The gut microbiota of Colombians differs from that of Americans, Europeans and Asians
详细信息    查看全文
  • 作者:Juan S Escobar (1)
    Bernadette Klotz (2) (3)
    Beatriz E Valdes (1) (4)
    Gloria M Agudelo (1) (5)

    1. Vidarium Nutrition
    ; Health and Wellness Research Center ; Grupo Nutresa ; Calle 8 sur #50-67 ; Medell铆n ; Colombia
    2. Faculty of Engineering
    ; University of La Sabana ; Km. 7 Autopista Norte de Bogot谩 ; Ch铆a ; Colombia
    3. Current address
    ; Instituto Alpina de Investigaci贸n ; Alpina S.A. ; Km. 3 v铆a Brice帽o-Sop贸 ; Sop贸 ; Colombia
    4. Current address
    ; Faculty of Health ; Instituci贸n Universitaria Colegio Mayor de Antioquia ; Carrera 78 #65-46 ; Medell铆n ; Colombia
    5. Current address
    ; Nutrition and Dietetic School ; University of Antioquia ; Calle 67 #53-108 ; Medell铆n ; Colombia
  • 关键词:Bacterial diversity ; Microbiome ; Geography ; Firmicutes ; Bacteroidetes ; Obesity ; Pyrosequencing ; Latin America ; Colombia
  • 刊名:BMC Microbiology
  • 出版年:2014
  • 出版时间:December 2014
  • 年:2014
  • 卷:14
  • 期:1
  • 全文大小:654 KB
  • 参考文献:Structure, function and diversity of the healthy human microbiome. Nature 486: pp. 207-214
    1. Pray, L, Pillsbury, L, Tomayko, E (2012) The Human Microbiome, Diet, and Health: Workshop Summary. National Academy of Sciences, Washington, D. C.
    2. Eckburg, PB, Bik, EM, Bernstein, CN, Purdom, E, Dethlefsen, L, Sargent, M, Gill, SR, Nelson, KE, Relman, DA (2005) Diversity of the human intestinal microbial flora. Science 308: pp. 1635-1638
    3. Backhed, F, Ley, RE, Sonnenburg, JL, Peterson, DA, Gordon, JI (2005) Host-bacterial mutualism in the human intestine. Science 307: pp. 1915-1920
    4. Guarner, F, Malagelada, JR (2003) Gut flora in health and disease. Lancet 361: pp. 512-519
    5. Mazmanian, SK, Liu, CH, Tzianabos, AO, Kasper, DL (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122: pp. 107-118
    6. Backhed, F, Ding, H, Wang, T, Hooper, LV, Koh, GY, Nagy, A, Semenkovich, CF, Gordon, JI (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101: pp. 15718-15723
    7. Ley, RE (2010) Obesity and the human microbiome. Curr Opin Gastroenterol 26: pp. 5-11
    8. Wen, L, Ley, RE, Volchkov, PY, Stranges, PB, Avanesyan, L, Stonebraker, AC, Hu, C, Wong, FS, Szot, GL, Bluestone, JA, Gordon, JI, Chervonsky, AV (2008) Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455: pp. 1109-1113
    9. Larsen, N, Vogensen, FK, Berg, FW, Nielsen, DS, Andreasen, AS, Pedersen, BK, Al-Soud, WA, Sorensen, SJ, Hansen, LH, Jakobsen, M (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 5: pp. e9085
    10. Mai, V, Colbert, LH, Perkins, SN, Schatzkin, A, Hursting, SD (2007) Intestinal microbiota: a potential diet-responsive prevention target in ApcMin mice. Mol Carcinog 46: pp. 42-48
    11. Clarke, SF, Murphy, EF, Nilaweera, K, Ross, PR, Shanahan, F, O鈥橳oole, PW, Cotter, PD (2012) The gut microbiota and its relationship to diet and obesity: new insights. Gut Microbes 3: pp. 186-202
    12. Scott KP, Gratz SW, Sheridan PO, Flint HJ, Duncan SH: The influence of diet on the gut microbiota. / Pharmacol Res 2012. In press
    13. Cox, LM, Blaser, MJ (2013) Pathways in microbe-induced obesity. Cell Metab 17: pp. 883-894
    14. Turnbaugh, PJ, Backhed, F, Fulton, L, Gordon, JI (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3: pp. 213-223
    15. Turnbaugh, PJ, Ley, RE, Mahowald, MA, Magrini, V, Mardis, ER, Gordon, JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: pp. 1027-1031
    16. Ley, RE, Backhed, F, Turnbaugh, P, Lozupone, CA, Knight, RD, Gordon, JI (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102: pp. 11070-11075
