Metagenome Assembled Genome of a Putative Phage from a Continental Cheese Production Facility
Disciplines
Bacteria | Bacteriology | Biochemistry | Bioinformatics | Biotechnology | Computational Biology | Genomics | Molecular Biology | Molecular Genetics | Virology | Viruses
Abstract (300 words maximum)
Next-generation sequencing (NGS) has been providing new opportunities in the elucidation of microbiomes, especially in fermented foods. The goal of this study is to find new phages from a production facility for continental cheeses to further understand its microbiome. After sequencing with Illumina NextSeq 500, the Teagasc Food Research Centre from Ireland deposited the data under BioProject PRJEB22242 in NCBI Sequence Read Archive (SRA). ERR2102097 from the above BioProject was selected for our study to identify novel phages. After adapter trimming with fastp, metaviralspades was used for de novo assembly of reads into contigs and scaffolds, which potentially contain metagenome-assembled genomes (MAGs) for phages. Mobile genetic elements, such as plasmids and viruses, from contigs and scaffolds were then identified by geNomad, along with taxonomic assignments. One scaffold thus generated contains 21,935 nucleotides in length and a G + C content of 36%. Metaviralspades also reported a coverage of 48,144.931673 for this scaffold. This scaffold has been predicted by geNomad as a member in the class of Caudoviricetes. Similarity search with BLASTN against nt revealed 95.56% identity to Lactococcus phage 62606 as the most related entry, which was originally isolated from dairy products and is also a member of Caudoviricetes. Within the pharokka pipeline, PHANOTATE predicted 41 open-reading frames (ORFs). The most noteworthy categories include: nucleotide metabolism with four ORFs, lysis with two ORFs, and phage head/packaging with five ORFs, as well as a large terminase subunit of 526 amino acids. CheckV reported that the assembly is at a completeness of 100% with the presence of direct terminal repeats (DTR). It also reported that the minimum information about an uncultivated virus genome (MIUVIG) quality is “High-Quality.” This MAG is therefore considered as the complete genome a of phage. In conclusion, this study thus suggests the discovery of a novel phage that infects the genus of Lactococcus from a production facility for continental-style cheeses.
Academic department under which the project should be listed
CSM - Molecular and Cellular Biology
Primary Investigator (PI) Name
Tsai-Tien Tseng
Metagenome Assembled Genome of a Putative Phage from a Continental Cheese Production Facility
Next-generation sequencing (NGS) has been providing new opportunities in the elucidation of microbiomes, especially in fermented foods. The goal of this study is to find new phages from a production facility for continental cheeses to further understand its microbiome. After sequencing with Illumina NextSeq 500, the Teagasc Food Research Centre from Ireland deposited the data under BioProject PRJEB22242 in NCBI Sequence Read Archive (SRA). ERR2102097 from the above BioProject was selected for our study to identify novel phages. After adapter trimming with fastp, metaviralspades was used for de novo assembly of reads into contigs and scaffolds, which potentially contain metagenome-assembled genomes (MAGs) for phages. Mobile genetic elements, such as plasmids and viruses, from contigs and scaffolds were then identified by geNomad, along with taxonomic assignments. One scaffold thus generated contains 21,935 nucleotides in length and a G + C content of 36%. Metaviralspades also reported a coverage of 48,144.931673 for this scaffold. This scaffold has been predicted by geNomad as a member in the class of Caudoviricetes. Similarity search with BLASTN against nt revealed 95.56% identity to Lactococcus phage 62606 as the most related entry, which was originally isolated from dairy products and is also a member of Caudoviricetes. Within the pharokka pipeline, PHANOTATE predicted 41 open-reading frames (ORFs). The most noteworthy categories include: nucleotide metabolism with four ORFs, lysis with two ORFs, and phage head/packaging with five ORFs, as well as a large terminase subunit of 526 amino acids. CheckV reported that the assembly is at a completeness of 100% with the presence of direct terminal repeats (DTR). It also reported that the minimum information about an uncultivated virus genome (MIUVIG) quality is “High-Quality.” This MAG is therefore considered as the complete genome a of phage. In conclusion, this study thus suggests the discovery of a novel phage that infects the genus of Lactococcus from a production facility for continental-style cheeses.