Document Type

Honors Thesis


Mollecular and Cellular Biology


Pauline Kamath

Committee Members

Benjamin King, Mark Brewer, Melanie Prentice

Graduation Year

May 2023

Publication Date

Spring 2023


Infectious diseases have a tremendous global impact, adversely affecting the health and well-being of humans, domestic livestock, and wildlife. Consequently, pathogen surveillance in wild animals is essential for managing the risk of disease transmission to humans and domesticated animals, as well as for understanding host-pathogen interactions. However, pathogen detection methods are often focused on one to a few pathogen species, which limits our understanding of the distributions and effects of multiple co-infecting pathogens on host individuals and populations. In this study, I employed a metagenomic sequencing approach to (1) characterize the microbial community in a white-tailed deer (Odocoileus virginianus) that had succumbed to pneumonia, and (2) evaluate an adaptive sampling sequencing approach that more efficiently targets microbial sequences by excluding the host genome during sequencing. I first performed metagenomic sequencing on DNA extracted from deer lung tissue and then sequenced the same sample using the adaptive sampling approach on a MinION platform (Oxford Nanopore). The results from the metagenomic sequencing were compared to that from the adaptive sampling approach. While the expectation was to see an increase in microbes identified using the adaptive sampling approach, I found a similar list of microbial species using both the adaptive and standard approaches. However, we also found that the adaptive sequencing approach was more efficient in identifying a similar set of microbes in a shorter time frame and could be more cost-effective. This study validated the use of the adaptive sampling method as a more rapid tool for sequencing pathogens while also showing limitations in the ability to identify a broader range of microbes