Journal of Gastroenterology

, Volume 50, Issue 2, pp 167–179 | Cite as

Microbial mucosal colonic shifts associated with the development of colorectal cancer reveal the presence of different bacterial and archaeal biomarkers

  • L. Mira-Pascual
  • R. Cabrera-Rubio
  • S. Ocon
  • P. Costales
  • A. Parra
  • A. Suarez
  • F. Moris
  • L. Rodrigo
  • A. Mira
  • M. C. ColladoEmail author
Original Article—Alimentary Tract



Epidemiological studies demonstrate a link between gastrointestinal cancers and environmental factors such as diet. It has been suggested that environmental cancer risk is determined by the interaction between diet and microbes. Thus, the purpose of this study was to examine the hypothesis that microbiota composition during colorectal cancer (CRC) progression might differ depending on the stage of the disease.


A total of 28 age-matched and sex-matched subjects, seven with CRC adenocarcinoma, 11 with tubular adenomas and ten healthy subjects with intact colon, were included into the study. Microbiomes from mucosal and fecal samples were analyzed with 16S ribosomal RNA gene pyrosequencing, together with quantitative PCR of specific bacteria and archaea.


The principal coordinates analysis clearly separated healthy tissue samples from polyps and tumors, supporting the presence of specific bacterial consortia that are associated with affected sites and that can serve as potential biomarkers of CRC progression. A higher presence of Fusobacterium nucleatum and Enterobacteriaceae was found by qPCR in samples from CRC compared to healthy controls. We observed a correlation between CRC process development and levels of Methanobacteriales (R = 0.537, P = 0.007) and Methanobrevibacterium (R = 0.574, P = 0.03) in fecal samples.


Differences in microbial and archaeal composition between mucosal samples from healthy and disease tissues were observed in tubular adenoma and adenocarcinoma. In addition, microbiota from mucosal samples represented the underlying dysbiosis, whereas fecal samples seem not to be appropriate to detect shifts in microbial composition. CRC risk is influenced by microbial composition, showing differences according to disease progression step and tumor severity.


Colorectal cancer (CRC) Adenoma Adenocarcinoma Microbiota Bacteria Archaea Feces Mucosal tissue 



EntreChem S.L. also acknowledges funding from FICYT (project IE-09-314).

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

535_2014_963_MOESM1_ESM.doc (66 kb)
Supplementary material 1 (DOC 66 kb)


