S3303 New Insights into the Microbiota of the Upper Gastrointestinal Tract

Abstract

INTRODUCTION: High throughput DNA sequencing has greatly increased our knowledge of the microbial populations of the mouth and colon, but data on the duodenum are sparse. In this study, we explore the microbiota of the human duodenum and compare it with the stomach and saliva. METHODS: Routine esophagogastroduodenoscopy (EGD) was performed on 35 patients aged 18–82, 69% were women. Indications were gastroesophageal reflux disease (GERD) (n = 11), dyspepsia (n = 9), and dysphagia (n = 9). Fours patients had gastroparesis confirmed by gastric emptying study. Patients with dysphagia had achalasia and were regarded as “controls”, based on the evidence that achalasia occurs due to the loss of the neuronal function the esophageal smooth muscles with no mucosal pathology beyond the GE junction. Saliva samples were obtained immediately prior to the endoscopy. Mucosal bacteria were collected using a standard cytology brush (Olympus®) from the second part of the duodenum and the gastric antrum. Laboratory analysis was conducted to determine the composition of bacterial species by PCR amplification of 16S rRNA genes followed by Illumina MiSeq DNA sequencing. Gastric and duodenal biopsies were obtained for conventional pathological examination. RESULTS: The control group had the following phylum profile: 77% Firmicutes, 13% Proteobacteria, 6.3% Bacteroidetes, 1.9% Actinobacteria, 1.6% Fusobacteria. At the genus level, the composition was: 47% Veillonella, 12% Streptococcus, 5% Prevotella (Bacteroidetes), 3.2% Lactobacillus, 1.9% Megasphaer, 1.5% Selenomonas (Firmicutes), 1.1% Fusobacterium (Fusobacteria).The data was analyzed by grouping the patients with GERD, dyspepsia, gastroparesis, under one umbrella as “dyspepsia” and compared to those with achalasia. No difference was observed in overall bacterial diversity between both groups by PCR. However, Principal Coordinated Analysis comparing dyspepsia vs. controls showed a distinct separation (P < 0.05), suggesting that dyspeptic patients have a “cluster” of microbiota with different composition from controls. CONCLUSION: We explored the upper gut microbiota and found that duodenal microbiota is significantly altered in patients with dyspepsia. The dysbiosis in dyspeptic patients may have pro-inflammatory implications contributing to their symptoms, opening the door for new therapeutic approaches to address this microbial imbalance.