Disciplines
Bioinformatics | Computational Biology | Other Food Science
Abstract (300 words maximum)
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, SPAdes, and SeaView. Novel reads that are unrelated to previously characterized phages were first isolated by Kraken2. MetaVelvet, Edena and SPAdes were used to provide contigs that represent potentially new phage sequences via de novo assembly. Functional characterization of these contigs were carried out with blastn and tblastx to identify similar open reading frames from databases. SeaView was also used to visualize evolutionary lineages between potentially new phages and previously uncharacterized ones with multiple alignments and phylogenetic trees. As a result, we will present preliminary data that revealed several contigs from a novel phage with potential functions of capsid and terminase that are like ones from Streptococcus phage Str-PAP-1, along with several hypothetical proteins. Its tail protein and helicase were found to be closely related to a phage that infects Streptococcus gallolyticus. In addition to above, another contig contains an open-reading frame for PblA that shares similarity with bacterial adhesins from Streptococcus mitis for attaching to human platelets. In conclusion, our study further characterized the virosphere of the nunu microbiome. And this putatively identified phage have the potential to serve as a biocontrol agent in food processing facilities.
Academic department under which the project should be listed
CSM - Molecular and Cellular Biology
Primary Investigator (PI) Name
Tsai-Tien Tseng
In Silico Identification of a Streptococcus Phage from an Unpasteurized Dairy Product
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, SPAdes, and SeaView. Novel reads that are unrelated to previously characterized phages were first isolated by Kraken2. MetaVelvet, Edena and SPAdes were used to provide contigs that represent potentially new phage sequences via de novo assembly. Functional characterization of these contigs were carried out with blastn and tblastx to identify similar open reading frames from databases. SeaView was also used to visualize evolutionary lineages between potentially new phages and previously uncharacterized ones with multiple alignments and phylogenetic trees. As a result, we will present preliminary data that revealed several contigs from a novel phage with potential functions of capsid and terminase that are like ones from Streptococcus phage Str-PAP-1, along with several hypothetical proteins. Its tail protein and helicase were found to be closely related to a phage that infects Streptococcus gallolyticus. In addition to above, another contig contains an open-reading frame for PblA that shares similarity with bacterial adhesins from Streptococcus mitis for attaching to human platelets. In conclusion, our study further characterized the virosphere of the nunu microbiome. And this putatively identified phage have the potential to serve as a biocontrol agent in food processing facilities.