Obesity, diabetes, and the gut microbiome: an updated review

References

• World Health Organization. Obesity and overweight. 2018. [cited 2018 Feb 9]. Available from: http://www.who.int/mediacentre/factsheets/fs311/en/
   Google Scholar
• World Health Organization/International Association for the Study of Obesity/International Obesity Takforce. The Asia Pacific perspective: redefining obesity and its treatment. 2000. [cited 2018 Feb 9].  Available from: http://www.wpro.who.int/nutrition/documents/docs/Redefiningobesity.pdf
   Google Scholar
• Department of Health and Human Services, Centers for Disease Control and Prevention. Body mass index: considerations for practitioners. [cited 2018 Feb 9]. Available from: https://www.cdc.gov/obesity/downloads/bmiforpactitioners.pdf
   Google Scholar
• Obesity: preventing and managing the global epidemic. Geneva: World Health Organization; 2000. (Report of a WHO Consultation; WHO Technical Report Series 894). [cited 2018 Feb 9]. Available from: http://www.who.int/nutrition/publications/obesity/WHO_TRS_894/en/
   Google Scholar
• Stenvinkel P, Zoccali C, Ikizler TA. Obesity in CKD–what should nephrologists know? J Am Soc Nephrol. 2013;24(11):1727–1736.
   PubMed Web of Science ®Google Scholar
• van Leiden HA, Dekker JM, Moll AC, et al. Blood pressure, lipids, and obesity are associated with retinopathy. Diabetes Care. 2002;25(8):1320.
   PubMed Web of Science ®Google Scholar
• Lauby-Secretan B, Scoccianti C, Loomis D, et al. Body fatness and cancer - viewpoint of the IARC working group. N Engl J Med. 2016;375(8):794–798.
   PubMed Web of Science ®Google Scholar
• Centers for Disease Control and Prevention. Adult obesity facts - overweight & obesity; 2017 Aug 29. [cited 2018 Feb 9]. Available from: https://www.cdc.gov/obesity/data/adult.html
   Google Scholar
• American Diabetes Association. Diagnosis and classification of diabetes mellitus. Diabetes Care. 2010;33(Suppl 1):S62–SS9.
   PubMed Web of Science ®Google Scholar
• International Diabetes Federation. IDF diabetes atlas. 8th ed. Brussels: International Diabetes Federation; 2017. Available from: http://www.diabetesatlas.org
   Google Scholar
• World Health Organization. Diabetes; 2017 Nov 1. [cited 2018 Feb 9].  Available from: http://www.who.int/mediacentre/factsheets/fs312/en/
   Google Scholar
• Mathers CD, Loncar D. Projections of global mortality and burden of disease from 2002 to 2030. PLoS Med. 2006;3(11):e442.
   PubMed Web of Science ®Google Scholar
• Weinsier RL, Hunter GR, Heini AF, et al. The etiology of obesity: relative contribution of metabolic factors, diet, and physical activity. Am J Med. 1998;105(2):145–150.
   PubMed Web of Science ®Google Scholar
• Molarius A, Seidell JC, Sans S, et al. Educational level, relative body weight, and changes in their association over 10 years: an international perspective from the WHO MONICA Project. Am J Public Health. 2000;90(8):1260–1268.
   PubMed Web of Science ®Google Scholar
• Barlow GM, Yu A, Mathur R. Role of the gut microbiome in obesity and diabetes mellitus. Nutr Clin Pract. 2015;30(6):787–797.
   PubMed Web of Science ®Google Scholar
• Barlow GM, Lin EA, Mathur R. An overview of the roles of the gut microbiome in obesity and diabetes. In: Bagchi D, Nair S, editors. Nutritional and therapeutic interventions for diabetes and metabolic syndrome. 2nd ed. Cambridge, MA: Academic Press; 2018. p. 65–91.
   Google Scholar
• Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):e1002533.
   PubMed Web of Science ®Google Scholar
• Jandhyala SM, Talukdar R, Subramanyam C, et al. Role of the normal gut microbiota. World J Gastroenterol. 2015;21(29):8787–8803.
