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Profile of the gut microbiota of adults with obesity: a systematic review



Recently, relationship between gut microbiota composition and development of obesity has been pointed. However, the gut microbiota composition of individual with obesity is not known yet. Therefore, this systematic review aimed to evaluate differences in profile of gut microbiota between individuals with obesity and individuals with normal weight. A search performed on August 2019 in the databases Pubmed, Scopus, Web of Science, Cochrane library, Lilacs and gray literature using the terms: “microbiota”, “microbiome”, “obesity”, “obesity morbid”, and “humans”. Studies assessing the gut microbiota composition in adults with obesity and lean were included. Quality assessment was performed by Newcastle–Ottawa Quality Assessment Scale. Of the 12,496 studies, 32 were eligible and included in this review. Individuals with obesity have a greater Firmicutes/Bacteroidetes ratio, Firmicutes, Fusobacteria, Proteobacteria, Mollicutes, Lactobacillus (reuteri), and less Verrucomicrobia (Akkermansia muciniphila), Faecalibacterium (prausnitzii), Bacteroidetes, Methanobrevibacter smithii, Lactobacillus plantarum and paracasei. In addition, some bacteria had positive correlation and others negative correlation with obesity. Individuals with obesity showed profile of gut microbiota different than individual lean. These results may help in advances of the diagnosis and treatment of obesity.

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Fig. 1


  1. 1.

    World Health Organization (WHO). Fact sheet: obesity and overweight. no. 311. 2017. Accessed 20 Dec 2018.

  2. 2.

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

    CAS  PubMed  Google Scholar 

  3. 3.

    Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Addendum: enterotypes of the human gut microbiome. Nature. 2011;473:174–80.

    CAS  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–8.

    PubMed  PubMed Central  Google Scholar 

  5. 5.

    Gerritsen J, Smidt H, Rijkers GT, de Vos WM. Intestinal microbiota in human health and disease: the impact of probiotics. Genes Nutr. 2011;6:209–40.

    PubMed  PubMed Central  Google Scholar 

  6. 6.

    Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. The gut microbiota as an environmental factor that regales fat storage. Proc Natl Acad Sci USA. 2004;204:15718–23.

    Google Scholar 

  7. 7.

    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  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Murphy EF, Bäckhed F, Fulton L, Gordon JI. Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut. 2010;59:1635–42.

    CAS  PubMed  Google Scholar 

  9. 9.

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

    CAS  PubMed  Google Scholar 

  10. 10.

    Kolida A, Syzenko G, Moseiko V, Budovska L, Puchkov K, Perederiy V, et al. Association between body mass index and Firmicutes/Bcateroidetes ratio in an adult Ukranian population. BMC Microbiol. 2017;17:120.

    Google Scholar 

  11. 11.

    Schwiertz A, Taras D, Schäfer K, Beijer S, Bos NA, Donus C, et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 2010;18:190–5.

    PubMed  Google Scholar 

  12. 12.

    Kocelak P, Zak-Golab A, Zahorska-Markiewicz B, Aptekorz M, Zientara M, Martirosian G, et al. Resting energy expenditure and gut microbiota in obese and normal weight subjects. Eur Rev Med Pharm Sci. 2013;17:2816–21.

    CAS  Google Scholar 

  13. 13.

    Yasir M, Angelakis E, Bibi F, Azhar E, Bachar D, Lagier JC, et al. Comparison of the gut microbiota of people in France an Saudi Arabia. Nutr Diabetes. 2015;5:e153.

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, et al. Correlation between body mass index and gut concentration of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibactersmithii and Echerichia coli. Int J Obes. 2013;37:1460–6.

    CAS  Google Scholar 

  15. 15.

    Moher D, Shamseer L, Clarke M, Ghersi D, Liberati A, Petticrew M, et al. Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst Rev. 2015;4:1.

    PubMed  PubMed Central  Google Scholar 

  16. 16.

