Testing the Luedemann hypothesis: the discovery of novel antimicrobials from slow-growing microbes from nutrient-limited environments

George Luedemann is known throughout the antimicrobial community as one of the discoverers of the natural product antibiotic gentamicin. He subsequently hypothesized that slow-growing organisms inhabiting inhospitable, nutrient-limited environments may represent an enriched source of previously undescribed microbes that produce novel antimicrobials to create a competitive advantage over faster-growing rival organisms. Accordingly, 750 slow-growing microorganisms were isolated from desert rock surfaces and archived prior to Dr. Luedemann's passing in 2000. Here, we describe the characterization and antimicrobial screening of the first 147 members of the Luedemann collection. 16S rRNA and whole-genome sequencing revealed that the pilot isolate set is highly diverse and includes novel microbial species belonging to genera commonly associated with soil samples, including <i>Geodermatophilus</i>, <i>Streptomyces</i>, and <i>Micromonospora</i>. Antimicrobial screening and comparative genomics indicate that at least six members are likely to produce novel antimicrobials with activity toward the ESKAPE pathogens, <i>Vibrio cholerae</i> and/or <i>Mycobacterium smegmatis</i>. Indeed, we show that the library member "9005BA" produces a newly identified phenazine, pyocyanin A, which displays potent (0.625 µg/mL), selective bactericidal activity toward <i>Acinetobacter baumannii</i> and efficacy in animals. Genetic and biochemical assays revealed that the antimicrobial activity of pyocyanin A is likely to be mediated by oxidative stress and can be overcome by altering bacterial respiration and/or efflux. Taken together, the data suggest that slow-growing organisms inhabiting nutrient-limited environments represent a previously overlooked rich source of microbial and antimicrobial agent diversity.IMPORTANCEThe discovery and study of novel bacterial species offer an opportunity to identify new microbial biological processes, molecular mechanisms, and secondary metabolites, such as new antibiotics. Our work indicates that slow-growing organisms inhabiting nutrient-limited environments may represent an enriched source of novel microbial species. Furthermore, we find that a subset of these organisms is likely to produce corresponding novel antimicrobials, presumably as a means to outcompete faster-growing rival organisms. Indeed, we show that a putative new <i>Streptomyces</i> species is capable of producing a previously undescribed antimicrobial, pyocyanin A, with potent, selective antibacterial toward <i>Acinetobacter baumannii</i>, a prominent cause of antibiotic-resistant infections.