   PubMed Web of Science ®Google Scholar
• Sears CL. A dynamic partnership: celebrating our gut flora. Anaerobe. 2005;11(5):247–251.
   PubMed Web of Science ®Google Scholar
• Gaci N, Borrel G, Tottey W, et al. Archaea and the human gut: new beginning of an old story. World J Gastroenterol. 2014;20(43):16062–16078.
   PubMed Web of Science ®Google Scholar
• Lozupone CA, Stombaugh JI, Gordon JI, et al. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489(7415):220–230.
   PubMed Web of Science ®Google Scholar
• Reyes A, Semenkovich NP, Whiteson K, et al. Going viral: next generation sequencing applied to human gut phage populations. Nat Rev Microbiol. 2012;10(9):607–617.
   PubMed Web of Science ®Google Scholar
• Brooks L, Viardot A, Tsakmaki A, et al. Fermentable carbohydrate stimulates FFAR2-dependent colonic PYY cell expansion to increase satiety. Mol Metab. 2017;6(1):48–60.
   PubMed Web of Science ®Google Scholar
• Everard A, Belzer C, Geurts L, et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci USA. 2013;110(22):9066–9071.
   PubMed Web of Science ®Google Scholar
• Kau AL, Ahern PP, Griffin NW, et al. Human nutrition, the gut microbiome, and immune system: envisioning the future. Nature. 2011;474(7351):327–336.
   PubMed Web of Science ®Google Scholar
• Bäckhed F, Ley RE, Sonnenburg JL, et al. Host-bacterial mutualism in the human intestine. Science. 2005;307(5717):1915–1920.
   PubMed Web of Science ®Google Scholar
• Blanton LV, Charbonneau MR, Salih T, et al. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science. 2016;351(6275).
   PubMed Web of Science ®Google Scholar
• DeGruttola AK, Low D, Mizoguchi A, et al. Current understanding of dysbiosis in disease in human and animal models. Inflamm Bowel Dis. 2016;22(5):1137–1150.
   PubMed Web of Science ®Google Scholar
• Carding S, Verbeke K, Vipond DT, et al. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis. 2015;26. DOI:10.3402/mehd.v26.26191
   PubMed Web of Science ®Google Scholar
• Voigt RM, Forsyth CB, Green SJ, et al. Circadian disorganization alters intestinal microbiota. PLOS ONE. 2014;9(5):e97500.
   PubMed Web of Science ®Google Scholar
• Mathur R, Barlow GM. Obesity and the microbiome. Expert Rev Gastroenterol Hepatol. 2015;9(8):1087–1099.
   PubMed Web of Science ®Google Scholar
• O’Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep. 2006;7(7):688–693.
   PubMed Web of Science ®Google Scholar
• Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355–1359.
   PubMed Web of Science ®Google Scholar
• Hooper LV, Midtvedt T, Gordon JI. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu Rev Nutr. 2002;22:283–307.
   PubMed Web of Science ®Google Scholar
• Backhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA. 2004;101(44):15718–15723.
   PubMed Web of Science ®Google Scholar
• Ridlon JM, Kang DJ, Hylemon PB. Bile salt biotransformations by human intestinal bacteria. J Lipid Res. 2006;47(2):241–259.
   PubMed Web of Science ®Google Scholar
• Aitman T, Dhillon P, Geurts AM. A RATional choice for translational research? Dis Model Mech. 2016;9(10):1069–1072.
   PubMed Web of Science ®Google Scholar
• Shimoyama M, Laulederkind SJF, De Pons J, et al. Exploring human disease using the rat genome database. Dis Model Mech. 2016;9(10):1089–1095.
   PubMed Web of Science ®Google Scholar
• Aagaard K, Ma J, Antony KM, et al. The placenta harbors a unique microbiome. Sci Transl Med. 2014;6(237):237ra65.
   PubMed Web of Science ®Google Scholar
• Collado MC, Rautava S, Aakko J, et al. Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci Rep. 2016;6:23129.
   PubMed Web of Science ®Google Scholar
• Rodriguez JM, Murphy K, Stanton C, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis. 2015;26:26050.
