Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2017

Microbial colonisation of the oesophageal, gastric and duodenal mucosa (#159)

Erin Shanahan 1 2 , Anh Do 3 , Paraic O Cuiv 1 , Teressa Hansen 2 , Natasha Koloski 2 4 , Mark Morrison 1 , Gerald Holtmann 2 3
  1. Diamantina Institute, The University of Queensland, Brisbane, Australia
  2. Princess Alexandra Hospital, Woolloongabba, QLD, Australia
  3. School of Medicine, The University of Queensland, Brisbane, Australia
  4. Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia

The mucosa associated microbiota (MAM) of the upper gastrointestinal (GI) tract, including the oesophagus, stomach and duodenum, is of increasing interest in conditions such as oesophageal and gastric cancer, chronic liver disease and functional gut disorders.  While studies of the upper GI microbiota reveal similarities with the oral cavity, we do not fully understand the MAM biogeography from oesophagus to small intestine.  In addition, it is unclear whether the microbes identified are resident, or the result of flow through.  This study therefore aimed to characterise the upper GI MAM, and improve our understanding of microbial colonisation of this region.

Patients (n=50) undergoing endoscopy for iron deficiency or dyspepsia were recruited with consent.  Biopsies were obtained from oesophageal, gastric and duodenal mucosa, using the Brisbane Aseptic Biopsy forceps which exclude oral/luminal contamination.  The MAM was profiled via sequencing of 16S rRNA gene (Illumina MiSeq). Bioinformatics was performed using QIIME.  Community profiles were compared to published datasets of saliva and ileal mucosa.  An additional duodenal biopsy was utilised for microbial culture.

The oesophageal, gastric and duodenal MAM was dominated by Streptococcus, Prevotella and Veillonella.  The three sites displayed a high degree of similarity, with only Streptococcus significantly increased in the oesophagus compared to gastric and duodenal samples (p<0.001).  Alpha diversity was similar across the three mucosal sites, and in multivariate analyses, the sites could not be significantly differentiated. When compared to saliva and the terminal ileum, the upper GI samples all clustered with saliva.  Utilising a variety of culture conditions, a panel of bacterial isolates from the duodenal mucosa was obtained with some displaying bile tolerance.

These results highlight similarities between the oesophageal, gastric and duodenal MAM, and overlap with the oral microbiota.  This suggests input from the oral cavity may play a role in seeding the GI mucosa.  However, isolation of a variety of duodenal bacterial strains suggests mucosal colonisation, and strain adaptation to this niche is currently under investigation.