  1. 1.
    Cunningham D, Atki W, Lenz HJ, Lynch HT, Minsky B, Nordlinger B, Starling N. Colorectal cancer. Lancet. 2010;375:1030–47.PubMedCrossRefGoogle Scholar
  2. 2.
    Regula J, Rupinski M, Kraszewska E, Polkowski M, Pachlewski J, Orlowska J, et al. Colonoscopy in colorectal cancer screening for detection of advanced neoplasia. N Engl J Med. 2006;355:1863–72.PubMedCrossRefGoogle Scholar
  3. 3.
    Bamia C, Lagiou P, Buckland G, Grioni S, Agnoli C, Taylor AJ, et al. Mediterranean diet and colorectal cancer risk: results form a European cohort. Eur J Epidemiol. 2013;28:317–28.PubMedCrossRefGoogle Scholar
  4. 4.
    Sobhani I, Amiot A, Le Baleur Y, Levy M, Auriault ML, Van Nhieu JT, et al. Microbial dysbiosis and colon carcinogenesis: could colon cancer be considered a bacteria-related disease? Therap Adv Gastroenterol. 2013;6:215–29.PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Gaboriau-Routhiau V, Lécuyer E, Cerf-Bensussan N. Role of microbiota in postnatal maturation of intestinal T-cell responses. Curr Opin Gastroenterol. 2011;27(6):502–8.PubMedCrossRefGoogle Scholar
  6. 6.
    O’Keefe SJ, Chung D, Mahmoud N, Sepulveda AR, Manafe M, et al. Why do African Americans get more colon cancer than Native Africans? J Nutr. 2007;137:S75–82.Google Scholar
  7. 7.
    Man SM, Kaakoush NO, Mitchell HM. The role of bacteria and pattern-recognition receptor’s in Crohn’s disease. Nat Rev Gastroenterol Hepatol. 2011;8:152–68.PubMedCrossRefGoogle Scholar
  8. 8.
    Candela M, Guidotti M, Fabbri A, Brigidi P, Franceschi C, Fiorentini C. Human intestinal microbiota: cross talk with the host and its potential role in colorectal cancer. Crit Rev Micro. 2011;37:1–14.CrossRefGoogle Scholar
  9. 9.
    Giardiello FM, Brensinger JD, Petersen GM. AGA technical review on hereditary colorectal cancer and genetic testing. Gastroenterology. 2001;21:198–213.Google Scholar
  10. 10.
    Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature. 2012;482(7384):179–85.PubMedCentralPubMedGoogle Scholar
  11. 11.
    Marchesi JR, Dutilh BE, Hall N, Peters WHM, Roelofs R, et al. Towards the human colorectal cancer microbiome. PLoS ONE. 2011;6(5):e20447.PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Hu B, Elinav E, Huber S, Strowig T, Hao L, Hafemann A, et al. Microbiota-induced activation of epithelial IL-6 signaling links inflammasome-driven inflammation with transmissible cancer. PNAS. 2013;110(24):9682–7.CrossRefGoogle Scholar
  13. 13.
    Sobhani I, Tap J, Roudot-Thoraval F, Roperch JP, Letulle S, Langella P, Corthier G, Tran Van Nhieu J, Furet JP. Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS ONE. 2011;6(1):e16393.PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS ONE. 2012;7(6):e39743.PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Scanlan PD, Shanahan F, Clune Y, Collins JK, O’Sullivan GC, O’Riordan M, et al. Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol. 2008;10:789–98.PubMedCrossRefGoogle Scholar
  16. 16.
    Parkin D. The global health burden of infection-associated cancers in the year 2002. Int J Cancer. 2006;118:3030–44.PubMedCrossRefGoogle Scholar
  17. 17.
    Castellarin M, Warren R, Freeman J, Dreolini L, Krzywinski M, Strauss J, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 2012;22:299–306.PubMedCentralPubMedCrossRefGoogle Scholar
  18. 18.
    Derrien M, Vaughan EE, Plugge CM, de Vos WM. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol. 2004;54(Pt 5):1469–76.PubMedCrossRefGoogle Scholar
  19. 19.
    Scanlan PD, Shanahan F, Marchesi JR. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol. 2008;20(8):79.CrossRefGoogle Scholar
  20. 20.
    Azcárate-Peril MA, Sikes M, Bruno-Bárcena JM. The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer? Am J Physiol Gastrointest Liver Physiol. 2011;301(3):G401–24.PubMedCentralPubMedCrossRefGoogle Scholar
  21. 21.
    Cabrera-Rubio R, Garcia-Núñez M, Setó L, Antó JM, Moya A, Monsó E, Mira A. Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease. J Clin Microbiol. 2012;50:3562–8.PubMedCentralPubMedCrossRefGoogle Scholar
  22. 22.
    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–41.PubMedCentralPubMedCrossRefGoogle Scholar
  23. 23.
    Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37:D141–5.PubMedCentralPubMedCrossRefGoogle Scholar
  24. 24.
    Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer K, et al. The all-species living tree PROJECT: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol. 2008;31:241–50.PubMedCrossRefGoogle Scholar
  25. 25.
    Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71(12):8228–35.PubMedCentralPubMedCrossRefGoogle Scholar
  26. 26.
    Collado MC, Isolauri E, Laitinen K, Salminen S. Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr. 2008;88:894–9.PubMedGoogle Scholar
  27. 27.
    Yu Y, Lee C, Kim J, Hwang S. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng. 2005;89(6):670–9.PubMedCrossRefGoogle Scholar
  28. 28.
    Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe. 2013;14(2):207–15.PubMedCentralPubMedCrossRefGoogle Scholar
  29. 29.
    Turner ND, Ritchie LE, Bresalier RS, Chapkin RS. The microbiome and colorectal neoplasia: environmental modifiers of dysbiosis. Curr Gastroenterol Rep. 2013;15(9):346.PubMedCrossRefGoogle Scholar
  30. 30.
    Vipperia K, O’Keefe SJ. The microbiota and its metabolites in colonic mucosal health and cancer risk. Nutr Clin Practice. 2013;27:624–35.CrossRefGoogle Scholar
  31. 31.
    Wu N, Yang X, Zhang R, Li J, Xiao X, Hu Y, et al. Dysbiosis signature of fecal microbiota in colorectal cancer patients. Microb Ecol. 2013;66(2):462–70.PubMedCrossRefGoogle Scholar
  32. 32.
