subjects has demonstrated the causal role of intestinal microbes in regulating host energy homeostasis and the development of metabolic pathologies. Experimental studies have even identified single cultured bacteria that influence metabolic responses, including underlying molecular mechanisms and bioactive molecules. All these findings speak in favor of the importance of the gut microbiota for host metabolism. In the present chapter, we summarize data in a critical manner and discuss key notions pertaining to the impact of gut microbial communities on host metabolism and ensuing implications for the development of metabolic disorders.


  1. Abrams, G. D., & Bishop, J. E. (1967). Effect of the normal microbial flora on gastrointestinal motility. Proceedings of the Society for Experimental Biology and Medicine, 126, 301–304.PubMedPubMedCentralCrossRefGoogle Scholar
  2. Abu-Shanab, A., & Quigley, E. M. (2010). The role of the gut microbiota in nonalcoholic fatty liver disease. Nature Reviews. Gastroenterology & Hepatology, 7, 691–701.CrossRefGoogle Scholar
  3. Ajslev, T. A., Andersen, C. S., Gamborg, M., Sorensen, T. I., & Jess, T. (2011). Childhood overweight after establishment of the gut microbiota: The role of delivery mode, pre-pregnancy weight and early administration of antibiotics. International Journal of Obesity, 35, 522–529.PubMedPubMedCentralCrossRefGoogle Scholar
  4. Alves, M. M., Pereira, M. A., Sousa, D. Z., Cavaleiro, A. J., Picavet, M., Smidt, H., et al. (2009). Waste lipids to energy: How to optimize methane production from long-chain fatty acids (LCFA). Microbial Biotechnology, 2, 538–550.PubMedPubMedCentralCrossRefGoogle Scholar
  5. Amato, A., Baldassano, S., & Mule, F. (2016). GLP2: An underestimated signal for improving glycaemic control and insulin sensitivity. The Journal of Endocrinology, 229, R57–R66.PubMedPubMedCentralCrossRefGoogle Scholar
  6. Angelakis, E., & Raoult, D. (2010). The increase of Lactobacillus species in the gut flora of newborn broiler chicks and ducks is associated with weight gain. PLoS One, 5, e10463.PubMedPubMedCentralCrossRefGoogle Scholar
  7. Arrieta, M. C., Walter, J., & Finlay, B. B. (2016). Human microbiota-associated mice: A model with challenges. Cell Host & Microbe, 19, 575–578.CrossRefGoogle Scholar
  8. Azad, M. B., Bridgman, S. L., Becker, A. B., & Kozyrskyj, A. L. (2014). Infant antibiotic exposure and the development of childhood overweight and central adiposity. International Journal of Obesity, 38, 1290–1298.PubMedPubMedCentralCrossRefGoogle Scholar
  9. Backhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., et al. (2004). The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences of the United States of America, 101, 15718–15723.PubMedPubMedCentralGoogle Scholar
  10. Backhed, F., Manchester, J. K., Semenkovich, C. F., & Gordon, J. I. (2007). Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proceedings of the National Academy of Sciences of the United States of America, 104, 979–984.PubMedPubMedCentralCrossRefGoogle Scholar
  11. Bajaj, J. S., Kassam, Z., Fagan, A., Gavis, E. A., Liu, E., Cox, I. J., et al. (2017, December). Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: A randomized clinical trial. Hepatology, 66(6), 1727–1738.PubMedPubMedCentralCrossRefGoogle Scholar
  12. Barret, K., Brooks, H., Boitano, S., & Barman, S. (2010). Digestion, absorption, and nutritional principles (Chapter 27). In Ganong’s review of medical physiology. In Lange medical book, pp. 451–467.Google Scholar
  13. Bassaganya-Riera, J., & Hontecillas, R. (2006). CLA and n-3 PUFA differentially modulate clinical activity and colonic PPAR-responsive gene expression in a pig model of experimental IBD. Clinical Nutrition, 25, 454–465.PubMedPubMedCentralCrossRefGoogle Scholar
  14. Bjorneklett, A., Viddal, K. O., Midtvedt, T., & Nygaard, K. (1981). Intestinal and gastric bypass. Changes in intestinal microecology after surgical treatment of morbid obesity in man. Scand J Gastroenterol, 16, 681–687.PubMedPubMedCentralCrossRefGoogle Scholar
  15. Blachier, F., Beaumont, M., Andriamihaja, M., Davila, A. M., Lan, A., Grauso, M., et al. (2017). Changes in the luminal environment of the colonic epithelial cells and physiopathological consequences. The American Journal of Pathology, 187, 476–486.PubMedPubMedCentralCrossRefGoogle Scholar
  16. Blanton, L. V., Charbonneau, M. R., Salih, T., Barratt, M. J., Venkatesh, S., Ilkaveya, O., et al. (2016). Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science, 351.Google Scholar
  17. Booth, C. C., Alldis, D., & Read, A. E. (1961). Studies on the site of fat absorption: 2 Fat balances after resection of varying amounts of the small intestine in man. Gut, 2, 168–174.PubMedPubMedCentralCrossRefGoogle Scholar
  18. Brown, J. M., Chung, S., Sawyer, J. K., Degirolamo, C., Alger, H. M., Nguyen, T., et al. (2008). Inhibition of stearoyl-coenzyme A desaturase 1 dissociates insulin resistance and obesity from atherosclerosis. Circulation, 118, 1467–1475.PubMedPubMedCentralCrossRefGoogle Scholar
  19. Brun, P., Castagliuolo, I., Di Leo, V., Buda, A., Pinzani, M., Palu, G., et al. (2007). Increased intestinal permeability in obese mice: New evidence in the pathogenesis of nonalcoholic steatohepatitis. American Journal of Physiology. Gastrointestinal and Liver Physiology, 292, G518–G525.PubMedPubMedCentralCrossRefGoogle Scholar
  20. Buckley, C. D., Gilroy, D. W., & Serhan, C. N. (2014). Proresolving lipid mediators and mechanisms in the resolution of acute inflammation. Immunity, 40, 315–327.PubMedPubMedCentralCrossRefGoogle Scholar
