CRISPR-Armed Phages: Design, Mechanisms, Applications, and Prospects in Precision Microbiome Engineering

The dysregulation of microbial communities poses severe threats to host health and ecological stability, yet traditional microbiome modulation strategies lack specificity and often exacerbate dysbiosis. The CRISPR-Cas system offers unprecedented potential for targeted microbiome regulation due to its sequence-specific nucleic acid recognition and cleavage capabilities, but its translation is hindered by inefficient and non-specific delivery. As natural bacterial predators with inherent host specificity, bacteriophages have emerged as ideal carriers to address this delivery bottleneck. The development of CRISPR-armed phages combines the targeted delivery of phages and the precision editing advantages of CRISPR-Cas systems. This review systematically elaborates on the design and mechanism of CRISPR-armed phages for microbiome engineering. CRISPR-Cas systems were classified on the basis of their structural and functional characteristics, as well as their regulatory effects, in detail after phage delivery. The engineering strategies of integrative and non-integrative phage vectors were then discussed, followed by their applications in ecological regulation and genetic regulation of the microbiome. The current limitations were finally analyzed, such as narrow phage host range, bacterial phage resistance, and low editing efficiency. This review provides a comprehensive theoretical framework to promote the development of CRISPR-armed phages, aiming to advance precision microbiome engineering for human health.