PoMeLo

PoMeLo identifies metabolic gaps in the genomes of pathogenic bacteria by leveraging a centralized public database of high-quality genomes and annotations, enabling comparison across large numbers of genomes and placing results in a phylogenetic context.

Key Features:

• Genome comparison: PoMeLo allows comparison of an unlimited number of genomes across individual genes and pathways.
• Predicted Metabolic Loss scoring: Each pathway is assigned a Predicted Metabolic Loss (PML) score to assess the magnitude of genome streamlining.
• Phylogenetic context: PoMeLo optionally places results in an evolutionary context by including phylogenetic relationships in visual outputs.
• Phylogenetically-weighted genome size analysis: PoMeLo can compute phylogenetically-weighted mean genome sizes to identify genome streamlining events.
• Tabular and visual outputs: PoMeLo generates tabular and visual outputs for comparing predicted metabolic capacity between groups of bacteria and individual species.

Scientific Applications:

• Metabolic gap identification: PoMeLo identifies metabolic gaps in pathogenic bacterial genomes to assess pathogen dependency on host metabolism.
• Genome streamlining characterization: PoMeLo characterizes genome streamlining, gene loss, and metabolic pathway degradation in pathogenic bacteria evolving in nutrient-rich host environments.
• Host-directed therapeutic target identification: PoMeLo identifies potential targets for host-directed therapeutics by revealing metabolic dependencies.
• Comparative pathogen genomics: PoMeLo enables comparison of predicted metabolic capacity across groups of bacteria and individual species, as demonstrated in pathogenic Treponema species.

Methodology:

PoMeLo uses an evolutionary genomics-guided computational approach with a centralized public database of high-quality genomes and annotations. Each pathway is assigned a Predicted Metabolic Loss (PML) score. Phylogenetically-weighted mean genome sizes are computed to identify genome streamlining events.