Baquero F, Nombela C. The microbiome as a human organ. Clin Microbiol Infect. 2012;4:2–4.
Article
Google Scholar
Whitman WBCD, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci. 1998;95:6578–83.
CAS
Article
PubMed
PubMed Central
Google Scholar
Blaut M, Clavel T. Metabolic diversity of the intestinal microbiota: implications for health and disease. J Nutr. 2007;137:751S–5.
CAS
PubMed
Google Scholar
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.
Article
PubMed
PubMed Central
Google Scholar
Nieuwdorp M, Gilijamse PW, Pai N, Kaplan LM. Role of the microbiome in energy regulation and metabolism. Gastroenterology. 2014;146:1525–33.
CAS
Article
PubMed
Google Scholar
Hooper LV, Macpherson AJ. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat Rev Immunol. 2010;10:159–69.
CAS
Article
PubMed
Google Scholar
Turner JR. Intestinal mucosal barrier function in health and disease. Nat Rev Immunol. 2009;9:799–809.
CAS
Article
PubMed
Google Scholar
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.
Article
PubMed
Google Scholar
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.
CAS
Article
PubMed
Google Scholar
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.
Mullin GE. Gut Microbiome imbalance: pathways to weight gain and illness. Alternative and Complementary Therapies. 2015;21(4):161–62.
WHO. BMI classification. In: World Health Organization; 2015. http://apps.who.int/bmi/index.jsp?introPage=intro_3.htm
Consortium THMP. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.
Article
Google Scholar
Tremaroli V, Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012;489:242–9.
CAS
Article
PubMed
Google Scholar
Calle EE, Thun MJ. Obesity and cancer. Oncogene. 2004;23:6365–78.
CAS
Article
PubMed
Google Scholar
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.
Article
PubMed
Google Scholar
Mullin GE. The gut balance revolution: boost your metabolism, restore your inner ecology, and lose the weight for good! Emmaus: Rodale; 2015.
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.
CAS
Article
PubMed
Google Scholar
Jiménez E, Marín ML, Martín R, et al. Is meconium from healthy newborns actually sterile? Res Microbiol. 2008;159:187–93.
Article
PubMed
Google Scholar
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.
CAS
Article
PubMed
Google Scholar
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.
Article
PubMed
PubMed Central
Google Scholar
Ley RE. Obesity and the human microbiome. Curr Opin Gastroenterol. 2010;26:5–11.
Article
PubMed
Google Scholar
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.
CAS
Article
PubMed
PubMed Central
Google Scholar
Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457:480–4.
CAS
Article
PubMed
Google Scholar
Schwiertz A, Taras D, Schafer K, et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 2010;18:190–5.
Article
PubMed
Google Scholar
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.
CAS
PubMed
Google Scholar
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.
CAS
Article
Google Scholar
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.
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.
CAS
Article
PubMed
Google Scholar
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.
Article
Google Scholar
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.
CAS
Article
PubMed
PubMed Central
Google Scholar
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.
CAS
PubMed
Google Scholar
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.
CAS
Article
Google Scholar
Santacruz A, Marcos A, Warnberg J, et al. Interplay between weight loss and gut microbiota composition in overweight adolescents. Obesity. 2009;17:1906–15.
Article
PubMed
Google Scholar
Sotos M, Nadal I, Marti A, et al. Gut microbes and obesity in adolescents. Proceed Nutr Soc. 2008;67:null-null.
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.
Article
PubMed
Google Scholar
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.
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.
CAS
Article
PubMed
PubMed Central
Google Scholar
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.
Article
PubMed
PubMed Central
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Article
PubMed
Google Scholar
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.
Article
PubMed
PubMed Central
Google Scholar
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.
CAS
Article
PubMed
PubMed Central
Google Scholar
Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022–3.
CAS
Article
PubMed
Google Scholar
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.
CAS
Article
PubMed
Google Scholar
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.
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.
Article
Google Scholar
Million M, Raoult D. The role of the manipulation of the gut microbiota in obesity. Curr Infect Dis Rep. 2012;15:25–30.
Article
Google Scholar
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.
Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr. 1995;125:1401–12.
CAS
PubMed
Google Scholar
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.
CAS
Article
PubMed
Google Scholar
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.
CAS
PubMed
Google Scholar
Cani PD, Delzenne NM. The role of the gut microbiota in energy metabolism and metabolic disease. Curr Pharm Des. 2009;15:1546–58.
CAS
Article
PubMed
Google Scholar
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.
CAS
Article
PubMed
PubMed Central
Google Scholar
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.
Article
Google Scholar
Begley M, Hill C, Gahan CG. Bile salt hydrolase activity in probiotics. Appl Environ Microbiol. 2006;72:1729–38.
CAS
Article
PubMed
PubMed Central
Google Scholar
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.
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.
CAS
Article
PubMed
PubMed Central
Google Scholar
Cho I, Yamanishi S, Cox L, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012;488:621–6.
CAS
Article
PubMed
PubMed Central
Google Scholar
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.
CAS
Article
PubMed
PubMed Central
Google Scholar
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.
Atherton JC, Blaser MJ. Coadaptation of helicobacter pylori and humans: ancient history, modern implications. J Clin Invest. 2009;119:2475–87.
CAS
Article
PubMed
PubMed Central
Google Scholar
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.
Article
Google Scholar
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.
Article
PubMed
Google Scholar
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.
Article
PubMed
Google Scholar
Mullin GE. Probiotics in digestive disease. Nutr Clin Pract. 2012;27(2):300–2.
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.
Article
PubMed
Google Scholar
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.
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.
CAS
Article
PubMed
PubMed Central
Google Scholar