Date of Award

Summer 8-2022

Level of Access Assigned by Author

Open-Access Thesis

Degree Name

Master of Science (MS)


Animal Sciences


Suzanne Ishaq

Second Committee Member

Erin Grey

Third Committee Member

Caitlin Howell

Additional Committee Members

Juan Romero

Emma Perry


Animals have trillions of microorganisms living in or on many body sites, these communities of microorganisms are called microbiomes. Microbiomes are typically host-specific, and a lot of information about the host can be determined from investigating them. Microbiome research has many real-world applications, and this thesis utilizes the One Health perspective, which acknowledges the connection of humans, animals, and environments, and emphasizes the need for collaborative, interdisciplinary research. The first interdisciplinary project is an investigation into the bacteria in wild and cultured Atlantic deep-sea scallop, Placopecten magellanicus larvae. Adults in hatcheries can be induced to spawn, but the last two weeks of the larval maturation phase are plagued by massive animal death. The reasons for this are unknown, but research into other scallop and aquaculture species point to loss from bacterial infections and altered functionality of host- associated microbial communities. This pilot study used 16S rDNA sequencing to identify bacterial communities in wild larvae, cultured larvae, and tank biofilms. Tank biofilms were also cultured for the presence of common aquatic pathogenic Vibrio species of bacteria using selective media. We assessed the similarities between bacteria associated with these three sample types, to determine the role of environmental microbes in establishing a microbial community in scallop larvae. These results, along with future work, will be able to inform the hatcheries on methods that will hopefully increase the larval survival in these facilities. The second chapter of the thesis reviews Cryptosporidium species of protozoa. Cryptosporidium spp. are apicomplexan parasites responsible for cryptosporidiosis, the leading cause of diarrheal-related death in young children and neonatal calves (Bos taurus). Cryptosporidium parvum is the most common zoonotic species that infects livestock and humans, but dozens of species have been identified. The detection of oocysts has historically relied on microscopy and molecular identification, but these can be hampered by the difficulty of processing the sample substrate or a lack of species or strain resolution. Further, Cryptosporidium is difficult to maintain in culture for in-depth study. Because of its ubiquity in the environment, range of host species, and ease of transmission, eradication of the disease in livestock is unlikely. Consequently, understanding the modes of transmission, risk of infection, treatments, and research methods is essential to understanding the ecology of the protozoa to prevent outbreaks. The goal of this research is to emphasize the importance of exploring the relationships between animals, humans, and the environment, and microbes, host, and environment, as well as the need for collaboration to accomplish these types of interdisciplinary research projects. The scallop study focuses on connecting microbes to the host and the environment, and without collaborations from the scallop industry, we would not be able to apply our research to real-world problems. The Cryptosporidium review emphasizes the lack of research and knowledge to be able to minimize risk of outbreaks, and collaboration with farmers and other agriculture workers is needed to do this research as well as to implement disease prevention strategies.