   PubMed Web of Science ®Google Scholar
• Gritz EC, Bhandari V. The human neonatal gut microbiome: a brief review. Front Pediatr. 2015;3:17.
   PubMed Web of Science ®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 USA. 2010;107(26):11971–11975.
   PubMed Web of Science ®Google Scholar
• Azad MB, Konya T, Persaud RR, et al. Impact of maternal intrapartum antibiotics, method of birth and breastfeeding on gut microbiota during the first year of life: a prospective cohort study. BJOG. 2016;123(6):983–993.
   PubMed Web of Science ®Google Scholar
• Koenig JE, Spor A, Scalfone N, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA. 2011;108(Suppl 1):4578–4585.
   PubMed Web of Science ®Google Scholar
• Biagi E, Nylund L, Candela M, et al. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLOS ONE. 2010;5(5):e10667.
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457(7228):480–484.
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Ridaura VK, Faith JJ, et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1(6):6ra14–6ra.
   PubMed Web of Science ®Google Scholar
• Azad MB, Bridgman SL, Becker AB, et al. Infant antibiotic exposure and the development of childhood overweight and central adiposity. Int J Obes. 2014;38:1290.
   PubMed Web of Science ®Google Scholar
• Pannaraj PS, Li F, Cerini C, et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr. 2017;171(7):647–654.
   PubMed Web of Science ®Google Scholar
• Subramanian S, Huq S, Yatsunenko T, et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature. 2014;510(7505):417–421.
   PubMed Web of Science ®Google Scholar
• Yan J, Liu L, Zhu Y, et al. The association between breastfeeding and childhood obesity: a meta-analysis. BMC Public Health. 2014;14(1):1267.
   PubMedGoogle Scholar
• Horta BL, Loret de Mola C, Victora CG. Long‐term consequences of breastfeeding on cholesterol, obesity, systolic blood pressure and type 2 diabetes: a systematic review and meta‐analysis. Acta Paediatr. 2015;104(S467):30–37.
   PubMedGoogle Scholar
• Gohir W, Ratcliffe EM, Sloboda DM. Of the bugs that shape us: maternal obesity, the gut microbiome, and long-term disease risk. Pediatr Res. 2014;77:196.
   PubMed Web of Science ®Google Scholar
• Collado MC, Isolauri E, Laitinen K, et al. 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. Am J Clin Nutr. 2010;92(5):1023–1030.
   PubMed Web of Science ®Google Scholar
• Groer MW, Gregory KE, Louis-Jacques A, et al. The very low birth weight infant microbiome and childhood health. Birth Defect Res C. 2015;105(4):252–264.
   PubMedGoogle Scholar
• Cox LM, Blaser MJ. Antibiotics in early life and obesity. Nat Rev Endocrinol. 2014;11:182.
   PubMed Web of Science ®Google Scholar
• Festa A, D’Agostino R Jr, Williams K, et al. The relation of body fat mass and distribution to markers of chronic inflammation. Int J Obes. 2001;25:1407.
   PubMed Web of Science ®Google Scholar
• Park S, Kim YJ, Choi C-Y, et al. Bariatric surgery can reduce albuminuria in patients with severe obesity and normal kidney function by reducing systemic inflammation. Obes Surg. 2018;28(3):831–837.
   PubMed Web of Science ®Google Scholar
• Chatzigeorgiou A, Karalis KP, Bornstein SR, et al. Lymphocytes in obesity-related adipose tissue inflammation. Diabetologia. 2012;55(10):2583–2592.
   PubMed Web of Science ®Google Scholar
• Chassaing B, Kumar M, Baker MT, et al. Mammalian gut immunity. Biomed J. 2014;37(5):246–258.
   PubMedGoogle Scholar
• Chassaing B, Raja SM, Lewis JD, et al. Colonic microbiota encroachment correlates with dysglycemia in humans. Cell Mol Gastroenterol Hepatol. 2017;4(2):205–221.
   PubMed Web of Science ®Google Scholar
• Ringel Y. The gut microbiome in irritable bowel syndrome and other functional bowel disorders. Gastroenterol Clin North Am. 2017;46(1):91–101.
