Phage-based microbiome manipulation reveals ecological interactions within gut communities

Area of Science:

• Microbiology
• Synthetic Biology
• Ecology

Background:

• Understanding gut ecology requires tools for precise microbiome manipulation.
• Current methods lack specificity for targeting individual commensal species.

Purpose of the Study:

• To develop phage-based tools for targeted removal of Escherichia fergusonii (Ef) from complex gut microbial communities.
• To investigate the ecological role of Ef in preventing Salmonella invasion.
• To explore the genetic basis of phage resistance and its impact on microbial fitness.

Main Methods:

• Isolation of lytic phages targeting Ef.
• Construction of phage cocktails to overcome resistance.
• Generation of Ef knockout communities using phages.
• Transposon mutagenesis to create an Ef mutant library.
• Analysis of microbial fitness and community dynamics.

Main Results:

• A single phage induced resistance in Ef, but resistant strains had reduced fitness in communities.
• Phage cocktails achieved Ef knockout with minimal off-target effects.
• Ef was essential for preventing Salmonella invasion in knockout communities.
• Mutant library analysis revealed outer-membrane genes are crucial for Ef fitness and interspecies interactions.
• Interspecies competition significantly drives microbiome ecology.

Conclusions:

• Phage-mediated perturbation is a powerful framework for linking microbial species to community functions.
• Precision microbiome engineering using phages enables targeted manipulation and functional studies.
• Understanding interspecies warfare is key to deciphering microbiome dynamics and engineering microbial communities.