Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Chen, Weiguang ^a   Liu, Fanlong ^b   Ling, Zongxin ^a   Tong, Xiaojuan ^a   Xiang, Charlie ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ADULT; AGED; ARTICLE; BIFIDOBACTERIUM; CANCER GROWTH; CANCER PATIENT; CANCER RISK; CLINICAL ARTICLE; COLON FLORA; COLORECTAL CANCER; CONTROLLED STUDY; CORIOBACTERIACEAE; ENTEROCOCCUS FAECALIS; ERYSIPELOTRICHACEAE; FEMALE; FUSOBACTERIUM; GENETIC ANALYSIS; HUMAN; HUMAN TISSUE; INTESTINE FLORA; LACTOBACILLALES; MALE; MICROBIAL COMMUNITY; PEPTOSTREPTOCOCCUS; PORPHYROMONAS; PREVOTELLACEAE; PYROSEQUENCING;

BASE SEQUENCE; CASE-CONTROL STUDIES; COLORECTAL NEOPLASMS; DNA PRIMERS; HUMANS; INTESTINAL MUCOSA; INTESTINES; POLYMERASE CHAIN REACTION;

BACTERIA (MICROORGANISMS); BACTEROIDETES; BIFIDOBACTERIUM; CORIOBACTERIACEAE; ERYSIPELOTRICHACEAE; FAECALIBACTERIUM; FIRMICUTES; FUSOBACTERIUM; LACTOBACILLALES; MOGIBACTERIUM; PEPTOSTREPTOCOCCUS; PORPHYROMONAS; PREVOTELLACEAE; PROTEOBACTERIA;

EID: 84862997111     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039743     Document Type: Article

References (61)