   PubMed Web of Science ®Google Scholar
• Vijay-Kumar M, Sanders CJ, Taylor RT, et al. Deletion of TLR5 results in spontaneous colitis in mice. J Clin Invest. 2007;117(12):3909–3921.
   PubMed Web of Science ®Google Scholar
• Means TK, Hayashi F, Smith KD, et al. The toll-like receptor 5 stimulus bacterial flagellin induces maturation and chemokine production in human dendritic cells. J Immunol. 2003;170(10):5165–5175.
   PubMed Web of Science ®Google Scholar
• O’Neill LA, Golenbock D, Bowie AG. The history of toll-like receptors – redefining innate immunity. Nat Rev Immunol. 2013;13:453–460.
   PubMed Web of Science ®Google Scholar
• Cani PD, Amar J, Iglesias MA, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes. 2007;56(7):1761–1772.
   PubMed Web of Science ®Google Scholar
• Saberi M, Woods NB, de Luca C, et al. Hematopoietic cell-specific deletion of toll-like receptor 4 ameliorates hepatic and adipose tissue insulin resistance in high-fat-fed mice. Cell Metab. 2009;10(5):419–429.
   PubMed Web of Science ®Google Scholar
• Poggi M, Bastelica D, Gual P, et al. C3H/HeJ mice carrying a toll-like receptor 4 mutation are protected against the development of insulin resistance in white adipose tissue in response to a high-fat diet. Diabetologia. 2007;50(6):1267–1276.
   PubMed Web of Science ®Google Scholar
• Cani PD, Neyrinck AM, Fava F, et al. Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia. 2007;50(11):2374–2383.
   PubMed Web of Science ®Google Scholar
• Vijay-Kumar M, Aitken JD, Carvalho FA, et al. Metabolic syndrome and altered gut microbiota in mice lacking toll-like receptor 5. Science. 2010;328(5975):228–231.
   PubMed Web of Science ®Google Scholar
• Creely SJ, McTernan PG, Kusminski CM, et al. Lipopolysaccharide activates an innate immune system response in human adipose tissue in obesity and type 2 diabetes. Am J Physiol Endocrinol Metab. 2007;292(3):E740–E747.
   PubMed Web of Science ®Google Scholar
• Dasu MR, Devaraj S, Park S, et al. Increased toll-like receptor (TLR) activation and TLR ligands in recently diagnosed type 2 diabetic subjects. Diabetes Care. 2010;33(4):861–868.
   PubMed Web of Science ®Google Scholar
• van der Crabben SN, Blümer RM, Stegenga ME, et al. Early endotoxemia increases peripheral and hepatic insulin sensitivity in healthy humans. J Clin Endocrinol Metab. 2009;94(2):463–468.
   PubMed Web of Science ®Google Scholar
• Mead JR, Irvine SA, Ramji DP. Lipoprotein lipase: structure, function, regulation, and role in disease. J Mol Med. 2002;80(12):753–769.
   PubMed Web of Science ®Google Scholar
• Cryer A. Lipoprotein lipase and the uptake of lipids by adipose cells during development. Reprod Nutr Dev. 1985;25(1B):255–270.
   PubMedGoogle Scholar
• Kusunoki M, Tsutsumi K, Iwata K, et al. NO-1886 (ibrolipim), a lipoprotein lipase activator, increases the expression of uncoupling protein 3 in skeletal muscle and suppresses fat accumulation in high-fat diet-induced obesity in rats. Metabolism. 2005;54(12):1587–1592.
   PubMed Web of Science ®Google Scholar
• Bäckhed F, Manchester JK, Semenkovich CF, et al. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci USA. 2007;104(3):979–984.
   PubMed Web of Science ®Google Scholar
• Roy CC, Kien CL, Bouthillier L, et al. Short-chain fatty acids: ready for prime time? Nutr Clin Pract. 2006;21(4):351–366.
   PubMedGoogle Scholar
• Macfarlane S, Macfarlane GT. Regulation of short-chain fatty acid production. Proc Nutr Soc. 2003;62(1):67–72.
