Microorganisms use toxins to kill competing microorganisms or eukaryotic cells. Polymorphic toxins are proteins that encode carboxy-terminal toxin domains. Here we developed a computational approach to identify previously undiscovered, conserved toxin domains of polymorphic toxins within 105,438 microbial genomes. We validated nine short toxins, showing that they cause cell death upon heterologous expression in either Escherichia coli or Saccharomyces cerevisiae. Five cognate immunity genes that neutralize the toxins were also discovered. The toxins are encoded by 2.2% of sequenced bacteria. A subset of the toxins exhibited potent antifungal activity against various pathogenic fungi but not against two invertebrate model organisms or macrophages. Experimental validation suggested that these toxins probably target the cell membrane or DNA or inhibit cell division. Further characterization and structural analysis of two toxin–immunity protein complexes confirmed DNase activity. These findings expand our knowledge of microbial toxins involved in inter-microbial competition that may have the potential for clinical and biotechnological applications.

微生物利用毒素杀死竞争微生物或真核细胞。多态性毒素是编码羧基末端毒素结构域的蛋白质。在这里，我们开发了一种计算方法来识别 105,438 个微生物基因组中以前未发现的多态性毒素的保守毒素结构域。我们验证了 9 种短毒素，表明它们在大肠杆菌或酿酒酵母中异源表达时会导致细胞死亡。还发现了五个中和毒素的同源免疫基因。毒素由 2.2% 的测序细菌编码。毒素的一个子集对各种病原真菌表现出有效的抗真菌活性，但对两种无脊椎动物模式生物或巨噬细胞没有。实验验证表明，这些毒素可能靶向细胞膜或 DNA 或抑制细胞分裂。两种毒素免疫蛋白复合物的进一步表征和结构分析证实了 DNase 活性。这些发现扩展了我们对参与微生物间竞争的微生物毒素的了解，这些毒素可能具有临床和生物技术应用的潜力。