  21. Bui, T. P., Ritari, J., Boeren, S., de Waard, P., Plugge, C. M., & de Vos, W. M. (2015). Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal. Nature Communications, 6, 10062.PubMedPubMedCentralCrossRefGoogle Scholar
  22. Cani, P. D., Neyrinck, A. M., Fava, F., Knauf, C., Burcelin, R. G., Tuohy, K. M., et al. (2007). Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia, 50, 2374–2383.PubMedCrossRefGoogle Scholar
  23. Cani, P. D., Possemiers, S., Van de Wiele, T., Guiot, Y., Everard, A., Rottier, O., et al. (2009). Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. Gut, 58, 1091–1103.PubMedPubMedCentralCrossRefGoogle Scholar
  24. Charbonneau, M. R., O’Donnell, D., Blanton, L. V., Totten, S. M., Davis, J. C., Barratt, M. J., et al. (2016). Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition. Cell, 164, 859–871.PubMedPubMedCentralCrossRefGoogle Scholar
  25. Cherbuy, C., Darcy-Vrillon, B., Morel, M. T., Pegorier, J. P., & Duee, P. H. (1995). Effect of germfree state on the capacities of isolated rat colonocytes to metabolize n-butyrate, glucose, and glutamine. Gastroenterology, 109, 1890–1899.PubMedPubMedCentralCrossRefGoogle Scholar
  26. Clavel, T., Desmarchelier, C., Haller, D., Gerard, P., Rohn, S., Lepage, P., et al. (2014). Intestinal microbiota in metabolic diseases: From bacterial community structure and functions to species of pathophysiological relevance. Gut Microbes, 5, 544–551.PubMedPubMedCentralCrossRefGoogle Scholar
  27. Collado, M. C., Isolauri, E., Laitinen, K., & Salminen, S. (2010). Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: A prospective follow-up study initiated in early pregnancy. The American Journal of Clinical Nutrition, 92, 1023–1030.PubMedCrossRefGoogle Scholar
  28. Cotillard, A., Kennedy, S. P., Kong, L. C., Prifti, E., Pons, N., Le Chatelier, E., et al. (2013). Dietary intervention impact on gut microbial gene richness. Nature, 500, 585–588.CrossRefPubMedGoogle Scholar
  29. Cox, L. M., & Blaser, M. J. (2015). Antibiotics in early life and obesity. Nature Reviews. Endocrinology, 11, 182–190.PubMedCrossRefGoogle Scholar
  30. Damms-Machado, A., Louis, S., Schnitzer, A., Volynets, V., Rings, A., Basrai, M., et al. (2017). Gut permeability is related to body weight, fatty liver disease, and insulin resistance in obese individuals undergoing weight reduction. The American Journal of Clinical Nutrition, 105, 127–135.PubMedPubMedCentralCrossRefGoogle Scholar
  31. Daniel, H., Gholami, A. M., Berry, D., Desmarchelier, C., Hahne, H., Loh, G., et al. (2014). High-fat diet alters gut microbiota physiology in mice. The ISME Journal, 8, 295–308.PubMedPubMedCentralCrossRefGoogle Scholar
  32. David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505, 559–563.PubMedPubMedCentralCrossRefGoogle Scholar
  33. De Filippis, F., Pellegrini, N., Laghi, L., Gobbetti, M., & Ercolini, D. (2016). Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns. Microbiome, 4, 57.PubMedPubMedCentralCrossRefGoogle Scholar
  34. de Groot, P. F., Frissen, M. N., de Clercq, N. C., & Nieuwdorp, M. (2017). Fecal microbiota transplantation in metabolic syndrome: History, present and future. Gut Microbes, 8, 253–267.PubMedPubMedCentralCrossRefGoogle Scholar
  35. De Vadder, F., Kovatcheva-Datchary, P., Goncalves, D., Vinera, J., Zitoun, C., Duchampt, A., et al. (2014). Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell, 156, 84–96.PubMedPubMedCentralCrossRefGoogle Scholar
  36. Degen, C., Ecker, J., Piegholdt, S., Liebisch, G., Schmitz, G., & Jahreis, G. (2011). Metabolic and growth inhibitory effects of conjugated fatty acids in the cell line HT-29 with special regard to the conversion of t11,t13-CLA. Biochimica et Biophysica Acta, 1811, 1070–1080.PubMedPubMedCentralCrossRefGoogle Scholar
  37. den Besten, G., van Eunen, K., Groen, A. K., Venema, K., Reijngoud, D. J., & Bakker, B. M. (2013). The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. Journal of Lipid Research, 54, 2325–2340.CrossRefGoogle Scholar
  38. Derrien, M., Vaughan, E. E., Plugge, C. M., & de Vos, W. M. (2004). Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. International Journal of Systematic and Evolutionary Microbiology, 54, 1469–1476.PubMedPubMedCentralCrossRefGoogle Scholar
  39. Derrien, M., Collado, M. C., Ben-Amor, K., Salminen, S., & de Vos, W. M. (2008). The Mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Applied and Environmental Microbiology, 74, 1646–1648.PubMedPubMedCentralCrossRefGoogle Scholar
  40. Devillard, E., McIntosh, F. M., Duncan, S. H., & Wallace, R. J. (2007). Metabolism of linoleic acid by human gut bacteria: Different routes for biosynthesis of conjugated linoleic acid. Journal of Bacteriology, 189, 2566–2570.PubMedPubMedCentralCrossRefGoogle Scholar
  41. Dubos, R. J., & Schaedler, R. W. (1960). The effect of the intestinal flora on the growth rate of mice, and on their susceptibility to experimental infections. The Journal of Experimental Medicine, 111, 407–417.PubMedPubMedCentralCrossRefGoogle Scholar
  42. Dubos, R., Lee, C. J., & Costello, R. (1969). Lasting biological effects of early environmental influences. V. Viability, growth, and longevity. The Journal of Experimental Medicine, 130, 963–977.PubMedPubMedCentralCrossRefGoogle Scholar
  43. Duncan, S. H., Belenguer, A., Holtrop, G., Johnstone, A. M., Flint, H. J., & Lobley, G. E. (2007). Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Applied and Environmental Microbiology, 73, 1073–1078.PubMedPubMedCentralCrossRefGoogle Scholar