    17. Murphy, EF, Cotter, PD, Healy, S, Marques, TM, O鈥橲ullivan, O, Fouhy, F, Clarke, SF, O鈥橳oole, PW, Quigley, EM, Stanton, C, Ross, PR, O鈥橠oherty, RM, Shanahan, F (2010) Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut 59: pp. 1635-1642
    18. Turnbaugh, PJ, Ridaura, VK, Faith, JJ, Rey, FE, Knight, R, Gordon, JI (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1: pp. 6ra-14ra
    19. Ley, RE, Turnbaugh, PJ, Klein, S, Gordon, JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: pp. 1022-1023
    20. Collado, MC, Isolauri, E, Laitinen, K, Salminen, S (2008) Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr 88: pp. 894-899
    21. Duncan, SH, Lobley, GE, Holtrop, G, Ince, J, Johnstone, AM, Louis, P, Flint, HJ (2008) Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 32: pp. 1720-1724
    22. Ismail, NA, Ragab, SH, ElBaky, AA, Shoeib, ARS, Alhosary, Y, Fekry, D (2011) Frequency of Firmicutes and Bacteroidetes in gut microbiota in obese and normal weight Egyptian children and adults. Archives of Med Sci 7: pp. 501-507
    23. Schwiertz, A, Taras, D, Schafer, K, Beijer, S, Bos, NA, Donus, C, Hardt, PD (2010) Microbiota and SCFA in lean and overweight healthy subjects. Obesity 18: pp. 190-195
    24. Tims, S, Derom, C, Jonkers, DM, Vlietinck, R, Saris, WH, Kleerebezem, M, Vos, WM, Zoetendal, EG (2012) Microbiota conservation and BMI signatures in adult monozygotic twins. ISME J 7: pp. 707-717
    25. Qin, J, Li, R, Raes, J, Arumugam, M, Burgdorf, KS, Manichanh, C, Nielsen, T, Pons, N, Levenez, F, Yamada, T, Mende, DR, Li, J, Xu, J, Li, S, Li, D, Cao, J, Wang, B, Liang, H, Zheng, H, Xie, Y, Tap, J, Lepage, P, Bertalan, M, Batto, JM, Hansen, T, Paslier, D, Linneberg, A, Nielsen, HB, Pelletier, E, Renault, P (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: pp. 59-65
    26. Arumugam, M, Raes, J, Pelletier, E, Paslier, D, Yamada, T, Mende, DR, Fernandes, GR, Tap, J, Bruls, T, Batto, JM, Bertalan, M, Borruel, N, Casellas, F, Fernandez, L, Gautier, L, Hansen, T, Hattori, M, Hayashi, T, Kleerebezem, M, Kurokawa, K, Leclerc, M, Levenez, F, Manichanh, C, Nielsen, HB, Nielsen, T, Pons, N, Poulain, J, Qin, J, Sicheritz-Ponten, T, Tims, S (2011) Enterotypes of the human gut microbiome. Nature 473: pp. 174-180
    27. Mueller, S, Saunier, K, Hanisch, C, Norin, E, Alm, L, Midtvedt, T, Cresci, A, Silvi, S, Orpianesi, C, Verdenelli, MC, Clavel, T, Koebnick, C, Zunft, HJF, Dor茅, J, Blaut, M (2006) Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl Environ Microbiol 72: pp. 1027-1033
    28. Lay, C, Rigottier-Gois, L, Holmstrom, K, Rajilic, M, Vaughan, EE, Vos, WM, Collins, MD, Thiel, R, Namsolleck, P, Blaut, M, Dore, J (2005) Colonic microbiota signatures across five northern European countries. Appl Environ Microbiol 71: pp. 4153-4155
    29. Schloissnig, S, Arumugam, M, Sunagawa, S, Mitreva, M, Tap, J, Zhu, A, Waller, A, Mende, DR, Kultima, JR, Martin, J, Kota, K, Sunyaev, SR, Weinstock, GM, Bork, P (2013) Genomic variation landscape of the human gut microbiome. Nature 493: pp. 45-50
    30. Yatsunenko, T, Rey, FE, Manary, MJ, Trehan, I, Dominguez-Bello, MG, Contreras, M, Magris, M, Hidalgo, G, Baldassano, RN, Anokhin, AP, Heath, AC, Warner, B, Reeder, J, Kuczynski, J, Caporaso, JG, Lozupone, CA, Lauber, C, Clemente, JC, Knights, D, Knight, R, Gordon, JI (2012) Human gut microbiome viewed across age and geography. Nature 486: pp. 222-227
    31. Schnorr, SL, Candela, M, Rampelli, S, Centanni, M, Consolandi, C, Basaglia, G, Turroni, S, Biagi, E, Peano, C, Severgnini, M, Fiori, J, Gotti, R, Bellis, G, Luiselli, D, Brigidi, P, Mabulla, A, Marlowe, F, Henry, AG, Crittenden, AN (2014) Gut microbiome of the Hadza hunter-gatherers. Nat Commun 5: pp. 3654
