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Full-Text Articles in Computational Biology
In Silico Identification Of A Streptococcus Phage From An Unpasteurized Dairy Product
In Silico Identification Of A Streptococcus Phage From An Unpasteurized Dairy Product
Symposium of Student Scholars
This study aimed to identify novel phages from a West African dairy product, nunu, to better understand the uncharacterized virosphere of a food microbiome. Nunu is a yogurt-like product from spontaneous fermentation of unpasteurized cow milk without a standardized starter culture. Phages and their bacterial hosts make up a microbiome, where their collective metagenome can be studied in silico, or computationally, after next generation sequencing (NGS). The targeted dataset for our study can be found in the Sequence Read Archives under the accession number of ERX2041567. This study utilized several bioinformatics software tools with customized settings: Kraken2, MetaVelvet, Edena, NCBI-BLAST, …
In Silico Isolation Of A Novel Phage For Food Safety Applications Against Pathogenic E. Coli, Daisy Mcgrath
In Silico Isolation Of A Novel Phage For Food Safety Applications Against Pathogenic E. Coli, Daisy Mcgrath
Symposium of Student Scholars
With the advent of next-generation sequencing (NGS) on metagenomes, the elucidation of all genetic material from microbiomes has prompted a renewed interest towards uncultivated members of the virosphere. We describe the discovery of a novel phage from a metagenomic dataset on the West African fermented dairy product, nunu, with a custom bioinformatics workflow to potentially serve as a biocontrol agent against pathogenic E. coli. Initial dataset of ERR2014814 from NCBI was first subjected to Kraken2 to extract novel sequencing reads for further de novo assembly into contigs by MetaVelvet. Resultant contigs served as potential partial phage genomes, then searched …