  44. Duncan, S. H., Lobley, G. E., Holtrop, G., Ince, J., Johnstone, A. M., Louis, P., et al. (2008). Human colonic microbiota associated with diet, obesity and weight loss. International Journal of Obesity, 32, 1720–1724.PubMedPubMedCentralCrossRefGoogle Scholar
  45. Ecker, J., & Liebisch, G. (2014). Application of stable isotopes to investigate the metabolism of fatty acids, glycerophospholipid and sphingolipid species. Progress in Lipid Research, 54, 14–31.PubMedPubMedCentralCrossRefGoogle Scholar
  46. Ecker, J., Liebisch, G., Patsch, W., & Schmitz, G. (2009). The conjugated linoleic acid isomer trans-9,trans-11 is a dietary occurring agonist of liver X receptor alpha. Biochemical and Biophysical Research Communications, 388, 660–666.PubMedPubMedCentralCrossRefGoogle Scholar
  47. Ecker, J., Liebisch, G., Englmaier, M., Grandl, M., Robenek, H., & Schmitz, G. (2010a). Induction of fatty acid synthesis is a key requirement for phagocytic differentiation of human monocytes. Proceedings of the National Academy of Sciences of the United States of America, 107, 7817–7822.PubMedPubMedCentralCrossRefGoogle Scholar
  48. Ecker, J., Liebisch, G., Scherer, M., & Schmitz, G. (2010b). Differential effects of conjugated linoleic acid isomers on macrophage glycerophospholipid metabolism. Journal of Lipid Research, 51, 2686–2694.PubMedPubMedCentralCrossRefGoogle Scholar
  49. Edmonson, M. B., & Eickhoff, J. C. (2017). Weight gain and obesity in infants and young children exposed to prolonged antibiotic prophylaxis. JAMA Pediatrics, 171, 150–156.PubMedPubMedCentralCrossRefGoogle Scholar
  50. Erbay, E., Babaev, V. R., Mayers, J. R., Makowski, L., Charles, K. N., Snitow, M. E., et al. (2009). Reducing endoplasmic reticulum stress through a macrophage lipid chaperone alleviates atherosclerosis. Nature Medicine, 15, 1383–1391.PubMedPubMedCentralCrossRefGoogle Scholar
  51. Ernst, R., Ejsing, C. S., & Antonny, B. (2016). Homeoviscous adaptation and the regulation of membrane lipids. Journal of Molecular Biology, 428, 4776–4791.PubMedPubMedCentralCrossRefGoogle Scholar
  52. Everard, A., Belzer, C., Geurts, L., Ouwerkerk, J. P., Druart, C., Bindels, L. B., et al. (2013). Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proceedings of the National Academy of Sciences of the United States of America, 110, 9066–9071.PubMedPubMedCentralCrossRefGoogle Scholar
  53. Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., et al. (2016). Population-level analysis of gut microbiome variation. Science, 352, 560–564.PubMedPubMedCentralCrossRefGoogle Scholar
  54. Fava, F., Gitau, R., Griffin, B. A., Gibson, G. R., Tuohy, K. M., & Lovegrove, J. A. (2013). The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome ‘at-risk’ population. International Journal of Obesity, 37, 216–223.PubMedPubMedCentralCrossRefGoogle Scholar
  55. Fei, N., & Zhao, L. (2013). An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. The ISME Journal, 7, 880–884.PubMedPubMedCentralCrossRefGoogle Scholar
  56. Ferolla, S. M., Couto, C. A., Costa-Silva, L., Armiliato, G. N., Pereira, C. A., Martins, F. S., et al. (2016). Beneficial effect of synbiotic supplementation on hepatic steatosis and anthropometric parameters, but not on gut permeability in a population with nonalcoholic steatohepatitis. Nutrients, 8.Google Scholar
  57. Fleissner, C. K., Huebel, N., Abd El-Bary, M. M., Loh, G., Klaus, S., & Blaut, M. (2010). Absence of intestinal microbiota does not protect mice from diet-induced obesity. The British Journal of Nutrition, 104, 919–929.PubMedPubMedCentralCrossRefGoogle Scholar
  58. Foote, A. P., & Freetly, H. C. (2016). Effect of abomasal butyrate infusion on net nutrient flux across the portal-drained viscera and liver of growing lambs. Journal of Animal Science, 94, 2962–2972.PubMedPubMedCentralCrossRefGoogle Scholar
  59. Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., et al. (2015). Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature, 528, 262–266.PubMedPubMedCentralCrossRefGoogle Scholar
  60. Fuller, R. (1989). Probiotics in man and animals. The Journal of Applied Bacteriology, 66, 365–378.PubMedPubMedCentralCrossRefGoogle Scholar
  61. Furet, J. P., Kong, L. C., Tap, J., Poitou, C., Basdevant, A., Bouillot, J. L., et al. (2010). Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: Links with metabolic and low-grade inflammation markers. Diabetes, 59, 3049–3057.PubMedPubMedCentralCrossRefGoogle Scholar
  62. Garidou, L., Pomie, C., Klopp, P., Waget, A., Charpentier, J., Aloulou, M., et al. (2015). The gut microbiota regulates intestinal CD4 T cells expressing RORgammat and controls metabolic disease. Cell Metabolism, 22, 100–112.PubMedPubMedCentralCrossRefGoogle Scholar
  63. Glatz, J. F., Luiken, J. J., & Bonen, A. (2010). Membrane fatty acid transporters as regulators of lipid metabolism: Implications for metabolic disease. Physiological Reviews, 90, 367–417.PubMedPubMedCentralCrossRefGoogle Scholar
  64. Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., et al. (2014). Human genetics shape the gut microbiome. Cell, 159, 789–799.PubMedPubMedCentralCrossRefGoogle Scholar
  65. Grasset, E., Puel, A., Charpentier, J., Collet, X., Christensen, J. E., Terce, F., et al. (2017). A specific gut microbiota dysbiosis of type 2 diabetic mice induces GLP-1 resistance through an enteric NO-dependent and gut-brain axis mechanism. Cell Metabolism, 26, 278.PubMedPubMedCentralCrossRefGoogle Scholar
