Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization

Scientific Reports

Volumn 8, Issue 1, 2018, Pages

  de la Cuesta Zuluaga, Jacobo ^a,d   Corrales Agudelo, Vanessa ^a   Velásquez Mejía, Eliana P ^a   Carmona, Jenny A ^b,e   Abad, José M ^c   Escobar, Juan S ^a  

^a Grupo Empresarial Nutresa   (Colombia)

^b Dinámica IPS Especialista en Ayudas Diagnósticas   (Colombia)

^c EPS SURA   (Colombia)

^d MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^e SURA Colombia   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ADULT; BACTERIAL GENOME; BACTERIUM; CARDIOVASCULAR DISEASE; CLASSIFICATION; COLOMBIA; FEMALE; GENETICS; HUMAN; INTESTINE FLORA; MALE; METABOLIC DISORDER; MICROBIOLOGY; MIDDLE AGED; OBESITY; YOUNG ADULT;

ADOLESCENT; ADULT; BACTERIA; CARDIOVASCULAR DISEASES; COLOMBIA; FEMALE; GASTROINTESTINAL MICROBIOME; GENOME, BACTERIAL; HUMANS; MALE; METABOLIC DISEASES; MIDDLE AGED; OBESITY; YOUNG ADULT;

EID: 85050824876     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-018-29687-x     Document Type: Article

References (56)

