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Characterization of the Equine Intestinal Microbiota by High Throughput Sequencing.

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Title: Characterization of the Equine Intestinal Microbiota by High Throughput Sequencing.
Author: Costa, Marcio
Department: Department of Pathobiology
Program: Pathobiology
Advisor: Weese, J Scott
Abstract: This study was performed to characterize the intestinal microbiota of horses by the use of new sequencing technologies, which allow for a broader coverage of the organisms inhabiting complex ecosystems. The first study of this thesis characterized the fecal microbiota of healthy horses and horses with undifferentiated colitis. Actinobacteria, Spirochaetes and Clostridia were significantly more abundant in healthy horses, while Fusobacteria were more abundant in horses with colitis. Members of the Lachnospiraceae were the most frequently shared organisms among healthy individuals. The second study of this thesis found that newborn foals have a rich and diverse bacterial community during the first day of life, comprised by several low abundant genera that were unique at this age. The microbiota present during the first month of life was less diverse compared to older animals, with the majority of organisms classified as Akkermansia spp.. After 60 days of life, bacterial structure tended to remain stable, but differences in community membership were still present between nine month old animals and adult mares. The third study investigated changes in the fecal microbiota associated with antimicrobial administration. Significant changes of population structure and community membership were observed after the use of penicillin, ceftiofur and trimethoprim sulfadiazine, with the last drug causing the most marked changes and significant decrease of richness and diversity. Changes induced by antimicrobial administration were specific for each drug. Recover of the intestinal microbiota was observed, but differences were still evident 30 days after the beginning of the trial. In the last study, we characterized the microbiota present in different intestinal compartments of healthy horses. As expected, marked differences were present among compartments. Lactobacillus spp. and Sarcina spp. predominated in the stomach, Streptococcus spp. in the duodenum, Actinobacillus and Clostridium sensu stricto, in the ileum and “5 genus incertae sedis” from the large colon through feces. There was a significant increase in diversity towards the distal gut with a stable profile observed from the cecum through feces. Our results demonstrated the complexity of the intestinal microbiota in horses and the consequences that factors like age and antimicrobial usage have on this ecosystem.
URI: http://hdl.handle.net/10214/8188
Date: 2014-06


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