  66. Hamilton, M. K., Boudry, G., Lemay, D. G., & Raybould, H. E. (2015). Changes in intestinal barrier function and gut microbiota in high-fat diet-fed rats are dynamic and region dependent. American Journal of Physiology. Gastrointestinal and Liver Physiology, 308, G840–G851.PubMedPubMedCentralCrossRefGoogle Scholar
  67. Hansen, C. H., Krych, L., Nielsen, D. S., Vogensen, F. K., Hansen, L. H., Sorensen, S. J., et al. (2012). Early life treatment with vancomycin propagates Akkermansia muciniphila and reduces diabetes incidence in the NOD mouse. Diabetologia, 55, 2285–2294.PubMedPubMedCentralCrossRefGoogle Scholar
  68. Henao-Mejia, J., Elinav, E., Jin, C., Hao, L., Mehal, W. Z., Strowig, T., et al. (2012). Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature, 482, 179–185.PubMedPubMedCentralCrossRefGoogle Scholar
  69. Hersoug, L. G., Moller, P., & Loft, S. (2016). Gut microbiota-derived lipopolysaccharide uptake and trafficking to adipose tissue: Implications for inflammation and obesity. Obesity Reviews, 17, 297–312.PubMedPubMedCentralCrossRefGoogle Scholar
  70. Heymann, F., & Tacke, F. (2016). Immunology in the liver – From homeostasis to disease. Nature Reviews. Gastroenterology and Hepatology, 13, 88–110.PubMedPubMedCentralCrossRefGoogle Scholar
  71. Hodson, L., & Fielding, B. A. (2013). Stearoyl-CoA desaturase: Rogue or innocent bystander? Progress in Lipid Research, 52, 15–42.PubMedPubMedCentralCrossRefGoogle Scholar
  72. Horton, J. D., Goldstein, J. L., & Brown, M. S. (2002). SREBPs: Activators of the complete program of cholesterol and fatty acid synthesis in the liver. The Journal of Clinical Investigation, 109, 1125–1131.PubMedPubMedCentralCrossRefGoogle Scholar
  73. Hussain, M. M. (2014). Intestinal lipid absorption and lipoprotein formation. Current Opinion in Lipidology, 25, 200–206.PubMedPubMedCentralCrossRefGoogle Scholar
  74. Hussain, M. M., Leung, T. M., Zhou, L., & Abu-Merhi, S. (2013). Regulating intestinal function to reduce atherogenic lipoproteins. Clinical Lipidology, 8, 481–490.CrossRefGoogle Scholar
  75. Itoh, T., Fairall, L., Amin, K., Inaba, Y., Szanto, A., Balint, B. L., et al. (2008). Structural basis for the activation of PPARgamma by oxidized fatty acids. Nature Structural and Molecular Biology, 15, 924–931.PubMedPubMedCentralCrossRefGoogle Scholar
  76. Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., et al. (2009). Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell, 139, 485–498.PubMedPubMedCentralCrossRefGoogle Scholar
  77. Johnson, E. L., Heaver, S. L., Walters, W. A., & Ley, R. E. (2017). Microbiome and metabolic disease: Revisiting the bacterial phylum Bacteroidetes. The Journal of Molecular Medicine (Berlin), 95, 1–8.CrossRefGoogle Scholar
  78. Jumpertz, R., Le, D. S., Turnbaugh, P. J., Trinidad, C., Bogardus, C., Gordon, J. I., et al. (2011). Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. The American Journal of Clinical Nutrition, 94, 58–65.PubMedPubMedCentralCrossRefGoogle Scholar
  79. Kalliomaki, M., Collado, M. C., Salminen, S., & Isolauri, E. (2008). Early differences in fecal microbiota composition in children may predict overweight. The American Journal of Clinical Nutrition, 87, 534–538.PubMedPubMedCentralCrossRefGoogle Scholar
  80. Karl, J. P., Margolis, L. M., Madslien, E. H., Murphy, N. E., Castellani, J. W., Gundersen, Y., et al. (2017). Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiological stress. American Journal of Physiology. Gastrointestinal and Liver Physiology, 312, G559–G571.PubMedPubMedCentralCrossRefGoogle Scholar
  81. Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011). Human nutrition, the gut microbiome and the immune system. Nature, 474, 327–336.PubMedPubMedCentralCrossRefGoogle Scholar
  82. Kelley, N. S., Hubbard, N. E., & Erickson, K. L. (2007). Conjugated linoleic acid isomers and cancer. The Journal of Nutrition, 137, 2599–2607.PubMedPubMedCentralCrossRefGoogle Scholar
  83. Kimura, I., Ozawa, K., Inoue, D., Imamura, T., Kimura, K., Maeda, T., et al. (2013). The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43. Nature Communications, 4, 1829.PubMedPubMedCentralCrossRefGoogle Scholar
  84. Kishino, S., Takeuchi, M., Park, S. B., Hirata, A., Kitamura, N., Kunisawa, J., et al. (2013). Polyunsaturated fatty acid saturation by gut lactic acid bacteria affecting host lipid composition. Proceedings of the National Academy of Sciences of the United States of America, 110, 17808–17813.PubMedPubMedCentralCrossRefGoogle Scholar
  85. Kless, C., Muller, V. M., Schuppel, V. L., Lichtenegger, M., Rychlik, M., Daniel, H., et al. (2015). Diet-induced obesity causes metabolic impairment independent of alterations in gut barrier integrity. Molecular Nutrition and Food Research, 59, 968–978.PubMedPubMedCentralCrossRefGoogle Scholar
  86. Kootte, R. S., Levin, E., Salojarvi, J., Smits, L. P., Hartstra, A. V., Udayappan, S. D., et al. (2017). Improvement of insulin sensitivity after lean donor feces in metabolic syndrome is driven by baseline intestinal microbiota composition. Cell Metabolism, 26, 611–619 e616.PubMedPubMedCentralCrossRefGoogle Scholar
  87. Kovatcheva-Datchary, P., Nilsson, A., Akrami, R., Lee, Y. S., De Vadder, F., Arora, T., et al. (2015). Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of prevotella. Cell Metabolism, 22, 971–982.PubMedPubMedCentralCrossRefGoogle Scholar
