Characterization of fecal microbiota across seven Chinese ethnic groups by quantitative polymerase chain reaction

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Kwok, Lai Yu ^a   Zhang, Jiachao ^a   Guo, Zhuang ^a   Gesudu, Qimu ^a   Zheng, Yi ^a   Qiao, Jianmin ^a   Huo, Dongxue ^a   Zhang, Heping ^a  

^a Inner Mongolia Agricultural University   (Mongolia)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; ATOPOBIUM; BACTEROIDES FRAGILIS; BIFIDOBACTERIUM; CHINESE; CLOSTRIDIUM; CLOSTRIDIUM COCCOIDES; CLOSTRIDIUM LEPTUM; CLOSTRIDIUM PERFRINGENS; CONTROLLED STUDY; DESULFOVIBRIO; ENTEROBACTERIACEAE; ETHNIC DIFFERENCE; FECES MICROFLORA; FEMALE; HUMAN; LACTOBACILLUS; MALE; NONHUMAN; NORMAL HUMAN; POLYMERASE CHAIN REACTION; PREVOTELLA; QUANTITATIVE POLYMERASE CHAIN REACTION; BACTERIAL COUNT; CHINA; ETHNIC GROUP; FECES; MICROBIOLOGY; MICROFLORA; NUCLEOTIDE SEQUENCE; PROCEDURES;

PRIMER DNA;

BASE SEQUENCE; CHINA; COLONY COUNT, MICROBIAL; DNA PRIMERS; ETHNIC GROUPS; FECES; HUMANS; MICROBIOTA; POLYMERASE CHAIN REACTION;

EID: 84899093426     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093631     Document Type: Article

References (44)

1. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Hostbacterial mutualism in the human intestine. Science 307: 1915-1920. doi:10.1126/science.1104816.
2. Baquero F, Nombela C (2012) The microbiome as a human organ. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis 18 Suppl 4: 2-4. doi:10.1111/j.1469-0691.2012.03916.x.
3. Round JL, Mazmanian SK (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9: 313-323. doi:10.1038/nri2515.
4. Sekirov I, Russell SL, Antunes LCM, Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90: 859-904. doi:10.1152/physrev.00045.2009.
5. Clemente JC, Ursell LK, Parfrey LW, Knight R (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148: 1258-1270. doi:10.1016/j.cell.2012.01.035.
6. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031. doi:10.1038/nature05414. (Pubitemid 46018515)
7. Larsen N, Vogensen FK, van den Berg FWJ, Nielsen DS, Andreasen AS, et al. (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PloS One 5: e9085. doi:10.1371/journal.pone.0009085.
8. Hörmannsperger G, Clavel T, Haller D (2012) Gut matters: microbe-host interactions in allergic diseases. J Allergy Clin Immunol 129: 1452-1459. doi:10.1016/j.jaci.2011.12.993.
9. Scher JU, Abramson SB (2011) The microbiome and rheumatoid arthritis. Nat Rev Rheumatol 7: 569-578. doi:10.1038/nrrheum.2011.121.
10. Kuwahara T, Ogura Y, Oshima K, Kurokawa K, Ooka T, et al. (2011) The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing. DNA Res Int J Rapid Publ Rep Genes Genomes 18: 291-303. doi:10.1093/dnares/ dsr022.
11. Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, et al. (2011) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5: 220-230. doi:10.1038/ismej.2010.118.
12. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638. doi:10.1126/science.1110591. (Pubitemid 40807514)
13. Nam Y-D, Jung M-J, Roh SW, Kim M-S, Bae J-W (2011) Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PloS One 6: e22109. doi:10.1371/journal.pone.0022109.
14. Peris-Bondia F, Latorre A, Artacho A, Moya A, D'Auria G (2011) The active human gut microbiota differs from the total microbiota. PloS One 6: e22448. doi:10.1371/journal.pone.0022448.
15. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, et al. (2011) Enterotypes of the human gut microbiome. Nature 473: 174-180. doi:10.1038/nature09944.
16. Lay C, Rigottier-Gois L, Holmstrøm K, Rajilic M, Vaughan EE, et al. (2005) Colonic microbiota signatures across five northern European countries. Appl Environ Microbiol 71: 4153-4155. doi:10.1128/AEM.71.7.4153-4155. 2005. (Pubitemid 40980596)
17. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, et al. (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: 14691-14696. doi:10.1073/pnas.1005963107.
18. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, et al. (2012) Human gut microbiome viewed across age and geography. Nature 486: 222-227. doi:10.1038/nature11053.
19. Inglis GD, Thomas MC, Thomas DK, Kalmokoff ML, Brooks SPJ, et al. (2012) Molecular methods to measure intestinal bacteria: a review. J AOAC Int 95: 5-23.
20. Dethlefsen L, Relman DA (2011) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 108 Suppl 1: 4554-4561. doi:10.1073/pnas.1000087107.
21. Hammer Ø, Ryan PD, Harper DAT (2001) PAST: Paleontological Statistics software package for education and data analysis. Palaeontol Electron 4: 9.
22. Kirkma TW (1996) Statistics to Use. Available: http://www.physics.csbsju. edu/stats/. Accessed 2013 June 27
23. Mueller S, Saunier K, Hanisch C, Norin E, Alm L, et al. (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: 1027-1033. doi:10.1128/AEM.72.2.1027-1033.2006. (Pubitemid 43271206)
24. Su B, Xiao J, Underhill P, Deka R, Zhang W, et al. (1999) Y-Chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age. Am J Hum Genet 65: 1718-1724. doi:10.1086/302680. (Pubitemid 30468685)
25. Yao Y-G, Nie L, Harpending H, Fu Y-X, Yuan Z-G, et al. (2002) Genetic relationship of Chinese ethnic populations revealed by mtDNA sequence diversity. Am J Phys Anthropol 118: 63-76. doi:10.1002/ajpa.10052. (Pubitemid 34327047)
26. Yao Y-G, Kong Q-P, Wang C-Y, Zhu C-L, Zhang Y-P (2004) Different matrilineal contributions to genetic structure of ethnic groups in the silk road region in china. Mol Biol Evol 21: 2265-2280. doi:10.1093/molbev/msh238. (Pubitemid 39488897)
27. Lin H, Fan H, Zhang F, Huang X, Lin K, et al. (2010) Genetic relationships of ethnic minorities in Southwest China revealed by microsatellite markers. PloS One 5: e9895. doi:10.1371/journal.pone.0009895.
28. Chen J, Zheng H, Bei J-X, Sun L, Jia W, et al. (2009) Genetic structure of the Han Chinese population revealed by genome-wide SNP variation. Am J Hum Genet 85: 775-785. doi:10.1016/j.ajhg.2009.10.016.
29. Chu JY, Huang W, Kuang SQ, Wang JM, Xu JJ, et al. (1998) Genetic relationship of populations in China. Proc Natl Acad Sci U S A 95: 11763-11768. (Pubitemid 28460488)
30. Yao Y-G, Kong Q-P, Bandelt H-J, Kivisild T, Zhang Y-P (2002) Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet 70: 635-651. doi:10.1086/338999. (Pubitemid 34177919)
31. Unger J (1997) Not quite Han?: the ethnic minorities of China's southwest. Bull Concerned Asian Sch 29: 67-78.
32. Zhai F, He Y, Wang Z, Hu Y (2007) [Status and characteristic of dietary intake of 12 minority nationalities in China]. Wei Sheng Yan Jiu 36: 539-541.
33. Ge K, Zhai F, Wang Q (1997) Effect of nationality on dietary pattern and meal behavior in China. Am J Clin Nutr 65: 1290S-1294S. (Pubitemid 27152601)
34. Mariat D, Firmesse O, Levenez F, Guimarǎes V, Sokol H, et al. (2009) The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9: 123. doi:10.1186/1471-2180-9-123.
35. Duncan SH, Flint HJ (2013) Probiotics and prebiotics and health in ageing populations. Maturitas. Available: http://linkinghub.elsevier.com/retrieve/pii/ S0378512213000492. Accessed 2013 April 14.
36. Maukonen J, Simões C, Saarela M (2012) The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples. FEMS Microbiol Ecol 79: 697-708. doi:10.1111/j.1574-6941.2011.01257.x.
37. Nechvatal JM, Ram JL, Basson MD, Namprachan P, Niec SR, et al. (2008) Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. J Microbiol Methods 72: 124-132. doi:10.1016/j.mimet.2007.11.007.
38. Matsuki T, Watanabe K, Fujimoto J, Takada T, Tanaka R (2004) Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl Environ Microbiol 70: 7220-7228. doi:10.1128/AEM.70.12.7220-7228.2004. (Pubitemid 39643786)
39. Matsuki T, Watanabe K, Fujimoto J, Miyamoto Y, Takada T, et al. (2002) Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl Environ Microbiol 68: 5445-5451. (Pubitemid 35265679)
40. Kikuchi E, Miyamoto Y, Narushima S, Itoh K (2002) Design of species-specific primers to identify 13 species of Clostridium harbored in human intestinal tracts. Microbiol Immunol 46: 353-358. (Pubitemid 34535009)
41. Fite A, Macfarlane GT, Cummings JH, Hopkins MJ, Kong SC, et al. (2004) Identification and quantitation of mucosal and faecal desulfovibrios using real time polymerase chain reaction. Gut 53: 523-529. (Pubitemid 38372976)
42. Matsuda K, Tsuji H, Asahara T, Kado Y, Nomoto K (2007) Sensitive quantitative detection of commensal bacteria by rRNA-targeted reverse transcription-PCR. Appl Environ Microbiol 73: 32-39. doi:10.1128/AEM.01224-06. (Pubitemid 46079932)
43. Rinttilä T, Kassinen A, Malinen E, Krogius L, Palva A (2004) Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. J Appl Microbiol 97: 1166-1177. doi:10.1111/j.1365-2672.2004.02409.x. (Pubitemid 39573940)
44. Bartosch S, Fite A, Macfarlane GT, McMurdo MET (2004) Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota. Appl Environ Microbiol 70: 3575-3581. doi:10.1128/AEM.70. 6.3575-3581.2004. (Pubitemid 38745906)