Master of Science, The Ohio State University, 2020, Animal Sciences
Necrotic enteritis (NE) is a multifactorial disease caused by Clostridium perfringens. A way to examine treatments on NE is through methods like body weight gain or lesion scores. Quantification of C. perfringens could be additional measurement. In experiment 3.1, four published extraction protocols, and a new protocol were compared to determine which would be ideal for extracting bacterial DNA. After extraction, DNA concentrations were measured with quality assessed, and a qPCR standard curve was established for each protocol. For Protocols 1 to 5, mean DNA yields and A260/280/A260/230 ratios were 459.02μg/g and 2.18/1.26, 989.66μg/g and 2.07/2.06, 110.71μg/g and 1.58/0.89, 437.03μg/g and 2.07/1.93 and 1,794.90μg/g and 1.91/1.42, respectively. Amplification efficiency percentages and standard curve regression coefficient values for Protocols 1 to 5 were 84.69%/1.00, 79.76%/0.99, 100.30%/1.00, 80.93%/0.99 and 95.76%/0.99, respectively. There was extensive variation in DNA quantity, quality, and PCR efficiency, highlighting challenges of DNA extraction from intestinal samples. Protocol 2 was identified as ideal based on DNA quantity and quality, and low standard deviations between qPCR samples. Experiments 4.1 and 4.2 compared qPCR and direct plating of fecal, ileal and cecal samples for C. perfringens quantification. In experiment 4.1, two groups were compared; an un-inoculated control and an inoculated group, while in experiment 4.2, the two groups compared were an un-inoculated control, fed a corn-based diet and an inoculated rye-based diet group. For quantifying C. perfringens, qPCR and two recently developed selective agar types were compared, with results analyzed by ANOVA factorials and Tukey's Honestly Significant Difference test. All methods were further evaluated using relative standard deviation of CFU/g percentage (RSD%) values. In experiment 4.1, quantification method was a significant variable (p<0.05), with significant differences between qPCR and C. p (open full item for complete abstract)
Committee: Lisa Bielke (Advisor); Thaddeus Ezeji (Committee Member); Zhongtang Yu (Committee Member)
Subjects: Animal Diseases; Microbiology; Molecular Biology