1. de Vos, W. M. & De Vos, E. A. J. J. Role of the intestinal microbiome in health and disease: From correlation to causation. Nutr. Rev. 70, 45–56 (2012)
2. Zmora, N., Zeevi, D., Korem, T., Segal, E. & Elinav, E. Perspective Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease. Cell Host Microbe 19, 12–20 (2015)
3. The Human Microbiome Project Consortium et al. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012)
4. De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and ruralAfrica. Proc. Natl. Acad. Sci. 107, 14691–14696 (2010)
5. Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012)
6. Schnorr, S. L. et al. Gut microbiome of the Hadza hunter-gatherers. Nat. Commun. 5, 3654 (2014)
7. Obregon-Tito, A. J. et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat. Commun. 6, 1–9 (2015)
8. Dugas, L. R., Fuller, M., Gilbert, J. & Layden, B. T. The obese gut microbiome across the epidemiologic transition. Emerg. Themes Epidemiol. 13, 2 (2016)
9. Popkin, B. M. The nutrition transition and its health implications in lower-income countries. Public health nutrition 1, 5–21 (1998)
10. Instituto Colombiano de Bienestar Familiar et al. Encuesta Nacional de la Situación Nutricional en Colombia 2010 ENSIN (2011)
11. Silva-Arias, A. C. & González-Román, P. A Spatial Analysis Of Internal Migrations In Colombia (2000–2005). Rev. Fac. Ciencias Económicas Investig. y Reflexión 17, 123–144 (2009)
12. Hallal, P. C. et al. Global physical activity levels: surveillance progress, pitfalls, and prospects. Lancet 380, 247–257 (2012)
13. Martínez, J. C. Factores asociados a la mortalidad por enfermedades no transmisibles en Colombia, 2008–2012. Biomédica 36 (2016)
14. Escobar, J. S., Klotz, B., Valdes, B. E. & Agudelo, G. M. The gut microbiota of Colombians differs from that of Americans, Europeans and Asians. BMC Microbiol. 14, 311 (2014)
15. Wang, S. et al. Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet. 4, e1000037 (2008)
16. Rishishwar, L. et al. Ancestry, admixture and fitness in Colombian genomes. Sci. Rep. 5, 12376 (2015)
17. Mancabelli, L. et al. Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations. Environ. Microbiol. 19, 1379–1390 (2017)
18. Pasolli, E. et al. Accessible, curated metagenomic data through Experiment Hub. Nature Methods 14, 1023–1024 (2017)
19. Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011)
20. Koren, O. et al. A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. PLoS Comput. Biol. 9, e1002863 (2013)
21. Claesson, M. J. et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178–184 (2012)
22. Flemer, B. et al. Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut 66, 633–643 (2017)
23. Friedman, J. & Alm, E. J. Inferring Correlation Networks from Genomic Survey Data. PLoS Comput. Biol. 8, e1002687 (2012)
24. O’Keefe, S. J. D. et al. Fat, fibre and cancer risk in African Americans and rural Africans. Nat. Commun. 6 (2015)
25. Everard, A. et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc. Natl. Acad. Sci. USA 110, 9066–9071 (2013)
26. Shin, N. R., Whon, T. W. & Bae, J. W. Proteobacteria: Microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 33, 496–503 (2015)
27. Cani, P. D. et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56, 1761–1772 (2007)
28. Jie, Z. et al. The gut microbiome in atherosclerotic cardiovascular disease. Nat. Commun. 8, 845 (2017)
29. Koren, O. et al. Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc. Natl. Acad. Sci. USA 108, 4592–8 (2011)
30. Wang, T. et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 6, 320–329 (2011)
31. Brook, I. Anaerobic Infections Diagnosis and Management. (CRC Press, Inc., 2007)
32. Pimentel, M., Gunsalus, R. P., Rao, S. S. & Zhang, H. Methanogens in Human Health and Disease. Am. J. Gastroenterol. Suppl. 1, 28–33 (2012)
33. Morrison, D. J. & Preston, T. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes 7, 189–200 (2016)
34. Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480–487 (2009)
35. Gorvitovskaia, A., Holmes, S. P. & Huse, S. M. Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome 4, 15 (2016)
36. Avila, M., Ojcius, D. M., Yilmaz, Ö. & Yilmaz, O. The oral microbiota: living with a permanent guest. DNA Cell Biol. 28, 405–11 (2009)
37. Nardone, G. & Compare, D. The human gastric microbiota: Is it time to rethink the pathogenesis of stomach diseases? United Eur. Gastroenterol. J. 3, 255–260 (2015)
38. Guinane, C. M. & Cotter, P. D. Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therap. Adv. Gastroenterol. 6, 295–308 (2013)
39. Rigsbee, L. et al. Quantitative Profiling of Gut Microbiota of Children With Diarrhea-Predominant Irritable Bowel Syndrome. Am. J. Gastroenterol. 107, 1740–1751 (2012)
40. Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc. Natl. Acad. Sci. USA 111, E2329–38 (2014)
41. Meehan, C. J. & Beiko, R. G. A Phylogenomic View of Ecological Specialization in the Lachnospiraceae, a Family of Digestive Tract-Associated Bacteria. Genome Biol. Evol. 6, 703–713 (2014)
42. Dao, M. C. et al. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut 65, 426–436 (2016)
43. Ridaura, V. K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (80-.). 341, 1241214 (2013)
44. Schwiertz, A. et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity 18, 190–195 (2010)
45. Goodrich, J. K. et al. Human genetics shape the gut microbiome. Cell 159, 789–799 (2014)
46. Konikoff, T. & Gophna, U. Oscillospira: a central, enigmatic component of the human gut microbiota. Trends Microbiol. 24, 523–524 (2016)
47. Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220–230 (2012)
48. Siri, W. Body composition from fluid spaces and density: Analysis of methods. Techniques for Measuring Body Composition 1, (Washington, DC: National Academy of Sciences, 1961)
49. Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013)
50. Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41 (2013)
51. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011)
52. DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006)
53. Evans, J., Sheneman, L. & Foster, J. Relaxed neighbor joining: A fast distance-based phylogenetic tree construction method. J. Mol. Evol. 62, 785–792 (2006)
54. Chen, J. et al. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics 28, 2106–2113 (2012)
55. Aßhauer, K. P., Wemheuer, B., Daniel, R. & Meinicke, P. Tax4Fun: Predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics 31, 2882–2884 (2015)
56. Darzi, Y., Falony, G., Vieira-Silva, S. & Raes, J. Towards biome-specific analysis of meta-omics data. ISME J. 10, 1025–1028 (2016)