  88. Kubeck, R., Bonet-Ripoll, C., Hoffmann, C., Walker, A., Muller, V. M., Schuppel, V. L., et al. (2016). Dietary fat and gut microbiota interactions determine diet-induced obesity in mice. Molecular Metabolism, 5, 1162–1174.PubMedPubMedCentralCrossRefGoogle Scholar
  89. Kuhnt, K., Wagner, A., Kraft, J., Basu, S., & Jahreis, G. (2006). Dietary supplementation with 11trans- and 12trans-18:1 and oxidative stress in humans. The American Journal of Clinical Nutrition, 84, 981–988.PubMedPubMedCentralCrossRefGoogle Scholar
  90. Kumar, M., Nagpal, R., Kumar, R., Hemalatha, R., Verma, V., Kumar, A., et al. (2012). Cholesterol-lowering probiotics as potential biotherapeutics for metabolic diseases. Experimental Diabetes Research, 2012, 902917.PubMedPubMedCentralCrossRefGoogle Scholar
  91. Lagkouvardos, I., Overmann, J., & Clavel, T. (2017). Cultured microbes represent a substantial fraction of the human and mouse gut microbiota. Gut Microbes, 8(5), 493–503.PubMedPubMedCentralCrossRefGoogle Scholar
  92. Lahtinen, S. J., Davis, E., & Ouwehand, A. C. (2012). Lactobacillus species causing obesity in humans: Where is the evidence? Beneficial Microbes, 3, 171–174.PubMedCrossRefGoogle Scholar
  93. Lambert, J. E., Parnell, J. A., Eksteen, B., Raman, M., Bomhof, M. R., Rioux, K. P., et al. (2015). Gut microbiota manipulation with prebiotics in patients with non-alcoholic fatty liver disease: A randomized controlled trial protocol. BMC Gastroenterology, 15, 169.PubMedPubMedCentralCrossRefGoogle Scholar
  94. Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., et al. (2013). Richness of human gut microbiome correlates with metabolic markers. Nature, 500, 541–546.PubMedCrossRefGoogle Scholar
  95. Le Roy, T., Llopis, M., Lepage, P., Bruneau, A., Rabot, S., Bevilacqua, C., et al. (2013). Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice. Gut, 62, 1787–1794.PubMedPubMedCentralCrossRefGoogle Scholar
  96. Lee, T., Clavel, T., Smirnov, K., Schmidt, A., Lagkouvardos, I., Walker, A., et al. (2017). Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut, 66, 863–871.PubMedPubMedCentralCrossRefGoogle Scholar
  97. Lefebvre, P., Cariou, B., Lien, F., Kuipers, F., & Staels, B. (2009). Role of bile acids and bile acid receptors in metabolic regulation. Physiological Reviews, 89, 147–191.PubMedPubMedCentralCrossRefGoogle Scholar
  98. Ley, R. E., Backhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005). Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences of the United States of America, 102, 11070–11075.PubMedPubMedCentralCrossRefGoogle Scholar
  99. Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006). Microbial ecology: Human gut microbes associated with obesity. Nature, 444, 1022–1023.PubMedPubMedCentralCrossRefGoogle Scholar
  100. Liebisch, G., Ejsing, C. S., & Ekroos, K. (2015). Identification and annotation of lipid species in metabolomics studies need improvement. Clinical Chemistry, 61, 1542–1544.PubMedCrossRefGoogle Scholar
  101. Liebisch, G., Ekroos, K., Hermansson, M., & Ejsing, C. S. (2017). Reporting of lipidomics data should be standardized. Biochimica et Biophysica Acta, 1862, 747–751.PubMedCrossRefGoogle Scholar
  102. Liou, A. P., Paziuk, M., Luevano, J. M., Jr., Machineni, S., Turnbaugh, P. J., & Kaplan, L. M. (2013). Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Science Translational Medicine, 5, 178ra141.CrossRefGoogle Scholar
  103. Louis, P., & Flint, H. J. (2017). Formation of propionate and butyrate by the human colonic microbiota. Environmental Microbiology, 19, 29–41.PubMedCrossRefGoogle Scholar
  104. Ma, H., Sales, V. M., Wolf, A. R., Subramanian, S., Matthews, T. J., Chen, M., et al. (2017). Attenuated effects of bile acids on glucose metabolism and insulin sensitivity in a male mouse model of prenatal undernutrition. Endocrinology, 158, 2441–2452.PubMedPubMedCentralCrossRefGoogle Scholar
  105. Mardinoglu, A., Wu, H., Bjornson, E., Zhang, C., Hakkarainen, A., Rasanen, S. M., et al. (2018). An integrated understanding of the rapid metabolic benefits of a carbohydrate-restricted diet on hepatic steatosis in humans. Cell Metabolism, 27(3), 559–571.e5.PubMedCrossRefGoogle Scholar
  106. Martinez, I., Stegen, J. C., Maldonado-Gomez, M. X., Eren, A. M., Siba, P. M., Greenhill, A. R., et al. (2015). The gut microbiota of rural papua new guineans: Composition, diversity patterns, and ecological processes. Cell Reports, 11, 527–538.PubMedCrossRefGoogle Scholar
  107. Matis, G., Kulcsar, A., Turowski, V., Febel, H., Neogrady, Z., & Huber, K. (2015). Effects of oral butyrate application on insulin signaling in various tissues of chickens. Domestic Animal Endocrinology, 50, 26–31.PubMedCrossRefGoogle Scholar
  108. Matsuzaka, T., Shimano, H., Yahagi, N., Kato, T., Atsumi, A., Yamamoto, T., et al. (2007). Crucial role of a long-chain fatty acid elongase, Elovl6, in obesity-induced insulin resistance. Nature Medicine, 13, 1193–1202.PubMedCrossRefGoogle Scholar
  109. McIntosh, F. M., Shingfield, K. J., Devillard, E., Russell, W. R., & Wallace, R. J. (2009). Mechanism of conjugated linoleic acid and vaccenic acid formation in human faecal suspensions and pure cultures of intestinal bacteria. Microbiology, 155, 285–294.PubMedCrossRefGoogle Scholar
  110. Million, M., Maraninchi, M., Henry, M., Armougom, F., Richet, H., Carrieri, P., et al. (2012). Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii. International Journal of Obesity, 36, 817–825.PubMedPubMedCentralCrossRefGoogle Scholar
  111. Mitchell, P. L., & McLeod, R. S. (2008). Conjugated linoleic acid and atherosclerosis: Studies in animal models. Biochemistry and Cell Biology, 86, 293–301.PubMedPubMedCentralCrossRefGoogle Scholar
