Bacterial chromosomes may contain up to 20% phage DNA that encodes diverse proteins ranging from those for photosynthesis to those for autoimmunity; hence, phages contribute greatly to the metabolic potential of pathogens. Active prophages carrying genes encoding virulence factors and antibiotic resistance can be excised from the host chromosome to form active phages and are transmissible among different bacterial hosts upon SOS responses. Cryptic prophages are artifacts of mutagenesis in which lysogenic phage are captured in the bacterial chromosome: they may excise but they do not form active phage particles or lyse their captors. Hence, cryptic prophages are relatively permanent reservoirs of genes, many of which benefit pathogens, in ways we are just beginning to discern. Here we explore the role of active prophage- and cryptic prophage-derived proteins in terms of (i) virulence, (ii) antibiotic resistance, and (iii) antibiotic tolerance; antibiotic tolerance occurs as a result of the non-heritable phenotype of dormancy which is a result of activation of toxins of toxin/antitoxin loci that are frequently encoded in cryptic prophages. Therefore, cryptic prophages are promising targets for drug development.

细菌染色体可能包含高达20％的噬菌体DNA，该DNA编码各种蛋白质，从用于光合作用的蛋白质到用于自身免疫的蛋白质。因此，噬菌体极大地促进了病原体的代谢潜能。携带编码毒力因子和抗生素抗性基因的主动噬​​菌体可以从宿主染色体上切下以形成活跃的噬菌体，并在SOS反应后可在不同细菌宿主之间传播。隐性噬菌体是诱变的产物，其中溶源性噬菌体被捕获在细菌染色体中：它们可以切除，但不会形成活性噬菌体颗粒或裂解其捕获物。因此，隐性噬菌体是相对永久的基因库，其中许多以我们刚刚开始辨别的方式使病原体受益。在这里，我们从（i）毒力，（ii）抗生素耐药性和（iii）抗生素耐受性方面探讨了活性的原噬菌体和隐含的原噬菌体来源的蛋白质的作用。抗生素的耐受性是由于休眠的非遗传表型而产生的，休眠的表型是毒素/抗毒素基因座的毒素被激活的结果，而毒素/抗毒素基因座的毒素通常在隐性原噬菌体中编码。因此，隐性预言是药物开发的有希望的目标。