Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures

Shanahan, E. R., Zhong, L., Talley, N. J., Morrison, M. and Holtmann, G. (2016) Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures. Alimentary Pharmacology and Therapeutics, 43 11: 1186-1196. doi:10.1111/apt.13622


Author Shanahan, E. R.
Zhong, L.
Talley, N. J.
Morrison, M.
Holtmann, G.
Title Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures
Journal name Alimentary Pharmacology and Therapeutics   Check publisher's open access policy
ISSN 1365-2036
0269-2813
Publication date 2016-06
Year available 2016
Sub-type Article (original research)
DOI 10.1111/apt.13622
Open Access Status Not Open Access
Volume 43
Issue 11
Start page 1186
End page 1196
Total pages 11
Place of publication Chichester, West Sussex, United Kingdom
Publisher Wiley-Blackwell Publishing
Collection year 2017
Language eng
Formatted abstract
Background: The mucosa-associated microbiota appears to be highly relevant to host-microbe interactions in the gastrointestinal (GI) tract. Thus, precise characterisation of the mucosa-associated microbiota may provide important insights for diagnostic and therapeutic development. However, for technical reasons, mucosal biopsies taken during standard endoscopic procedures are potentially contaminated by GI luminal contents.

Aim: To develop and validate a biopsy device that minimises contamination during sampling of the mucosa-associated microbiota.

Methods: A new, encased biopsy forceps was developed, the Brisbane Aseptic Biopsy Device (BABD). This comprises sterile forceps encased by a sheath with a plug at the tip, allowing targeted, aseptic sampling of the mucosa. Matched duodenal biopsies were obtained using the BABD, standard biopsy forceps, and a sterile brush, from patients undergoing upper GI endoscopy for iron deficiency (n = 6). Total genomic deoxyribonucleic acid (gDNA) was extracted from samples and bacterial 16S rRNA gene libraries sequenced to investigate the mucosa-associated microbiota.

Results: Microbial DNA was recovered from biopsies obtained by the BABD, confirming the presence of a duodenal mucosa-associated microbiota. This microbiota was dominated by the genus Streptococcus, with lower levels of Prevotella, Veillonella and Neisseria. At the individual patient level, substantial differences were observed between matched samples obtained using the different devices. A greater degree of bacterial diversity was observed in samples collected using the standard forceps, indicating the BABD affords collection of samples more representative of the mucosa-associated microbiota, by precluding luminal cross-contamination.

Conclusions: Cross-contamination can occur when mucosal biopsies are taken during standard endoscopic procedures. Utilising the novel Brisbane Aseptic Biopsy Device can reduce cross-contamination, and it offers improved opportunities to more precisely examine host-mucosa-associated microbiota interactions
Keyword Mucosa-associated microbiota
Gastrointestinal (GI) tract
Brisbane Aseptic Biopsy Device (BABD)
Geno-mic deoxyribonucleic acid (gDNA)
Microbial DNA
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Health and Rehabilitation Sciences Publications
UQ Diamantina Institute Publications
 
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