The Gut Microbiome and Obesity


The gut microbiome consists of trillions of bacteria which play an important role in human metabolism. Animal and human studies have implicated distortion of the normal microbial balance in obesity and metabolic syndrome. Bacteria causing weight gain are thought to induce the expression of genes related to lipid and carbohydrate metabolism thereby leading to greater energy harvest from the diet. There is a large body of evidence demonstrating that alteration in the proportion of Bacteroidetes and Firmicutes leads to the development of obesity, but this has been recently challenged. It is likely that the influence of gut microbiome on obesity is much more complex than simply an imbalance in the proportion of these phyla of bacteria. Modulation of the gut microbiome through diet, pre- and probiotics, antibiotics, surgery, and fecal transplantation has the potential to majorly impact the obesity epidemic.

This is a preview of subscription content, log in to check access.

Access options

Buy single article

Instant unlimited access to the full article PDF.

US$ 39.95

Price includes VAT for USA

Subscribe to journal

Immediate online access to all issues from 2019. Subscription will auto renew annually.

US$ 99

This is the net price. Taxes to be calculated in checkout.

Fig. 1


    Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance

    1. 1.

      Baquero F, Nombela C. The microbiome as a human organ. Clin Microbiol Infect. 2012;4:2–4.

    2. 2.

      Whitman WBCD, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci. 1998;95:6578–83.

    3. 3.

      Blaut M, Clavel T. Metabolic diversity of the intestinal microbiota: implications for health and disease. J Nutr. 2007;137:751S–5.

    4. 4.

      Bäckhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 2004;101:15718–23.

    5. 5.

      Nieuwdorp M, Gilijamse PW, Pai N, Kaplan LM. Role of the microbiome in energy regulation and metabolism. Gastroenterology. 2014;146:1525–33.

    6. 6.

      Hooper LV, Macpherson AJ. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat Rev Immunol. 2010;10:159–69.

    7. 7.

      Turner JR. Intestinal mucosal barrier function in health and disease. Nat Rev Immunol. 2009;9:799–809.

    8. 8.

      Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–131.

    9. 9.

      Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut. 2016;65:57–62.

    10. 10.

      Okeke F, Roland BC, Mullin GE. The role of the gut microbiome in the pathogenesis and treatment of obesity. Glob Adv Health Med. 2014;3(3):44–57.

    11. 11.

      Mullin GE. Gut Microbiome imbalance: pathways to weight gain and illness. Alternative and Complementary Therapies. 2015;21(4):161–62.

    12. 12.

      WHO. BMI classification. In: World Health Organization; 2015.

    13. 13.

      Consortium THMP. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.

    14. 14.

      Tremaroli V, Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012;489:242–9.

    15. 15.

      Calle EE, Thun MJ. Obesity and cancer. Oncogene. 2004;23:6365–78.

    16. 16.

      Calle EE, Rodriguez C, Walker-Thurmond K, Thun MJ. Overweight, obesity, and mortality from cancer in a prospectively studied cohort of U.S. adults. New Engl J Med. 2003;348:1625–38.

    17. 17.

      Mullin GE. The gut balance revolution: boost your metabolism, restore your inner ecology, and lose the weight for good! Emmaus: Rodale; 2015.

    18. 18.•

      Wallace JG, Gohir W, Sloboda DM. The impact of early life gut colonization on metabolic and obesogenic outcomes: what have animal models shown us? J Dev Orig Health Dis. 2016;7:15–24. This paper reviews early gut colonization in animal models focusing especially on the role of the early gut microbiome in impacting disease later in life.

    19. 19.

      Jiménez E, Marín ML, Martín R, et al. Is meconium from healthy newborns actually sterile? Res Microbiol. 2008;159:187–93.

    20. 20.

      Wang M, Radlowski EC, Monaco MH, Fahey GC, Gaskins HR, Donovan SM. Mode of delivery and early nutrition modulate microbial colonization and fermentation products in neonatal piglets. J Nutr. 2013;143:795–803.

    21. 21.

      Bäckhed F, Manchester JK, Semenkovich CF, Gordon JI. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci. 2007;104:979–84.

    22. 22.

      Ley RE. Obesity and the human microbiome. Curr Opin Gastroenterol. 2010;26:5–11.

    23. 23.

      Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A. 2005;102:11070–5.

    24. 24.

      Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457:480–4.

    25. 25.

      Schwiertz A, Taras D, Schafer K, et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 2010;18:190–5.

    26. 26.

      Collado MC, Isolauri E, Laitinen K, Salminen S. Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr. 2008;88:894–9.

    27. 27.

      Duncan SH, Lobley GE, Holtrop G, et al. Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes. 2008;32:1720–4.

    28. 28.

