Presentation Title

Evaluating the Effectiveness of Metagenome Plasmid Enrichment by Bioinformatically Comparing a Metagenome and Plasmidome from a Mine Reclamation Site

Format of Presentation

Poster to be presented the Friday of the conference

Abstract

Metagenomic analysis of environmental DNA tells us a great deal about the metabolic capacity of the resident microorganisms; however, assembling environmental metagenomes is time consuming, and requires a high level of sequencing commitment. In the context of tracking bacterial pathogens and monitoring antimicrobial and metal resistance genes, a more efficient method might be to enrich plasmids from metagenomes and sequence them, allowing for higher sample throughput. To put this idea to the test, metagenomic DNA isolated from samples originating from a mine reclamation site historically treated with biosolids was treated with plasmid-safe DNase to remove non-circular DNA and generate a “plasmidome”. Both the metagenome and plasmidome were sequenced using Ion Torrent S5 XL sequencing technology, generating 6.91 Gb and 5.89 Gb, respectively. Data were annotated in MG-RAST, and the proportion of antibiotic resistance, metal resistance, and pathogenesis genes in both the metagenome and plasmidome was determined. The plasmidome was found to have over 7.1 million identified protein features and over 5.8 million identified functional categories. From here, methods to assemble the plasmids from the metagenome and plasmidome will be developed to determine if small circular plasmids were in fact enriched using DNase treatments.

Department

Biological Sciences

Faculty Advisor

Jonathan Van Hamme

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Evaluating the Effectiveness of Metagenome Plasmid Enrichment by Bioinformatically Comparing a Metagenome and Plasmidome from a Mine Reclamation Site

Metagenomic analysis of environmental DNA tells us a great deal about the metabolic capacity of the resident microorganisms; however, assembling environmental metagenomes is time consuming, and requires a high level of sequencing commitment. In the context of tracking bacterial pathogens and monitoring antimicrobial and metal resistance genes, a more efficient method might be to enrich plasmids from metagenomes and sequence them, allowing for higher sample throughput. To put this idea to the test, metagenomic DNA isolated from samples originating from a mine reclamation site historically treated with biosolids was treated with plasmid-safe DNase to remove non-circular DNA and generate a “plasmidome”. Both the metagenome and plasmidome were sequenced using Ion Torrent S5 XL sequencing technology, generating 6.91 Gb and 5.89 Gb, respectively. Data were annotated in MG-RAST, and the proportion of antibiotic resistance, metal resistance, and pathogenesis genes in both the metagenome and plasmidome was determined. The plasmidome was found to have over 7.1 million identified protein features and over 5.8 million identified functional categories. From here, methods to assemble the plasmids from the metagenome and plasmidome will be developed to determine if small circular plasmids were in fact enriched using DNase treatments.