Co-occurrence of anaerobic bacteria in colorectal carcinomas

Microbiome

Volumn 1, Issue 1, 2013, Pages

  Warren, René L ^a   Freeman, Douglas J ^a   Pleasance, Stephen ^a   Watson, Peter ^a   Moore, Richard A ^a,b   Cochrane, Kyla ^c   Allen Vercoe, Emma ^c   Holt, Robert A ^a,b,d  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b SIMON FRASER UNIVERSITY   (Canada)

^c UNIVERSITY OF GUELPH   (Canada)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Anaerobe; Cancer; Emerging pathogens; Host microbe interaction; Microbial genomics; Microbiome

Indexed keywords

BETA LACTAMASE; HLA ANTIGEN CLASS 1; INTERLEUKIN 8; MULTIDRUG RESISTANCE PROTEIN;

ANAEROBIC BACTERIUM; ARTICLE; BACTERIAL VIRULENCE; CAMPYLOBACTER; CAMPYLOBACTER SHOWAE; COLORECTAL CARCINOMA; CONTROLLED STUDY; ELECTRON MICROSCOPY; FUSOBACTERIUM NUCLEATUM; GENE EXPRESSION; GENE SEQUENCE; HUMAN; HUMAN TISSUE; LEPTOTRICHIA; MAJOR CLINICAL STUDY; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTOMICS;

BACTERIA (MICROORGANISMS); CAMPYLOBACTER; CAMPYLOBACTER SHOWAE; FUSOBACTERIUM; FUSOBACTERIUM NUCLEATUM; LEPTOTRICHIA; NEGIBACTERIA;

EID: 84896066661     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/2049-2618-1-16     Document Type: Article

References (48)

