Panos G. Kalatzis

Introduction: Bacteriophages are emerging as viable food safety tools, yet their global implementation is hindered by regulatory fragmentation and a lack of harmonized data standards. This review addresses the gap between scientific maturity and governance readiness by evaluating manufacturing quality, safety requirements, and international oversight frameworks. Methods: A narrative review was conducted through a structured search of databases including PubMed, Scopus, Web of Science, and Google Scholar (up to December 2025). We analyzed scientific research and publicly available regulatory documents from agencies such as the FDA, EFSA, USDA, Health Canada, and FSANZ to identify authorization routes and manufacturing standards. Results: Commercial phage products are primarily approved as processing aids in jurisdictions like the United States, Canada, and Australia/New Zealand. We identified convergent technical requirements across these regions, including genomic integrity (absence of toxins and antimicrobial resistance genes), purity, potency, and matrix-validated efficacy. However, significant gaps remain in unified terminology, environmental risk assessment, and post-market monitoring for resistance emergence. Conclusions: To facilitate global adoption, a One Health-oriented governance cycle is proposed. This includes establishing interoperable phage seed banks, standardized dossier formats, and adaptive lifecycle controls (phagovigilance) to ensure long-term efficacy and public trust.

Phages are typically classified as temperate, integrating into host genomes, or lytic, replicating and killing bacteria; for this reason, lytic phages are not expected in bacterial genome sequences. Here we analyse 3.6 million bacterial genome assemblies from 1,226 species and find 119,510 lytic phage genomes, which we term bacterial assembly-associated phage sequences. This represents a ~5-fold increase in the number of phages with associated hosts and raises questions about fundamental aspects of phage biology. Our analyses of bacterial assembly-associated phage sequences revealed previously undescribed phage clusters, including clusters distantly related to Salmonella Goslarviruses in Escherichia coli and Shigella , while also substantially expanding known genera such as Seoulvirus (from 16 to >300 members). Close relatives of lytic phages used therapeutically were also detected, suggesting clinical isolate sequencing unknowingly archives potential phage candidates. The discovery of complete, lytic phage genomes within bacterial assemblies challenges assumptions about the nature of the lytic lifestyle and reveals an untapped reservoir of phages.

Non-tailed phages remain an underexplored group in marine environments, as tailed phages have dominated sequence and culture collections. However, recent surveys indicate that non-tailed phages might be more abundant than tailed phages, and with different effects on microbial mortality and gene transfer. Here, we report the structural characterization of bacteriophage NO16, a non-tailed vibriophage, one of the simplest members of the Double Jelly Roll (DJR) lineage. Mass spectrometry analyses indicate that the virion is composed of at least nine different proteins. NO16 has a pseudo T = 21 capsid, similar to other phages in the lineage but differs in the organization of minor capsid proteins, mainly in terms of membrane-capsid contacts. The DJR major capsid protein GP19 is stabilized by a cation in the base as previously observed in corticovirus PM2, and by strong electrostatic interactions between monomers. Notably, localized reconstruction reveals a symmetry mismatch at the vertex, where two trimeric GP13 spikes are anchored to a pentamer of the penton base GP14. GP13 presents carbohydrate-binding modules and putative glycosylase activity, indicating implications for host entry. Finally, we use structural and functional predictions for NO16 non-structural proteins to propose a complete atlas of the NO16 infectious cycle.

Bacteriophages are the most abundant biological entities in the oceans and play key roles in bacterial activity, diversity and evolution. While extensive research has been conducted on the role of tailed viruses (Class: Caudoviricetes), very little is known about the distribution and functions of the non-tailed viruses (Class: Tectiliviricetes). The recent discovery of the lytic Autolykiviridae family demonstrated the potential importance of this structural lineage, emphasizing the need for further exploration of the role of this group of marine viruses. Here, we report the novel family of temperate phages under the class of Tectiliviricetes, which we propose to name “Asemoviridae” with phage NO16 as a main representative. These phages are widely distributed across geographical regions and isolation sources and found inside the genomes of at least 30 species of Vibrio, in addition to the original V. anguillarum isolation host. Genomic analysis identified dif-like sites, suggesting that NO16 prophages recombine with the bacterial genome based on the XerCD site-specific recombination mechanism. The interactions between the NO16 phage and its V. anguillarum host were linked to cell density and phage–host ratio. High cell density and low phage predation levels were shown to favor the temperate over the lytic lifestyle for NO16 viruses, and their spontaneous induction rate was highly variable between different V. anguillarum lysogenic strains. NO16 prophages coexist with the V. anguillarum host in a mutualistic interaction by rendering fitness properties to the host, such as increased virulence and biofilm formation through lysogenic conversion, likely contributing to their global distribution.

