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.研究目标：尽管近端胃肠道（gastrointestinal, GI）菌群已被证实与维持机体健康、预防疾病密切相关，但相较于远端胃肠道，健康个体中该微生物群落的相关研究仍较为匮乏。本研究旨在表征健康个体多个近端胃肠道位点的菌群随时间的变化特征。 研究结果：本研究招募8名健康空腹志愿者，累计完成10次入院采样。研究采用带有多组抽吸端口的四腔导管经口插管，可同步采集胃、十二指肠及多个空肠位点的样本。每小时采集一次液体样本（采样总时长<7小时），用于检测美沙拉嗪（t=0时给药）浓度、pH值，以及基于16S rRNA基因的微生物群落组成。结果显示，近端胃肠道各位点均以厚壁菌门（Firmicutes）为优势菌群，且其群落组成与粪便菌群存在显著差异。个体内的菌群随时间的相似度高于个体间；与稳定性更强的空肠位点相比，胃和十二指肠的菌群个体内变异性最高。在十二指肠（而非胃）中，我们观察到菌群组成随pH变化出现显著波动；线性混合模型分析显示，多个链球菌属（Streptococcus）操作分类单元（Operational Taxonomic Unit，OTU）与pH呈正相关，而多个普雷沃氏菌属（Prevotella）和巴斯德菌科（Pasteurellaceae，变形菌门Proteobacteria）操作分类单元则与pH呈负相关。此外，十二指肠和胃内的美沙拉嗪浓度仅与极少数操作分类单元存在显著相关性。 研究结论：相较于粪便菌群，胃、十二指肠及空肠内的菌群组成具有显著特异性。与空肠或胃相比，十二指肠菌群的短期波动与pH变化显著相关。