    32. Filippo, C, Cavalieri, D, Paola, M, Ramazzotti, M, Poullet, JB, Massart, S, Collini, S, Pieraccini, G, Lionetti, P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107: pp. 14691-14696
    33. Suzuki, TA, Worobey, M (2014) Geographical variation of human gut microbial composition. Biol Lett 10: pp. 20131037
    34. Mai, V, McCrary, QM, Sinha, R, Glei, M (2009) Associations between dietary habits and body mass index with gut microbiota composition and fecal water genotoxicity: an observational study in African American and Caucasian American volunteers. Nutritional J 8: pp. 49
    35. Cox, LM, Cho, I, Young, SA, Anderson, WH, Waters, BJ, Hung, SC, Gao, Z, Mahana, D, Bihan, M, Alekseyenko, AV, Meth茅, BA, Blaser, MJ (2013) The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota. FASEB J 27: pp. 692-702
    36. Faith, JJ, McNulty, NP, Rey, FE, Gordon, JI (2011) Predicting a human gut microbiota鈥檚 response to diet in gnotobiotic mice. Science 333: pp. 101-104
    37. Cotillard, A, Kennedy, SP, Kong, LC, Prifti, E, Pons, N, Chatelier, E, Almeida, M, Quinquis, B, Levenez, F, Galleron, N, Gougis, S, Rizkalla, S, Batto, JM, Renault, P, Dor茅, J, Zucker, JD, Cl茅ment, K, Ehrlich, SD (2013) Dietary intervention impact on gut microbial gene richness. Nature 500: pp. 585-588
    38. David, LA, Maurice, CF, Carmody, RN, Gootenberg, DB, Button, JE, Wolfe, BE, Ling, AV, Devlin, AS, Varma, Y, Fischbach, MA, Biddinger, SB, Dutton, RJ, Turnbaugh, PJ (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505: pp. 559-563
    39. Zoetendal, EG, Akkermans, ADL, Akkermans-van Vliet, WM, Visser, JAGM, Vos, WM (2001) The host genotype affects the bacterial community in the human gastrointestinal tract. Microbial Ecology Health Dis 13: pp. 129-134
    40. Turnbaugh, PJ, Hamady, M, Yatsunenko, T, Cantarel, BL, Duncan, A, Ley, RE, Sogin, ML, Jones, WJ, Roe, BA, Affourtit, JP, Egholm, M, Henrissat, B, Heath, AC, Knight, R, Gordon, JI (2009) A core gut microbiome in obese and lean twins. Nature 457: pp. 480-487
    41. Claesson, MJ, Cusack, S, O鈥橲ullivan, O, Greene-Diniz, R, Weerd, H, Flannery, E, Marchesi, JR, Falush, D, Dinan, T, Fitzgerald, G, Stanton, C, Sinderen, D, O鈥機onnor, M, Harnedy, N, O鈥機onnor, K, Henry, C, O鈥橫ahony, D, Fitzgerald, AP, Shanahan, D, Twomey, C, Hill, C, Ross, RP, O鈥橳oole, PW (2011) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A 108: pp. 4586-4591
    42. Palmer, C, Bik, EM, DiGiulio, DB, Relman, DA, Brown, PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5: pp. e177
    43. Antonopoulos, DA, Huse, SM, Morrison, HG, Schmidt, TM, Sogin, ML, Young, VB (2009) Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun 77: pp. 2367-2375
    44. Dethlefsen, L, Huse, S, Sogin, ML, Relman, DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6: pp. e280
    45. Ubeda, C, Pamer, EG (2012) Antibiotics, microbiota, and immune defense. Trends Immunol 33: pp. 459-466
    46. Jernberg, C, Lofmark, S, Edlund, C, Jansson, JK (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1: pp. 56-66
    47. Biasucci, G, Rubini, M, Riboni, S, Morelli, L, Bessi, E, Retetangos, C (2010) Mode of delivery affects the bacterial community in the newborn gut. Early Hum Dev 86: pp. 13-15
    48. Dominguez-Bello, MG, Costello, EK, Contreras, M, Magris, M, Hidalgo, G, Fierer, N, Knight, R (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 107: pp. 11971-11975
