Bacterial biogeography of the human digestive tract

Scientific Reports

Volumn 1, Issue , 2011, Pages

  Stearns, Jennifer C ^a,e   Lynch, Michael D J ^a,b   Senadheera, Dilani B ^c   Tenenbaum, Howard C ^c   Goldberg, Michael B ^c   Cvitkovitch, Dennis G ^c   Croitoru, Kenneth ^d   Moreno Hagelsieb, Gabriel ^b   Neufeld, Josh D ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b WILFRID LAURIER UNIVERSITY   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d MOUNT SINAI HOSPITAL   (Canada)

^e MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA 16S;

ADULT; ANTIBODY SPECIFICITY; ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; FEMALE; GASTROINTESTINAL TRACT; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MALE; METAGENOME; MICROBIOLOGY; PHYLOGENY;

ADULT; BACTERIA; BIODIVERSITY; FEMALE; GASTROINTESTINAL TRACT; HUMANS; MALE; METAGENOME; ORGAN SPECIFICITY; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

EID: 84859747964     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep00170     Document Type: Article

References (54)

1. Mazmanian, S. K., Liu, C. H., Tzianabos, A. O. & Kasper, D. L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107-118 (2005). (Pubitemid 40977944)
2. Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A. & Gordon, J. I. Hostbacterial mutualism in the human intestine. Science 307, 1915-1920 (2005).
3. Beck, J. D. et al. Periodontal disease and coronary heart disease: a reappraisal of the exposure. Circulation 112, 19-24 (2005). (Pubitemid 40962564)
4. Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl. Acad. Sci. U. S. A. 105, 16731-16736 (2008).
5. Vijay-Kumar, M. et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-Like Receptor 5. Science 328, 228-231 (2010).
6. Bercik, P. et al. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology 141, 599-609 (2011).
7. Bercik, P. et al. Chronic gastrointestinal inflammation induces anxiety-like behavior and alters central nervous system biochemistry in mice. Gastroenterology 139, 2102-2112 (2010).
8. Dewhirst, F. E. et al. The human oral microbiome. J. Bacteriol. 192, 5002-5017 (2010).
9. Lazarevic, V. et al. Metagenomic study of the oral microbiota by Illumina highthroughput sequencing. J. Microbiol. Meth. 79, 266-271 (2009).
10. Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A. & Brown, P. O. Development of the human infant intestinal microbiota. PLoS Biol. 5, e177 (2007).
11. Dominguez-Bello, M. G. et al. 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, 11971-11975 (2010).
12. Turnbaugh, P. et al. A core gut microbiome in obese and lean twins. Nature 457, 480-484 (2009).
13. Keijser, B. J. F. et al. Pyrosequencing analysis of the oral microflora of healthy adults. J. Dent. Res. 87, 1016-1020 (2008).
14. Willing, B. et al. A pyrosequencing study in twins shows that GImicrobial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844-1854 (2010).
15. Wade, W. G. Has the use of molecular methods for the characterization of the human oral microbiome changed our understanding of the role of bacteria in the pathogenesis of periodontal disease? J. Clin. Periodont. 38, 7-16 (2011).
16. Bik, E. M. et al. Molecular analysis of the bacterial microbiota in the human stomach. Proc. Natl. Acad. Sci. U. S. A. 103, 732-737 (2006). (Pubitemid 43153094)
17. Costello, E. K. et al. Bacterial community variation in human body habitats across space and time. Science 326, 1694-1697 (2009).
18. Grice, E. A. et al. Topographical and temporal diversity of the human skin microbiome. Science 324, 1190-1192 (2009).
19. Fierer, N., Hamady, M., Lauber, C. L. & Knight, R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc. Natl. Acad. Sci. U. S. A. 105, 17994-17999 (2008).
20. Caporaso, J. G. et al. Moving pictures of the human microbiome. Genome Biol. 12, R50 (2011).
21. Andersson, A. F. et al. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3, e2836 (2008).
