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An Investigation into the Fecal Microbiota of Domestic Rabbits (Oryctolagus cuniculus) and Factors Influencing its Composition

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Title: An Investigation into the Fecal Microbiota of Domestic Rabbits (Oryctolagus cuniculus) and Factors Influencing its Composition
Author: Kylie, Jennifer
Department: Department of Pathobiology
Program: Pathobiology
Advisor: Turner, Patricia V.
Abstract: The rabbit enteric microbiota plays a key role in maintaining rabbit health, including helping to digest the forage-based diet and aiding in immune system regulation and development. Changes in the enteric microbiota composition may result in enteritis. The primary goals of the current study were to characterize the fecal microbiota of healthy rabbits and identify factors that may contribute to microbiota changes. Fecal samples (n=191) were collected from adult and weanling rabbits raised for a variety of purposes (commercial meat, laboratories, shelters, and companions) during summer and winter months. Fecal bacterial DNA was extracted and analysed using 16s rRNA gene sequencing to identify composition and variations in the microbiota. Additionally, culture and susceptibility testing was conducted to identify whether antimicrobial-resistant Escherichia coli and Salmonella enterica isolates were present, and, if present, whether they were associated with routine antimicrobial use, and whether routine antimicrobial use was associated with changes in the fecal microbiota. In all rabbit samples examined, Firmicutes was the predominant phylum detected. Relative proportions of Proteobacteria were increased significantly in commercial meat rabbits (p<0.01) and during the summer (p=0.02). Relative proportions of Verrucomicrobia were decreased significantly in commercial meat rabbits (p<0.01) and during the summer months (p=0.03). Additional changes included a significantly lower proportion of Lentisphaerae in commercial meat rabbit feces than in companion or shelter rabbits, increases in relative proportions of Actinobacteria (p=0.03), Bacteroidetes (p=0.03), and Denococcus-Thermus (p=0.04) during the summer, and increases in Firmicutes (p=0.04) during the winter. Minimal microbiota changes were noted between adult and weanling rabbits, regardless of whether antimicrobials were routinely administered. At least one antimicrobial resistant isolate of E. coli was identified from 56% of commercial meat farms (n=27), and from 25% of laboratory (n=8) and shelter (n=4) facilities. Salmonella Kentucky was the only antimicrobial resistant S. enterica serovar identified and from only one farm. Antimicrobial resistance was most commonly identified against tetracycline. This body of work provides significant insight into the composition of the enteric microbiota of clinically healthy domestic rabbits from a range of sources and potential underlying causes of variations.
URI: http://hdl.handle.net/10214/10004
Date: 2016-08
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