Microbiota along gastrointestinal tract of humans

Background: Homeostasis of the gastrointestinal tract depends on a healthy bacterial microbiota, with alterations in microbiota composition suggested to contribute to diseases. To unravel bacterial contribution to disease pathology, a thorough understanding of the microbiota of the complete gastrointestinal tract is essential. To date, most microbial analyses have either focused on faecal samples, or on the microbial constitution of one gastrointestinal location instead of different locations within one individual. Objective: We aimed to analyse the mucosal microbiome along the entire gastrointestinal tract within the same individuals. Methods: Mucosal biopsies were taken from nine different sites in 14 individuals undergoing antegrade and subsequent retrograde double-balloon enteroscopy. The bacterial composition was characterised using 16 S rRNA sequencing with Illumina Miseq. Results: At double-balloon enteroscopy, one individual had a caecal adenocarcinoma and one individual had Peutz-Jeghers polyps. The composition of the microbiota distinctively changed along the gastrointestinal tract with larger bacterial load, diversity and abundance of Firmicutes and Bacteroidetes in the lower gastrointestinal tract than the upper gastrointestinal tract, which was predominated by Proteobacteria and Firmicutes. Conclusions: We show that gastrointestinal location is a larger determinant of mucosal microbial diversity than inter-person differences. These data provide a baseline for further studies investigating gastrointestinal microbiota-related disease. Keywords: Colonic microflora; colon; gastrointestinal tract; intestinal microbiology; small bowel.

背景：胃肠道稳态依赖于健康的细菌菌群，菌群组成的改变被认为与疾病发生相关。若要阐明细菌在疾病病理中的作用，全面了解整个胃肠道的菌群特征至关重要。迄今为止，多数微生物组研究要么仅聚焦于粪便样本，要么仅针对单一个体的某一胃肠道部位开展菌群构成分析，而非同一受试者的不同胃肠道部位。
研究目的：本研究旨在分析同一受试者整个胃肠道各段的黏膜微生物组。
研究方法：本研究纳入14名接受顺行及后续逆行双气囊小肠镜（double-balloon enteroscopy）检查的受试者，从其胃肠道的9个不同部位采集黏膜活检组织。采用Illumina Miseq平台进行16S rRNA测序，以表征细菌群落组成。
研究结果：双气囊小肠镜检查过程中，1名受试者被检出盲肠腺癌，另1名受试者检出波伊茨-耶格息肉（Peutz-Jeghers polyps）。胃肠道各段的菌群组成呈现显著的阶段性变化：下消化道的细菌载量、群落多样性以及厚壁菌门（Firmicutes）和拟杆菌门（Bacteroidetes）的丰度均显著高于上消化道；而上消化道则以变形菌门（Proteobacteria）和厚壁菌门为优势菌群。
研究结论：本研究证实，相较于个体间差异，胃肠道部位是影响黏膜微生物群落多样性的更主要决定因素。本研究数据为后续开展胃肠道菌群相关疾病研究提供了基准参照。
关键词：结肠菌群（Colonic microflora）；结肠（colon）；胃肠道（gastrointestinal tract）；肠道微生物学（intestinal microbiology）；小肠（small bowel）。