An integrated multi-omic approach for discovery and dereplication of bioactive microbial natural products

Soil bacteria are a major source of clinically useful antibiotics, yet the majority of soil-dwelling micro-organisms remain uncultivable by standard laboratory methods. To access this untapped microbial diversity, we employed microbial diffusion chambers to isolate bacteria from ten Australian soil samples. A total of 1,218 bacterial isolates were recovered, representing a diverse collection spanning 61 genera from 32 families, covering the major known phyla of soil bacteria. Antibiotic activity screening revealed that 16% of isolates inhibited the growth of at least 1 of Escherichia coli or Staphylococcus aureus, with 120 isolates displaying activity against multidrug-resistant pathogens including methicillin-resistant S. aureus and vancomycin-resistant Enterococcus faecium. Mass spectrometry-based dereplication using GNPS identified known antibiotics in 33% of bioactive strains, including actinomycin D, nonactins and valinomycin. Genomic analysis confirmed the presence of corresponding biosynthetic gene clusters, while targeted analysis of selected strains uncovered production of additional antibiotics such as nigericin and streptothricin that were not initially detected by MS. Our results demonstrate that diffusion chambers enhance bacterial recovery from soil and show the benefits of a combined pipeline including bioactivity screening, MS and genomics for effective antibiotic dereplication and discovery.