   PubMed Web of Science ®Google Scholar
• Smith PM, Howitt MR, Panikov N, et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science. 2013;341(6145):569–573.
   PubMed Web of Science ®Google Scholar
• Tolhurst G, Heffron H, Lam YS, et al. Short-chain fatty acids stimulate glucagon-like peptide-1 secretion via the G-protein-coupled receptor FFAR2. Diabetes. 2012;61(2):364–371.
   PubMed Web of Science ®Google Scholar
• Lin HV, Frassetto A, Kowalik EJ Jr, et al. Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms. PLoS One. 2012;7(4):e35240.
   PubMed Web of Science ®Google Scholar
• Gill PA, van Zelm MC, Muir JG, et al. Review article: short chain fatty acids as potential therapeutic agents in human gastrointestinal and inflammatory disorders. Aliment Pharmacol Ther. 2018;48(1):15–34.
   PubMed Web of Science ®Google Scholar
• Gao Z, Yin J, Zhang J, et al. Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes. 2009;58(7):1509–1517.
   PubMed Web of Science ®Google Scholar
• Gao Z, Yin J, Zhang J, et al. Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes. 2009;58(7):1509–1517.
   PubMed Web of Science ®Google Scholar
• Byndloss MX, Olsan EE, Rivera-Chávez F, et al. Microbiota-activated PPAR-gamma signaling inhibits dysbiotic Enterobacteriaceae expansion. Science. 2017;357(6351):570–575.
   PubMed Web of Science ®Google Scholar
• Cani PD. Gut cell metabolism shapes the microbiome. Science. 2017;357(6351):548–549.
   PubMed Web of Science ®Google Scholar
• Cani PD. Human gut microbiome: hopes, threats and promises. Gut. 2018;67(9):1716–1725.
   PubMed Web of Science ®Google Scholar
• Natarajan N, Pluznick JL. From microbe to man: the role of microbial short chain fatty acid metabolites in host cell biology. Am J Physiol Cell Physiol. 2014;307(11):C979–C985.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Chen F, Wu W, et al. GPR43 mediates microbiota metabolite SCFA regulation of antimicrobial peptide expression in intestinal epithelial cells via activation of mTOR and STAT3. Mucosal Immunol. 2018;11(3):752–762.
   PubMed Web of Science ®Google Scholar
• Hartmann P, Chen P, Wang HJ, et al. Deficiency of intestinal mucin‐2 ameliorates experimental alcoholic liver disease in mice. Hepatology. 2013;58(1):108–119.
   PubMed Web of Science ®Google Scholar
• Brun P, Castagliuolo I, De Leo V, et al. Increased intestinal permeability in obese mice: new evidence in the pathogenesis of nonalcoholic steatohepatitis. Am J Physiol Gastrointest Liver Physiol. 2007;292(2):G518–G525.
   PubMed Web of Science ®Google Scholar
• Willemsen LE, Koetsier MA, van Deventer SJ, et al. Short chain fatty acids stimulate epithelial mucin 2 expression through differential effects on prostaglandin E(1) and E(2) production by intestinal myofibroblasts. Gut. 2003;52(10):1442–1447.
   PubMed Web of Science ®Google Scholar
• Wang HB, Wang PY, Wang X, et al. Butyrate enhances intestinal epithelial barrier function via up-regulation of tight junction protein claudin-1 transcription. Dig Dis Sci. 2012;57(12):3126–3135.
   PubMed Web of Science ®Google Scholar
• Stappenbeck TS, Hooper LV, Gordon JI. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci USA. 2002;99(24):15451–15455.
   PubMed Web of Science ®Google Scholar
• Zoetendal EG, Akkermans ADL, Akkermans-van Vliet WM, et al. The host genotype affects the bacterial community in the human gastronintestinal tract. Micro Ecol Health Dis. 2001;13(3):129–134.
   Google Scholar
• Jumpertz R, Le DS, Turnbaugh PJ, et al. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am J Clin Nutr. 2011;94(1):58–65.
   PubMed Web of Science ®Google Scholar
• Wu GD, Chen J, Hoffmann C, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105–108.