      Armougom F, Henry M, Vialettes B, Raccah D, Raoult D. Monitoring bacterial community of human gut microbiota reveals an increase in lactobacillus in obese patients and methanogens in anorexic patients. PLoS One. 2009;4(9):e7125. doi:10.1371/journal.pone.0007125.

    29. 29.

      Balamurugan R, George G, Kabeerdoss J, Hepsiba J, Chandragunasekaran AM, Ramakrishna BS. Quantitative differences in intestinal Faecalibacterium prausnitzii in obese Indian children. Br J Nutr. 2010;103:335–8.

    30. 30.

      Damms-Machado A, Mitra S, Schollenberger AE, et al. Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption. Biomed Res Int. 2015;806248:1.

    31. 31.

      Furet J-P, Kong L-C, Tap J, et al. Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers. Diabetes. 2010;59:3049–57.

    32. 32.

      Kalliomaki M, Collado MC, Salminen S, Isolauri E. Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr. 2008;87:534–8.

    33. 33.

      Nadal I, Santacruz A, Marcos A, et al. Shifts in clostridia, bacteroides and immunoglobulin-coating fecal bacteria associated with weight loss in obese adolescents. Int J Obes. 2009;33:758–67.

    34. 34.

      Santacruz A, Marcos A, Warnberg J, et al. Interplay between weight loss and gut microbiota composition in overweight adolescents. Obesity. 2009;17:1906–15.

    35. 35.

      Sotos M, Nadal I, Marti A, et al. Gut microbes and obesity in adolescents. Proceed Nutr Soc. 2008;67:null-null.

    36. 36.

      Woodard GA, Encarnacion B, Downey JR, et al. Probiotics improve outcomes after Roux-en-Y gastric bypass surgery: a prospective randomized trial. J Gastrointest Surg. 2009;13:1198–204.

    37. 37.

      Zhang H, DiBaise JK, Zuccolo A, et al. Human gut microbiota in obesity and after gastric bypass. Proceedings of the National Academy of Sciences; 2009.

    38. 38.•

      Albenberg LG, Wu GD. Diet and the intestinal microbiome: associations, functions, and implications for health and disease. Gastroenterology. 2014;146:1564–72. This paper reviews the role of diet in impacting gut microbiome and its contribution in the pathogenesis of various disorders including obesity, coronary artery disease and inflammatory bowel disease.

    39. 39.

      Dominguez-Bello MG, Costello EK, Contreras M, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci. 2010;107:11971–5.

    40. 40.

      Wang M, Li M, Chapkin RS, Ivanov I, Donovan SM. Fecal microbiome and metabolites differ between breast and formula-fed human infants. FASEB J. 2013;27:850–4.

    41. 41.

      Koenig JE, Spor A, Scalfone N, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci. 2011;108:4578–85.

    42. 42.

      De Filippo C, Cavalieri D, Di Paola M, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci. 2010;107:14691–6.

    43. 43.

      Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008;3:213–23.

    44. 44.

      Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022–3.

    45. 45.••

      Chassaing B, Koren O, Goodrich JK, et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature. 2015;519:92–6. This study was one of the first studies focusing on dietary emulsifiers which are commonly used in the food industry. The authors demonstrated that the use of relatively low concentrations of two commonly used emulsifiers, carboxymethylcellulose and polysorbate-80, induced alterations in the gut flora associated with the development of colitis and onset of metabolic syndrome with increase in adiposity and weight and impaired glycemic control which was transmissible by fecal transplantation into germ free mice.

    46. 46.

      Singh M, Mullin GE. Diet and environmental influences on the gut microbiome. In: Cohen A, vom Saal F editors. Integrative Environmental Medicine. Oxford: Univ Press; 2016.

    47. 47.

      Brahe LK, Astrup A, Larsen LH. Can we prevent obesity-related metabolic diseases by dietary modulation of the gut microbiota? Advan Nutrit Int Rev J. 2016;7:90–101.

    48. 48.

      Million M, Raoult D. The role of the manipulation of the gut microbiota in obesity. Curr Infect Dis Rep. 2012;15:25–30.

    49. 49.

      Pineiro M, Asp NG, Reid G, Macfarlane S, Morelli L, Brunser O, Tuohy K. FAO Technical meeting on prebiotics. J Clin Gastroenterol. 2008;42(Suppl 3 Pt 2):S156–9.

    50. 50.

      Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr. 1995;125:1401–12.

    51. 51.

      Jackson KG, Taylor GR, Clohessy AM, Williams CM. The effect of the daily intake of inulin on fasting lipid, insulin and glucose concentrations in middle-aged men and women. Br J Nutr. 1999;82:23–30.

    52. 52.

      Delzenne NM, Cani PD, Neyrinck AM. Modulation of glucagon-like peptide 1 and energy metabolism by inulin and oligofructose: experimental data. J Nutr. 2007;137:2547S–51.

