eggNOG 6.0: enabling comparative genomics across 12 535 organisms

Abstract: BackgroundThe avian gut virome plays a crucial role in shaping the gastrointestinal microbial ecosystem of birds. However, its taxonomic and functional diversity remains poorly characterized due to the absence of a dedicated reference database. This limitation hampers our understanding of the complex interactions among viruses, their bacterial hosts, and the overarching avian host, as well as viral contributions to gut microbial ecology.ResultsTo address this gap, we developed the Avian Virome Database (AvianViromeDB) by integrating 2,692 gut metagenomic samples from poultry and wild birds. This effort yielded 252,752 viral contigs, which are clustered into 61,608 high-quality, species-level viral operational taxonomic units (vOTUs). Taxonomic analysis revealed that 99.05% of these vOTUs belonged to the class Caudoviricetes, yet only 4.69% could be assigned to known viral families—suggesting over 95% likely represent novel viral lineages. Prediction of prokaryotic hosts indicated that these viruses primarily target core gut microbiota, particularly Bacillota and Bacteroidota, both central to carbohydrate metabolism. Functional annotation uncovered tens of thousands of auxiliary metabolic genes (AMGs), with enrichments in glycolysis, amino acid metabolism, and nucleotide biosynthesis pathways.ConclusionThese findings demonstrate that avian gut viruses may modulate microbial communities both through direct lysis of their bacterial hosts (“top-down” control) and by altering host metabolism via AMGs (“bottom-up” modulation). The resulting high-quality genome catalog reveals the remarkable diversity and functional potential of the avian gut virome, offering a valuable resource for future research into avian microbial ecology and the intricate interplay between viruses, bacteria, and their avian hosts. The AvianViromeDB is publicly accessible at: https://phagebyte.github.io/avianviromedb.

TL;DR: This study reveals the evolutionary tale of tailocins in Pectobacterium, a globally present phytopathogen, showing genus-wide homologous recombination and inversions of tail fiber genes, which enables tailocin polymorphism and host range specificity.

Abstract: Supplementary Material 1

TL;DR: The protein interactome of E. coli carbohydrate metabolism regulates carbohydrate metabolism by modulating enzyme activity and stoichiometry.

TL;DR: The content has been expanded and the quality improved irrespective of whether or not the KOs appear in the three molecular network databases, and the newly introduced addendum category of the GENES database is a collection of individual proteins whose functions are experimentally characterized and from which an increasing number of KOs are defined.

TL;DR: Changes to the text-mining system, a new scoring-mode for physical interactions, as well as extensive user interface features for customizing, extending and sharing protein networks are described.

TL;DR: The UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal and a credit-based publication submission interface was developed.

TL;DR: The Pfam database is a widely used resource for classifying protein sequences into families and domains and the reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family.