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A SHOTGUN METAGENOMIC APPROACH TO THE BIOSYNTHESIS OF MARINE NATURAL PRODUCTS
Title
A SHOTGUN METAGENOMIC APPROACH TO THE BIOSYNTHESIS OF MARINE NATURAL PRODUCTS.
Creator
Miller-Xavier, René Kathleen, Mincer, Tracy, Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
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...
Show moreGenomics 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.
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Date Issued
2023
PURL
http://purl.flvc.org/fau/fd/FA00014186
Subject Headings
Marine natural products, Metagenomics
Format
Document (PDF)
DNA fingerprinting of human oral microbiome: a first step towards development of early diagnosis of oral diseases
Title
DNA fingerprinting of human oral microbiome: a first step towards development of early diagnosis of oral diseases.
Creator
Chakraborty, Shreyasee, Graduate College
Date Issued
2013-04-12
PURL
http://purl.flvc.org/fcla/dt/3361916
Subject Headings
DNA fingerprinting, Mouth--Diseases, Metagenomics
Format
Document (PDF)
EVALUATION OF THE CONTRIBUTION METAGENOMIC SHOTGUN SEQUENCING HAS IN ASSESSING POLLUTION SOURCE AND DEFINING PUBLIC HEALTH AND ENVIRONMENTAL RISKS
Title
EVALUATION OF THE CONTRIBUTION METAGENOMIC SHOTGUN SEQUENCING HAS IN ASSESSING POLLUTION SOURCE AND DEFINING PUBLIC HEALTH AND ENVIRONMENTAL RISKS.
Creator
Mercer, Brian, Esiobu, Nawdiuto, Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
Abstract/Description
State-approved membrane filtration (MF) techniques for water quality assessments were contrasted with metagenomic shotgun sequencing (MSS) protocols to evaluate their efficacy in providing precise health-risk indices for surface waters. Using MSS, the relative numerical abundance of pathogenic bacteria, virulence and antibiotic resistance genes revealed the status and potential pollution sources in samples studied. Traditional culture methods (TCM) showed possible fecal contamination, while...
Show moreState-approved membrane filtration (MF) techniques for water quality assessments were contrasted with metagenomic shotgun sequencing (MSS) protocols to evaluate their efficacy in providing precise health-risk indices for surface waters. Using MSS, the relative numerical abundance of pathogenic bacteria, virulence and antibiotic resistance genes revealed the status and potential pollution sources in samples studied. Traditional culture methods (TCM) showed possible fecal contamination, while MSS clearly distinguished between fecal and environmental bacteria contamination sources, and pinpointed actual risks from pathogens. RNA MSS to detect all viable microorganisms and qPCR of fecal biomarkers were used to assess the possible environmental risk between runoff drainage canals and a swamp area with no anthropogenic impact. Results revealed higher levels of pathogenic bacteria, viruses, and virulence and antibiotic resistance genes in the canal samples. The data underscore the potential utility of MSS in precision risk assessment for public and biodiversity health and tracking of environmental microbiome shifts by field managers and policy makers.
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Date Issued
2020
PURL
http://purl.flvc.org/fau/fd/FA00013573
Subject Headings
Metagenomics, Public health--Risk assessment, Environmental risks, Water quality--Evaluation, Metagenomics--methods
Format
Document (PDF)