22. Bartram, A. K., Lynch, M. D. J., Stearns, J. C., Moreno-Hagelsieb, G. & Neufeld, J. D. Generation of multi-million 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl. Environ. Microbiol. 77, 3846-3852 (2011).
23. Huse, S., Welch, D., Morrison, H. & Sogin, M. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12, 1889-1898 (2010).
24. Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659 (2006). (Pubitemid 43985301)
25. Gloor, G. et al. Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products. PLoS ONE e15406 (2010).
26. Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. U. S. A. 102, 11070-11075 (2005). (Pubitemid 41105994)
27. Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635-1638 (2005). (Pubitemid 40807514)
28. Sears, C. L. A dynamic partnership: celebrating our gut flora. Anaerobe 11, 247-251 (2005). (Pubitemid 41138226)
29. Bik, E. M. et al. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J 4, 962-974 (2010).
30. Belda-Ferre, P. et al. The oral metagenome in health and disease. ISME J In press (2011).
31. Ling, Z. et al. Analysis of oral microbiota in children with dental caries by PCRDGGE and barcoded pyrosequencing. Microb. Ecol. 60, 677-690 (2010).
32. Lawson, R. D. & Coyle, W. J. The noncolonic microbiome: does it really matter? Curr. Gastroenterol. Rep. 12, 259-262 (2010).
33. Kunin, V., Engelbrektson, A., Ochman, H. & Hugenholtz, P. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12, 118-123 (2010).
34. Guarner, F. & Malagelada, J. R. Gut flora in health and disease. The Lancet 361, 512-519 (2003). (Pubitemid 36173720)
35. Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
36. Dinis, J. M. et al. In search of an uncultured human-associated TM7 bacterium in the environment. PLoS ONE 6, e21280 (2011).
37. Paster, B. J. et al. Bacterial diversity in human subgingival plaque. J. Bacteriol. 183, 3770-3783 (2001). (Pubitemid 32510445)
38. Kazor, C. E. et al. Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients. J. Clin. Microbiol. 41, 558-563 (2003). (Pubitemid 36184161)
39. Kumar, P. S. et al. New bacterial species associated with chronic periodontitis. J. Dent. Res. 82, 338-344 (2003). (Pubitemid 41756823)
40. Pei, Z. et al. Bacterial biota in the human distal esophagus. Proc. Natl. Acad. Sci. U. S. A. 101, 4250-4255 (2004). (Pubitemid 38405915)
41. Kuehbacher, T. et al. Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease. J. Med. Microbiol. 57, 1569-1576 (2008).
42. Fredricks, D. N., Fiedler, T. L., Thomas, K. K., Oakley, B. B. & Marrazzo, J. M. Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis. J. Clin. Microbiol. 45, 3270-3276 (2007). (Pubitemid 47585650)
43. Gao, Z., Tseng, C.-h., Pei, Z. & Blaser, M. J. Molecular analysis of human forearm superficial skin bacterial biota. Proc. Natl. Acad. Sci. U. S. A. 104, 2927-2932 (2007). (Pubitemid 46327980)
44. Sogin, M. L. et al. Microbial diversity in the deep sea and the underexplored "rare biosphere" Proc. Natl. Acad. Sci. U. S. A. 103, 12115-12120 (2006). (Pubitemid 44215820)
45. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Na?̈ve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267 (2007). (Pubitemid 47326658)
46. Lane, D. J. in Nucleic acid techniques in bacterial systematics. (eds E. Stackebrandt & M. Goodfellow) 115-175 (John Wiley & Sons, Inc, 1991).
47. Muyzer, G., de Waal, E. C. & Uitterlinden, A. G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695-700 (1993). (Pubitemid 23072343)
48. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
49. Wickham, H. ggplot2: elegant graphics for data analysis. (Springer-Verlag New York Inc, 2009).
50. R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing Vienna Austria ISBN 3 (2008).
51. 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).
52. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336 (2010).
53. Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641-1650 (2009).
54. Rambaut, A. & Drummond, A. FigTree v1. 3. 1. Institute of Evolutionary Biology, University of Edinburgh (2010).