    49. Huurre, A, Kalliomaki, M, Rautava, S, Rinne, M, Salminen, S, Isolauri, E (2008) Mode of delivery - effects on gut microbiota and humoral immunity. Neonatology 93: pp. 236-240
    50. Pandey, PK, Verma, P, Kumar, H, Bavdekar, A, Patole, MS, Shouche, YS (2012) Comparative analysis of fecal microflora of healthy full-term Indian infants born with different methods of delivery (vaginal vs cesarean): Acinetobacter sp. prevalence in vaginally born infants. J Biosci 37: pp. 989-998
    51. Nermes, M, Niinivirta, K, Nylund, L, Laitinen, K, Matom盲ki, J, Salminen, S, Isolauri, E (2013) Perinatal pet exposure, faecal microbiota, and wheezy bronchitis: is there a connection?. ISRN Allergy 2013: pp. 827934
    52. Song, SJ, Lauber, C, Costello, EK, Lozupone, CA, Humphrey, G, Berg-Lyons, D, Caporaso, JG, Knights, D, Clemente, JC, Nakielny, S, Gordon, JI, Fierer, N, Knight, R (2013) Cohabiting family members share microbiota with one another and with their dogs. eLife 2: pp. e00458
    53. Rojas, W, Parra, MV, Campo, O, Caro, MA, Lopera, JG, Arias, W, Duque, C, Naranjo, A, Garcia, J, Vergara, C, Lopera, J, Hernandez, E, Valencia, A, Caicedo, Y, Cuartas, M, Guti茅rrez, J, L贸pez, S, Ruiz-Linares, A, Bedoya, G (2010) Genetic make up and structure of Colombian populations by means of uniparental and biparental DNA markers. Am J Phys Anthropol 143: pp. 13-20
    54. Moreno-Estrada, A, Gravel, S, Zakharia, F, McCauley, JL, Byrnes, JK, Gignoux, CR, Ortiz-Tello, PA, Mart铆nez, RJ, Hedges, DJ, Morris, RW, Eng, C, Sandoval, K, Acevedo-Acevedo, S, Norman, PJ, Layrisse, Z, Parham, P, Mart铆nez-Cruzado, JC, Gonz谩lez Burchard, E, Cuccaro, ML, Martin, ER, Bustamante, CD (2013) Reconstructing the population genetic history of the Caribbean. PLoS Genet 9: pp. e1003925
    55. Gravel, S, Zakharia, F, Moreno-Estrada, A, Byrnes, JK, Muzzio, M, Rodriguez-Flores, JL, Kenny, EE, Gignoux, CR, Maples, BK, Guiblet, W, Dutil, J, Via, M, Sandoval, K, Bedoya, G, Oleksyk, TK, Ruiz-Linares, A, Burchard, EG, Martinez-Cruzado, JC, Bustamante, CD (2013) Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet 9: pp. e1004023
    Encuesta Nacional de la Situaci贸n Nutricional en Colombia, 2005. Instituto Colombiano de Bienestar Familiar, Bogot谩
    Encuesta Nacional de la Situaci贸n Nutricional en Colombia 2010 ENSIN. Instituto Colombiano de Bienestar Familiar, Bogot谩
    56. Duncan, SH, Belenguer, A, Holtrop, G, Johnstone, AM, Flint, HJ, Lobley, GE (2007) Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol 73: pp. 1073-1078
    57. Zhang, H, DiBaise, JK, Zuccolo, A, Kudrna, D, Braidotti, M, Yu, Y, Parameswaran, P, Crowell, MD, Wing, R, Rittmann, BE, Krajmalnik-Brown, R (2009) Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci U S A 106: pp. 2365-2370
    58. Walker, AW, Ince, J, Duncan, SH, Webster, LM, Holtrop, G, Ze, X, Brown, D, Stares, MD, Scott, P, Bergerat, A, Louis, P, McIntosh, F, Johnstone, AM, Lobley, GE, Parkhill, J, Flint, HJ (2011) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5: pp. 220-230
    59. Nam, YD, Jung, MJ, Roh, SW, Kim, MS, Bae, JW (2011) Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PLoS One 6: pp. e22109
    60. Lohman, TG, Roche, AF, Martorell, R (1988) Anthropometric Standardization Reference Manual. Human Kinetics Books, Champaign, IL
    61. Gontcharova, VYE, Wolcott, RD, Hollister, EB, Gentry, TJ, Dowd, SE (2010) Black Box Chimera Check (B2C2): a windows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets. Open Microbiol J 4: pp. 6
    62. Edgar, RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: pp. 2460-2461
    63. Caporaso, JG, Bittinger, K, Bushman, FD, DeSantis, TZ, Andersen, GL, Knight, R (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: pp. 266-267
