Dynamics of phage-host interactions in Bacteroides fragilis resolved by single-cell transcriptomics

Area of Science:

• Microbiology
• Genomics
• Systems Biology

Background:

• Bacteriophage-host interactions are complex and often studied in bulk, masking individual cell variations.
• Understanding bacterial defenses against phages is crucial for controlling infections and developing phage therapies.

Purpose of the Study:

• To investigate the dynamics of lytic phage infection in individual bacterial cells using single-cell RNA sequencing.
• To identify bacterial subpopulations and genetic factors conferring resistance to phage infection.
• To establish bacterial single-cell RNA sequencing as a tool for studying host-phage interactions.

Main Methods:

• Profiling transcriptomes of approximately 50,000 individual Bacteroides fragilis cells infected with a lytic bacteriophage using single-cell RNA sequencing.
• Quantifying asynchronous phage infection progression and reconstructing the infection timeline at the single-cell level.
• Analyzing host and phage transcriptomic changes during infection to identify resistance mechanisms.

Main Results:

• Discovered phenotypic subpopulations of bacteria that remained uninfected during phage exposure.
• Identified phase-variable capsular polysaccharide (CPS) biosynthesis pathways and fimbrial genes as key determinants of phage susceptibility.
• Revealed genome-wide phase variation and stochasticity contributing to bacterial survival and regrowth without new mutations.

Conclusions:

• Bacterial single-cell RNA sequencing is a powerful platform for dissecting host-phage dynamics.
• Phase variation and stochasticity play significant roles in bacterial defense against phages.
• Understanding these mechanisms can inform strategies for managing bacterial infections and enhancing phage therapy efficacy.