  112. Miyazaki, M., & Ntambi, J. M. (2003). Role of stearoyl-coenzyme A desaturase in lipid metabolism. Prostaglandins, Leukotrienes, and Essential Fatty Acids, 68, 113–121.PubMedPubMedCentralCrossRefGoogle Scholar
  113. Moller, D. E. (2001). New drug targets for type 2 diabetes and the metabolic syndrome. Nature, 414, 821–827.PubMedPubMedCentralCrossRefGoogle Scholar
  114. Moya-Camarena, S. Y., Vanden Heuvel, J. P., Blanchard, S. G., Leesnitzer, L. A., & Belury, M. A. (1999). Conjugated linoleic acid is a potent naturally occurring ligand and activator of PPARalpha. Journal of Lipid Research, 40, 1426–1433.PubMedPubMedCentralGoogle Scholar
  115. Mudaliar, S., Henry, R. R., Sanyal, A. J., Morrow, L., Marschall, H. U., Kipnes, M., et al. (2013). Efficacy and safety of the farnesoid X receptor agonist obeticholic acid in patients with type 2 diabetes and nonalcoholic fatty liver disease. Gastroenterology, 145, 574–582 e571.PubMedPubMedCentralCrossRefGoogle Scholar
  116. Mueller, N. T., Whyatt, R., Hoepner, L., Oberfield, S., Dominguez-Bello, M. G., Widen, E. M., et al. (2015). Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. International Journal of Obesity, 39, 665–670.PubMedPubMedCentralCrossRefGoogle Scholar
  117. Muller, V. M., Zietek, T., Rohm, F., Fiamoncini, J., Lagkouvardos, I., Haller, D., et al. (2016). Gut barrier impairment by high-fat diet in mice depends on housing conditions. Molecular Nutrition and Food Research, 60, 897–908.PubMedPubMedCentralCrossRefGoogle Scholar
  118. Nishizawa, Y., Imaizumi, T., Tanishita, H., Yano, I., Kawai, Y., & Mormii, H. (1988). Relationship of fat deposition and intestinal microflora in VMH rats. International Journal of Obesity, 12, 103–110.PubMedPubMedCentralGoogle Scholar
  119. Ogasawara, Y., Itakura, E., Kono, N., Mizushima, N., Arai, H., Nara, A., et al. (2014). Stearoyl-CoA desaturase 1 activity is required for autophagosome formation. The Journal of Biological Chemistry, 289, 23938–23950.PubMedPubMedCentralCrossRefGoogle Scholar
  120. Ott, B., Skurk, T., Hastreiter, L., Lagkouvardos, I., Fischer, S., Buttner, J., et al. (2017). Effect of caloric restriction on gut permeability, inflammation markers, and fecal microbiota in obese women. Scientific Reports, 7, 11955.PubMedPubMedCentralCrossRefGoogle Scholar
  121. Paramsothy, S., Kamm, M. A., Kaakoush, N. O., Walsh, A. J., van den Bogaerde, J., Samuel, D., et al. (2017). Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: A randomised placebo-controlled trial. Lancet, 389, 1218–1228.PubMedPubMedCentralCrossRefGoogle Scholar
  122. Parseus, A., Sommer, N., Sommer, F., Caesar, R., Molinaro, A., Stahlman, M., et al. (2017). Microbiota-induced obesity requires farnesoid X receptor. Gut, 66, 429–437.PubMedPubMedCentralCrossRefGoogle Scholar
  123. Pascal, V., Pozuelo, M., Borruel, N., Casellas, F., Campos, D., Santiago, A., et al. (2017). A microbial signature for Crohn’s disease. Gut, 66, 813–822.PubMedPubMedCentralCrossRefGoogle Scholar
  124. Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A., et al. (2016). Human gut microbes impact host serum metabolome and insulin sensitivity. Nature, 535, 376–381.PubMedPubMedCentralCrossRefGoogle Scholar
  125. Pereira, S. L., Leonard, A. E., & Mukerji, P. (2003). Recent advances in the study of fatty acid desaturases from animals and lower eukaryotes. Prostaglandins, Leukotrienes, and Essential Fatty Acids, 68, 97–106.PubMedPubMedCentralCrossRefGoogle Scholar
  126. Perez-Munoz, M. E., Arrieta, M. C., Ramer-Tait, A. E., & Walter, J. (2017). A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: Implications for research on the pioneer infant microbiome. Microbiome, 5, 48.PubMedPubMedCentralCrossRefGoogle Scholar
  127. Peterson, L. W., & Artis, D. (2014). Intestinal epithelial cells: Regulators of barrier function and immune homeostasis. Nature Reviews. Immunology, 14, 141–153.PubMedPubMedCentralCrossRefGoogle Scholar
  128. Pinot, M., Vanni, S., Pagnotta, S., Lacas-Gervais, S., Payet, L. A., Ferreira, T., et al. (2014). Lipid cell biology. Polyunsaturated phospholipids facilitate membrane deformation and fission by endocytic proteins. Science, 345, 693–697.PubMedPubMedCentralCrossRefGoogle Scholar
  129. Pleasants, J. R. (1968). Characteristics of the germ-free animal. In M. E. Coates, H. A. Gordon, & B. S. Wostmann (Eds.), The germ-free animal in research. London and New York: Academic Press.Google Scholar
  130. Plovier, H., Everard, A., Druart, C., Depommier, C., Van Hul, M., Geurts, L., et al. (2017). A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice. Nature Medicine, 23, 107–113.PubMedPubMedCentralCrossRefGoogle Scholar
  131. Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., et al. (2012). A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature, 490, 55–60.PubMedPubMedCentralCrossRefGoogle Scholar
  132. Reijnders, D., Goossens, G. H., Hermes, G. D., Neis, E. P., van der Beek, C. M., Most, J., et al. (2016). Effects of gut microbiota manipulation by antibiotics on host metabolism in obese humans: A randomized double-blind placebo-controlled trial. Cell Metabolism, 24, 63–74.PubMedPubMedCentralCrossRefGoogle Scholar
  133. Rettger, L. F. (1915). The influence of milk feeding on mortality and growth, and on the character of the intestinal flora. The Journal of Experimental Medicine, 21, 365–388.PubMedPubMedCentralCrossRefGoogle Scholar
