Oantigenet

Oantigenet is a community-driven database and analytical framework designed to catalog and study O-antigen gene clusters (O-AGCs) in Gram-negative bacteria. The project aims to integrate genome sequences, annotations, and serotype information to enable comparative analyses of O-antigen biosynthesis and diversity.

O-AGCs encode the enzymes and transport proteins required to assemble and export the O-antigen portion of lipopolysaccharide. Typical content includes wzx and wzy genes for assembly, wzm and wzt for transport, and a diverse set of glycosyltransferases and sugar-modifying enzymes. Oantigenet organizes clusters by species, serotype, and locus type, linking each cluster to reference serotype designations when available.

Data sources and curation involve genomes from public repositories such as NCBI RefSeq and ENA, along with experimental serotype data from the literature. The database uses standardized locus tags and nomenclature to facilitate cross-study comparisons, and applies curator review to maintain data quality.

Key features include search by organism, serotype, gene content, or enzyme families; a locus map viewer; tools for multiple sequence alignment and phylogenetic analysis; visualization of gene content across clusters; serotype prediction from whole-genome sequences; and an API for programmatic access. Data can be downloaded in common formats, and community contributions go through a validation workflow.

Applications span epidemiology and outbreak tracking, vaccine and diagnostic design, and evolutionary studies of O-antigen variation. Limitations include horizontal gene transfer and recombination that complicate phylogeny, and incomplete assemblies that hinder cluster reconstruction.

Governance is community-based with versioned releases, contributor guidelines, and open-access data and software. Oantigenet invites collaboration from microbiologists, bioinformaticians, and clinicians.