Pasteurellosis in farmed lumpsuckers, Cyclopterus lumpus, has emerged as a serious disease in Norwegian aquaculture in recent years. Genomic characterization of the causative agent is essential in understanding the biology of the bacteria involved and in devising an efficient preventive strategy. The genomes of two clinical Pasteurella atlantica isolates were sequenced (≈2.3 Mbp), and phylogenetic analysis confirmed their position as a novel species within the Pasteurellaceae. In silico analyses revealed 11 genomic islands and 5 prophages, highlighting the potential of mobile elements as driving forces in the evolution of this species. The previously documented pathogenicity of P. atlantica is strongly supported by the current study, and 17 target genes were recognized as putative primary drivers of pathogenicity. The expression level of a predicted vaccine target, an uncharacterized adhesin protein, was significantly increased in both broth culture and following the exposure of P. atlantica to lumpsucker head kidney leucocytes. Based on in silico and functional analyses, the strongest gene target candidates will be prioritized in future vaccine development efforts to prevent future pasteurellosis outbreaks.

Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine Vibrios has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. The results of our multi-omics approach, incorporating transcriptome and metabolome analyses of Vibrio alginolyticus phage-resistant strains, corroborate this prospect. Our results provide insights into phage-tolerant strains diminishing the expression of phage receptors ompF, lamB, and btuB. The same pattern was observed for genes encoding natural nutrient channels, such as rbsA, ptsG, tryP, livH, lysE, and hisp, meaning that the cell needs to readjust its biochemistry to achieve phage resistance. The results showed reprogramming of bacterial metabolism by transcript regulations in key-metabolic pathways, such as the tricarboxylic acid cycle (TCA) and lysine biosynthesis, as well as the content of intracellular metabolites belonging to processes that could also significantly affect the cell physiology. Finally, SNP analysis in resistant strains revealed no evidence of amino acid alterations in the studied putative bacterial phage receptors, but several SNPs were detected in genes involved in transcriptional regulation. This phenomenon appears to be a phage-specific, fine-tuned metabolic engineering, imposed by the different phage genera the bacteria have interacted with, updating the role of lytic phages in microbial marine ecology.

Vibrio anguillarum is a marine pathogenic bacterium that causes vibriosis in fish and shellfish. Although prophage-like sequences have been predicted in V. anguillarum strains, many are not characterized, and it is not known if they retain the functional capacity to form infectious particles that can infect and lysogenize other bacterial hosts. In this study, the genome sequences of 28 V. anguillarum strains revealed 55 different prophage-related elements. Chemical and spontaneous induction allowed a collection of 42 phage isolates, which were classified in seven different groups according to a multiplex PCR assay. One shared prophage sequence, p41 (group III), was present in 17 V. anguillarum strains, suggesting that this specific element is very dynamically exchanged among V. anguillarum populations. Interestingly, the host range of genetically identical phages was highly dependent on the strains used for proliferation, indicating that phenotypic properties of phages were partly regulated by the host. Finally, experimental evidence displayed that the induced phage ɸVa_90-11-287_p41 was able to lysogenize V. anguillarum strain Ba35, and subsequently spontaneously become released from the lysogenized cells, demonstrating an efficient transfer of the phage among V. anguillarum strains. Altogether, the results showed large genetic and functional diversity and broad distribution of prophages in V. anguillarum, and demonstrated the potential of prophages as drivers of evolution in V. anguillarum strains.

A rare nontailed virus designated NO16 was isolated against Vibrio anguillarum , a major aquaculture pathogen for both fish and shellfish. Here, we announce the 10,594-bp genome sequence of Vibrio phage NO16 with a 23-gene content.

Edwardsiella-associated outbreaks are increasingly reported on both marine and freshwater aquaculture setups, accounting for severe financial and biomass losses. E. tarda, E. ictaluri, and E. hoshinae have been the traditional causative agents of edwardsiellosis in aquaculture, however, intensive studies due to the significance of the disease have just recently revealed two more species, E. piscicida and E. anguillarum. Whole genome sequencing that was conducted on the strain EA011113, isolated from farmed Diplodus puntazzo after an edwardsiellosis outbreak in Greece, confirmed it as a new clinical strain of E. anguillarum. Extensive phylogenetic analysis showed that this Greek strain is closely related to an Israeli E. piscicida-like clinical strain, isolated from diseased groupers, Epinephelus aeneus and E. marginatus in Red Sea. Bioinformatic analyses of E. anguillarum strain EA011113 unveiled a wide repertoire of potential virulence factors, the effect of which was corroborated by the mortalities that the strain induced in adult zebrafish, Danio rerio, under different levels of infection intensity (LD₅₀ after 48 h: 1.85 × 10⁴ cfu/fish). This strain was non-motile and according to electron microscopy lacked flagella, a fact that is not typical for E. anguillarum. Comparative genomic analysis revealed a deletion of 36 nt found in the flagellar biosynthetic gene (FlhB) that could explain that trait. Further in silico analysis revealed an intact prophage that was integrated in the bacterial genome. Following spontaneous induction, the phage was isolated, purified, characterized and independently sequenced, confirming its viability as a free, inducible virion as well. Separate genomic analysis of the prophage implies a plausible case of lysogenic conversion. Focusing on edwardsiellosis as a rapidly emerging aquaculture disease on a global scale, this work offers some insight into the virulence, fitness, and potential lysogenic conversion of a of a newly described, yet highly pathogenic, strain of E. anguillarum.