Home LiteratureArticle Details
PMID: 27383980 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Review

Diet-microbiota interactions as moderators of human metabolism.

Nature ·Vol. 535 ·No. 7610 ·2016-00-07 ·Pages 56-64

Sonnenburg JL, Bäckhed F

Abstract

It is widely accepted that obesity and associated metabolic diseases, including type 2 diabetes, are intimately linked to diet. However, the gut microbiota has also become a focus for research at the intersection of diet and metabolic health. Mechanisms that link the gut microbiota with obesity are coming to light through a powerful combination of translation-focused animal models and studies in humans. A body of knowledge is accumulating that points to the gut microbiota as a mediator of dietary impact on the host metabolic status. Efforts are focusing on the establishment of causal relationships in people and the prospect of therapeutic interventions such as personalized nutrition.

MeSH Terms
Animals Diabetes Mellitus, Type 2/diet therapy,metabolism,microbiology Diet Fatty Acids/metabolism Gastrointestinal Microbiome/physiology Humans Inflammation/diet therapy,metabolism,microbiology Metabolic Diseases/diet therapy,metabolism,microbiology Metabolism Obesity/diet therapy,metabolism,microbiology Precision Medicine/methods Signal Transduction
Chemicals
Fatty Acids
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Sonnenburg Justin L
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.
Bäckhed Fredrik
Wallenberg Laboratory for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden. | Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
References (127)
127 references, click to expand
  1. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43.
    Nature. 2009 Oct 29;461(7268):1282-6 PMID: 19865172
  2. Linking long-term dietary patterns with gut microbial enterotypes.
    Science. 2011 Oct 7;334(6052):105-8 PMID: 21885731
  3. CD8+ effector T cells contribute to macrophage recruitment and adipose tissue inflammation in obesity.
    Nat Med. 2009 Aug;15(8):914-20 PMID: 19633658
  4. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells.
    Nature. 2013 Dec 19;504(7480):446-50 PMID: 24226770
  5. Biodiversity loss and its impact on humanity.
    Nature. 2012 Jun 06;486(7401):59-67 PMID: 22678280
  6. Effects of lactulose and other laxatives on ileal and colonic pH as measured by a radiotelemetry device.
    Gut. 1974 Dec;15(12):999-1004 PMID: 4448417
  7. Human genetics shape the gut microbiome.
    Cell. 2014 Nov 6;159(4):789-99 PMID: 25417156
  8. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice.
    Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):979-84 PMID: 17210919
  9. Human symbionts inject and neutralize antibacterial toxins to persist in the gut.
    Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3639-44 PMID: 26957597
  10. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome.
    Nature. 2015 Mar 5;519(7541):92-6 PMID: 25731162
  11. HUMAN MICROBIOTA. Small molecules from the human microbiota.
    Science. 2015 Jul 24;349(6246):1254766 PMID: 26206939
  12. Personalized Nutrition by Prediction of Glycemic Responses.
    Cell. 2015 Nov 19;163(5):1079-94 PMID: 26590418
  13. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor.
    Science. 2013 Feb 1;339(6119):548-54 PMID: 23363771
  14. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis.
    Nat Med. 2014 Feb;20(2):159-66 PMID: 24390308
  15. Microbiota-induced obesity requires farnesoid X receptor.
    Gut. 2017 Mar;66(3):429-437 PMID: 26740296
  16. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome.
    Cell Host Microbe. 2008 Apr 17;3(4):213-23 PMID: 18407065
  17. Serum indoxyl sulfate is associated with vascular disease and mortality in chronic kidney disease patients.
    Clin J Am Soc Nephrol. 2009 Oct;4(10):1551-8 PMID: 19696217
  18. The gut microbiota as an environmental factor that regulates fat storage.
    Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15718-23 PMID: 15505215
  19. Dominant and diet-responsive groups of bacteria within the human colonic microbiota.
    ISME J. 2011 Feb;5(2):220-30 PMID: 20686513
  20. Uremic solutes from colon microbes.
    Kidney Int. 2012 May;81(10):949-54 PMID: 22318422
  21. p-Cresol and cardiovascular risk in mild-to-moderate kidney disease.
