The gut microbiome provides important metabolic functions for the host animal. Bacterial dysbiosis as a result of bacterial, viral, and parasitic gastrointestinal infections can adversely affect the metabolism, productivity, and overall health. The objective of this study is to characterize the commensal microbiome present in the lumen and the mucosal surface of the duodenum of cattle, as we hypothesize that due to metabolic processes and or host proprieties, there are differences in the natural microbiota present in the mucosal surface and luminal contents of the bovine duodenum. Duodenal lumen contents and mucosal biopsies were collected from six dairy crossbred yearling steers. A flexible video-endoscope was used to harvest biopsy samples via a T shaped intestinal cannula. In order to assess as much environmental and individual steer microbiota variation as possible, each animal was sampled three times over a 6 week period. The DNA was extracted from the samples and submitted for16S rRNA gene Ion Torrent PGM bacterial sequencing. A detailed descriptive analysis from phylum to genus taxonomic level was reported. Differences in the microbiome population between two different sites within the duodenum were successfully characterized. A great and significant microbiota diversity was found between the luminal and mucosal biopsy At the phylum taxonomic level, Firmicutes, and Bacteroidetes composed over 80% of the microbiome. Further analysis at lower taxonomic levels, class, family, and genus, showed distinct diversity and distribution of the microbiome. Characterizing the gastrointestinal microbiome in vivo is imperative. The novelty of this study is the use of live cattle undergoing customary husbandry allowing real-time analysis of the duodenum microbiome contributing to the literature with respect to the bovine duodenum microbiome.

肠道微生物组为宿主动物提供重要的代谢功能。细菌性，病毒性和寄生性胃肠道感染导致的细菌性营养不良会不利地影响新陈代谢，生产力和整体健康。这项研究的目的是鉴定牛十二指肠腔和黏膜表面的共生微生物组，因为我们假设由于代谢过程和/或宿主的存在，黏膜表面的天然微生物群存在差异和牛十二指肠的腔内物质。从六只奶牛杂交一岁ste牛中收集十二指肠管腔内容物和黏膜活检。柔性视频内窥镜用于收集活检样本通过T形肠套管。为了评估尽可能多的环境和个体操舵菌群变异，每只动物在6周的时间内采样了3次。从样品中提取DNA并提交16S rRNA基因Ion Torrent PGM细菌测序。报告了从门类到分类学级别的详细描述性分析。十二指肠内两个不同部位之间的微生物组数量差异已得到成功表征。在腔内和粘膜活检之间发现了巨大而显着的微生物群多样性。在门类分类学水平上，纤毛虫和拟杆菌属占微生物组的80％以上。在较低的分类学水平，分类，家族和属下进行的进一步分析表明，微生物组具有明显的多样性和分布。体内势在必行。这项研究的新颖性是使用经过常规饲养的活牛，可以实时分析十二指肠微生物组，从而为有关牛十二指肠微生物组的文献做出了贡献。