Protein toxins are key molecular weapons in biology that are used to destroy neighboring cells. Bacteria use protein toxins to kill or inhibit growth of prokaryotic and eukaryotic cells using various modes of action that target essential cellular components, such as nuecleic acids, the translation machinery, cell wall, and cell membrane. The toxins are responsible for shaping microbiomes and for severe infectious diseases of animals and plants. Toxinome is a comprehensive and updated bacterial protein toxin database that contains toxins from various resources and classes. Toxinome includes a total of 2 million known toxins encoded by 59,475 bacterial genomes across the tree of life. It includes gene-related and protein-related information of toxins, and bacterial immunity proteins that inhibit toxin function. The Toxinome resource can be freely used by the academic non-profit research community interested in bacterial toxins and can guide toxin discovery and function elucidation, and infectious disease diagnosis. Users from commercial organizations are requested to contact Dr. Asaf Levy from the Hebrew University of Jerusalem: alevy at mail.huji.ac.il.