The PubMLST.org website and the Bacterial Isolate Genome Sequence Database (BIGSdb) software are open-access tools that integrate population sequence data with provenance and phenotype information for over 100 microbial species and genera. BIGSdb, published in 2010, enables the inclusion of all levels of sequence data, from single gene sequences to complete genomes. The system uses a gene-by-gene analysis approach, where each deposited sequence is annotated and curated to identify and catalog genes and their variants. This platform supports a wide range of applications, including predicting antimicrobial resistance, cross-reactivity with vaccine antigens, and functional activities leading to key phenotypes. BIGSdb has no limitations on the number of sequences, genetic loci, allelic variants, or schemes, allowing for the expansion of genetic variation catalogs. The software includes a RESTful API for third-party applications and data analysis pipelines, facilitating web-accessible analyses and integration with other tools. The PubMLST databases have been widely used for epidemiological surveillance, vaccine development, evolutionary analysis, and functional studies, with a focus on bacterial pathogens.The PubMLST.org website and the Bacterial Isolate Genome Sequence Database (BIGSdb) software are open-access tools that integrate population sequence data with provenance and phenotype information for over 100 microbial species and genera. BIGSdb, published in 2010, enables the inclusion of all levels of sequence data, from single gene sequences to complete genomes. The system uses a gene-by-gene analysis approach, where each deposited sequence is annotated and curated to identify and catalog genes and their variants. This platform supports a wide range of applications, including predicting antimicrobial resistance, cross-reactivity with vaccine antigens, and functional activities leading to key phenotypes. BIGSdb has no limitations on the number of sequences, genetic loci, allelic variants, or schemes, allowing for the expansion of genetic variation catalogs. The software includes a RESTful API for third-party applications and data analysis pipelines, facilitating web-accessible analyses and integration with other tools. The PubMLST databases have been widely used for epidemiological surveillance, vaccine development, evolutionary analysis, and functional studies, with a focus on bacterial pathogens.