The Promise and Pitfalls of Prophages

Area of Science:

• Microbiology
• Genomics
• Bioenergetics

Background:

• Phages significantly influence microbial ecosystems, with temperate phages conferring benefits via lysogenic conversion.
• Prophages contribute to bacterial genotypic and phenotypic diversity but impose a metabolic cost on host cells.
• Quantifying the energetic balance of prophage-host interactions has been a long-standing challenge.

Approach:

• Analyzed over 2.5 million prophages from 500,000 bacterial genome assemblies.
• Investigated prophage density and carrying capacity across diverse bacterial genomes.
• Estimated the energetic cost of prophage maintenance in terms of cellular energy and ATP production.

Key Points:

• A uniform normalized prophage density was observed across bacterial genomes larger than 2 Mbp.
• A consistent carrying capacity for phage DNA relative to bacterial DNA was identified.
• Each prophage was estimated to consume approximately 2.4% of cellular energy (0.9 ATP/bp/hour).

Conclusions:

• The energetic benefits bacteria gain from prophages likely balance the costs of their maintenance.
• Disparities in prophage identification across taxonomic, geographic, and temporal datasets offer new avenues for phage discovery.
• This research provides a framework for identifying phages in diverse environmental and bacterial samples.