Actinomyces Genomic DNA Extraction for Biosynthetic Gene Clusters and Associated Secondary Metabolites
Poster Number
19B
Faculty Mentor Name
Skylar Carlson and Paul Orwin
Research or Creativity Area
Natural Sciences
Abstract
Bacterial genomes serve as a blueprint for secondary metabolism, defining which molecules bacteria are capable of making. Secondary metabolites are organic compounds produced by microbes that are not directly involved in normal growth and development. These small molecules exhibit biological activities including antimicrobial, antioxidant, and anticancer properties. In our study, we focused on Actinomyces in the Carlson lab microbial library. This class of bacteria dedicates a significant portion of the genome to the biosynthesis of secondary metabolites. Thanks to advances in sequencing technology, scientists are able to directly access this information without sending samples away to be sequenced. The nanopore is a USB capable device smaller than a cellphone. The goal of this project is to optimize the extraction of genomic DNA from Actinomyces. The genomic DNA is then sequenced on the nanopore sequencer, assembled into a genome to identify the biosynthetic gene clusters, predict its small molecule output, and verify the structure outputs experimentally. Our Actinomyces grow on a shaking platform for 3-7 days in a starch-yeast-peptone medium. We used a modification of an Actinomyces DNA isolation protocol from Actinobase, aiming to preserve long, high-quality DNA fragments suitable for long-read nanopore sequencing. Using this protocol, DNA was successfully extracted and sequenced with the nanopore technology. Assembly software was then used to identify overlaps between DNA fragments, improving confidence in the reconstructed genomes. Sequencing and assembly of these long reads provides a foundation for further investigation into biosynthetic gene clusters and their correlation with the production of specific secondary metabolites. Collected DNA segments will be used to analyze and predict compounds Actinomyces genome encodes for. We will then cultivate the bacteria in a variety of media to confirm these predicted metabolite products are produced and assess their biological activities. In future work, we plan to integrate mass spectrometry analysis to identify the secondary metabolites produced by Actinomyces, strengthening our understanding of the relationship between biosynthetic gene clusters and secondary metabolite production, and ultimately contributing to the discovery and characterization of biologically significant compounds.
Location
University of the Pacific, DeRosa University Center
Start Date
24-4-2026 11:00 AM
End Date
24-4-2026 2:00 PM
Actinomyces Genomic DNA Extraction for Biosynthetic Gene Clusters and Associated Secondary Metabolites
University of the Pacific, DeRosa University Center
Bacterial genomes serve as a blueprint for secondary metabolism, defining which molecules bacteria are capable of making. Secondary metabolites are organic compounds produced by microbes that are not directly involved in normal growth and development. These small molecules exhibit biological activities including antimicrobial, antioxidant, and anticancer properties. In our study, we focused on Actinomyces in the Carlson lab microbial library. This class of bacteria dedicates a significant portion of the genome to the biosynthesis of secondary metabolites. Thanks to advances in sequencing technology, scientists are able to directly access this information without sending samples away to be sequenced. The nanopore is a USB capable device smaller than a cellphone. The goal of this project is to optimize the extraction of genomic DNA from Actinomyces. The genomic DNA is then sequenced on the nanopore sequencer, assembled into a genome to identify the biosynthetic gene clusters, predict its small molecule output, and verify the structure outputs experimentally. Our Actinomyces grow on a shaking platform for 3-7 days in a starch-yeast-peptone medium. We used a modification of an Actinomyces DNA isolation protocol from Actinobase, aiming to preserve long, high-quality DNA fragments suitable for long-read nanopore sequencing. Using this protocol, DNA was successfully extracted and sequenced with the nanopore technology. Assembly software was then used to identify overlaps between DNA fragments, improving confidence in the reconstructed genomes. Sequencing and assembly of these long reads provides a foundation for further investigation into biosynthetic gene clusters and their correlation with the production of specific secondary metabolites. Collected DNA segments will be used to analyze and predict compounds Actinomyces genome encodes for. We will then cultivate the bacteria in a variety of media to confirm these predicted metabolite products are produced and assess their biological activities. In future work, we plan to integrate mass spectrometry analysis to identify the secondary metabolites produced by Actinomyces, strengthening our understanding of the relationship between biosynthetic gene clusters and secondary metabolite production, and ultimately contributing to the discovery and characterization of biologically significant compounds.
