Towards the human colorectal cancer microbiome

PLoS ONE

Volumn 6, Issue 5, 2011, Pages

  Marchesi, Julian R ^a   Dutilh, Bas E ^b,c   Hall, Neil ^d   Peters, Wilbert H M ^e   Roelofs, Rian ^e   Boleij, Annemarie ^e   Tjalsma, Harold ^e  

^a CARDIFF UNIVERSITY   (United Kingdom)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^c SAN DIEGO STATE UNIVERSITY   (United States)

^d UNIVERSITY OF LIVERPOOL   (United Kingdom)

^e RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RIBOSOME RNA; RNA 16S; SPACER DNA;

ADULT; AGED; ARTICLE; BACTERIAL COLONIZATION; COLORECTAL CANCER; COMMENSAL; CONTROLLED STUDY; CORIOBACTERIACEAE; CORRELATIONAL STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; ENTEROBACTERIACEAE; FEMALE; HUMAN; HUMAN TISSUE; INTESTINE FLORA; MALE; METABOLIC BALANCE; MICROBIOME; NONHUMAN; PHYSIOLOGICAL PROCESS; PYROSEQUENCING; REGULATORY RNA SEQUENCE; TUMOR MICROENVIRONMENT; BACTERIUM ADHERENCE; COLORECTAL TUMOR; DNA FINGERPRINTING; GENETICS; INTESTINE MUCOSA; METAGENOME; MICROBIOLOGY; MIDDLE AGED; PATHOLOGY; RIBOSOME; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); ENTEROBACTERIACEAE;

AGED; BACTERIAL ADHESION; COLORECTAL NEOPLASMS; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA FINGERPRINTING; DNA, INTERGENIC; FEMALE; HUMANS; INTESTINAL MUCOSA; MALE; METAGENOME; MIDDLE AGED; RIBOSOMES; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA;

EID: 79956359184     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020447     Document Type: Article

References (57)

