PROBEAT: PRObiotic Bacterial gEnome Analysis Toolkit.

Whole-genome sequencing has become a central approach for investigating candidate probiotic bacterial isolates, but probiogenomic analysis often requires multiple independent tools, manual marker-gene searches and study-specific interpretation of heterogeneous outputs. PROBEAT (PRObiotic Bacterial gEnome Analysis Toolkit), a Dockerized workflow for the integrated and reproducible genome-based characterization of candidate probiotic isolates. PROBEAT combines standard bacterial genome analysis with specialized probiotic-oriented features, covering read processing, genome assembly and quality assessment, taxonomic confirmation, genome annotation, safety screening, functional and metabolic profiling, probiotic marker detection and automated visualization. A key feature of PROBEAT is a custom Probiotic Gene Markers database containing more than 400 gene aliases organized into 320 curated marker records and 32 functional categories. The workflow automatically converts raw sequencing data into a structured PDF booklet report that integrates safety, taxonomy, metabolism, functional annotation and probiotic-oriented data. PROBEAT reduces the technical burden of bacterial genome analysis and provides a reproducible framework for standardized genome-based assessment of probiotic potential, while supporting functional annotation rather than clinical claims.