    Clin J Am Soc Nephrol. 2010 Jul;5(7):1182-9 PMID: 20430946
  22. A metagenome-wide association study of gut microbiota in type 2 diabetes.
    Nature. 2012 Oct 4;490(7418):55-60 PMID: 23023125
  23. The effect of microbial colonization on the host proteome varies by gastrointestinal location.
    ISME J. 2016 May;10 (5):1170-81 PMID: 26574685
  24. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation.
    Nature. 2013 Dec 19;504(7480):451-5 PMID: 24226773
  25. Gut-derived lipopolysaccharide augments adipose macrophage accumulation but is not essential for impaired glucose or insulin tolerance in mice.
    Gut. 2012 Dec;61(12):1701-7 PMID: 22535377
  26. Artificial sweeteners induce glucose intolerance by altering the gut microbiota.
    Nature. 2014 Oct 9;514(7521):181-6 PMID: 25231862
  27. 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. 2005 Jul;71(7):3692-700 PMID: 16000778
  28. Intestinal farnesoid X receptor signaling promotes nonalcoholic fatty liver disease.
    J Clin Invest. 2015 Jan;125(1):386-402 PMID: 25500885
  29. The convergence of carbohydrate active gene repertoires in human gut microbes.
    Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15076-81 PMID: 18806222
  30. Antibiotics in early life alter the murine colonic microbiome and adiposity.
    Nature. 2012 Aug 30;488(7413):621-6 PMID: 22914093
  31. Host remodeling of the gut microbiome and metabolic changes during pregnancy.
    Cell. 2012 Aug 3;150(3):470-80 PMID: 22863002
  32. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.
    Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6 PMID: 20679230
  33. Richness of human gut microbiome correlates with metabolic markers.
    Nature. 2013 Aug 29;500(7464):541-6 PMID: 23985870
  34. Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41.
    Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16767-72 PMID: 18931303
  35. The Gut Microbiota Regulates Intestinal CD4 T Cells Expressing RORγt and Controls Metabolic Disease.
    Cell Metab. 2015 Jul 7;22(1):100-12 PMID: 26154056
  36. A high-fat meal induces low-grade endotoxemia: evidence of a novel mechanism of postprandial inflammation.
    Am J Clin Nutr. 2007 Nov;86(5):1286-92 PMID: 17991637
  37. Genetic deficiency and pharmacological stabilization of mast cells reduce diet-induced obesity and diabetes in mice.
    Nat Med. 2009 Aug;15(8):940-5 PMID: 19633655
  38. Obesity alters gut microbial ecology.
    Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11070-5 PMID: 16033867
  39. Absence of intestinal microbiota does not protect mice from diet-induced obesity.
    Br J Nutr. 2010 Sep;104(6):919-29 PMID: 20441670
  40. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk.
    N Engl J Med. 2013 Apr 25;368(17):1575-84 PMID: 23614584
  41. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome.
    Gastroenterology. 2012 Oct;143(4):913-6.e7 PMID: 22728514
  42. Gut microbiota from twins discordant for obesity modulate metabolism in mice.
    Science. 2013 Sep 6;341(6150):1241214 PMID: 24009397
  43. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist.
    Cell Metab. 2013 Feb 5;17 (2):225-35 PMID: 23395169
  44. An obesity-associated gut microbiome with increased capacity for energy harvest.
    Nature. 2006 Dec 21;444(7122):1027-31 PMID: 17183312
  45. Structure, function and diversity of the healthy human microbiome.
    Nature. 2012 Jun 13;486(7402):207-14 PMID: 22699609
  46. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans.