   PubMed Web of Science ®Google Scholar
• Fabbiano S, Suárez-Zamorano N, Chevalier C, et al. Functional gut microbiota remodeling contributes to the caloric restriction-induced metabolic improvements. Cell Metab. 2018;28:1–15.
   PubMedGoogle Scholar
• Wang S, Huang M, You X, et al. Gut microbiota mediates the anti-obesity effect of calorie restriction in mice. Sci Rep. 2018;8(1):13037.
   PubMed Web of Science ®Google Scholar
• Ley RE, Bäckhead F, Turnbaugh P, et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA. 2005;102(31):11070–11075.
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Ley RE, Mahowald MA, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444(7122):1027–1031.
   PubMed Web of Science ®Google Scholar
• Ley RE, Turnbaugh PJ, Klein S, et al. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444(7122):1022–1023.
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2008;457(7288):480–484.
   PubMedGoogle Scholar
• Fernandes J, Su W, Rahat-Rozenbloom S, et al. Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans. Nutr Diabetes. 2014;4(6):e121.
   PubMedGoogle Scholar
• Schwiertz A, Taras D, Schäfer K, et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 2010;18(1):190–195.
   PubMed Web of Science ®Google Scholar
• Gao R, Zhu C, Li H, et al. Dysbiosis signatures of gut microbiota along the sequence from healthy, young patients to those with overweight and obesity. Obesity. 2018;26(2):351–361.
   PubMed Web of Science ®Google Scholar
• Allin KH, Tremaroli V, Caesar R, et al. Aberrant intestinal microbiota in individuals with prediabetes. Diabetologia. 2018;61(4):810–820.
   PubMed Web of Science ®Google Scholar
• Jia L, Li D, Feng N, et al. Anti-diabetic effects of Clostridium butyricum CGMCC0313.1 through promoting the growth of gut butyrate-producing bacteria in type 2 diabetic mice. Sci Rep. 2017;7(1):7046.
   PubMedGoogle Scholar
• Qin J, Li Y, Cai Z, et al. A metagenome-wide association of study of gut microbiota in type 2 diabetes. Nature. 2012;490:55–60.
   PubMed Web of Science ®Google Scholar
• Hippe B, Remely M, Aumueller E, et al. Faecalibacterium prausnitzii phylotypes in type two diabetic, obese, and lean control subjects. Benef Microbes. 2016;7(4):511–517.
   PubMed Web of Science ®Google Scholar
• Kim G, Deepinder F, Morales W, et al. Methanobrevibacter smithii is the predominant methanogen in patients with constipation-predominant IBS and methane on breath. Dig Dis Sci. 2012;57(12):3213–3218.
   PubMed Web of Science ®Google Scholar
• Kang DW, DiBaise JK, Ilhan ZE, et al. Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone. Anaerobe. 2015;33:33–41.
   PubMed Web of Science ®Google Scholar
• Million M, Angelakis E, Maraninchi M, et al. Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli. Int J Obes. 2013;37(11):1460–1466.
   PubMed Web of Science ®Google Scholar
• Million M, Maraninchi M, Henry M, et al. Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibavter smithii. Int J Obes. 2012;36(6):817–825.
   PubMed Web of Science ®Google Scholar
• Armougom F, Henry M, Vialettes B, et al. 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.
   PubMed Web of Science ®Google Scholar
• Zhang H, DiBaise JK, Zuccolo A, et al. Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA. 2009;106(7):2365–2370.
   PubMed Web of Science ®Google Scholar
• Patil DP, Dhotre DP, Chavan SG, et al. Molecular analysis of gut microbiota in obesity among Indian individuals. J Biosci. 2012;37(4):647–657.
   PubMed Web of Science ®Google Scholar
• Mbakwa CA, Penders J, Savelkoul PH, et al. Gut colonization with methanobrevibacter smithii is associated with childhood weight development. Obesity. 2015;23(12):2508–2516.
   PubMed Web of Science ®Google Scholar
• Basseri RJ, Basseri B, Pimentel M, et al. Intestinal methane production in obese individuals is associated with higher body mass index. Gastroenterol Hepatol. 2012;8(1):22–28.