    53. 53.

      Cani PD, Delzenne NM. The role of the gut microbiota in energy metabolism and metabolic disease. Curr Pharm Des. 2009;15:1546–58.

    54. 54.

      Kaczmarczyk MM, Miller MJ, Freund GG. The health benefits of dietary fiber: beyond the usual suspects of type 2 diabetes mellitus, cardiovascular disease and colon cancer. Metabolism. 2012;61:1058–66.

    55. 55.

      Rowland I, Capurso L, Collins K, et al. Current level of consensus on probiotic science—report of an expert meeting—London, 23 November 2009. Gut Microbe. 2010;1:436–9.

    56. 56.

      Begley M, Hill C, Gahan CG. Bile salt hydrolase activity in probiotics. Appl Environ Microbiol. 2006;72:1729–38.

    57. 57.

      Mullin GE, Delzenne NM. The human gut micobiome and its role in obesity and the metabolic syndrome. In: Mullin GE, Cheskin L, Matarese L, editors. Integrative weight management. New York: Springer Publ; 2014.

    58. 58.

      Butaye P, Devriese LA, Haesebrouck F. Antimicrobial growth promoters used in animal feed: effects of less well known antibiotics on gram-positive bacteria. Clin Microbiol Rev. 2003;16:175–88.

    59. 59.

      Cho I, Yamanishi S, Cox L, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012;488:621–6.

    60. 60.••

      Cox Laura M, Yamanishi S, Sohn J, et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell. 2014;158:705–21. This study focused on the effect of low dose penicillin in weaning mice which caused changes in the ileal expression of genes involved in immunity as well as enhancement in the effect of diet induced obesity by its effects of gene expression in the liver, metabolic hormone levels and visceral adiposity with the trait being transferrable to germ free showing that the altered microbiota and not the antibiotics per se cause promotion of adiposity.

    61. 61.

      Thuny F, Richet H, Casalta JP, Angelakis E, Habib G, Raoult D. Vancomycin treatment of infective endocarditis is linked with recently acquired obesity. PLoS One. 2010;5:0009074.

    62. 62.

      Atherton JC, Blaser MJ. Coadaptation of helicobacter pylori and humans: ancient history, modern implications. J Clin Invest. 2009;119:2475–87.

    63. 63.

      Francois F, Roper J, Joseph N, et al. The effect of H. pylori eradication on meal-associated changes in plasma ghrelin and leptin. BMC Gastroenterol. 2011;11:11–37.

    64. 64.

      Zhang Y, Du T, Chen X, Yu X, Tu L, Zhang C. Association between helicobacter pylori infection and overweight or obesity in a Chinese population. J Infect Dev Ctries. 2015;9:945–53.

    65. 65.

      Xu C, Yan M, Sun Y, et al. Prevalence of helicobacter pylori infection and its relation with body mass index in a Chinese population. Helicobacter. 2014;19:437–42.

    66. 66.

      Mullin GE. Probiotics in digestive disease. Nutr Clin Pract. 2012;27(2):300–2.

    67. 67.

      van Nood E, Vrieze A, Nieuwdorp M, et al. Duodenal infusion of donor feces for recurrent clostridium difficile. N Engl J Med. 2013;368:407–15.

    68. 68.•

      Alang N, Kelly CR. Weight gain after fecal microbiota transplantation. Open Forum Infect Dis. 2015;2. The authors report a case of a 32 year old woman with a 41 lb unintentional weight gain following fecal transplantation from a related, overweight donor which highlights the importance of further studies to study the long term risks and benefits of fecal transplantation.

    69. 69.•

      Sweeney TE, Morton JM. The human gut microbiome: a review of the effect of obesity and surgically induced weight loss. JAMA Surg. 2013;148:563–9. This review focuses on the changes in the distal gut microbiome after Roux-en-Y gastric bypass and weight loss and discusses further clinical applications of studies of the distal gut microbiome.

    Download references

    Author information

    Correspondence to Gerard E. Mullin.

    Ethics declarations

    Conflict of Interest

    George Kunnackal John and Gerard E. Mullin declare that they have no conflict of interest.

    Human and Animal Rights and Informed Consent

    This article does not contain any studies with human or animal subjects performed by any of the authors.

    Additional information

    This article is part of the Topical Collection on Integrative Care

    Rights and permissions

    Reprints and Permissions

    About this article

    Verify currency and authenticity via CrossMark

    Cite this article

    John, G.K., Mullin, G.E. The Gut Microbiome and Obesity. Curr Oncol Rep 18, 45 (2016) doi:10.1007/s11912-016-0528-7

    Download citation


    • Microbiome
    • Obesity
    • Microbiota
    • Diet
    • Prebiotic
    • Probiotic
    • Microbial balance
    • Bacteroidetes
    • Firmicutes