Discovery of a new cinnamycin analog from an Actinomadura sp. isolated from meerkat feces

The rapid global spread of antibiotic resistance emphasizes the need for new effective therapeutics. The isolation of strains, e.g. of the actinomycetes, from unexplored habitats could potentially provide access to new or endemic species as the new sources for novel secondary metabolites. Here, we investigate an antibiotic-producing isolate from a meerkat (Suricata suricatta) fecal sample with regard to its antimicrobial activity.

Diluted fecal samples were plated on MYM agar. Actinobacteria were isolated based on colony and cell morphology. The isolate was phylogenetically classified based on the 16S rDNA sequence. Mature colonies were overlayed with soft agar containing Gram-negative, Gram-positive or fungal species. Cell extracts from liquid cultures as well as colonies were analyzed regarding their antibiotic spectrum by applying a panel of whole cell biosensors, in which an antibiotic-inducible promoter is fused to the luciferase cassette. The potential antibiotic biosynthetic gene clusters (BGC) were identified by genome mining. During the plate-based biosensor screens, we identified naturally resistant Bacillus subtilis colonies growing in the zone of inhibition. After repeating rounds of selection, highly resistant spontaneous mutant strains were subjected to whole genome sequencing.

16S rDNA sequencing identified the isolate as Actinomadura coerulea. The isolate showed a strong and broad range of antibacterial activity against Gram-positive bacteria, including pathogens, as well as an antifungal effect. The secondary metabolites of the isolate potentially inhibit replication, block translation, and interfere with bacterial cell wall integrity. Amongst others, we identified loss of function mutations in pssA, encoding a phosphatidylserine synthase. Based on the function of PssA and genome mining, the BGC for a novel cinnamycin analog was identified. Detailed follow-up studies are currently ongoing.

Our approach demonstrates that combining the exploration of niche habitats for actinomycetes with whole-cell biosensor screening and characterization of natural resistance development provides a promising strategy for identifying novel antibiotics.