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

Abstract

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.

Keywords

CRISPR-Cas system / Engineered bacteriophage / Microbiome engineering / Targeted delivery / Precision regulation

Statement of the Use of Generative AI and AI-Assisted Technologies in the Writing Process

During the preparation of this manuscript, the author(s) used DeepSeek in order to refine the English expressions and optimize linguistic accuracy. After using this tool/service, the author(s) reviewed and edited the content as needed and take(s) full responsibility for the content of the published article.

Acknowledgments

All illustrations in this study were created with the aid of the BioRender platform (©BioRender: biorender.com), and we hereby express our gratitude for its user-friendly design tools.

Author Contributions

Y.Y.: Writing—review & editing, Writing—original draft, Visualization. J.S.: Writing—original draft, Conceptualization. Z.X.: Writing—review & editing, Funding acquisition, Conceptualization.

Ethics Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The datasets generated during the current study are available from the corresponding author on reasonable request.

Funding

This research was funded by the National Natural Science Foundation of China grant number [22478059].

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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