Extending colonic mucosal microbiome analysis - Assessment of colonic lavage as a proxy for endoscopic colonic biopsies

Euan Watt, Matthew R. Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I Murray, Emad El-Omar, Georgina L Hold

Research output: Contribution to journalArticle

14 Citations (Scopus)
7 Downloads (Pure)

Abstract

Background
Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size. We collected paired colonic biopsies and lavage samples from subjects who were attending for colorectal cancer screening colonoscopy.

Results
Next-generation sequencing and qPCR validation were performed with multiple bioinformatics analyses to determine the composition and predict function of the microbiota. Colonic lavage samples contained significantly higher numbers of operational taxonomic units (OTUs) compared to corresponding biopsy samples, however, diversity and evenness between lavage and biopsy samples were similar. The differences seen were driven by the presence of 12 OTUs which were in higher relative abundance in biopsies and were either not present or in low relative abundance in lavage samples, whilst a further 3 OTUs were present in higher amounts in the lavage samples compared to biopsy samples. However, predicted functional community profiling based on 16S ribosomal ribonucleic acid (rRNA) data indicated minimal differences between sample types.
Original languageEnglish
Article number61
JournalMicrobiome
Volume4
DOIs
Publication statusPublished - 25 Nov 2016

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Therapeutic Irrigation
Microbiota
Proxy
Biopsy
Colonoscopy
Computational Biology
Early Detection of Cancer
Sample Size
Colorectal Neoplasms
RNA

Keywords

  • colonic lavage
  • colonic biopsies
  • microbiome analysis
  • next-generation sequencing

Cite this

Extending colonic mucosal microbiome analysis - Assessment of colonic lavage as a proxy for endoscopic colonic biopsies. / Watt, Euan; Gemmell, Matthew R.; Berry, Susan; Glaire, Mark; Farquharson, Freda; Louis, Petra; Murray, Graeme I; El-Omar, Emad; Hold, Georgina L.

In: Microbiome, Vol. 4, 61, 25.11.2016.

Research output: Contribution to journalArticle

Watt, Euan ; Gemmell, Matthew R. ; Berry, Susan ; Glaire, Mark ; Farquharson, Freda ; Louis, Petra ; Murray, Graeme I ; El-Omar, Emad ; Hold, Georgina L. / Extending colonic mucosal microbiome analysis - Assessment of colonic lavage as a proxy for endoscopic colonic biopsies. In: Microbiome. 2016 ; Vol. 4.
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abstract = "BackgroundSequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size. We collected paired colonic biopsies and lavage samples from subjects who were attending for colorectal cancer screening colonoscopy.ResultsNext-generation sequencing and qPCR validation were performed with multiple bioinformatics analyses to determine the composition and predict function of the microbiota. Colonic lavage samples contained significantly higher numbers of operational taxonomic units (OTUs) compared to corresponding biopsy samples, however, diversity and evenness between lavage and biopsy samples were similar. The differences seen were driven by the presence of 12 OTUs which were in higher relative abundance in biopsies and were either not present or in low relative abundance in lavage samples, whilst a further 3 OTUs were present in higher amounts in the lavage samples compared to biopsy samples. However, predicted functional community profiling based on 16S ribosomal ribonucleic acid (rRNA) data indicated minimal differences between sample types.",
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AU - Berry, Susan

AU - Glaire, Mark

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AU - Louis, Petra

AU - Murray, Graeme I

AU - El-Omar, Emad

AU - Hold, Georgina L

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