Bioprospecting Soil Microorganisms as a Source of Antimicrobial Compounds Active Against ESKAPE Pathogens

ABSTRACT

The escalating global crisis of antimicrobial resistance (AMR), particularly among the ESKAPE group, necessitates the discovery of novel therapeutic agents. Soil ecosystems represent a vast, under‐explored repository of microbial secondary metabolites with potent antimicrobial properties. This study aimed to identify soil‐derived bacteria with inhibitory activity through a large‐scale bioprospecting effort within the MicroMundo@UCM service‐learning project. Primary screening of 6403 isolates against Kocuria rhizophila and Escherichia coli identified 261 with inhibitory activity, including 45 with inhibition halos greater than 6 mm. Secondary screening showed that 58% of these isolates retained activity against at least one of the tested bacterial pathogens, most frequently Staphylococcus aureus . Based on inhibition halo size and antimicrobial spectrum, the most active isolates were identified by 16S rRNA gene sequencing as Bacillus pumilus , Paenibacillus peoriae and Bacillus cereus . Notably, the P. peoriae isolate indicates broad‐spectrum activity. Organic extracts obtained from these isolates successfully reproduced the inhibitory activity, indicating that the antibiosis was mediated by stable, diffusible secondary metabolites. Furthermore, minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays showed that these extracts exert a definitive bactericidal mechanism against the tested clinical strains. This study suggests that competition‐based screening of soil bacteria enables the identification of isolates producing diffusible antibacterial metabolites active against clinically relevant ESKAPE pathogens. Moreover, it proves that large‐scale soil bioprospecting and citizen science are valuable complementary strategies for discovering new antibacterial‐producing microorganisms, highlighting the potential of this approach despite the inherent limitations of primary screening.