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The Identification and Genomic Analysis of MunkgeeRoachy: A Novel Gordonia rubripertincta Bacteriophage Isolated from Soil

Author

Ashley M. Janke, Nova Southeastern UniversityFollow

Date of Award

2024

Document Type

Honors Thesis - NSU Access Only

Degree Type

Bachelors of Science

Degree Name

Biology

Department

Halmos College of Arts and Sciences and the Guy Harvey Oceanographic Research Center

Honors College

Farquhar Honors College Thesis

Honors College Dean

Andrea Nevins, Ph.D., M.F.A.

Home College Dean

Holly Lynn Baumgartner, Ph.D.

Faculty Advisor

Julie Torruellas Garcia, Ph.D.

Abstract

There are many bacteria that are growing resistant to antibiotics. Therefore, there is an urgent need for alternative therapies. Bacteriophage therapy, the use of viruses to treat bacterial infections, is a promising alternative. The bacterium Gordonia rubripertincta is gram-positive and is typically found in soil and aquatic habitats. Gordonia species are rapidly becoming associated with human and animal diseases. Infections of G. rubripertincta have typically been found after various surgical procedures such as the applications of catheters, or the use of heart-lung machines. These infections are difficult to treat and require a more effective solution. The goal of this project was to isolate a bacteriophage that infects G. rubripertincta from a soil sample and then analyze its genome. In this experiment, a soil sample was collected at Wolf Lake Park in Davie, Florida to isolate bacteriophage that eliminated G. rubripertincta. The phage was isolated from the soil sample using a direct isolation method. Phage purification was conducted to ensure that a unique phage was present in the sample. To purify the phage, isolated plaques were picked, diluted, and subjected to additional plaque assays. The phage (MungkeeRoachy) was successfully isolated after three rounds of purification. Webbed plates were created to produce a high concentration of phage lysate. The phage sample of MunkgeeRoachy was imaged with Cryo-EM. Based on morphology, they were classified as being Siphoviridae. The DNA was extracted and sequenced. The bacteriophage's classification was determined to be a CT cluster with a genome length of 45912 base pairs with 71 genes. After manual genome annotation, there were 69 genes in total. There were two genes that were deleted from the auto-annotation, six start sites were changed, and 23 of the gene functions were altered. Genes 60 and 69 are suspected orphams. Genes 23 and 41 potentially have special gene functions, such as holin and helix-turn-helix DNA binding domain. Future applications can entail using this bacteriophage as an advantage for phage therapy for G. rubripertintca infections.

NSUWorks Citation

Ashley M. Janke. 2024. The Identification and Genomic Analysis of MunkgeeRoachy: A Novel Gordonia rubripertincta Bacteriophage Isolated from Soil. Capstone. Nova Southeastern University. Retrieved from NSUWorks, Halmos College of Arts and Sciences and the Guy Harvey Oceanographic Research Center. (41)
https://nsuworks.nova.edu/honors_theses/41.