    Wells G, Shea B, O’Connell D, Robertson J, Peterson J, Welch V, et al. The Newcastle-Ottawa scale (NOS) for assessing the quailty of nonrandomised studies in meta-analyses. 2000. Accessed 26 Sep 2018.

  17. 17.

    Simões CD, Maukonen J, Kaprio J, Rissanen A, Pietiläinen KH, Saarela M. Habitual dietary intake is associated with stool with stool microbiota composition in monozygotic twins. J Nutr. 2013;143:417–23.

    PubMed  Google Scholar 

  18. 18.

    Bezerra BTS. Avaliação da microbiota intestinal e sua relação com parâmetros metabólicos em mulheres com obesidade mórbida. Florianópolis: Dissertação (Mestrado), Universidade Federal de Santa Catarina; 2013.

  19. 19.

    Zak-Golab A, Kocelak P, Aptekorz M, Zientara M, Juszczyk L, Martirosian G, et al. Gut microbiota, microinflammation, metabolic profile, and zonulin concentration in obese and normal weight subjects. Int J endocrinol. 2013;2013:674106.

    PubMed  PubMed Central  Google Scholar 

  20. 20.

    Dorminianni C, Sinha R, Goedert JJ, Pei Z, Yang L, Hayes RB, et al. Sex, body mass index, and dietary fiber intake influence the human gut microbiome. PLoS ONE. 2015;10:e0124599.

    Google Scholar 

  21. 21.

    Fernandéz-Navarro T, Salazar N, Gutiérrez-Díaz I, de los Reyes-Gavilán CG, Gueimonde M, González S. Different intestinal microbial profile in over-weight and obese subjects consuming a diet with low content of fiber and antioxidants. Nutrients. 2017;9:551.

    PubMed Central  Google Scholar 

  22. 22.

    Gao R, Zhu C, Li H, Yin M, Pan C, Huang L, et al. Dysbiosis signatures of gut microbiota along the sequence from health, young patients to those with overweight and obesity. Obesity. 2017;26:351–61.

    PubMed  Google Scholar 

  23. 23.

    Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, et al. Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. Nat Med. 2017;23:859–68.

    CAS  PubMed  Google Scholar 

  24. 24.

    Verdam FJ, Fuentes S, Jonge C, Zoetendal EG, Erbil R, Greve JW, et al. Human intestinal microbiota composition is associated with local and systemic inflammation in obesity. Obesity. 2013;21:E607–E615.

    CAS  PubMed  PubMed Central  Google Scholar 

  25. 25.

    De La Cuesta-Zuluaga J, Corrales-Agudelo V, Carmona JA, Abad JM, Excobar JS. Body size phenotypes comprehensively assess cardiometabolic risk and refine the association between obesity and gut microbiota. Int J Obes. 2018;42:424–32.

    Google Scholar 

  26. 26.

    Kasai C, Sugimoto K, Moritani I, Tanaka J, Oya Y, Inoue H, et al. Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing. BMC Gastroenterol. 2015;15:100.

    PubMed  PubMed Central  Google Scholar 

  27. 27.

    Nistal E, Sáez de Miera LE, Ballesteros-Pomar M, Sánchez-Campos S, Álvarez-Cuellas B, Aparicio-Cabezudo M, et al. Alteration of the intestinal microbiota associated with the development of obesity in patients. Rev ACAD. 2017;33:13–20.

    Google Scholar 

  28. 28.

    Rahat-Rozenbloom S, Fernandes J, Gloor GB, Wolever TM. Evidence for greater production of colonic short-chain fatty acids in overweight than lean humans. Int J Obes. 2014;38:1525–31.

    CAS  Google Scholar 

  29. 29.

    Santos VM. Avaliação da participação dos micro-organismos da classe Mollicutes na microbiota intestinal de mulheres eutróficas e obesas. São Paulo: Dissertação (Mestrado), Universidade de São Paulo; 2015.

  30. 30.