    64. DeSantis, TZ, Hugenholtz, P, Larsen, N, Rojas, M, Brodie, EL, Keller, K, Huber, T, Dalevi, D, Hu, P, Andersen, GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: pp. 5069-5072
    65. Wang, Q, Garrity, GM, Tiedje, JM, Cole, JR (2007) Na茂ve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: pp. 5261-5267
    66. Caporaso, JG, Kuczynski, J, Stombaugh, J, Bittinger, K, Bushman, FD, Costello, EK, Fierer, N, Gonzalez Pena, A, Goodrich, JK, Gordon, JI, Huttley, GA, Kelley, ST, Knights, D, Koenig, JE, Ley, RE, Lozupone, CA, McDonald, D, Muegge, BD, Pirrung, M, Reeder, J, Sevinsky, JR, Turnbaugh, PJ, Walters, WA, Widmann, J, Yatsunenko, T, Zaneveld, J, Knight, R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: pp. 335-336
    67. Richter, M, Rossell贸-M贸ra, R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106: pp. 19126-19131
    68. Kim, M, Oh, HS, Park, SC, Chun, J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64: pp. 346-351
    69. Kim, SW, Suda, W, Kim, S, Oshima, K, Fukuda, S, Ohno, H, Morita, H, Hattori, M (2013) Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res 20: pp. 241-253
    70. Subramanian, S, Huq, S, Yatsunenko, T, Haque, R, Mahfuz, M, Alam, MA, Benezra, A, DeStefano, J, Meier, MF, Muegge, BD, Barratt, MJ, VanArendonk, LG, Zhang, Q, Province, MA, Petri, WA, Ahmed, T, Gordon, JI (2014) Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510: pp. 417-421
    71. Hartmann, M, Howes, CG, Abarenkov, K, Mohn, WW, Nilsson, RH (2010) V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences. J Microbiol Methods 83: pp. 250-253
    72. Lozupone, C, Knight, R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: pp. 8228-8235
    73. Hamady, M, Lozupone, C, Knight, R (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: pp. 17-27
    74. Verhoeven, KJF, Simonsen, KL, McIntyre, LM (2005) Implementing false discovery rate control: increasing your power. Oikos 108: pp. 643-647
    A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria
    75. Grime, JP (1998) Benefits of plant diversity to ecosystems: immediate, filter and founder effects. J Ecol 86: pp. 902-910
    76. Kostic, AD, Gevers, D, Pedamallu, CS, Michaud, M, Duke, F, Earl, AM, Ojesina, AI, Jung, J, Bass, AJ, Tabernero, J, Baselga, J, Liu, C, Shivdasani, RA, Ogino, S, Birren, BW, Huttenhower, C, Garrett, WS, Meyerson, M (2012) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 22: pp. 292-298
    77. Garrett, WS, Gallini, CA, Yatsunenko, T, Michaud, M, DuBois, A, Delaney, ML, Punit, S, Karlsson, M, Bry, L, Glickman, JN, Gordon, JI, Onderdonk, AB, Glimcher, LH (2010) Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8: pp. 292-300
    78. Bibiloni, R, Schiffrin, EJ (2010) Intestinal host-microbe interactions under physiological and pathological conditions. Int J Inflamm 2010: pp. 386956
    79. Hu, B, Elinav, E, Huber, S, Strowig, T, Hao, L, Hafemann, A, Jin, C, Eisenbarth, SC, Flavell, RA (2013) Microbiota-induced activation of epithelial IL-6 signaling links inflammasome-driven inflammation with transmissible cancer. Proc Natl Acad Sci U S A 110: pp. 9862-9867
    80. Ridaura, VK, Faith, JJ, Rey, FE, Cheng, J, Duncan, AE, Kau, AL, Griffin, NW, Lombard, V, Henrissat, B, Bain, JR, Muehlbauer, MJ, Ilkayeva, O, Semenkovich, CF, Funai, K, Hayashi, DK, Lyle, BJ, Martini, MC, Ursell, LK, Clemente, JC, Treuren, W, Walters, WA, Knight, R, Newgard, CB, Heath, AC, Gordon, JI (2013) Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341: pp. 1241214