    Science. 2011 May 20;332(6032):970-4 PMID: 21596990
  47. Human gut microbiome viewed across age and geography.
    Nature. 2012 May 09;486(7402):222-7 PMID: 22699611
  48. Duodenal infusion of donor feces for recurrent Clostridium difficile.
    N Engl J Med. 2013 Jan 31;368(5):407-15 PMID: 23323867
  49. High-fat diet: bacteria interactions promote intestinal inflammation which precedes and correlates with obesity and insulin resistance in mouse.
    PLoS One. 2010 Aug 16;5(8):e12191 PMID: 20808947
  50. Microbiota and SCFA in lean and overweight healthy subjects.
    Obesity (Silver Spring). 2010 Jan;18(1):190-5 PMID: 19498350
  51. Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis.
    Cell. 2015 Dec 17;163(7):1585-95 PMID: 26687352
  52. Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites.
    Nat Commun. 2015 Jun 23;6:7320 PMID: 26102221
  53. Bacterial colonization factors control specificity and stability of the gut microbiota.
    Nature. 2013 Sep 19;501(7467):426-9 PMID: 23955152
  54. Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men.
    ISME J. 2014 Nov;8(11):2218-30 PMID: 24763370
  55. Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-like receptor 4.
    Immunity. 2014 Aug 21;41(2):296-310 PMID: 25065623
  56. Inhibition of histone deacetylase activity by butyrate.
    J Nutr. 2003 Jul;133(7 Suppl):2485S-2493S PMID: 12840228
  57. Chronic inflammation in fat plays a crucial role in the development of obesity-related insulin resistance.
    J Clin Invest. 2003 Dec;112(12):1821-30 PMID: 14679177
  58. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice.
    Nature. 2012 Jul 5;487(7405):104-8 PMID: 22722865
  59. Dyslipidemia in type 2 diabetes mellitus.
    Nat Clin Pract Endocrinol Metab. 2009 Mar;5(3):150-9 PMID: 19229235
  60. Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.
    PLoS One. 2012;7(6):e37818 PMID: 22719852
  61. Evolution of mammals and their gut microbes.
    Science. 2008 Jun 20;320(5883):1647-51 PMID: 18497261
  62. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota.
    Nature. 2010 Apr 8;464(7290):908-12 PMID: 20376150
  63. Childhood overweight after establishment of the gut microbiota: the role of delivery mode, pre-pregnancy weight and early administration of antibiotics.
    Int J Obes (Lond). 2011 Apr;35(4):522-9 PMID: 21386800
  64. Dietary intervention impact on gut microbial gene richness.
    Nature. 2013 Aug 29;500(7464):585-8 PMID: 23985875
  65. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates.
    Cell Metab. 2014 Nov 4;20(5):779-86 PMID: 25156449
  66. Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters.
    Nat Med. 2009 Aug;15(8):930-9 PMID: 19633656
  67. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders.
    Cell. 2013 Dec 19;155(7):1451-63 PMID: 24315484
  68. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis.
    Science. 2013 Aug 2;341(6145):569-73 PMID: 23828891
  69. Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella.
    Cell Metab. 2015 Dec 1;22(6):971-82 PMID: 26552345
  70. Microbiome remodelling leads to inhibition of intestinal farnesoid X receptor signalling and decreased obesity.
    Nat Commun. 2013;4:2384 PMID: 24064762
  71. p-Cresyl sulfate promotes insulin resistance associated with CKD.
    J Am Soc Nephrol. 2013 Jan;24(1):88-99 PMID: 23274953
  72. Obesity is associated with macrophage accumulation in adipose tissue.
    J Clin Invest. 2003 Dec;112(12):1796-808 PMID: 14679176
  73. Bariatric surgery and long-term cardiovascular events.
    JAMA. 2012 Jan 4;307(1):56-65 PMID: 22215166
  74. Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota.
    Curr Biol. 2015 Jun 29;25(13):1682-93 PMID: 25981789
  75. An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses.
    Cell. 2015 Oct 8;163(2):381-93 PMID: 26411290
  76. Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity.
