You are here
A SHOTGUN METAGENOMIC APPROACH TO THE BIOSYNTHESIS OF MARINE NATURAL PRODUCTS
| Title: | A SHOTGUN METAGENOMIC APPROACH TO THE BIOSYNTHESIS OF MARINE NATURAL PRODUCTS. |
 41 views 17 downloads |
|---|---|---|
| Name(s): |
Miller-Xavier, René Kathleen , author Mincer, Tracy, Thesis advisor Florida Atlantic University, Degree grantor Department of Biological Sciences Charles E. Schmidt College of Science |
|
| Type of Resource: | text | |
| Genre: | Electronic Thesis Or Dissertation | |
| Date Created: | 2023 | |
| Date Issued: | 2023 | |
| Publisher: | Florida Atlantic University | |
| Place of Publication: | Boca Raton, Fla. | |
| Physical Form: | application/pdf | |
| Extent: | 271 p. | |
| Language(s): | English | |
| Abstract/Description: | Genomics has been revolutionized by improved sequencing technologies, allowing for the detailed exploration of microbial dark matter and complex microscopic ecosystems. The bottleneck in genomic workflows has shifted from high-throughput sequencing to data analysis. This dissertation developed the Florida Center for Coastal and Human Health Shotgun Metagenomics Workflow (FCHsm) that is easy to use and tailor to unique datasets. This work acts as the beta-testing for the workflow, as it analyzes disparate biomes (environmental and host microbiomes) at varying sequencing depths (shallow and deep). FCHsm was used to resolve molecular dynamics and mine trans-kingdom metagenomes for secondary metabolic biosynthetic gene clusters (BGCs) in two marine environments— Indian River Lagoon toxic harmful algal blooms (IRL HABs) and the medicinal Leiodermatium sponge holobiont. First, an in silico mock dataset was analyzed to benchmark the FCHsm workflow. Sourmash, coupled with the Genome Taxonomy Database, outcompeted the other taxonomic profilers by accurately predicting the size of the mock metagenome (450 genomes) and recalling the highest number of species (82 %) and strains (44 %). Nonpareil calculated the sequencing effort needed for 100 % coverage for all the datasets and correctly estimated the 75 Gbp of sequencing needed for almost 100 % coverage of the mock metagenomes (99.5 %). Next, the trans-kingdom metagenomes of the IRL were explored, and potential HAB biomarkers were identified. | |
| Identifier: | FA00014186 (IID) | |
| Degree granted: | Dissertation (PhD)--Florida Atlantic University, 2023. | |
| Collection: | FAU Electronic Theses and Dissertations Collection | |
| Note(s): | Includes bibliography. | |
| Subject(s): |
Marine natural products Metagenomics |
|
| Persistent Link to This Record: | http://purl.flvc.org/fau/fd/FA00014186 | |
| Use and Reproduction: | Copyright © is held by the author with permission granted to Florida Atlantic University to digitize, archive and distribute this item for non-profit research and educational purposes. Any reuse of this item in excess of fair use or other copyright exemptions requires permission of the copyright holder. | |
| Host Institution: | FAU | |
| Is Part of Series: | Florida Atlantic University Digital Library Collections. |
