BacMap 3.0: a comprehensive knowledgebase of annotated bacterial genomes

BacMap 3.0 (https://bacmap.ca) is a comprehensive, freely accessible resource integrating 23 524 bacterial and archaeal species, 32 866 genomes, >100 million genes, 1756 primary metabolic pathways, and 45 284 metabolites within one interactive platform. Despite the extraordinary growth of bacterial and archaeal genome sequencing, relevant data remain distributed across numerous specialized databases, impeding comprehensive genome-to-function analysis. While existing microbial resources generally emphasize genome annotation, taxonomy, metabolic pathways, or phenotypes separately, BacMap 3.0 unifies these complementary information layers within an organism-centred framework. It resolves this fragmentation by consolidating genomic, functional, structural, metabolic, phenotypic, ecological, and phylogenetic information into richly detailed, organism-specific "BacCards". Each BacCard combines an interactive genome map with extensive annotations covering bacterium-specific taxonomy, physiology, morphology, metabolism, protein structures, pathways, and metabolites. To facilitate data exploration, BacMap 3.0 supports taxonomic and phenotype-based browsing, chemical structure searches, interactive genome visualization, as well as gene, genome, 16S RNA, and protein BLAST searches. Building on earlier releases devoted primarily to genome visualization, BacMap 3.0 increases organismal coverage by >13-fold and transforms BacMap into an integrated bacterial knowledgebase for genome-to-function investigation across multiple biological scales. By bringing diverse biological information together in a single searchable environment, BacMap 3.0 offers a powerful platform for comparative genomics, microbiome research, infectious disease investigation, and biotechnology with a goal of accelerating the interpretation of microbial diversity, biology, and function.