    Sci Transl Med. 2013 Mar 27;5(178):178ra41 PMID: 23536013
  77. Country-specific antibiotic use practices impact the human gut resistome.
    Genome Res. 2013 Jul;23(7):1163-9 PMID: 23568836
  78. The enzymes, regulation, and genetics of bile acid synthesis.
    Annu Rev Biochem. 2003;72:137-74 PMID: 12543708
  79. Quantitative Imaging of Gut Microbiota Spatial Organization.
    Cell Host Microbe. 2015 Oct 14;18(4):478-88 PMID: 26439864
  80. Modulation of the human gut microbiota by dietary fibres occurs at the species level.
    BMC Biol. 2016 Jan 11;14 :3 PMID: 26754945
  81. The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes.
    J Mol Biol. 2014 Nov 25;426(23):3851-65 PMID: 25026064
  82. Diversity of the human intestinal microbial flora.
    Science. 2005 Jun 10;308(5728):1635-8 PMID: 15831718
  83. Microbial ecology: human gut microbes associated with obesity.
    Nature. 2006 Dec 21;444(7122):1022-3 PMID: 17183309
  84. FXR is a molecular target for the effects of vertical sleeve gastrectomy.
    Nature. 2014 May 8;509(7499):183-8 PMID: 24670636
  85. A human gut microbial gene catalogue established by metagenomic sequencing.
    Nature. 2010 Mar 4;464(7285):59-65 PMID: 20203603
  86. Diet rapidly and reproducibly alters the human gut microbiome.
    Nature. 2014 Jan 23;505(7484):559-63 PMID: 24336217
  87. Association between dietary fiber and lower risk of all-cause mortality: a meta-analysis of cohort studies.
    Am J Epidemiol. 2015 Jan 15;181(2):83-91 PMID: 25552267
  88. The Regulation of the Intestinal Flora of Dogs through Diet.
    J Med Res. 1919 Jan;39(3):415-47 PMID: 19972470
  89. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.
    Sci Transl Med. 2009 Nov 11;1(6):6ra14 PMID: 20368178
  90. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease.
    Nature. 2011 Apr 7;472(7341):57-63 PMID: 21475195
  91. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.
    Gut. 2016 Jan;65(1):63-72 PMID: 25431456
  92. A G protein-coupled receptor responsive to bile acids.
    J Biol Chem. 2003 Mar 14;278(11):9435-40 PMID: 12524422
  93. Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia.
    Diabetologia. 2007 Nov;50(11):2374-83 PMID: 17823788
  94. An integrated catalog of reference genes in the human gut microbiome.
    Nat Biotechnol. 2014 Aug;32(8):834-41 PMID: 24997786
  95. Dietary intake, energy metabolism, and excretory losses of adult male germfree Wistar rats.
    Lab Anim Sci. 1983 Feb;33(1):46-50 PMID: 6834773
  96. Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults.
    Gut. 2015 Nov;64(11):1744-54 PMID: 25500202
  97. Gut microbiome of the Hadza hunter-gatherers.
    Nat Commun. 2014 Apr 15;5:3654 PMID: 24736369
  98. Germ-free C57BL/6J mice are resistant to high-fat-diet-induced insulin resistance and have altered cholesterol metabolism.
    FASEB J. 2010 Dec;24(12):4948-59 PMID: 20724524
  99. The contribution of the large intestine to energy supplies in man.
    Am J Clin Nutr. 1984 Feb;39(2):338-42 PMID: 6320630
  100. Targeting bile-acid signalling for metabolic diseases.
    Nat Rev Drug Discov. 2008 Aug;7(8):678-93 PMID: 18670431
  101. Diet-induced extinctions in the gut microbiota compound over generations.
    Nature. 2016 Jan 14;529(7585):212-5 PMID: 26762459
  102. Normalization of obesity-associated insulin resistance through immunotherapy.
    Nat Med. 2009 Aug;15(8):921-9 PMID: 19633657
  103. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon.
