In contrast to the spread of pathogenic species across different hosts (zoonoses), the use of microbial effectors from diverse environments holds transformative potential for treating diseases and control of microbiomes in biotechnological systems. Just as the "golden age" of antibiotic discovery opened new frontiers in medicine, broader screening of microbial effectors now offers the potential to treat pathogen-associated diseases. One advantage of many microbial effectors is their ability to target specific microorganisms, allowing for more precise treatment options and enhanced microbiome control. However, this specificity also increases the risk of resistance mechanisms, such as escape mutations, which require continuous adaptation of microbial effectors to maintain efficacy.