1. Azcarate-Peril MA, Sikes M, Bruno-Barcena JM, (2011) The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer? Am J Physiol Gastrointest Liver Physiol 301: G401-424.
2. Ley RE, Peterson DA, Gordon JI, (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124: 837-848.
3. Rowland IR, (2009) The role of the gastrointestinal microbiota in colorectal cancer. Curr Pharm Des 15: 1524-1527.
4. Candela M, Guidotti M, Fabbri A, Brigidi P, Franceschi C, et al. (2011) Human intestinal microbiota: cross-talk with the host and its potential role in colorectal cancer. Crit Rev Microbiol 37: 1-14.
5. Wei H, Dong L, Wang T, Zhang M, Hua W, et al. (2010) Structural shifts of gut microbiota as surrogate endpoints for monitoring host health changes induced by carcinogen exposure. FEMS Microbiol Ecol 73: 577-586.
6. Sobhani I, Tap J, Roudot-Thoraval F, Roperch JP, Letulle S, et al. (2011) Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS One 6: e16393.
7. Wang T, Cai G, Qiu Y, Fei N, Zhang M, et al. (2011) Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J.
8. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
9. Marchesi JR, Dutilh BE, Hall N, Peters WH, Roelofs R, et al. (2011) Towards the human colorectal cancer microbiome. PLoS One 6: e20447.
10. Ray K, (2011) Colorectal cancer: Fusobacterium nucleatum found in colon cancer tissue-could an infection cause colorectal cancer? Nat Rev Gastroenterol Hepatol 8: 662.
11. van der Waaij LA, Harmsen HJ, Madjipour M, Kroese FG, Zwiers M, et al. (2005) Bacterial population analysis of human colon and terminal ileum biopsies with 16S rRNA-based fluorescent probes: commensal bacteria live in suspension and have no direct contact with epithelial cells. Inflamm Bowel Dis 11: 865-871.
12. Mai V, Stine OC, Morris JG Jr, (2005) Timing in collection of stool samples. Science 310: 1118; author replay 1118.
13. Vanhoutte T, Huys G, Brandt E, Swings J, (2004) Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol 48: 437-446.
14. Ling Z, Kong J, Liu F, Zhu H, Chen X, et al. (2010) Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. BMC Genomics 11: 488.
15. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
16. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R, (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5: 235-237.
17. 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.
18. 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.
19. Brown KR, (1977) Diagnosis and management of anaerobic infections. Trop Doct 7: 111-114.
20. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
21. Lozupone C, Hamady M, Knight R, (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371.
22. Lozupone C, Knight R, (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
23. Chen Y, Yang F, Lu H, Wang B, Lei D, et al. (2011) Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology 54: 562-572.
24. Domenici E, Wille DR, Tozzi F, Prokopenko I, Miller S, et al. (2010) Plasma protein biomarkers for depression and schizophrenia by multi analyte profiling of case-control collections. PLoS One 5: e9166.
25. Perez-Enciso M, Tenenhaus M, (2003) Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach. Hum Genet 112: 581-592.
26. 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.
27. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, et al. (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12: R60.
28. Sears CL, Pardoll DM, (2011) Perspective: alpha-bugs, their microbial partners, and the link to colon cancer. J Infect Dis 203: 306-311.
29. Costello EK, Gordon JI, Secor SM, Knight R, (2010) Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J 4: 1375-1385.
30. Ley RE, Turnbaugh PJ, Klein S, Gordon JI, (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022-1023.
31. 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.
32. Paillard D, McKain N, Chaudhary LC, Walker ND, Pizette F, et al. (2007) Relation between phylogenetic position, lipid metabolism and butyrate production by different Butyrivibrio-like bacteria from the rumen. Antonie Van Leeuwenhoek 91: 417-422.
33. Joly F, Mayeur C, Bruneau A, Noordine ML, Meylheuc T, et al. (2010) Drastic changes in fecal and mucosa-associated microbiota in adult patients with short bowel syndrome. Biochimie 92: 753-761.
34. Beeckman DS, Vanrompay DC, (2010) Bacterial secretion systems with an emphasis on the chlamydial Type III secretion system. Curr Issues Mol Biol 12: 17-41.
35. Brown NF, Finlay BB, (2011) Potential origins and horizontal transfer of type III secretion systems and effectors. Mob Genet Elements 1: 118-121.
36. Ohkusa T, Sato N, Ogihara T, Morita K, Ogawa M, et al. (2002) Fusobacterium varium localized in the colonic mucosa of patients with ulcerative colitis stimulates species-specific antibody. J Gastroenterol Hepatol 17: 849-853.
37. Strauss J, Kaplan GG, Beck PL, Rioux K, Panaccione R, et al. (2011) Invasive potential of gut mucosa-derived fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm Bowel Dis.
38. Vartoukian SR, Palmer RM, Wade WG, (2007) The division "Synergistes" Anaerobe 13: 99-106.
39. Atarashi K, Tanoue T, Honda K, (2010) Induction of lamina propria Th17 cells by intestinal commensal bacteria. Vaccine 28: 8036-8038.
40. Ivanov, II, Atarashi K, Manel N, Brodie EL, Shima T, et al. (2009) Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139: 485-498.
41. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran 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.
42. Benus RF, Harmsen HJ, Welling GW, Spanjersberg R, Zijlstra JG, et al. (2010) Impact of digestive and oropharyngeal decontamination on the intestinal microbiota in ICU patients. Intensive Care Med 36: 1394-1402.
43. Dabard J, Bridonneau C, Phillipe C, Anglade P, Molle D, et al. (2001) Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces. Appl Environ Microbiol 67: 4111-4118.
44. Candela M, Perna F, Carnevali P, Vitali B, Ciati R, et al. (2008) Interaction of probiotic Lactobacillus and Bifidobacterium strains with human intestinal epithelial cells: adhesion properties, competition against enteropathogens and modulation of IL-8 production. Int J Food Microbiol 125: 286-292.
45. Ohkusa T, Okayasu I, Ogihara T, Morita K, Ogawa M, et al. (2003) Induction of experimental ulcerative colitis by Fusobacterium varium isolated from colonic mucosa of patients with ulcerative colitis. Gut 52: 79-83.
46. Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, et al. (2011) Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res.
47. Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, et al. (2011) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res.
48. Hajishengallis G, Liang S, Payne MA, Hashim A, Jotwani R, et al. (2011) Low-Abundance Biofilm Species Orchestrates Inflammatory Periodontal Disease through the Commensal Microbiota and Complement. Cell Host Microbe 10: 497-506.
49. Harris JI, Russell RR, Curtis MA, Aduse-Opoku J, Taylor JJ, (2002) Molecular mediators of Porphyromonas gingivalis-induced T-cell apoptosis. Oral Microbiol Immunol 17: 224-230.
50. Andrian E, Grenier D, Rouabhia M, (2006) Porphyromonas gingivalis-epithelial cell interactions in periodontitis. J Dent Res 85: 392-403.
51. Saleh M, Trinchieri G, (2011) Innate immune mechanisms of colitis and colitis-associated colorectal cancer. Nat Rev Immunol 11: 9-20.
52. Davis CD, Milner JA, (2009) Gastrointestinal microflora, food components and colon cancer prevention. J Nutr Biochem 20: 743-752.
53. Martinez I, Wallace G, Zhang C, Legge R, Benson AK, et al. (2009) Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota. Appl Environ Microbiol 75: 4175-4184.
54. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, et al. (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1: 6ra14.
55. Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, et al. (2009) Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci U S A 106: 2365-2370.
56. Fleissner CK, Huebel N, Abd El-Bary MM, Loh G, Klaus S, et al. (2010) Absence of intestinal microbiota does not protect mice from diet-induced obesity. Br J Nutr 104: 919-929.
57. Claus SP, Ellero SL, Berger B, Krause L, Bruttin A, et al. (2011) Colonization-induced host-gut microbial metabolic interaction. MBio 2: e00271-00210.
58. Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, et al. (2011) Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci U S A 108: 6252-6257.
59. Huycke MM, Gaskins HR, (2004) Commensal bacteria, redox stress, and colorectal cancer: mechanisms and models. Exp Biol Med (Maywood) 229: 586-597.
60. Muyzer G, Stams AJ, (2008) The ecology and biotechnology of sulphate-reducing bacteria. Nat Rev Microbiol 6: 441-454.
61. Scharlau D, Borowicki A, Habermann N, Hofmann T, Klenow S, et al. (2009) Mechanisms of primary cancer prevention by butyrate and other products formed during gut flora-mediated fermentation of dietary fibre. Mutat Res 682: 39-53.