1. Parkin DM. The global health burden of infection-associated cancers in the year 2002. Int J Cancer 2006, 118:3030-3044. 10.1002/ijc.21731, 16404738.
2. Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chénard C, Friedman JM, Suttle CA, Zhao Y, Holt RA. The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PLoS One 2011, 6:e19838. 10.1371/journal.pone.0019838, 3094400, 21603639.
3. Feng H, Shuda M, Chang Y, Moore PS. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 2008, 319:1096-1100. 10.1126/science.1152586, 2740911, 18202256.
4. Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 2012, 22:299-306. 10.1101/gr.126516.111, 3266037, 22009989.
5. 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. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 2012, 22:292-298. 10.1101/gr.126573.111, 3266036, 22009990.
6. McCoy AN, Araújo-Pérez F, Azcárate-Peril A, Yeh JJ, Sandler RS, Keku TO. Fusobacterium is associated with colorectal adenomas. PLoS One 2013, 8:e53653. 10.1371/journal.pone.0053653, 3546075, 23335968.
7. Han YW, Shi W, Huang GT, Kinder Haake S, Park NH, Kuramitsu H, Genco RJ. Interactions between periodontal bacteria and human oral epithelial cells: Fusobacterium nucleatum adheres to and invades epithelial cells. Infect Immun 2000, 68:3140-3146. 10.1128/IAI.68.6.3140-3146.2000, 97547, 10816455.
8. Krisanaprakornkit S, Kimball JR, Weinberg A, Darveau RP, Bainbridge BW, Dale BA. Inducible expression of human beta-defensin 2 by Fusobacterium nucleatum in oral epithelial cells: multiple signaling pathways and role of commensal bacteria in innate immunity and the epithelial barrier. Infect Immun 2000, 68:2907-2915. 10.1128/IAI.68.5.2907-2915.2000, 97503, 10768988.
9. Peyret-Lacombe A, Brunel G, Watts M, Charveron M, Duplan H. TLR2 sensing of F. nucleatum and S. sanguinis distinctly triggered gingival innate response. Cytokine 2009, 46:201-210. 10.1016/j.cyto.2009.01.006, 19299164.
10. Signat B, Roques C, Poulet P, Duffaut D. Fusobacterium nucleatum in Periodontal Health and Disease. Curr Issues Mol Biol 2011, 13:25-36.
11. Swidsinski A, Dörffel Y, Loening-Baucke V, Theissig F, Rückert JC, Ismail M, Rau WA, Gaschler D, Weizenegger M, Kühn S, Schilling J, Dörffel WV. Acute appendicitis is characterised by local invasion with Fusobacterium nucleatum/necrophorum. Gut 2011, 60:34-40. 10.1136/gut.2009.191320, 19926616.
12. Strauss J, White A, Ambrose C, McDonald J, Allen-Vercoe E. Phenotypic and genotypic analyses of clinical Fusobacterium nucleatum and Fusobacterium periodonticum isolates from the human gut. Anaerobe 2008, 14:301-309. 10.1016/j.anaerobe.2008.12.003, 19114111.
13. Strauss J, Kaplan GG, Beck PL, Rioux K, Panaccione R, Devinney R, Lynch T, Allen-Vercoe E. Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm Bowel Dis 2011, 17:1971-1978. 10.1002/ibd.21606, 21830275.
14. Zilm PS, Rogers AH. Co-adhesion and biofilm formation by Fusobacterium nucleatum in response to growth pH. Anaerobe 2007, 13:146-152. 10.1016/j.anaerobe.2007.04.005, 17540586.
15. Fardini Y, Wang X, Témoin S, Nithianantham S, Lee D, Shoham M, Han YW. Fusobacterium nucleatum adhesin FadA binds vascular endothelial cadherin and alters endothelial integrity. Mol Microbiol 2011, 82:1468-1480. 10.1111/j.1365-2958.2011.07905.x, 3237733, 22040113.
16. Watson PH, Wilson-McManus JE, Barnes RO, Giesz SC, Png A, Hegele RG, Brinkman JN, Mackenzie IR, Huntsman DG, Junker A, Gilks B, Skarsgard E, Burgess M, Aparicio S, McManus BM. Evolutionary concepts in biobanking - the BC BioLibrary. J Transl Med 2009, 7:95. 10.1186/1479-5876-7-95, 2785772, 19909513.
17. Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, Steidl C, Holt RA, Jones S, Sun M, Leung G, Moore R, Severson T, Taylor GA, Teschendorff AE, Tse K, Turashvili G, Varhol R, Warren RL, Watson P, Zhao Y, Caldas C, Huntsman D, Hirst M, Marra MA, Aparicio S. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 2009, 461:809-813. 10.1038/nature08489, 19812674.
18. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, Yap D, Humphries RK, Griffith OL, Shah S, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao Y, Delaney A, Qian H, Birol I, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Aparicio S, Hirst M, Gascoyne RD, Marra MA. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet 2010, 42:181-185. 10.1038/ng.518, 2850970, 20081860.
19. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, et al. Ensembl 2011. Nucleic Acids Res 2011, 39:D800-D806. 10.1093/nar/gkq1064, 3013672, 21045057.
20. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26:589-595. 10.1093/bioinformatics/btp698, 2828108, 20080505.
