Skip to main content
SpringerLink
Log in

Molecular Analysis of the Microbiome in Colorectal Cancer

  • Protocol
  • First Online:
Colorectal Cancer

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1765))

Abstract

The human gut microbiota plays a major role in the development of colorectal cancer (CRC). Many studies have attempted to define links between microbiota residents, their function and disease development. We now have incredible molecular tools to allow us to study the gut microbiome however in order to make best use of these sophisticated approaches we need to ensure that samples are collected and processed using standardized and reproducible protocols. Here we provide an overview of molecular analysis methods and describe protocols for collecting and processing clinical samples for subsequent microbiome analysis.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Weisburger JH, Reddy BS, Narisawa T et al (1975) Germ-free status and colon tumor induction by N-methyl-N′-nitro-N-nitrosoguanidine. Proc Soc Exp Biol Med 148(4):1119–1121

    Article  CAS  PubMed  Google Scholar 

  2. Louis P, Hold GL, Flint HJ (2014) The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol 12(10):661–672

    Article  CAS  PubMed  Google Scholar 

  3. Hold GL, Garrett WS (2015) Gut microbiota: microbiota organisation a key to understanding CRC development. Nat Rev Gastroenterol Hepatol 12(3):128–129

    Article  CAS  PubMed  Google Scholar 

  4. Wang T, Cai G, Qiu Y et al (2012) Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J 6(2):320–329

    Article  CAS  PubMed  Google Scholar 

  5. Boleij A, van Gelder MM, Swinkels DW et al (2011) Clinical Importance of Streptococcus gallolyticus infection among colorectal cancer patients: systematic review and meta-analysis. Clin Infect Dis 53(9):870–878

    Article  CAS  PubMed  Google Scholar 

  6. Kostic AD, Chun E, Robertson L et al (2013) Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14(2):207–215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sears CL (2009) Enterotoxigenic Bacteroides fragilis: a rogue among symbiotes. Clin Microbiol Rev 22(2):349–369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Martin HM, Campbell BJ, Hart CA et al (2004) Enhanced Escherichia coli adherence and invasion in Crohn’s disease and colon cancer. Gastroenterology 127(1):80–93

    Article  CAS  PubMed  Google Scholar 

  9. Swidsinski A, Khilkin M, Kerjaschki D et al (1998) Association between intraepithelial Escherichia coli and colorectal cancer. Gastroenterology 115(2):281–286

    Article  CAS  PubMed  Google Scholar 

  10. Arthur JC, Perez-Chanona E, Mühlbauer M et al (2012) Intestinal inflammation targets cancer-inducing activity of the microbiota. Science 338(6103):120–123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Olsen GJ, Lane DJ, Giovannoni SJ et al (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40(1):337–365

    Article  CAS  PubMed  Google Scholar 

  12. Thomson J, Hansen R, Berry S et al (2011) Enterohepatic helicobacter in ulcerative colitis: potential pathogenic entities? PLoS One 6(2):e17184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Muyzer G, de Waal EC, Uitterlinden AG (1993) 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(3):695–700

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Zoetendal EG, Akkermans AD, De Vos WM (1998) Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 64(10):3854–3859

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Weisburg WG, Barns SM, Pelletier DA et al (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173(2):697–703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Giovannoni SJ, Britschgi TB, Moyer CL et al (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345(6270):60

    Article  CAS  PubMed  Google Scholar 

  17. Hold GL, Pryde SE, Russell VJ et al (2002) Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol 39(1):33–39

    Article  CAS  PubMed  Google Scholar 

  18. Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Rajilić-Stojanović M, Heilig HG, Molenaar D et al (2009) Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol 11(7):1736–1751

    Article  PubMed  PubMed Central  Google Scholar 

  20. Claesson MJ, O’Sullivan O, Wang Q et al (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 4(8):e6669

    Article  PubMed  PubMed Central  Google Scholar 

  21. Hansen R, Russell RK, Reiff C et al (2012) Microbiota of de-novo pediatric IBD: increased Faecalibacterium Prausnitzii and reduced bacterial diversity in Crohn's but not in ulcerative colitis. Am J Gastroenterol 107(12):1913–1922

    Article  CAS  PubMed  Google Scholar 

  22. Watt E, Gemmell MR, Berry S et al (2016) Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies. Microbiome 4(1):61

    Article  PubMed  PubMed Central  Google Scholar 

  23. Wheeler DA, Srinivasan M, Egholm M et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452(7189):872–876

    Article  CAS  PubMed  Google Scholar 

  24. Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285):59–65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Frank JA, Reich CI, Sharma S et al (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74(8):2461–2470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Mukhopadhya I, Hansen R, Meharg C et al (2015) The fungal microbiota of de-novo paediatric inflammatory bowel disease. Microbes Infect 17(4):304–310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Ghannoum MA, Jurevic RJ, Mukherjee PK et al (2010) Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 6(1):e1000713

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by grants from The Chief Scientist Office, Friends of Anchor, NHS Grampian Endowments, NHS Grampian Gastroenterology Endowment funds as well as donations from CRC patients.

Author information

Authors and Affiliations

  1. Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK

    Fiona Clegg, Susan H. Berry & Georgina L. Hold

  2. Department of Paediatric Gastroenterology, Royal Hospital for Children, Glasgow, UK

    Richard Hansen

Authors
  1. Fiona Clegg
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Susan H. Berry
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Richard Hansen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Georgina L. Hold
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Georgina L. Hold .

Editor information

Editors and Affiliations

  1. Laboratory of Intestinal Physiopathology, Department of Anatomy and Cell Biology, Faculty of Medicine and Health Science, Université de Sherbrooke, Sherbrooke, Québec, Canada

    Jean-François Beaulieu

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Clegg, F., Berry, S.H., Hansen, R., Hold, G.L. (2018). Molecular Analysis of the Microbiome in Colorectal Cancer. In: Beaulieu, JF. (eds) Colorectal Cancer. Methods in Molecular Biology, vol 1765. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7765-9_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7765-9_8

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7764-2

  • Online ISBN: 978-1-4939-7765-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation