This Is AuburnElectronic Theses and Dissertations

Taxonomic Profiling of the Lumen and Epimural Surface of the Duodenum, Rumen and Ileum Using a Cannulated Bovine Model





Stockler, Ricardo

Type of Degree

PhD Dissertation


General Veterinary Medicine


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. Although there are many peer reviewed studies focusing on the rumen microbiota and the impact on meat and milk production, limited information regarding the microbial populations in the upper small intestine of the bovine is available in the literature, especially studies that were conducted in the live animal. The ruminant gastrointestinal microbiome grants many physiological and unique functions that are considered essential to maintain overall homeostasis. The author hypothesizes that there are differences in the taxonomic distribution of the commensal microbiome between the lumen and the epimural surface of the bovine duodenum, rumen and ileum. This project involved the surgical fitting of ruminal, duodenal, and ileal indwelling cannulas to allow sample collection using a flexible video-endoscope, with the research units alive and undergoing ordinary husbandry. In the first study, using 16S rRNA gene phylogenetic analysis, the commensal microbiome present in the lumen and the mucosal surface of the duodenum of cattle was characterized and compared providing a detailed descriptive analysis from phylum to genus taxonomic level. Distinct differences in diversity and distribution of the microbiome were found between the luminal and mucosal biopsies at the phylum and lower taxonomic levels. In the second study, using the same technique, the commensal microbiome present in the lumen and the epimural surface of the rumen epithelium was characterized providing a detailed descriptive analysis from phylum to genus. A great and significant diversity of microbiota was found between the two locations. In agreement with the literature, the Firmicutes and Bacteroidetes bacterial phyla composed over 80% of the microbiome in the lumen contents whereas the Firmicutes, by itself, composed over 90% of the microbiome in the epimural surface of the rumen. Further analysis at lower taxonomic levels, class, family and genus, showed similar diversity and even distribution between the animals and throughout the study weeks. The technique validated by the first study, allowed the third study to mature. The objective of this study was to characterize the commensal microbiome present in the lumen and the mucosal surface of the ileum of cattle, as the ileum is the location of where many relevant infectious intestinal diseases occur. Firmicutes was the most predominant phyla in luminal and epimural locations followed by Bacteroidetes. The Firmicutes Bacteroidetes ratio varied between the animals, however, remained relatively consistent across individual cattle throughout the study period. In contrast with the rumen and duodenum, there appears to be no phylogenetic assemblage amongst the two collection sites despite the variation among the animals. Additionally, the author also hypothesize that the use of a systemic antimicrobial therapy does alter the microbiome characteristics associated with the lumen and epimural surface of the bovine ileum therefore, the microbiome was characterized following on-label administration of an approved systemic antimicrobial commonly used in bovine medicine.