    Selma MV, Romo-Vaquera M, García-Villalba R, González-Sarrías A, Tomás-Barberán FA, Espín JC. The human gut microbiota ecology associated with overweight and obesity determines ellagic acid metabolism. Food Funct. 2016;7:1769.

    CAS  PubMed  Google Scholar 

  31. 31.

    Jinatham V, Kullawong N, Kespechara K, Gentekaki E, Popluechai S. Comparison of gut microbiota between lean and obese adult Thai individuals. Microbiol Biotechnol Lett. 2018;46:277–87.

    Google Scholar 

  32. 32.

    Andoh A, Nishida A, Takahashi K, Inatomi O, Imaeda H, Bamba S, et al. Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population. J Clin Biochem Nutr. 2016;59:65–70.

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Zuo HJ, Xie ZM, Zhang WW, Li YR, Wang W, Ding XB, et al. Gut bacteria alteration in obese people and its relationship with gene polymorphism. World J Gastrointerol. 2011;17:1076–81.

    CAS  Google Scholar 

  34. 34.

    Escobar JS, Klotz B, Valdes BE, Agudelo GM. The gut microbiota of Colombians differs from that of Americans, Europeans and Asians. BMC Microbiol. 2014;14:311.

    PubMed  PubMed Central  Google Scholar 

  35. 35.

    Patil DP, Dhotre DP, Chavan SG, Sultan A, Jain DS, Lanjekar VB, et al. Molecular analysis of gut microbiota in obesity among Indian individuals. J Biosci. 2012;37:647–57.

    CAS  PubMed  Google Scholar 

  36. 36.

    Gao X, Zhang M, Xue J, Huang J, Zhuang R, Zhou X, et al. Body mass index diferences in the gut microbiota are gender specific. Front Microbiol. 2018;9:1250.

    PubMed  PubMed Central  Google Scholar 

  37. 37.

    Blasco G, Moreno-Navarrete JM, Rivero M, Pérez-Brocal V, Garre-Olmo J, Puig J, et al. The gut metagenome changes in parallel to waist circumference, brain iron deposition, and cognitive function. J Clin Endocrinol Metab. 2017;102:2962–73.

    PubMed  Google Scholar 

  38. 38.

    Sarmiento MRA, de Paula TO, Borges FM, Ferreira-Machado AB, Resende JA, Moreira APB, et al. Obesity, xenobiotic intake and antimicrobial-resistance genes in the human gastrointestinal tract: a comparative study of eutrophic, overweight and obese individuals. Genes. 2019;10:E349.

    PubMed  Google Scholar 

  39. 39.

    Teixeira TFS, Grzeskowiak LM, Salmien S, Laitinen K, Bressan J, Peluzio MCG. Faecal levels of Bifidobacterium and Clostridium coccoides but not plasma lipopolysaccharide are inversely related to insulin and HOMA index in women. Clin Nutr. 2013;32:1017–22.

    Google Scholar 

  40. 40.

    Munukka E, Wiklund P, Pekkala S, Völgyi E, Xu L, Cheng S, et al. Women with and without metabolic disorder differ in their gut microbiota composition. Obesity. 2012;20:1082–7.

    CAS  PubMed  Google Scholar 

  41. 41.

    Million M, Maraninchi M, Henry M, Armougom F, Richet H, Carrieri P, et al. Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii. Int J Obes. 2012;36:817–25.

    CAS  Google Scholar 

  42. 42.

    Fernandes J, Su W, Rahat-Rozenbloom S, Wolever TM, Cornelli EM. Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans. Nutr Diabetes. 2014;4:e121.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Hippe B, Remely M, Aumueller E, Pointner A, Magnet U, Haslberger AG. Faecalibacterium prausnitzii phylotype in type two diabetic, obese, and lean control subjects. Benf Microbes. 2016;7:511–7.

    CAS  Google Scholar 

  44. 44.

    Ottosson F, Brunkwall L, Ericson U, Nilsson PM, Almgren P, Fernandez C, et al. Connection between BMI-related plasma metabolite profile and gut microbiota. J Clin Endocrinol Metab. 2018;103:1491–501.

