Presentation Title

Utilizing a Next-Generation Sequencing Bioinformatics Pipeline to Analyze Antibiotic Resistomes in Coastal Microbial Communities

Faculty Mentor

Elinne Becket

Start Date

23-11-2019 1:00 PM

End Date

23-11-2019 1:15 PM

Location

Markstein 205

Session

oral 3

Type of Presentation

Oral Talk

Subject Area

biological_agricultural_sciences

Abstract

The ocean is an endpoint for anthropogenic runoff containing antibiotics and other wastes, and because of this, coastal microbiomes are acquiring and transferring more antibiotic resistance genes (ARGs) between each other and known pathogens through horizontal gene transfer. The ARGs present in these ocean bacteria have not yet been studied to the extent of other soil or clinical microbiomes, such as the gut microbiome. To study this, we generated a bioinformatics pipeline in our laboratory combining the informatics tools Bowtie2, samtools, and GROOT, which extracts ARGs from next-generation sequencing data using known ARG databases. Using this pipeline, we have identified ARGs from internally generated and publicly available next-generation sequencing data from coastal metagenomic samples across geographical regions, with the intention of analyzing the geographical distribution of ARGs. While our internal data (which came from samples enriched in DNA elements that carry ARGs) yielded deep coverage of multiple ARG classes, we observed little ARG coverage in total-DNA metagenome samples from publicly available ocean water samples, thereby hindering statistically sound inferences. Further pipeline developments and larger sample numbers will enable us to study the ocean antibiotic resistome more deeply and uncover patterns of ARG spread.

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Nov 23rd, 1:00 PM Nov 23rd, 1:15 PM

Utilizing a Next-Generation Sequencing Bioinformatics Pipeline to Analyze Antibiotic Resistomes in Coastal Microbial Communities

Markstein 205

The ocean is an endpoint for anthropogenic runoff containing antibiotics and other wastes, and because of this, coastal microbiomes are acquiring and transferring more antibiotic resistance genes (ARGs) between each other and known pathogens through horizontal gene transfer. The ARGs present in these ocean bacteria have not yet been studied to the extent of other soil or clinical microbiomes, such as the gut microbiome. To study this, we generated a bioinformatics pipeline in our laboratory combining the informatics tools Bowtie2, samtools, and GROOT, which extracts ARGs from next-generation sequencing data using known ARG databases. Using this pipeline, we have identified ARGs from internally generated and publicly available next-generation sequencing data from coastal metagenomic samples across geographical regions, with the intention of analyzing the geographical distribution of ARGs. While our internal data (which came from samples enriched in DNA elements that carry ARGs) yielded deep coverage of multiple ARG classes, we observed little ARG coverage in total-DNA metagenome samples from publicly available ocean water samples, thereby hindering statistically sound inferences. Further pipeline developments and larger sample numbers will enable us to study the ocean antibiotic resistome more deeply and uncover patterns of ARG spread.