   Google Scholar
• Mathur R, Amichai M, Chua KS, et al. Methane and hydrogen positivity on breath test is associated with greater body mass index and body fat. J Clin Endocrinol Metab. 2013;98(4):E698–E702.
   PubMed Web of Science ®Google Scholar
• Mathur R, Deepinder G, Kim G, et al. Methane-producing human subjects have higher serum glucose levels during oral glucose challenge than non-methane producers: a pilot study of the effects of enteric methanogens on glycemic regulation. Res J Endocrinol Metab. 2014;2(1):2.
   Google Scholar
• Mathur R, Chua KS, Mamelak M, et al. Metabolic effects of eradicating breath methane using antibiotics in prediabetic subjects with obesity. Obesity. 2016;24(3):576–582.
   PubMed Web of Science ®Google Scholar
• Mathur R, Mundi MS, Chua KS, et al. Intestinal methane production is associated with decreased weight loss following bariatric surgery. Obesity Res Clin Pract. 2016;10(6):728–733.
   PubMed Web of Science ®Google Scholar
• Samuel BS, Gordon JI. A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci USA. 2006;103(26):10011–10016.
   PubMed Web of Science ®Google Scholar
• Mathur R, Kim G, Morales W, et al. Intestinal Methanobrevibacter smithii but not total bacteria is related to diet-induced weight gain in rats. Obesity. 2013;21(4):748–754.
   PubMed Web of Science ®Google Scholar
• Obanda D, Page R, Guice J, et al. CD obseity-prone rats, but not obesity-resistant rats, robustly ferment resistant starch without increased weight or fat accretion. Obesity. 2018;26(3):570–577.
   PubMed Web of Science ®Google Scholar
• Zou J, Chassaing B, Singh V, et al. Fiber-mediated nourishment of gut microbiota protects against diet-induced obesity by restoring IL-22-mediated colonic health. Cell Host Microbe. 2018;23(1):41–53.e4.
   PubMed Web of Science ®Google Scholar
• Zhang Q, Yu H, Xiao X, et al. Inulin-type fructan improves diabetic phenotype and gut microbiota profiles in rats. Peer J. 2018;6:e4446.
   PubMed Web of Science ®Google Scholar
• Kinnebrew MA, Ubeda C, Zenewicz LA, et al. Bacterial flagellin stimulates TLR5-dependent defense against vancomycin-resistant Enterococcus infection. J Infect Dis. 2010;201(4):534–543.
   PubMed Web of Science ®Google Scholar
• Zenewicz LA, Yancopoulos GD, Valenzuela DM, et al. IL-22 but not IL-17 provides protection to hepatocytes during acute liver inflammation. Immunity. 2007;27(4):647–659.
   PubMed Web of Science ®Google Scholar
• Mistry RH, Gu F, Schols HA, et al. Effect of the prebiotic fiber inulin on cholesterol metabolism in wildtype mice. Sci Rep. 2018;8(1):13238.
   PubMedGoogle Scholar
• van der Beek CM, Canfora EE, Kip AM, et al. The prebiotic inulin improves substrate metabolism and promotes short-chain fatty acid production in overweight to obese men. Metabolism. 2018;87:25–35.
   PubMed Web of Science ®Google Scholar
• Wang J, Tang H, Zhang C, et al. Modulation of gut microbiota during probiotic-mediated attenuation of metabolic syndrome in high fat diet-fed mice. ISME J. 2015;9(1):1–15.
   PubMed Web of Science ®Google Scholar
• Million M, Angelakis E, Paul M, et al. Comparative meta-analysis of the effect of Lactobacillus species on weight gain in humans and animals. Microb Pathog. 2012;53(2):100–108.
   PubMed Web of Science ®Google Scholar
• Casacchia T, Scavello F, Rocca C, et al. Leopoldia comosa prevents metabolic disorders in rats with high-fat diet-induced obesity. Eur J Nutr. 2018.
   PubMedGoogle Scholar
• Casacchia T, Sofo A, Casaburi I, et al. Antioxidant, enzyme-inhibitory and antitumor activity of the wild dietary plant Muscari Comosum (L.). Mill Int J Plant Biol. 2017;8:6895.
