Table 1.

Benefits of genetic engineering of phages for therapy

Benefits	Supporting arguments	References
Enrichment of phages with selected lethal or regulatory genes from other phages or from bacteria and/or removal of undesired genes could potentiate the lytic and/or therapeutic efficacy and stability of phages, make them safer for use, and endow them with additional desired properties	No single natural phage combines all the features required of an ideal therapeutic agent	[122]
The development of GE derivatives of already well characterized phages approved for therapy could help shorten the procedures of new therapeutic phage acquisition and approval significantly and decrease their cost	The development of a therapeutic phage preparation, from the isolation of a desired phage to its approval for therapy in humans, is a time-consuming, costly, multistep process. All these steps have to be conducted anew for each natural isolate	[23, 75, 77, 134– 136]
The ongoing analysis of existing therapeutic phage candidates with the use of targeted mutagenesis may soon lead to the completion of their functional genomic maps and the identification of genes that should be removed/modified to produce GE phages with desired properties and infecting particular hosts	Phages targeting clinically relevant bacteria and meeting the criteria for therapeutic use usually belong to a few taxa only at the level of genus or subfamily. Several of them are related to model phages. Related phages differ mostly in genome regions required for the host-specific interaction	[80, 81, 87, 91, 119, 127, 137– 139]
The phage that infects a bacterium of a given species should be metabolically compatible with all strains of this species. Thus, if well characterized, it could serve as a universal scaffold to construct its derivatives differing, e.g., in strain specificity, stability, or other properties	The core genomes of diverse bacterial strains of a given species, which determine their basic metabolic functions, are conserved	[140 –142]
The Earth phageome, even if incompletely characterized, can serve as a source of genes or gene modules that can be analyzed functionally when incorporated to the genomes of well characterized phages and provide a much broader repertoire of functions than that encoded by the few well characterized phages	The enormous diversity of phages, reflected, e.g., by their genome size range and differences in morphological and physiological properties, limits the possibility of a phage pan-genome functional analysis. This excludes poorly characterized phages with potentially desired properties from implementation in therapy in a reasonable time span	[10, 11, 17, 87, 122, 143– 146]
The identification of genes of highly lytic phages responsible for their low therapeutic efficacy could allow genetic alterations, making such phages useful in therapy	Not all phages highly effective in bacterial lysis in the laboratory are therapeutically effective	[147– 150]
Modification of temperate phage genomes to remove lysogeny modules and undesired genes (e.g., encoding virulence factors) should allow benefit from the potential of these phages to infect and kill certain bacteria resistant to virulent phages	Certain strains of pathogenic bacteria are resistant to available virulent phages, while temperate phages infecting those strains are available or can be acquired by prophage induction	[22, 90, 151, 152]
Arming a temperate phage with genes encoding regulators of bacterial metabolism or functions disabling certain genes could allow such a phage to be used to modify human or animal microbiota by disarming pathogenic bacteria, re-sensitizing them to antibiotics, or selectively killing pathogenic strains of commensal bacterial species	Phages, especially temperate ones, are efficient regulators of human/animal microbiome composition and hence have an impact on human/animal health	[153– 156]

GE genetically engineered