Induction and Genome Analysis of HY01, a Newly Reported Prophage from an Emerging Shrimp Pathogen Vibrio campbellii

Vibrio campbellii is an emerging aquaculture pathogen that causes luminous vibriosis in farmed shrimp. Although prophages in various aquaculture pathogens have been widely reported, there is still limited knowledge regarding prophages in the genome of pathogenic V. campbellii. Here, we describe the full-genome sequence of a prophage named HY01, induced from the emerging shrimp pathogen V. campbellii HY01. The phage HY01 was induced by mitomycin C and was morphologically characterized as long tailed phage. V. campbellii phage HY01 is composed of 41,772 bp of dsDNA with a G+C content of 47.45%. A total of 60 open reading frames (ORFs) were identified, of which 31 could be predicted for their biological functions. Twenty seven out of 31 predicted protein coding regions were matched with several encoded proteins of various Enterobacteriaceae, Pseudomonadaceae, Vibrionaceae, and other phages of Gram-negative bacteria. Interestingly, the comparative genome analysis revealed that the phage HY01 was only distantly related to Vibrio phage Va_PF430-3_p42 of fish pathogen V. anguillarum but differed in genomic size and gene organization. The phylogenetic tree placed the phage together with Siphoviridae family. Additionally, a survey of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers revealed two matching sequences between phage HY01 genome and viral spacer sequence of Vibrio spp. The spacer results combined with the synteny results suggest that the evolution of V. campbellii phage HY01 is driven by the horizontal genetic exchange between bacterial families belonging to the class of Gammaproteobacteria.

A Novel Singleton Giant Phage Yong-XC31 Lytic to the Pyropia Pathogen Vibrio mediterranei

Vibrio mediterranei 117-T6 is extensively pathogenic to several Pyropia species, leading to the death of conchocelis. In this study, the first V. mediterranei phage (named Vibrio phage Yong-XC31, abbreviated as Yong-XC31) was isolated. Yong-XC31 is a giant phage containing an icosahedral head about 113 nm in diameter and a contractible tail about 219 nm in length. The latent period of Yong-XC31 is 30 min, and burst size is 64,227. Adsorption rate of Yong-XC31 to V. mediterranei 117-T6 can reach 93.8% in 2 min. The phage genome consisted of a linear, double-stranded 290,532 bp DNA molecule with a G + C content of 45.87%. Bioinformatic analyses predicted 318 open reading frames (ORFs), 80 of which had no similarity to protein sequences in current (26 January 2021) public databases. Yong-XC31 shared the highest pair-wise average nucleotide identity (ANI) value of 58.65% (below the ≥95% boundary to define a species) and the highest nucleotide sequence similarity of 11.71% (below the >50% boundary to define a genus) with the closest related phage. In the proteomic tree based on genome-wide sequence similarities, Yong-XC31 and three unclassified giant phages clustered in a monophyletic clade independently between the family Drexlerviridae and Herelleviridae. Results demonstrated Yong-XC31 as a new evolutionary lineage of phage. We propose a new phage family in Caudovirales order. This study provides new insights and fundamental data for the study and application of giant phages.