Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Area of Science:

• Microbiology
• Genomics
• Bacteriophage Therapy

Background:

• Cutibacterium acnes (C. acnes) is a key skin commensal linked to acne vulgaris.
• Restriction-modification (R-M) systems are DNA defense mechanisms, but their function in C. acnes is largely unknown.
• Understanding C. acnes R-M systems is vital for developing targeted therapies.

Purpose of the Study:

• To investigate the functionality of putative R-M systems in diverse C. acnes strains.
• To explore the role of R-M systems in C. acnes-bacteriophage interactions.
• To demonstrate the therapeutic potential of R-M systems in phage therapy for acne.

Main Methods:

• Methylome analysis of six C. acnes strains using Oxford Nanopore Technologies (ONT) sequencing.
• Recombinant expression and R-M knockout mutant generation to confirm methylation activity.
• Bacteriophage (PAD20) infection assays and specificity analysis.

Main Results:

• Identified active 6-methyladenine modification in C. acnes strain KPA171202, confirming functional R-M system.
• Demonstrated that phage specificity against C. acnes strains is influenced by host R-M system activity.
• Showcased selective killing of R-M deficient acne-prone C. acnes clades by phages propagated in R-M deficient strains.

Conclusions:

• Functional R-M systems are present in C. acnes and influence phage interactions.
• Phage therapy can be engineered by exploiting C. acnes R-M systems for targeted acne treatment.
• This mechanism offers a strategy to selectively eliminate pathogenic C. acnes while preserving beneficial strains.