   Google Scholar
• Cho YR, Lee JA, Kim YY, et al. Anti-obesity effects of Clausena excavate in high-fat diet-induced obese mice. Biomed Pharmacother. 2018;99:253–260.
   PubMed Web of Science ®Google Scholar
• Jernberg C, Lofmark S, Edlund C, et al. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 2007;1:56.
   PubMed Web of Science ®Google Scholar
• Li R, Wang H, Shi Q, et al. Effects of oral florfenicol and azithromycin on gut microbiota and adipogenesis in mice. PloS one. 2017;12(7):e0181690.
   PubMed Web of Science ®Google Scholar
• Cho I, Yamanishi S, Cox L, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012;488(7413):621–626.
   PubMed Web of Science ®Google Scholar
• Mahana D, Trent CM, Kurtz ZD, et al. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. Genome Med. 2016;8:48.
   PubMed Web of Science ®Google Scholar
• Vrieze A, Out C, Fuentes S, et al. Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity. J Hepatol. 2014;60(4):824–831.
   PubMed Web of Science ®Google Scholar
• Rejinders D, Goossens GH, Hermes GD, et al. Effects of gut microbiota manipulation by antibiotics on host metabolism in obese humans: a randomized double-blind placebo-controlled trial. Cell Metab. 2016;24(1):63–74.
   PubMed Web of Science ®Google Scholar
• Mikkelsen KH, Knop FK, Frost M, et al. Use of antibiotics and risk of type 2 diabetes: a population-based case-control study. J Clin Endocrinol Metab. 2015;100(10):3633–3640.
   PubMed Web of Science ®Google Scholar
• Buchwald H, Avidor Y, Braunwald E, et al. Bariatric surgery: a systematic review and meta-analysis. JAMA. 2004;292(14):1724–1737.
   PubMed Web of Science ®Google Scholar
• Ballantyne GH, Gumbs A, Modlin IM. Changes in insulin resistance following bariatric surgery and the adipoinsular axis: role of the adipocytokines, leptin, adiponectin and resistin. Obes Surg. 2005;15(5):692–699.
   PubMed Web of Science ®Google Scholar
• Osto M, Abegg K, Bueter M, et al. Roux-en-Y gastric bypass surgery in rats alters gut microbiota profile along the intestine. Physiol Behav. 2013;119:92–96.
   PubMed Web of Science ®Google Scholar
• Mavri A, Stegnar M, Sabovic M. Do baseline serum leptin levels predict weight regain after dieting in obese women? Diabetes Obes Metab. 2001;3(4):293–296.
   PubMed Web of Science ®Google Scholar
• Arora T, Seyfried F, Docherty NG, et al. Diabetes-associated microbiota in fa/fa rats is modified by Roux-en-Y gastric bypass. ISME J. 2017;11(9):2035–2046.
   PubMed Web of Science ®Google Scholar
• Kong LC, Tap J, Aron-Wisnewsky J, et al. Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes. Am J Clin Nutr. 2013;98(1):16–24.
   PubMed Web of Science ®Google Scholar
• Ridaura VK, Faith JJ, Rey FE, et al. Cultured gut microbiota from twins discordant for obesity modulate adiposity and metabolic phenotypes in mice. Science. 2013;341(6150). DOI:10.1126/science.1241214
   PubMed Web of Science ®Google Scholar
• Vrieze A, Van Nood E, Holleman F, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology. 2012;143(4):913–916.e7.
   PubMed Web of Science ®Google Scholar
• Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–227.
   PubMed Web of Science ®Google Scholar
• Fujisaka S, Avila-Pacheco J, Soto M, et al. Diet, genetics, and the gut microbiome drive dynamic changes in plasma metabolites. Cell Rep. 2018;22(11):3072–3086.
   PubMed Web of Science ®Google Scholar
• Weese JS, Martin H. Assessment of commercial probiotic bacterial contents and label accuracy. Can Vet J. 2011;52(1):43–46.
   PubMed Web of Science ®Google Scholar