Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies

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.ConclusionsWe propose that colonic lavage samples provide a relatively accurate representation of biopsy microbiota composition and should be considered where biopsy size is an issue.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0207-9) contains supplementary material, which is available to authorized users.

Microbial and metabolic multi‐omic correlations in systemic sclerosis patients

“…15 Another source of variability with respect to the study by Volkmann et al 16 is the sampling methodology: we analyzed stool samples, while the Volkmann et al analyzed colonic lavage. Each collection method has advantages and drawbacks: some authors claim that colonic lavage is more representative of the actual gut microbial ecology (as determined by biopsy) with respect to stool samples; 41 that bowel cleansing before sample collection may alter the gut microbiota. 42 Despite these considerations, and regardless of the specific findings, our results are in full accordance with other studies (see Refs.…”

Review article: the gut microbiome in inflammatory bowel disease—avenues for microbial management

“…When considering the issue of mucosal vs faecal populations, there is limited comparison of both sample types within the same patient cohort, highlighting a gap in our understanding. The current evidence would indicate that only limited differences exist between different mucosal sites, or between inflamed and uninflamed mucosa, but significant differences exist between mucosal and luminal microbial populations—even within healthy individuals . Table summarises publications which describe microbial composition between IBD (either CD or ulcerative colitis) and healthy controls, where next‐generation sequencing was used as the principal analysis tool (Table ).…”

Consensus on standard biobanking of gut microbiota

“…(b) Colonic lavage samples. Colonic lavage specimens can be used in place of endoscopic colonic biopsy samples for studies on gut microbiota . Before a colonoscopy, patients should drink a large amount of water to clean the colon.…”

“…Appropriate measures should be taken to treat the items used for sample collection and to eliminate potential nucleic acid contamination (eg, ultraviolet irradiation and selective enzymatic degradation). A blank control should always be set up during the collection and processing steps . Blood should be collected by venipuncture.…”

“…A blank control should always be set up during the collection and processing steps. 22,[24][25][26][27][28][29][30][31][32][33][35][36][37][38][39][40][41][42][43] Blood should be collected by venipuncture. The median cubital vein is recommended due to the low risk of contamination.…”