Metagenome Assembled Genome of a Novel Phage from a Small-Scale White Cheese Processing Facility
Disciplines
Bacteriology | Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Biology | Biotechnology | Food Science | Genetics and Genomics | Immunology and Infectious Disease | Microbiology | Virology
Abstract (300 words maximum)
Next-generation sequencing (NGS) has been providing new opportunities in finding new phages from metagenomic data sets. The surface metagenome from a small-scale white cheese processing facility was originally sequenced by FoodOmics Laboratory at Hacettepe University using Illumina NovaSeq 6000 and deposited in NCBI Sequence Read Archive (SRA) under the accession number of PRJNA951084. One specific run from the above experiment, SRR24234328, was downloaded from NCBI SRA and subjected to the following data mining protocol with the goal of identifying new phages. First, Metaviralspadeswas used for de novo assembly of sequencing reads after adapter trimming with fastp to generate contigs and scaffolds, which may contain metagenome assembled genomes (MAGs) for phages. Contigs and scaffolds were then subjected to identification of mobile genetic elements, including plasmids and viruses, by geNomad. GeNomadwas also utilized for taxonomic assignments of viral genomes. One scaffold thus generated contained 43,851 nucleotides in length and a G + C content of 52%. Metaviralspades also reported a coverage of 1,256.523580 for this contig. Prediction with geNomad revealed this scaffold as a member of the Autographiviridae family in the class of Caudoviricetes. Similarity search with BLASTN against nt_viruses revealed 90.41% identity to Enterobacterphage SDFMU_Pec as the most related entry, which is also a member of Autographiviridae. Among 74 open-reading frames (ORFs) predicted by PHANOTATE as implemented by the pharokka pipeline, the most noteworthy categories include: nucleotide metabolism with 11 ORFs, lysis with three ORFs, and phage head/packaging with nine ORFs, as well as a large terminase subunit of 616 amino acids. CheckV reported that the assembly is at a completeness of 100% with the presence of direct terminal repeats (DTR). CheckV also reported that the minimum information about an uncultivated virus genome (MIUVIG) quality is “High-Quality.” This MAG is therefore considered as a complete phage genome. In conclusion, this study suggests the discovery of a novel phage, which potentially infects the genus of Enterobacter, from the surface microbiome in a small-scale white cheese processing facility.
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 Novel Phage from a Small-Scale White Cheese Processing Facility
Next-generation sequencing (NGS) has been providing new opportunities in finding new phages from metagenomic data sets. The surface metagenome from a small-scale white cheese processing facility was originally sequenced by FoodOmics Laboratory at Hacettepe University using Illumina NovaSeq 6000 and deposited in NCBI Sequence Read Archive (SRA) under the accession number of PRJNA951084. One specific run from the above experiment, SRR24234328, was downloaded from NCBI SRA and subjected to the following data mining protocol with the goal of identifying new phages. First, Metaviralspadeswas used for de novo assembly of sequencing reads after adapter trimming with fastp to generate contigs and scaffolds, which may contain metagenome assembled genomes (MAGs) for phages. Contigs and scaffolds were then subjected to identification of mobile genetic elements, including plasmids and viruses, by geNomad. GeNomadwas also utilized for taxonomic assignments of viral genomes. One scaffold thus generated contained 43,851 nucleotides in length and a G + C content of 52%. Metaviralspades also reported a coverage of 1,256.523580 for this contig. Prediction with geNomad revealed this scaffold as a member of the Autographiviridae family in the class of Caudoviricetes. Similarity search with BLASTN against nt_viruses revealed 90.41% identity to Enterobacterphage SDFMU_Pec as the most related entry, which is also a member of Autographiviridae. Among 74 open-reading frames (ORFs) predicted by PHANOTATE as implemented by the pharokka pipeline, the most noteworthy categories include: nucleotide metabolism with 11 ORFs, lysis with three ORFs, and phage head/packaging with nine ORFs, as well as a large terminase subunit of 616 amino acids. CheckV reported that the assembly is at a completeness of 100% with the presence of direct terminal repeats (DTR). CheckV also reported that the minimum information about an uncultivated virus genome (MIUVIG) quality is “High-Quality.” This MAG is therefore considered as a complete phage genome. In conclusion, this study suggests the discovery of a novel phage, which potentially infects the genus of Enterobacter, from the surface microbiome in a small-scale white cheese processing facility.