Title: Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

Abstract

Mucosal biopsy is the most common sampling technique used to assess microbial communities associated with the intestinal mucosa. Biopsies disrupt the epithelium and can be associated with complications such as bleeding. Biopsies sample a limited area of the mucosa, which can lead to potential sampling bias. In contrast to the mucosal biopsy, the mucosal brush technique is less invasive and provides greater mucosal coverage, and if it can provide equivalent microbial community data, it would be preferable to mucosal biopsies. Results: We compared microbial samples collected from the intestinal mucosa using either a cytology brush or mucosal biopsy forceps. We collected paired samples from patients with ulcerative colitis (UC) who had previously undergone colectomy and ileal pouch anal anastomosis (IPAA), and profiled the microbial communities of the samples by sequencing V4-V6 or V4-V5 16S rRNA-encoding gene amplicons. Comparisons of 177 taxa in 16 brush-biopsy sample pairs had a mean R2 of 0.94. We found no taxa that varied significantly between the brush and biopsy samples after adjusting for multiple comparisons (false discovery rate ≤0.05). We also tested the reproducibility of DNA amplification and sequencing in 25 replicate pairs and found negligible variation (mean R2 = 0.99). A qPCR analysis ofmore » the two methods showed that the relative yields of bacterial DNA to human DNA were several-fold higher in the brush samples than in the biopsies. Conclusions: Mucosal brushing is preferred to mucosal biopsy for sampling the epithelial-associated microbiota. Although both techniques provide similar assessments of the microbial community composition, the brush sampling method has relatively more bacterial to host DNA, covers a larger surface area, and is less traumatic to the epithelium than the mucosal biopsy.« less

Authors:

Huse, Susan M. ^[1]; Young, Vincent B. ^[2]; Morrison, Hilary G. ^[3]; Antonopoulos, Dionysios A. ^[4]; Kwon, John ^[5]; Dalal, Sushila ^[5]; Arrieta, Rose ^[5]; Hubert, Nathaniel A. ^[5]; Shen, Lici ^[5]; Vineis, Joseph H. ^[3]; Koval, Jason C. ^[6]; Sogin, Mitchell L. ^[3]; Chang, Eugene B. ^[5]; Raffals, Laura E. ^[7]

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+ Show Author Affiliations

1. Brown University, Providence, RI (United States)
2. University of Michigan, Ann Arbor, MI (United States)
3. Marine Biological Laboratory, Woods Hole, MA (United States)
4. Argonne National Lab. (ANL), Argonne, IL (United States)
5. University of Chicago, IL (United States)
6. Argonne National Laboratory (ANL), Argonne, IL (United States)
7. Mayo Clinic, Rochester, MN (United States)

Publication Date:

Fri Feb 14 00:00:00 EST 2014

Research Org.:

Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); Crohn’s Colitis Foundation of America; Leona M. & Harry B. Helmsley Charitable Trust

OSTI Identifier:

1626689

Grant/Contract Number:  

AC02-06CH11357; UH2/3 DK083993; NIDDK DK 42086; DK097268; DK47722

Resource Type:

Accepted Manuscript

Journal Name:

Microbiome

Additional Journal Information:

Journal Volume: 2; Journal Issue: 1; Journal ID: ISSN 2049-2618

Publisher:

BioMed Central

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; microbiome; ulcerative colitis; mucosal biopsy; cytology brush; microbial sampling; mucosal brushing; microbiome methods Microbiome methods