The hidden prevalence and unique protein folds of huge phages

Abstract

Huge phages are remarkable for their expansive genomes ([≥]200 kbp, and up to 841 kbp to date), global distribution, and intricate functional repertoires. However, their study has been hindered by challenges in genome identification and the lack of a comprehensive reference database. Using vRep, we established the Huge Phage Genome Collection (HPGC), a curated resource of 7,295 non-redundant huge phage genomes spanning 4,613 species-level groups. Within HPGC, we identified an overlooked and prevalent clade, HP8026, which constitutes ~1.2% of human gut metagenomic reads, suggesting its potential in fecal contamination monitoring and a promissing modulator of gut microbiome dynamics. Complementing HPGC, we developed the Huge Phage Protein Structure Database (HPDB), which catalogs 15,594 structure clusters derived from 589,960 predicted proteomes. Notably, 40% of these clusters presented in huge phages only, exhibit specific protein folds. Additionally, 3% of the HPDB clusters were absent in other viral forms, including the plasmid-originated ArdC that could protect huge phages from the antiviral mechanisms of their hosts. Collectively, HPGC and HPDB provide a pioneering framework for exploring the evolution, functional innovation, and biotechnological potential of huge phages, while serving as indispensable references for viral ecology and structural biology.