Non-invasive approaches for esophageal microbiota analysis: a pilot study

Aims There is growing evidence that alterations in the composition of esophageal microbiota occur in gastroesophageal reflux disease (GERD). Recently non-invasive esophageal swabs have been introduced collecting a representative sample of the microbiota along the entire length of the esophagus [1].

Methods We aimed to profile the bacteriome of the esophagus and oral swabs in patients with symptoms of GERD. The collection of oral microbiota and esophageal microbiota by a minimally invasive tool EsophaCap was performed in 12 patients, who were followed up for GERD. The bacteriome was analyzed by sequencing the V1-V2 region of the 16S rRNA gene on the Illumina MiniSeq platform enabling classification up to the species level.

Results The analysis of the most abundant phyla in both analyzed samples (oral swabs and EsophaCap) corresponded to the typical bacteria composition of the upper GIT. Although the most abundant taxa overlapped between both sampling methods, the oral swabs did not cluster distinctly from EsophaCap samples. The samples collected by EsophaCap showed higher alpha diversity and the proportional abundances between both collection methods differed significantly. Besides, we observed statistically significant differences in the representation of the diagnostically important bacterial genera such as Prevotella (p<0.001) or Veillonella (p<0.001) that showed higher representation in EsophaCap samples compared to oral samples.

Conclusions The results of our pilot study suggest that EsophaCap, reflects more appropriately the bacterial structure of the upper GIT compared to oral swabs.

Publication History

Article published online:
14 April 2023

• 1 Elliott. et al. A non-endoscopic device to sample the oesophageal microbiota: a case-control study. L ancet Gastroenterol Hepatol. 2017; 2: 32-42