    Bibiloni R, Mangold M, Madsen KL, Fedorak RN, Tannock GW. The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn’s disease and ulcerative colitis patients. J Med Microbiol. 2006;55:1141–9.PubMedCrossRefGoogle Scholar
  33. 33.
    Ohigashi S, Sudo K, Kobayashi D, Takahashi T, Nomoto K, Onodera H. Significant changes in the intestinal environment after surgery in patients with colorectal cancer. J Gastrointest Surg. 2013;17(9):1657–64.PubMedCrossRefGoogle Scholar
  34. 34.
    Geng J, Fan H, Tang X, Zhai H, Zhang Z. Diversified pattern of the human colorectal cancer microbiome. Gut Pathog. 2013;5(1):2.PubMedCentralPubMedCrossRefGoogle Scholar
  35. 35.
    Balamurugan R, Rajendiran E, George S, Samuel GV, Ramakrishna BS. Real-time polymerase chain reaction quantification of specific butyrate-producing bacteria, Desulfovibrio and Enterococcus faecalis in the feces of patients with colorectal cancer. J Gastroenterol Hepatol. 2008;23(8 Pt 1):1298–303.PubMedCrossRefGoogle Scholar
  36. 36.
    Wang T, Cai G, Qiu Y, Fei N, Zhang M, Pang X, Jia W, Cai S, Zhao L. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 2012;6(2):320–9.PubMedCentralPubMedCrossRefGoogle Scholar
  37. 37.
    Shih DQ, Targan SR. Immunopathogenesis of inflammatory bowel disease. World J Gastroenterol. 2008;14(3):390–400.PubMedCentralPubMedCrossRefGoogle Scholar
  38. 38.
    Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL, Ryan EP. Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults. PLoS ONE. 2013;8(8):e70803.PubMedCentralPubMedCrossRefGoogle Scholar
  39. 39.
    Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 2011;22(2):299–306.PubMedCrossRefGoogle Scholar
  40. 40.
    Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 2011;22(2):292–8.PubMedCrossRefGoogle Scholar
  41. 41.
    McCoy AN, Araújo-Pérez F, Azcárate-Peril A, Yeh JJ, Sandler RS, Keku TO. Fusobacterium is associated with colorectal adenomas. PLoS ONE. 2013;8(1):e53653.PubMedCentralPubMedCrossRefGoogle Scholar
  42. 42.
    Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, Delzenne NM, et al. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes. 2008;57(6):1470–81.PubMedCrossRefGoogle Scholar
  43. 43.
    Kalliomäki M, Kirjavainen P, Eerola E, Kero P, Salminen S, Isolauri E. Distinct patterns of neonatal gut microflora in infants developing or not developing atopy. J Allergy Clin Immunol. 2001;107:129–34.PubMedCrossRefGoogle Scholar
  44. 44.
    Hotamisligil GS. Inflammation and metabolic disorders. Nature. 2006;444(7121):860–7.PubMedCrossRefGoogle Scholar
  45. 45.
    Strober W, Fuss IJ, Blumberg RS. The immunology of mucosal models of inflammation. Annu Rev Immunol. 2002;20:495–549.PubMedCrossRefGoogle Scholar
  46. 46.
    Cani PD, Osto M, Geurts L, Everard A. Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity. Gut Microbes. 2012;3(4):279–88.PubMedCentralPubMedCrossRefGoogle Scholar
  47. 47.
    Lyra A, Lahtinen S, Ouwehand AC. Gastrointestinal benefits of probiotics: clinical evidence. In: Salminen S, von Wright A, Lahtinen S, Ouwehand A, editors. Lactic acid bacteria: microbiological and functional aspects. 4th ed. Boca Raton: CRC Press; 2012. p. 509–23.Google Scholar
  48. 48.
    Geier MS, Butler RN, Howarth GS. Probiotics, prebiotics and synbiotics: role in chemoprevention for colorectal cancer? Cancer Biol Ther. 2006;5(10):1265–9.PubMedCrossRefGoogle Scholar
  49. 49.
    Collado MC, Isolauri E, Salminen S, Sanz Y. The impact of probiotic on gut health. Curr Drug Metab. 2009;10(1):68–78.PubMedCrossRefGoogle Scholar
  50. 50.
    Abell GCJ, Conlon MA, McOrist AL. Methanogenic archaea in adult human faecal samples are inversely related to butyrate concentration. Microb Ecol Health Dis. 2006;18:154–60.CrossRefGoogle Scholar
  51. 51.
    Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–8.PubMedCentralPubMedCrossRefGoogle Scholar
  52. 52.
    Mathur R, Amichai M, Chua KS, Mirocha J, Barlow GM, Pimentel M. Methane and hydrogen positivity on breath test is associated with greater body mass index and body fat. J Clin Endocrinol Metab. 2013;98(4):E698–702.PubMedCentralPubMedCrossRefGoogle Scholar
  53. 53.
    Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, et al. Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli. Int J Obes (Lond). 2013;37(11):1460–6.PubMedCentralCrossRefGoogle Scholar
  54. 54.
    Florin TH. Alkyl halides, super hydrogen production and the pathogenesis of pneumatosis cystoides coli. Gut. 1997;41:778–84.PubMedCentralPubMedCrossRefGoogle Scholar
  55. 55.
    Pique JM, Pallares M, Cuso E, Vilar-Bonet J, Gassull MA. Methane production and colon cancer. Gastroenterology. 1984;87:601–5.PubMedGoogle Scholar
  56. 56.
    Holma R, Osterlund P, Sairanen U, Blom M, Rautio M, Korpela R. Colonic methanogenesis in vivo and in vitro and fecal pH after resection of colorectal cancer and in healthy intact colon. Int J Colorectal Dis. 2012;27(2):171–8.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Japan 2014

Authors and Affiliations

  • L. Mira-Pascual
    • 1
  • R. Cabrera-Rubio
    • 2
  • S. Ocon
    • 3
  • P. Costales
    • 3
  • A. Parra
    • 4
  • A. Suarez
    • 4
  • F. Moris
    • 3
  • L. Rodrigo
    • 4
  • A. Mira
    • 2
  • M. C. Collado
    • 1
    Email author
  1. 1.Department of BiotechnologyInstitute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC)PaternaSpain
  2. 2.Department of Health and GenomicsCenter for Advanced Research in Public Health, CSISP-FISABIOValenciaSpain
  3. 3.Entrechem, S.L., Edificio Científico TecnológicoOviedoSpain
  4. 4.Department of GastroenterologyCentral University Hospital of AsturiasOviedoSpain

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