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The transition to organic farming is one of the most desirable achievements of our time. Rational use of modern organic farming approaches not only enables the reduction of costs and increased yields but also limits the risks associated with the use of pesticides and chemicals. Despite the widest practical application of numerous biocontrol agents based on Bacillus strains, their metabolome, including the main active substances, often remains unknown. In order to understand the basic principles of the functioning of the Bacillus velezensis K-3618 strain, widely used in organic farming, we studied its spectrum of antimicrobial metabolites in detail. It was shown that the main antimicrobial agents of the B. velezensis K-3618 are representatives of the macrolactin family. Macrolactins are a group of 24-membered lactones, including macrolactin A (MLN A) and its acylated analogs 7-O-malonyl macrolactin A (mal-MLN A) and 7-O-succinyl macrolactin A (suc-MLN A), mostly active against Gram-positive bacterial pathogens, including multidrug-resistant strains. Suc-MLN A was the most potent antimicrobial, highly active (MIC = 0.1 μg/mL) against the common human pathogen methicillin-resistant Staphylococcus aureus (MRSA). It was shown that the primary mechanism of action of MLN A-based macrolactins is protein translation inhibition. Acylated macrolactins outperform MLN A in the prokaryotic cell-free system, displaying high efficiency in low micromolar concentrations. We observed that acylated MLN A analogs undergo pathogen-mediated biotransformation to MLN F analogs, having the antimicrobial activity reduced by two orders of magnitude. Hence, both acylation of MLNs and stabilization of the MLN A core are essential for the creation of new synthetic MLNs with improved antimicrobial activity and stability. While the counteraction against the observed biotransformations is essential to create new macrolactin-based antimicrobials for clinical practice, we speculate that these degradability modes are essential for bacterial ecology, and they are highly conserved in many Bacillus species from various ecological niches.