This study was supported through GI Research funds and MRC Grant Ref: MR/M00533X/1 to GH.Peer reviewedPublisher PD

A Durban

A Jain

AC Ouwehand

AD Kostic

B Willing

CL O’Brien

E Pruesse

EG Zoetendal

EH Simpson

F Backhed

F Chierico Del

G Li

GL Hold

HJ Flint

HL Cash

I Mukhopadhya

I Rangel

J Handelsman

J Jalanka

J Qin

JJ Kozich

JM Choo

JR Marchesi

L Chen

L Drago

L Harrell

M Morotomi

MG Langille

MH McLean

N Segata

NA Kennedy

P Lepage

P Louis

PB Eckburg

PD Schloss

PJ Turnbaugh

R Bibiloni

R Hansen

RE Ley

RL Warren

RM Shobar

S Delgado

SJ Salter

T Vatanen

Team RC

TZ DeSantis

V Mai

Y Momozawa

Y Xie

Microbiome

English

PubMed

Euan Watt

Matthew R. Gemmell

Susan Berry

Mark Glaire

Freda Farquharson

Petra Louis

Graeme I. Murray

Emad El-Omar

Georgina L. Hold

Crossref

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

This study was supported through GI Research funds and MRC Grant Ref: MR/M00533X/1 to GH.Peer reviewe

Watt, Euan

Gemmell, Matthew R.

Berry, Susan

Glaire, Mark

Farquharson, Freda

Louis, Petra

Murray, Graeme I

El-Omar, Emad

Hold, Georgina L

Aberdeen University Research

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

Full account of figure production by R. (PDF 3.32 mb

Euan Watt (3444731)

Matthew Gemmell (3444737)

Susan Berry (653826)

Mark Glaire (3444728)

Freda Farquharson (3299991)

Petra Louis (526555)

Graeme Murray (368267)

Emad El-Omar (229332)

Georgina Hold (3444734)

The Francis Crick Institute

Additional file 12: of Extending colonic mucosal microbiome analysisâassessment of colonic lavage as a proxy for endoscopic colonic biopsies

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.CONCLUSIONS: 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

Watt, E

Gemmell, MR

Berry, S

Glaire, M

Farquharson, F

Louis, P

Murray, GI

El-Omar, E 

Hold, GL

UNSWorks

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

Springer - Publisher Connector

Rarefaction curve of all 46 samples following the removal of rare OTUs, defined as OTUs with 2 or less sequences across all the samples, which reduced the initial 131669 OTUs down to 17524) demonstrating sufficient sequencing depth. (PDF 28 kb

Additional file 3: Figure S2. of Extending colonic mucosal microbiome analysisâassessment of colonic lavage as a proxy for endoscopic colonic biopsies

https://figshare.com/articles/Additional_file_12_of_Extending_colonic_mucosal_microbiome_analysis_assessment_of_colonic_lavage_as_a_proxy_for_endoscopic_colonic_biopsies/4350470

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

Abstract

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Aberdeen University Research

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UNSWorks

Springer - Publisher Connector

The Francis Crick Institute