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.
Highlights
Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota
Paired samples (biopsy (Bx) and colonic lavage (CL)) were collected from 23 participants attending for colorectal cancer screening colonoscopy, but with no evidence of pathology seen during colonoscopy examination and subsequent histological analysis which was performed on all participants
The remaining liquid is bathing the colonic mucosa and tends to shift naturally around the bowel with the aid of peristalsis and the constant changes in the movement and posture of the subject. This lavage fluid is often encountered at the time of colonoscopy and is very easy to aspirate through a suction channel in the colonoscope and directly into a collecting tube. Both biopsies and colonic lavage samples were collected simultaneously, lavage followed by biopsy, observed relationships are representative of accurate comparisons between sample types and most likely reflect the scope of the majority of such samples available for collection for research studies
Summary
Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. Humans have evolved over millennia to develop this complex ecosystem of microorganisms, which provides critical health benefits including regulation of the immune system, metabolic processes and homeostatic control [1,2,3]. Disruption of this stable microbial balance has been associated with a wide range of disease states including inflammatory bowel disease [4,5,6] and colorectal cancer [7,8,9] as well.
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