    81. Armougom, F, Henry, M, Vialettes, B, Raccah, D, Raoult, D (2009) Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients. PLoS One 4: pp. e7125
    82. Santacruz, A, Collado, MC, Garcia-Valdes, L, Segura, MT, Martin-Lagos, JA, Anjos, T, Marti-Romero, M, Lopez, RM, Florido, J, Campoy, C, Sanz, Y (2010) Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. Br J Nutr 104: pp. 83-92
    83. Zupancic, ML, Cantarel, BL, Liu, Z, Drabek, EF, Ryan, KA, Cirimotich, S, Jones, C, Knight, R, Walters, WA, Knights, D, Mongodin, EF, Horenstein, RB, Mitchell, BD, Steinle, N, Snitker, S, Shuldiner, AR, Fraser, CM (2012) Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome. PLoS One 7: pp. e43052
    84. Kim, DW, Shim, JE, Paik, HY, Song, WO, Joung, H (2011) Nutritional intake of Korean population before and after adjusting for within-individual variations: 2001 Korean National Health and Nutrition Survey Data. Nutr Res Pract 5: pp. 266-274
    85. National Institute of Health and Nutrition: Outline for the Results of the National Health and Nutrition Survey Japan, 2007. [http://www0.nih.go.jp/eiken/english/research/pdf/nhns2007.pdf]
    86. What We Eat In America, NHANES 2009鈥?010: Documentation and Data Files [http://www.ars.usda.gov/Services/docs.htm?docid=18349]
    European Nutrition and Health Report 2009. European Commission, Health and Consumer Protection, Directorate-General, Vienna (Austria)
    87. Yoonna, L, Hae-Jeung, L, Haeng-Shin, L, Young-Ai, J, Cho-il, K (2008) Analytical dietary fiber database for the National Health and Nutrition Survey in Korea. J Food Composition Anal 21: pp. S35-S42
    88. McDonald, D, Price, MN, Goodrich, J, Nawrocki, EP, DeSantis, TZ, Probst, A, Andersen, GL, Knight, R, Hugenholtz, P (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6: pp. 610-618
    89. Bahl, MI, Bergstrom, A, Licht, TR (2012) Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett 329: pp. 193-197
    90. Hildebrandt, MA, Hoffmann, C, Sherrill-Mix, SA, Keilbaugh, SA, Hamady, M, Chen, YY, Knight, R, Ahima, RS, Bushman, F, Wu, GD (2009) High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137: pp. 1716-1724
    91. Mozes, S, Bujnakova, D, Sefcikova, Z, Kmet, V (2008) Developmental changes of gut microflora and enzyme activity in rat pups exposed to fat-rich diet. Obesity 16: pp. 2610-2615
    92. Guo, X, Xia, X, Tang, R, Zhou, J, Zhao, H, Wang, K (2008) Development of a real-time PCR method for Firmicutes and Bacteroidetes in faeces and its application to quantify intestinal population of obese and lean pigs. Lett Appl Microbiol 47: pp. 367-373
    93. Everard, A, Belzer, C, Geurts, L, Ouwerkerk, JP, Druart, C, Bindels, LB, Guiot, Y, Derrien, M, Muccioli, GG, Delzenne, NM, Schrenze, J, Cani, PD (2013) Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A 110: pp. 9066-9071
    94. Million, M, Thuny, F, Angelakis, E, Casalta, JP, Giorgi, R, Habib, G, Raoult, D (2013) Lactobacillus reuteri and Escherichia coli in the human gut microbiota may predict weight gain associated with vancomycin treatment. Nutrition & Diabetes 3: pp. e87
    95. Bhatt, AS, Freeman, SS, Herrera, AF, Pedamallu, CS, Gevers, D, Duke, F, Jung, J, Michaud, M, Walker, BJ, Young, S, Earl, AM, Kostic, AD, Ojesina, AI, Hasserjian, R, Ballen, KK, Chen, YB, Hobbs, G, Antin, JH, Soiffer, RJ, Baden, LR, Garrett, WS, Hornick, JL, Marty, FM, Meyerson, M (2013) Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome. N Engl J Med 369: pp. 517-528
    96. Raman, M, Ahmed, I, Gillevet, PM, Probert, CS, Ratcliffe, NM, Smith, S, Greenwood, R, Sikaroodi, M, Lam, V, Crotty, P, Bailey, J, Myers, RP, Rioux, KP (2013) Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol 11: pp. 868-875
