Intestinal microbiota fulfill important functions that contributed to their host ́s health, and can be affected by the presence of pathogens. White-tailed deer and cattle share pastures in many agro-ecosystems, and have been reported to share strains of both pathogenic E. coli and Salmonella, suggesting direct interaction and interspecific transmission of microorganisms. However, there is a lack of knowledge of the composition of white-tailed deer intestinal microbiota, the effects of pathogenic E. coli and Salmonella to the microbiota, and the differences in composition and pathogen response between deer and cattle microbiota. This thesis first characterized the microbiota of 67 fecal samples of white-tailed deer using 16S rDNA pyrosequencing. White-tailed deer intestinal microbiota is composed mainly by Firmicutes and Proteobacteria. Results revealed the importance of seasonal variability in microbial composition, and suggested that enterohemorrhagic E. coli (EHEC) and Salmonella affect intestinal microbiota composition of white-tailed deer. The second chapter compared the microbiota of deer and cattle, and contrasted their response to EHEC. Results revealed that the main difference in microbiota composition between both species was the abundance of Proteobacteria (0.82% in cattle vs. 20.25% in deer). Comparison of microbial abundance in EHEC-positive vs. -negative in cattle did not show major differences; while, white-tailed deer microbiota differed in composition at both phyla and genera level. Results demonstrate a different core microbiota between cattle and deer that shared an environment, and a different response to the presence of the EHEC.
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