A non-endoscopic device to sample the oesophageal microbiota: a case-control study

Background The strongest risk factor for oesophageal adenocarcinoma (OAC) is reflux disease, and the rising incidence coincides with the eradication of Helicobacter pylori, both of which may alter the oesophageal microbiota. We aimed to profile the microbiota at different stages of Barrett’s carcinogenesis and investigate the Cytosponge™ as a minimally invasive tool for sampling the oesophageal microbiota. Methods 16S rRNA gene amplicon sequencing was performed on 210 oesophageal samples from 86 patients representing the Barrett’s progression sequence (normal squamous controls, non-dysplastic and dysplastic Barrett’s oesophagus, and OAC), relevant negative controls and replicates on the Illumina MiSeq platform. Three different oesophageal sampling methods were compared for microbial DNA yield (qPCR), diversity and community composition: fresh frozen tissue, fresh frozen endoscopic brushings and the Cytosponge™ device. Findings There was decreased microbial diversity in OAC tissue compared to normal control patients as measured by the observed OTU richness, Chao estimated total richness and Shannon diversity index (all p<0·01). Lactobacillus fermentum was enriched in OAC (p=0·028), and lactic acid bacteria dominated the microenvironment in 7 (47%) of 15 OAC cases. Comparison of oesophageal sampling methods showed that the Cytosponge™ yielded more than ten-fold higher quantities of microbial DNA in comparison to endoscopic brushes (p<0·001) or biopsies (p<0·0001) using qPCR. The Cytosponge™ samples contained the majority of taxa detected in biopsy and brush samples, but were enriched for genera from the oral cavity and stomach, including Fusobacterium, Megasphaera, Campylobacter, Capnocytophaga and Dialister. The Cytosponge™ detected decreased microbial diversity in patients with high grade dysplasia in comparison to controls as measured by the observed OTU richness, Chao estimated total richness and Shannon diversity index (all p<0·05). Interpretation Alterations in microbial communities occur in the lower oesophagus in Barrett’s carcinogenesis, which can be detected at the pre-invasive stage of high grade dysplasia using the novel Cytosponge™.