#39 · Genomics

Coevolution and comparative genomics infer microbial interaction and symbiosis networks

The dominant thread is inference of relational structure from indirect genomic evidence rather than direct measurement of interactions. The siderophore study infers specific siderophore-receptor pairings from uncurated genomes via coevolution, reconstructing iron scavenging networks across nine bacterial taxa and revealing topological diversity in microbial exploitation. The lichen study is comparative rather than network-based: it analyzes 309 ascomycete genomes, 191 of them lichen symbionts, and links CAZyme repertoires to photobiont carbon subsidies. ECLIPSE embeds ESKAPE pan-proteomes in the Protein Universe Atlas sequence similarity network to find and rank dark proteins. What is new is the transfer of network-based reconstruction to genomic data spanning bacterial interaction, fungal symbiosis, and pathogen proteome scales. The items differ considerably in method, so this thread describes the dominant pattern rather than a feature shared by every item.