    Cell Metab. 2011 May 4;13(5):517-26 PMID: 21531334
  104. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota.
    Nat Rev Microbiol. 2013 Jul;11(7):497-504 PMID: 23748339
  105. Energy contributions of volatile fatty acids from the gastrointestinal tract in various species.
    Physiol Rev. 1990 Apr;70(2):567-90 PMID: 2181501
  106. The application of ecological theory toward an understanding of the human microbiome.
    Science. 2012 Jun 8;336(6086):1255-62 PMID: 22674335
  107. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis.
    Nat Med. 2013 May;19(5):576-85 PMID: 23563705
  108. Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling.
    Cell Metab. 2015 Oct 6;22(4):658-68 PMID: 26321659
  109. Ten-year trends in fiber and whole grain intakes and food sources for the United States population: National Health and Nutrition Examination Survey 2001-2010.
    Nutrients. 2015 Feb 09;7(2):1119-30 PMID: 25671414
  110. Microbial modulation of energy availability in the colon regulates intestinal transit.
    Cell Host Microbe. 2013 Nov 13;14(5):582-90 PMID: 24237703
  111. Microbial bile acid transformation.
    Am J Clin Nutr. 1974 Nov;27(11):1341-7 PMID: 4217103
  112. Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species.
    Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3627-32 PMID: 26951680
  113. Effects of bariatric surgery on mortality in Swedish obese subjects.
    N Engl J Med. 2007 Aug 23;357(8):741-52 PMID: 17715408
  114. Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut.
    Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20236-41 PMID: 24259713
  115. Modelling the emergent dynamics and major metabolites of the human colonic microbiota.
    Environ Microbiol. 2015 May;17(5):1615-30 PMID: 25142831
  116. The gut microbiota of rural papua new guineans: composition, diversity patterns, and ecological processes.
    Cell Rep. 2015 Apr 28;11(4):527-38 PMID: 25892234
  117. Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits.
    Cell. 2014 Jan 16;156(1-2):84-96 PMID: 24412651
  118. Metabolic endotoxemia initiates obesity and insulin resistance.
    Diabetes. 2007 Jul;56(7):1761-72 PMID: 17456850
  119. The microbiome of uncontacted Amerindians.
    Sci Adv. 2015 Apr 3;1(3):null PMID: 26229982
  120. Microbial regulation of glucose metabolism and cell-cycle progression in mammalian colonocytes.
    PLoS One. 2012;7(9):e46589 PMID: 23029553
  121. Dietary fiber intake and total mortality: a meta-analysis of prospective cohort studies.
    Am J Epidemiol. 2014 Sep 15;180(6):565-73 PMID: 25143474
  122. The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos.
    Cell Rep. 2016 Feb 23;14 (7):1655-61 PMID: 26854221
  123. Gut metagenome in European women with normal, impaired and diabetic glucose control.
    Nature. 2013 Jun 6;498(7452):99-103 PMID: 23719380
  124. Chylomicrons promote intestinal absorption of lipopolysaccharides.
    J Lipid Res. 2009 Jan;50(1):90-7 PMID: 18815435
  125. Subsistence strategies in traditional societies distinguish gut microbiomes.
    Nat Commun. 2015 Mar 25;6:6505 PMID: 25807110
  126. A core gut microbiome in obese and lean twins.
    Nature. 2009 Jan 22;457(7228):480-4 PMID: 19043404
  127. Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation.
    Cell Metab. 2015 Aug 4;22(2):228-38 PMID: 26244932
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
Published
2016-00-07
Pages
56-64
Language
English
Region
England
NLM ID
0410462
PMCID
PMC5991619
Subset
IM
Grants
European Research Council · 615362 · International
NIDDK NIH HHS · R01 DK085025 · United States
NIDDK NIH HHS · R01-DK085025 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com