  134. Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., et al. (2013). Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science, 341, 1241214.PubMedPubMedCentralCrossRefGoogle Scholar
  135. Ridlon, J. M., Kang, D. J., & Hylemon, P. B. (2006). Bile salt biotransformations by human intestinal bacteria. Journal of Lipid Research, 47, 241–259.PubMedPubMedCentralCrossRefGoogle Scholar
  136. Roediger, W. E. (1980). Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man. Gut, 21, 793–798.PubMedPubMedCentralCrossRefGoogle Scholar
  137. Russo, F., Linsalata, M., Clemente, C., Chiloiro, M., Orlando, A., Marconi, E., et al. (2012). Inulin-enriched pasta improves intestinal permeability and modifies the circulating levels of zonulin and glucagon-like peptide 2 in healthy young volunteers. Nutrition Research, 32, 940–946.PubMedPubMedCentralCrossRefGoogle Scholar
  138. Saari, A., Virta, L. J., Sankilampi, U., Dunkel, L., & Saxen, H. (2015). Antibiotic exposure in infancy and risk of being overweight in the first 24 months of life. Pediatrics, 135, 617–626.PubMedPubMedCentralCrossRefGoogle Scholar
  139. Santacruz, A., Collado, M. C., Garcia-Valdes, L., Segura, M. T., Martin-Lagos, J. A., Anjos, T., et al. (2010). Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. The British Journal of Nutrition, 104, 83–92.PubMedPubMedCentralCrossRefGoogle Scholar
  140. Sayin, S. I., Wahlstrom, A., Felin, J., Jantti, S., Marschall, H. U., Bamberg, K., et al. (2013). Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metabolism, 17, 225–235.PubMedPubMedCentralCrossRefGoogle Scholar
  141. Schmitz, G., & Ecker, J. (2008). The opposing effects of n-3 and n-6 fatty acids. Progress in Lipid Research, 47, 147–155.PubMedPubMedCentralCrossRefGoogle Scholar
  142. Schwarzer, M., Makki, K., Storelli, G., Machuca-Gayet, I., Srutkova, D., Hermanova, P., et al. (2016). Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition. Science, 351, 854–857.PubMedPubMedCentralCrossRefGoogle Scholar
  143. Schwiertz, A., Taras, D., Schafer, K., Beijer, S., Bos, N. A., Donus, C., et al. (2010). Microbiota and SCFA in lean and overweight healthy subjects. Obesity (Silver Spring), 18, 190–195.CrossRefGoogle Scholar
  144. Semova, I., Carten, J. D., Stombaugh, J., Mackey, L. C., Knight, R., Farber, S. A., et al. (2012). Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host and Microbe, 12, 277–288.PubMedPubMedCentralCrossRefGoogle Scholar
  145. Singh, V., Chassaing, B., Zhang, L., San Yeoh, B., Xiao, X., Kumar, M., et al. (2015). Microbiota-dependent hepatic lipogenesis mediated by stearoyl CoA desaturase 1 (SCD1) promotes metabolic syndrome in TLR5-deficient mice. Cell Metabolism, 22, 983–996.PubMedPubMedCentralCrossRefGoogle Scholar
  146. Smith, S., Witkowski, A., & Joshi, A. K. (2003). Structural and functional organization of the animal fatty acid synthase. Progress in Lipid Research, 42, 289–317.PubMedPubMedCentralCrossRefGoogle Scholar
  147. Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016). Diet-induced extinctions in the gut microbiota compound over generations. Nature, 529, 212–215.PubMedPubMedCentralCrossRefGoogle Scholar
  148. Steimle, A., Autenrieth, I. B., & Frick, J. S. (2016). Structure and function: Lipid A modifications in commensals and pathogens. International Journal of Medical Microbiology, 306, 290–301.PubMedPubMedCentralCrossRefGoogle Scholar
  149. Suarez-Zamorano, N., Fabbiano, S., Chevalier, C., Stojanovic, O., Colin, D. J., Stevanovic, A., et al. (2015). Microbiota depletion promotes browning of white adipose tissue and reduces obesity. Nature Medicine, 21, 1497–1501.PubMedPubMedCentralCrossRefGoogle Scholar
  150. Sze, M. A., & Schloss, P. D. (2016). Looking for a signal in the noise: Revisiting obesity and the microbiome. MBio, 7, e01018–e01016.PubMedPubMedCentralCrossRefGoogle Scholar
  151. Teixeira, T. F., Souza, N. C., Chiarello, P. G., Franceschini, S. C., Bressan, J., Ferreira, C. L., et al. (2012). Intestinal permeability parameters in obese patients are correlated with metabolic syndrome risk factors. Clinical Nutrition, 31, 735–740.PubMedPubMedCentralCrossRefGoogle Scholar
  152. Thomas, C., Pellicciari, R., Pruzanski, M., Auwerx, J., & Schoonjans, K. (2008). Targeting bile-acid signalling for metabolic diseases. Nature Reviews. Drug Discovery, 7, 678–693.PubMedPubMedCentralCrossRefGoogle Scholar
  153. Thorasin, T., Hoyles, L., & McCartney, A. L. (2015). Dynamics and diversity of the ‘Atopobium cluster’ in the human faecal microbiota, and phenotypic characterization of ‘Atopobium cluster’ isolates. Microbiology, 161, 565–579.PubMedPubMedCentralCrossRefGoogle Scholar
  154. Torres-Fuentes, C., Schellekens, H., Dinan, T. G., & Cryan, J. F. (2017). The microbiota-gut-brain axis in obesity. Lancet Gastroenterology and Hepatology, 2, 747–756.PubMedPubMedCentralCrossRefGoogle Scholar
  155. Tremaroli, V., Karlsson, F., Werling, M., Stahlman, M., Kovatcheva-Datchary, P., Olbers, T., et al. (2015). Roux-en-Y gastric bypass and vertical banded gastroplasty induce long-term changes on the human gut microbiome contributing to fat mass regulation. Cell Metabolism, 22, 228–238.PubMedPubMedCentralCrossRefGoogle Scholar
  156. Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444, 1027–1031.PubMedPubMedCentralCrossRefGoogle Scholar
  157. Turnbaugh, P. J., Backhed, F., Fulton, L., & Gordon, J. I. (2008). Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host and Microbe, 3, 213–223.PubMedPubMedCentralCrossRefGoogle Scholar