1. Hooper LV, Gordon JI, (2001) Commensal host-bacterial relationships in the gut. Science 292: 1115-1118.
2. Parkin DM, (2006) The global health burden of infection-associated cancers in the year 2002. In Int J Cancer 118: 3030-3044.
3. Mager DL, (2006) Bacteria and Cancer: Cause, Coincidence or Cure? J Transl Med 4: 14.
4. Zur Hausen H, (2006) Streptococcus bovis: causal or incidental involvement in cancer of the colon? Int J Cancer 119: xi-xii.
5. Rowland IR, (2009) The role of the gastrointestinal microbiota in colorectal cancer. Cur Pharm Des 15: 1524-1527.
6. Waisberg J, Matheus CdeO, Pimenta J, (2002) Infectious endocarditis from Streptococcus bovis associated with colonic carcinoma: case report and literature review. Arq Gastroenterol 39: 177-180.
7. Boleij A, Schaeps RM, Tjalsma H, (2009) Association between Streptococcus bovis and colon cancer. J Clin Microbiol 47: 516.
8. Seder CW, Kramer M, Long G, Uzieblo MR, Shanley CJ, et al. (2009) Clostridium septicum aortitis: Report of two cases and review of the literature. J Vasc Surg 49: 1304-1309.
9. Tjalsma H, Schöller-Guinard M, Lasonder E, Ruers TJ, Willems HL, et al. (2006) Profiling the humoral immune response in colon cancer patients: diagnostic antigens from Streptococcus bovis. Int J Cancer 119: 2127-2135.
10. Toprak NU, Yagci A, Gulluoglu BM, Akin ML, Demirkalem P, et al. (2006) A possible role of Bacteroides fragilis enterotoxin in the aetiology of colorectal cancer. Clin Microbiol Infect 12: 782-786.
11. Wang X, Allen TD, May RJ, Lightfoot S, Houchen CW, et al. (2008) Enterococcus faecalis induces aneuploidy and tetraploidy in colonic epithelial cells through a bystander effect. Cancer Res 68: 9909-9917.
12. Wu S, Rhee KJ, Albesiano E, Rabizadeh S, Wu X, et al. (2009) A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nat Med 15: 1016-1022.
13. Cuevas-Ramos G, Petit CR, Marcq I, Boury M, Oswald E, et al. (2010) Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells. Proc Natl Acad Sci U S A 107: 11537-11542.
14. Lee SH, Hu LL, Gonzalez-Navajas J, Seo GS, Shen C, et al. (2010) ERK activation drives intestinal tumorigenesis in Apc(min/+) mice. Nat Med 16: 665-670.
15. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the Human Intestinal Microbial Flora. Science 308: 1635-1638.
16. Green GL, Brostoff J, Hudspith B, Michael M, Mylonaki M, et al. (2006) Molecular characterization of the bacteria adherent to human colorectal mucosa. J Appl Microbiol 100: 460-469.
17. Dethlefsen L, Eckburg PB, Bik EM, Relman DA, (2006) Assembly of the human intestinal microbiota. Trends Ecol Evol 21: 517-523.
18. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, et al. (2009) Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697.
19. Scott-Conner CE, Christie DW, (1995) Cancer staging using the American Joint Committee on Cancer TNM System. J Am Coll Surg 181: 182-188.
20. Boon N, De Windt W, Verstraete W, Top EM, (2002) Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiol Ecol 39: 101-112.
21. Lane DJ, Stackebrandt E, Goodfellow M, (1991) 16S/23S rRNA Sequencing. Nucleic Acids Techniques in Bacterial Systematics Chichester John Wileyand Sons pp. 115-175.
22. Nubel U, Engelen B, Felske A, Snaidr J, Wieshuber A, et al. (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bact 178: 5636-5643.
23. Scanlan PD, Shanahan F, Clune Y, Collins JK, O'Sullivan GC, et al. (2008) Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol 10: 1382.
24. Borneman J, Triplett EW, (1997) Molecular microbial diversity in soils from eastern Amazonia: Evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63: 2647-2653.
25. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucl Acids Res 37: D141-145.
26. Huse SM, Welch DM, Morrison HG, Sogin ML, (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12: 1889-1898.
27. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: Open Source, Platform-independent, Community-supported Software for Describing and Comparing Microbial Communities. Appl Environ Microbiol 75: 7537-7541.
28. Huson DH, Richter DC, Mitra S, Auch AF, Schuster SC, (2009) Methods for comparative metagenomics. BMC Bioinformatics 10 (Suppl 1): S12.
29. Rudi K, Zimonja M, Kvenshagen B, Rugtveit J, Midtvedt T, et al. (2007) Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space. Appl Environ Microbiol 73: 2727-2734.
30. Rudi K, Zimonja M, Trosvik P, Næs T, (2007) Use of multivariate statistics for 16S rRNA gene analysis of microbial communities. Int J Food Microbiol 120: 95-99.
31. Rudi K, Zimonja M, Naes T, (2006) Alignment-independent bilinear multivariate modelling (AIBIMM) for global analyses of 16S rRNA gene phylogeny. Int J Syst Evol Microbiol 56: 1565-1575.
32. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
33. Kent WJ, (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
34. Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben Amor K, Akkermans AD, et al. (2002) Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 68: 3401-3407.
35. Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, et al. (2006) Rapid quantitative profiling of complex microbial populations. Nucleic Acids Research 34: e5.
36. Ahmed S, Macfarlane GT, Fite A, McBain AJ, Gilbert P, et al. (2007) Mucosa-Associated Bacterial Diversity in Relation to Human Terminal Ileum and Colonic Biopsy Samples. Appl Environ Microbiol 73: 7435-7442.
37. Boleij A, Roelofs R, Schaeps RM, Schülin T, Glaser P, Swinkels DW, et al. (2010) Increased exposure to bacterial antigen RpL7/L12 in early stage colorectal cancer patients. Cancer 116: 4014-22.
38. Sansonetti PJ, (2004) War and peace at mucosal surfaces. Nat Rev Immunol 4: 953-964.
39. Corfield AP, Myerscough N, Longman R, Sylvester P, Arul S, et al. (2000) Mucins and mucosal protection in the gastrointestinal tract: new prospects for mucins in the pathology of gastrointestinal disease. Gut 47: 589-594.
40. Dhawan P, Singh AB, Deane NG, No Y, Shiou SR, et al. (2005) Claudin-1 regulates cellular transformation and metastatic behavior in colon cancer. J Clin Invest 115: 1765-1776.
41. Hirayama A, Kami K, Sugimoto M, Sugawara M, Toki N, et al. (2009) Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry. Cancer Res 69: 4918-4925.
42. Righi V, Durante C, Cocchi M, Calabrese C, Di Febo G, et al. (2009) Discrimination of healthy and neoplastic human colon tissues by ex vivo HR-MAS NMR spectroscopy and chemometric analyses. J Proteome Res 8: 1859-1869.
43. Makivuokko H, Tiihonen K, Tynkkynen S, Paulin L, Rautonen N, (2009) The effect of age and non-steroidal anti-inflammatory drugs on human intestinal microbiota composition. Br J Nutr 103: 227-234.
44. Bordonaro M, Lazarova DL, Sartorelli AC, (2008) Butyrate and Wnt signaling: a possible solution to the puzzle of dietary fiber and colon cancer risk? Cell Cycle 7: 1178-1183.
45. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, et al. (2008) 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.
46. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, et al. (2009) Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 15: 1183-1189.
47. Jin JS, Kitahara M, Sakamoto M, Hattori M, Benno Y, (2009) Slackia equolifaciens sp. nov., a human intestinal bacterium capable of producing equol. Int J Syst Evol Microbiol 4: 4.
48. Choi EJ, Ahn WS, Bae SM, (2009) Equol induces apoptosis through cytochrome c-mediated caspases cascade in human breast cancer MDA-MB-453 cells. Chem Biol Interact 177: 7-11.
49. Qin JJ, Li RQ, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-U70.
50. DuPont HL, (2009) Clinical practice. Bacterial diarrhea. N Engl J Med 361: 1560-1569.
51. Shen X, Rawls J, Randall T, Burcal L, Mpande C, et al. (2010) Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes 1: 138-147.
52. Newman JV, Kosaka T, Sheppard BJ, Fox JG, Schauer DB, (2001) Bacterial infection promotes colon tumorigenesis in Apc(Min/+) mice. J Infect Dis 184: 227-230.
53. Maggio-Price L, Treuting P, Bielefeldt-Ohmann H, Seamons A, Drivdahl R, et al. (2009) Bacterial infection of Smad3/Rag2 double-null mice with transforming growth factor-beta dysregulation as a model for studying inflammation-associated colon cancer. Am J Pathol 174: 317-329.
54. Nougayrede JP, Homburg S, Taieb F, Boury M, Brzuszkiewicz E, et al. (2006) Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 313: 848-851.
55. Vogelstein B, Kinzler KW, (1993) The multistep nature of cancer. Trends Genet 9: 138-141.
56. Kang HY, Kim N, Park YS, Hwang JH, Kim JW, et al. (2006) Progression of atrophic gastritis and intestinal metaplasia drives Helicobacter pylori out of the gastric mucosa. Dig Dis Sci 51: 2310-2315.
57. Sobhani I, Tap J, Roudot-Thoraval F, Roperch JP, Letulle S, et al. (2011) Microbial Dysbiosis in Colorectal Cancer (CRC) Patients. PLoS One 6 (1): e16393.