    97. Wong, VW, Tse, CH, Lam, TT, Wong, GL, Chim, AM, Chu, WC, Yeung, DK, Law, PT, Kwan, HS, Yu, J, Sung, JJ, Chan, HL (2013) Molecular characterization of the fecal microbiota in patients with nonalcoholic steatohepatitis鈥揳 longitudinal study. PLoS One 8: pp. e62885
    98. Chen, W, Liu, F, Ling, Z, Tong, X, Xiang, C (2012) Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One 7: pp. e39743
    99. Passel, MW, Kant, R, Zoetendal, EG, Plugge, CM, Derrien, M, Malfatti, SA, Chain, PS, Woyke, T, Palva, A, Vos, WM, Smidt, H (2011) The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PLoS One 6: pp. e16876
    100. Axling, U, Olsson, C, Xu, J, Fernandez, C, Larsson, S, Strom, K, Ahrne, S, Holm, C, Molin, G, Berger, K (2012) Green tea powder and Lactobacillus plantarum affect gut microbiota, lipid metabolism and inflammation in high-fat fed C57BL/6聽J mice. Nutr Metab 9: pp. 105
    101. Karlsson, CLJ, Onnerfalt, J, Xu, J, Molin, G, Ahrne, S, Thorngren-Jerneck, K (2012) The microbiota of the gut in preschool children with normal and excessive body weight. Obesity 20: pp. 2257-2261
    102. Shin, NR, Lee, JC, Lee, HY, Kim, MS, Whon, TW, Lee, MS, Bae, JW (2013) An increase in the Akkermansia spp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice. Gut 63: pp. 727-735
  • 刊物主题:Microbiology; Biological Microscopy; Fungus Genetics; Parasitology; Virology; Life Sciences, general;
  • 出版者:BioMed Central
  • ISSN:1471-2180
文摘
Background The composition of the gut microbiota has recently been associated with health and disease, particularly with obesity. Some studies suggested a higher proportion of Firmicutes and a lower proportion of Bacteroidetes in obese compared to lean people; others found discordant patterns. Most studies, however, focused on Americans or Europeans, giving a limited picture of the gut microbiome. To determine the generality of previous observations and expand our knowledge of the human gut microbiota, it is important to replicate studies in overlooked populations. Thus, we describe here, for the first time, the gut microbiota of Colombian adults via the pyrosequencing of the 16S ribosomal DNA (rDNA), comparing it with results obtained in Americans, Europeans, Japanese and South Koreans, and testing the generality of previous observations concerning changes in Firmicutes and Bacteroidetes with increasing body mass index (BMI). Results We found that the composition of the gut microbiota of Colombians was significantly different from that of Americans, Europeans and Asians. The geographic origin of the population explained more variance in the composition of this bacterial community than BMI or gender. Concerning changes in Firmicutes and Bacteroidetes with obesity, in Colombians we found a tendency in Firmicutes to diminish with increasing BMI, whereas no change was observed in Bacteroidetes. A similar result was found in Americans. A more detailed inspection of the Colombian dataset revealed that five fiber-degrading bacteria, including Akkermansia, Dialister, Oscillospira, Ruminococcaceae and Clostridiales, became less abundant in obese subjects. Conclusion We contributed data from unstudied Colombians that showed that the geographic origin of the studied population had a greater impact on the composition of the gut microbiota than BMI or gender. Any strategy aiming to modulate or control obesity via manipulation of this bacterial community should consider this effect.

© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号

地址:北京市海淀区学院路29号 邮编:100083

电话:办公室:(+86 10)66554848;文献借阅、咨询服务、科技查新:66554700