Plating of DNA ladders, positive controls, a negative control, and samples prior to the detection step (gel electrophoresis) of a multiplex PCR assay

Author: Erika Shirer | Major: Animal Science | Semester: Spring 2024

In January of 2023, I began an undergraduate research project in the Animal Science Department under Dr. Charles Maxwell. Our overall goal is to examine whether dietary fiber and fiber-degrading enzymes introduced to swine will modulate their gut microbiome during periods of clinical illness. We utilized the first semester to determine what research we were to cover and then further adapted it over that same semester. We also planned what materials and media would be used during the trial. I also began having weekly meetings with my committee members.

I first learned that my mentor, Dr. Charles Maxwell, had availability for an undergraduate student to perform research in the spring of 2022. As a freshman transfer student, I was not yet a member of the Honors College, but I thought that research sounded interesting and planned on pursuing it regardless. In the fall of 2022, I began working as a Laboratory Assistant for UADA’s Swine Nutrition Lab. When I’m not working on my undergraduate research, I assist in Dr. Maxwell’s and Dr. Tsungcheng Tsai’s Swine Nutrition Lab which conducts monogastric nutrition research involving the maturation, nutrition, and management of swine, especially newborn pigs, through various processes. Being able to obtain a part-time job at the lab related to where I would conduct future research was a helpful way to integrate myself and gain a better understanding of what my project would cover. To have gained research and laboratory experience before gathering data for my Honors Thesis Project provided me with a basis of knowledge about animal welfare and the importance of the livestock industry.

Fast-forwarding to the fall of 2023, the dietary trial began. Piglets were blocked by weaning body weight and assigned randomly to dietary treatments. A four-phase feeding regimen which included dietary fiber and a stimbiotic was provided from weaning (day 0) till the end of phase three, a common diet was fed from the end of phase three to the end of the trial. On day five of postweaning, all pigs were orally inoculated with F18 enterotoxigenic Escherichia coli (ETEC). From there, fecal samples were collected from pigs before ETEC administration and two more times post-challenge.

Back in the laboratory, fecal samples were placed into sterilized filter bags with a peptone diluent and then homogenized in a stomacher. From there, a total coliform count was carried out which consisted of both red (gram-negative) and blue (gram-positive) colonies. Next, colonies were isolated in nutrient broth. To prepare for the polymerase chain reaction (PCR) assays that were to be carried out in the spring of 2024, nutrient broth containing the isolated bacteria was allocated into a microcentrifuge tube. Samples from day two of the fecal collection were to be utilized for PCR assays.

In the spring of 2024, my group and I began multiplex polymerase chain reaction (PCR) assays to detect and characterize pathogenic E. coli. From there, we will be able to identify the genotypic characterization of E. coli isolates from pigs experiencing post-weaning diarrhea (PWD). Through PCR, the use of multiple primer pairs in a reaction mixture allows us to amplify multiple target sequences.

In March, Dr. Tsungcheng Tsai, my committee member, and I traveled to Madison, Wisconsin for the 2024 American Society of Animal Science (ASAS) Midwest Section Meeting. There, I presented in an undergraduate poster competition regarding the “Effect of fiber and stimbiotic on growth performance and the gut microbiome in pigs challenged with F18 enterotoxigenic Escherichia coli (ETEC)”. The intended purpose was to present how pathogenic Escherichia coli affects growth and development during the early weaning period of the swine and to determine the effectiveness of dietary fiber sources and fiber-degrading enzymes on the sustainability of the ETEC challenge.

As for the future, I plan to attend veterinary school and subsequently graduate with a Doctor of Veterinary Medicine degree. Veterinary practices surrounding shelter, wildlife, small animal, and livestock medicine have recently piqued my interest. By exploring these specialties through shadowing and hands-on experience, I have been able to familiarize myself with the diverse responsibilities that different specialties are amenable to in their day-to-day practice. While I was not raised in an agricultural environment, my participation in laboratory, clinical, and production settings has confirmed my intent and desire to pursue a career in veterinary medicine.