title: Extending colonic mucosal microbiome analysis-assessment of colonic lavage as a proxy for endoscopic colonic biopsies.
abstract: 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.
  
  
  
  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.
  
  
  
  We propose that colonic lavage samples provide a relatively accurate representation of biopsy microbiota composition and should be considered where biopsy size is an issue.
authors.affiliation: Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
authors.forename: Euan
authors.initials: E
authors.lastname: Watt
authors.affiliation: Centre for Genome Enabled Biology and Medicine, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Gemmell
authors.affiliation: Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
authors.forename: Susan
authors.initials: S
authors.lastname: Berry
authors.affiliation: Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Glaire
authors.affiliation: Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
authors.forename: Freda
authors.initials: F
authors.lastname: Farquharson
authors.affiliation: Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
authors.forename: Petra
authors.initials: P
authors.lastname: Louis
authors.affiliation: Department of Pathology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
authors.forename: Graeme I
authors.initials: GI
authors.lastname: Murray
authors.affiliation: Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK.|St George and Sutherland Clinical School, University of New South Wales, St George Hospital, Short Street, Kogarah, Sydney, NSW 2217, Australia.
authors.forename: Emad
authors.initials: E
authors.lastname: El-Omar
authors.affiliation: Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK. g.l.hold@abdn.ac.uk.
authors.forename: Georgina L
authors.initials: GL
authors.lastname: Hold
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D001706:Biopsy / Q000379:methods*; D003106:Colon / Q000382:microbiology*; D003113:Colonoscopy / Q000379:methods; D019295:Computational Biology / Q000379:methods; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D007507:Therapeutic Irrigation / Q000379:methods*
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Colonic biopsies; Colonic lavage; Microbiome analysis; Next-generation sequencing