PRJNA495320
This project aimed to characterize the microbiota of the proximal gastrointestinal tract using a multi-lumen tube that samples aspirates at designated sites Raw sequence reads
Objectives: Although the microbiota in the proximal gastrointestinal (GI) tract has been implicated in maintaining health and preventing diseases, much of this microbial community remains understudied in healthy individuals compared to the distal GI tract. This study aimed to characterize the microbiota across multiple proximal GI sites over time in healthy individuals.Results: Healthy, fasted volunteers (N=8; 10 admissions total) were orally intubated with a four-lumen catheter with multiple aspiration ports, allowing sampling of stomach, duodenal, and multiple jejunal sites. Fluid was sampled hourly (<7 hours) to measure mesalamine (administered at t=0), pH, and 16S rRNA gene-based microbial composition. We observed a predominance of Firmicutes across proximal GI sites, with significant variation compared to stool. The microbiota was more similar within patients over time than across; the stomach and duodenal microbiota displayed highest intra-individual variability compared to jejunal sites, which were more stable across time. In the duodenum, but not the stomach, we observed significant fluctuations in microbial composition with changes in pH; linear mixed models identified positive correlations with multiple Streptococcus OTUs and negative correlations with multiple Prevotella and Pasteurellaceae (Proteobacteria) OTUs. Mesalamine concentration was significantly correlated with very few OTUs in the duodenum and stomach.Conclusion: Compared to the stool microbiota, the microbiota in the stomach, duodenum, and jejunum was distinct. Short-term fluctuations in the duodenal microbiota correlated with changes in pH compared to the jejunum or stomach.