  158. Ussar, S., Griffin, N. W., Bezy, O., Fujisaka, S., Vienberg, S., Softic, S., et al. (2015). Interactions between gut microbiota, host genetics and diet modulate the predisposition to obesity and metabolic syndrome. Cell Metabolism, 22, 516–530.PubMedPubMedCentralCrossRefGoogle Scholar
  159. van Meer, G., Voelker, D. R., & Feigenson, G. W. (2008). Membrane lipids: Where they are and how they behave. Nature Reviews. Molecular Cell Biology, 9, 112–124.PubMedPubMedCentralCrossRefGoogle Scholar
  160. van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., et al. (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. The New England Journal of Medicine, 368, 407–415.PubMedPubMedCentralCrossRefGoogle Scholar
  161. Velagapudi, V. R., Hezaveh, R., Reigstad, C. S., Gopalacharyulu, P., Yetukuri, L., Islam, S., et al. (2010). The gut microbiota modulates host energy and lipid metabolism in mice. Journal of Lipid Research, 51, 1101–1112.PubMedPubMedCentralCrossRefGoogle Scholar
  162. Vijay-Kumar, M., Aitken, J. D., Carvalho, F. A., Cullender, T. C., Mwangi, S., Srinivasan, S., et al. (2010). Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science, 328, 228–231.PubMedPubMedCentralCrossRefGoogle Scholar
  163. Vrieze, A., Van Nood, E., Holleman, F., Salojarvi, J., Kootte, R. S., Bartelsman, J. F., et al. (2012). Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology, 143, 913–916 e917.PubMedPubMedCentralCrossRefGoogle Scholar
  164. Wagner, V. E., Dey, N., Guruge, J., Hsiao, A., Ahern, P. P., Semenkovich, N. P., et al. (2016). Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition. Science Translational Medicine, 8, 366ra164.PubMedPubMedCentralCrossRefGoogle Scholar
  165. Wall, R., Ross, R. P., Shanahan, F., O’Mahony, L., O’Mahony, C., Coakley, M., et al. (2009). Metabolic activity of the enteric microbiota influences the fatty acid composition of murine and porcine liver and adipose tissues. The American Journal of Clinical Nutrition, 89, 1393–1401.PubMedPubMedCentralCrossRefGoogle Scholar
  166. Wallace, R. J., McKain, N., Shingfield, K. J., & Devillard, E. (2007). Isomers of conjugated linoleic acids are synthesized via different mechanisms in ruminal digesta and bacteria. Journal of Lipid Research, 48, 2247–2254.PubMedPubMedCentralCrossRefGoogle Scholar
  167. Wang, Z., Klipfell, E., Bennett, B. J., Koeth, R., Levison, B. S., Dugar, B., et al. (2011). Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature, 472, 57–63.PubMedPubMedCentralCrossRefGoogle Scholar
  168. Wang, X., Ota, N., Manzanillo, P., Kates, L., Zavala-Solorio, J., Eidenschenk, C., et al. (2014). Interleukin-22 alleviates metabolic disorders and restores mucosal immunity in diabetes. Nature, 514, 237–241.PubMedPubMedCentralCrossRefGoogle Scholar
  169. Wenk, M. R. (2010). Lipidomics: New tools and applications. Cell, 143, 888–895.PubMedPubMedCentralCrossRefGoogle Scholar
  170. Wostmann, B. S. (1975). Nutrition and metabolism of the germfree mammal. World Review of Nutrition and Dietetics, 22, 40–92.PubMedPubMedCentralCrossRefGoogle Scholar
  171. Woting, A., Pfeiffer, N., Loh, G., Klaus, S., & Blaut, M. (2014). Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models. MBio, 5, e01530-01514.CrossRefGoogle Scholar
  172. Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y. Y., Keilbaugh, S. A., et al. (2011). Linking long-term dietary patterns with gut microbial enterotypes. Science, 334, 105–108.PubMedPubMedCentralCrossRefGoogle Scholar
  173. Wu, H., Esteve, E., Tremaroli, V., Khan, M. T., Caesar, R., Manneras-Holm, L., et al. (2017). Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug. Nature Medicine, 23, 850–858.PubMedPubMedCentralCrossRefGoogle Scholar
  174. Xiao, S., Fei, N., Pang, X., Shen, J., Wang, L., Zhang, B., et al. (2014). A gut microbiota-targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome. FEMS Microbiology Ecology, 87, 357–367.PubMedPubMedCentralCrossRefGoogle Scholar
  175. Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., et al. (2012). Human gut microbiome viewed across age and geography. Nature, 486, 222–227.PubMedPubMedCentralCrossRefGoogle Scholar
  176. Zeevi, D., Korem, T., Zmora, N., Israeli, D., Rothschild, D., Weinberger, A., et al. (2015). Personalized nutrition by prediction of glycemic responses. Cell, 163, 1079–1094.PubMedCrossRefGoogle Scholar
  177. Zelante, T., Iannitti, R. G., Cunha, C., De Luca, A., Giovannini, G., Pieraccini, G., et al. (2013). Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity, 39, 372–385.CrossRefPubMedGoogle Scholar
  178. Zhou, D., Pan, Q., Xin, F. Z., Zhang, R. N., He, C. X., Chen, G. Y., et al. (2017). Sodium butyrate attenuates high-fat diet-induced steatohepatitis in mice by improving gut microbiota and gastrointestinal barrier. World Journal of Gastroenterology, 23, 60–75.PubMedPubMedCentralCrossRefGoogle Scholar
  179. Zietak, M., Kovatcheva-Datchary, P., Markiewicz, L. H., Stahlman, M., Kozak, L. P., & Backhed, F. (2016). Altered microbiota contributes to reduced diet-induced obesity upon cold exposure. Cell Metabolism, 23, 1216–1223.PubMedPubMedCentralCrossRefGoogle Scholar
  180. Zmora, N., Bashiardes, S., Levy, M., & Elinav, E. (2017). The role of the immune system in metabolic health and disease. Cell Metabolism, 25, 506–521.PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Functional Microbiome Research GroupInstitute of Medical Microbiology, University Hospital of RWTHAachenGermany
  2. 2.Department of Physiology of Human Nutrition, School of Life Sciences WeihenstephanTechnical University of MunichFreisingGermany

Personalised recommendations