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

• DOI: 10.1111/apt.13622
• Publication Date: 2016-04-18T10:44:09Z
• Authors: E. R. Shanahan; L. Zhong; N. J. Talley; M. Morrison; G. Holtmann
• Keywords: Veillonella; Intestinal mucosa; Prevotella; Endoscope

Summary Background The mucosa‐associated microbiota appears to be highly relevant host–microbe interactions in the gastrointestinal (GI) tract. Thus, precise characterisation of may provide important insights for diagnostic and therapeutic development. However, technical reasons, mucosal biopsies taken during standard endoscopic procedures are potentially contaminated by GI luminal contents. Aim To develop validate a biopsy device that minimises contamination sampling microbiota. Methods A new, encased forceps was developed, Brisbane Aseptic Biopsy Device (BABD). This comprises sterile sheath with plug at tip, allowing targeted, aseptic mucosa. Matched duodenal were obtained using BABD, forceps, brush, from patients undergoing upper endoscopy iron deficiency ( n = 6). Total genomic deoxyribonucleic acid (gDNA) extracted samples bacterial 16S rRNA gene libraries sequenced investigate Results Microbial DNA recovered confirming presence dominated genus Streptococcus , lower levels Prevotella Veillonella Neisseria . At individual patient level, substantial differences observed between matched different devices. greater degree diversity collected indicating BABD affords collection more representative microbiota, precluding cross‐contamination. Conclusions Cross‐contamination can occur when procedures. Utilising novel reduce cross‐contamination, it offers improved opportunities precisely examine host–mucosa‐associated interactions.