    PubMed  Google Scholar 

  45. 45.

    Davis SC, Yadav JS, Barrow SD, Robertson BK. Gut microbiome diversity influenced more by the Westernized dietary regime than the body mass index as assessed using effect size statistic. Microbiol Open. 2017;6:1–17.

    Google Scholar 

  46. 46.

    Gomes AC, Hoffmann C, Mota JF. The human gut microbiota: metabolism and perspective in obesity. Gut Microbes. 2018;9:308–25.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Cultured gut microbiota from twins discordant for obesity modulate adiposity and metabolomic phenotypes in mice. Science. 2013;341:1–22.

    Google Scholar 

  48. 48.

    Negpal R, Newman TM, Wang S, Jain S, Lovato JF, Yadav H. Obesity-linked gut microbiota dysbiosis associated with derangements in gut permeability and intestinal cellular homeostasis independent of diet. J Diabetes Res. 2018;2018:3462092.

    Google Scholar 

  49. 49.

    Ibrahim M, Anishetty S. A meta-metabolome network of carbohydrate metabolism: interactions between gut microbiota and host. Biochem Biophys Res Commun. 2012;428:278–84.

    CAS  PubMed  Google Scholar 

  50. 50.

    Drissi F, Merhej V, Angelakis E, Kaoutari AE, Carrière F, Henrissat B, et al. Comparative genomic analysis of Lactobacillus species associated with weight gain or weight protection. Nutr Diabetes. 2014;4:e109.

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Shi NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015;33:496–503.

    Google Scholar 

  52. 52.

    Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J. 2017;11:841–52.

    PubMed  PubMed Central  Google Scholar 

  53. 53.

    Derrien M, Blzer C, de Vos WM. Akkermansia muciniphila and its role in regulation host functions. Micro Pathog. 2017;106:171–81.

    Google Scholar 

  54. 54.

    Henderson G, Cox F, Kittelmann S, Miri VH, Zethof M, Noel SJ, et al. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS ONE. 2013;8:e74787.

    CAS  PubMed  PubMed Central  Google Scholar 

  55. 55.

    Rodríguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Micro Ecol Health Dis. 2015;69:52–60.

    Google Scholar 

  56. 56.

    Sun L, Ma L, Ma Y, Zhang F, Zhao C, Nie Y. Insights into the role of gut microbiota in obesity: pathogenesis, mechanisms, and therapeutic perspectives. Protein Cell. 2018;9:397–403.

    PubMed  PubMed Central  Google Scholar 

  57. 57.

    Bell DS. Changes seen in gut bacteria content and distribution with obesity: causation or association? Postgrad Med. 2015;127:863–8.

    PubMed  Google Scholar 

  58. 58.

    Segafredo FB, Blume CA, Moehlecke M, Giongo A, Casagrande DS, Spolidoro JVN, et al. Weight-loss interventions and gut microbiota changes in overweight and obese patients: a systematic review. Obes Rer. 2017;18:823–51.

    Google Scholar 

  59. 59.

    Pajecki D, de Oliveira LC, Sabino EC, Souza-Basqueira M, Dantas ACB, Nunes GC, et al. Changes in the intestinal microbiota of superobese patients after bariatric surgery. Clinical. 2019;74:e1198.

    Google Scholar 

  60. 60.

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

    PubMed  PubMed Central  Google Scholar 

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This research was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES)—Finance code 001, and Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (Faperj). The funders were not involved in the design until publication of study.

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LC and ELR: conceived and design of the study; LC and DM: protocol of search and acquisition of data; LC: drafting the article; All authors: revised and approval of the version to be submitted.

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Correspondence to Louise Crovesy.

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Crovesy, L., Masterson, D. & Rosado, E.L. Profile of the gut microbiota of adults with obesity: a systematic review. Eur J Clin Nutr 74, 1251–1262 (2020).

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