21. International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945. 10.1038/nature03001, 15496913, International Human Genome Sequencing Consortium.
22. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res 2008, 36:D25-D30. 10.1093/nar/gkn320, 2238942, 18073190.
23. Human Microbiome Jumpstart Reference Strains C, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, et al. A catalog of reference genomes from the human microbiome. Science 2010, 328:994-999. 2940224, 20489017.
24. White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 2009, 5:e1000352. 10.1371/journal.pcbi.1000352, 2661018, 19360128.
25. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2:2366-2382. 10.1038/nprot.2007.324, 3685583, 17947979.
26. Chessel D, Dufour AB, Thioulouse J. The ade4 package-I - One-table methods. R News 2004, 4:5-10.
27. Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA. Derivation of HLA types from shotgun sequence datasets. Genome Med 2012, 4:95. 10.1186/gm396, 3580435, 23228053.
28. Warren RL, Holt RA. Targeted assembly of short sequence reads. PLoS One 2011, 6:e19816. 10.1371/journal.pone.0019816, 3092772, 21589938.
29. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
30. Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG. The IMGT/HLA database. Nucleic Acids Res 2011, 39:D1171-D1176. 10.1093/nar/gkq998, 3013815, 21071412.
31. Gonzalez-Galarza FF, Christmas S, Middleton D, Jones AR. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acid Res 2011, 39:D913-D919. 10.1093/nar/gkq1128, 3013710, 21062830.
32. Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA. Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res 2011, 21:790-797. 10.1101/gr.115428.110, 3083096, 21349924.
33. Etoh Y, Dewhirst FE, Paster BJ, Yamamoto A, Goto N. Campylobacter showae sp. nov., isolated from the human oral cavity. Int J Syst Bacteriol 1993, 43:631-639. 10.1099/00207713-43-4-631, 7694633.
34. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829. 10.1101/gr.074492.107, 2336801, 18349386.
35. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, et al. NIH HMP Working Group The NIH Human Microbiome Project. Genome Res 2009, 19:2317-2323. 2792171, 19819907, NIH HMP Working Group.
36. 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, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65. 10.1038/nature08821, 20203603.
37. Iyer VN, Klee HJ, Nester EW. Units of genetic expression in the virulence region of plant tumor-inducing plasmid of Agrobacterium tumefaciens. Mol Gen Genet 1982, 188:418-424. 10.1007/BF00330043, 6298572.
38. Alvarez-Martinez CE, Christie PJ. Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 2009, 73:775-808. 2786583, 19946141.
39. Censini S, Lange C, Xiang Z, Crabtree JE, Ghiara P, Borodovsky M, Rappuoli R, Covacci A. Cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proc Natl Acad Sci USA 1996, 93:14648-14653. 10.1073/pnas.93.25.14648, 26189, 8962108.
40. Suerbaum S, Josenhans C. Helicobacter pylori evolution and phenotypic diversification in a changing host. Nat Rev Microbiol 2007, 5:441-452. 10.1038/nrmicro1658, 17505524.
41. Macuch PJ, Tanner AC. Campylobacter species in health, gingivitis, and periodontitis. J Dent Res 2000, 79:785-792. 10.1177/00220345000790021301, 10728981.
42. Eribe ER, Olsen I. Leptotrichia species in human infections. Anaerobe 2008, 14:131-137. 10.1016/j.anaerobe.2008.04.004, 18539056.
43. Weinberger M, Wu T, Rubin M, Gill VJ, Pizzo PA. Leptotrichia buccalis bacteremia in patients with cancer: report of four cases and review. Rev Infect Dis 1991, 13:201-206. 10.1093/clinids/13.2.201, 2041949.
44. Brauner A, Brandt L, Frisan T, Thelestam M, Ekbom A. Is there a risk of cancer development after Campylobacter infection?. Scand J Gastroenterol 2010, 45:893-897. 10.3109/00365521003734133, 20334473.
45. Kolenbrander PE, Andersen RN, Moore LV. Coaggregation of Fusobacterium nucleatum, Selenomonas flueggei, Selenomonas infelix, Selenomonas noxia, and Selenomonas sputigena with strains from 11 genera of oral bacteria. Infect Immun 1989, 57:3194-3203. 260789, 2777378.
46. Bolstad AI, Jensen HB, Bakken V. Taxonomy, biology, and periodontal aspects of Fusobacterium nucleatum. Clin Microbiol Rev 1996, 9:55-71. 172882, 8665477.
47. Edwards AM, Grossman TJ, Rudney JD. Fusobacterium nucleatum transports noninvasive Streptococcus cristatus into human epithelial cells. Infect Immun 2006, 74:654-662. 10.1128/IAI.74.1.654-662.2006, 1346643, 16369022.
48. Zhang G, Chen R, Rudney JD. Streptococcus cristatus modulates the Fusobacterium nucleatum-induced epithelial interleukin-8 response through the nuclear factor-kappa B pathway. J Periodontal Res 2011, 46:558-567.