Genome mining and characterisation of multiple bioactive compounds from a Burkholderia gladioli isolate collection

Burkholderia are Gram-negative bacteria with varied lifestyles and versatile phenotypes including the production of bioactive natural products [1]. Burkholderia gladioli has previously been shown to produce bioactive secondary metabolites such as bongkrekic acid [2] and toxoflavin [3]. To fully understand the potential of B. gladioli to produce novel natural products, a collection of 88 isolates was genome-sequenced using Illumina technology; and a reference 8.4 Mb genome was produced using single molecule real time sequencing. Genomic analysis of the B. gladioli collection revealed a wealth of secondary metabolite biosynthetic clusters (˜18% of genomic capacity) including terpene, nonribosomal peptide and polyketide biosynthesis. A core genome phylogenetic tree was constructed, and the biosynthesis capabilities mapped onto this tree, to assign the diversity of secondary metabolite biosynthesis within B. gladioli. Correlation of genomic potential with active secondary metabolite production was performed by extraction of growth media, thin layer chromatography, and microbial overlay analysis; multiple bioactive compounds were identified with activity against multidrug resistant bacteria and yeast. A novel macrolide antibiotic, designated gladiolin, with broad spectrum activity was identified in B. gladioli strain BCC238. The structure of gladiolin was elucidated, and shown by insertional mutagenesis to be the product of a 139 kb trans-AT PKS cluster, present in 34 of the 88 genomes analysed. In contrast, the additional bioactivity of strain BCC0238 was attributed to toxoflavin and its biosynthetic pathway was conserved in all 88 B. gladioli genomes. In conclusion, bioinformatic analysis revealed that the Burkholderia genus and B. gladioli holds great potential for natural product discovery and novel antibiotic production. However, with the majority of the predicted biosynthetic pathways being silent, strategies for activation will be required to release this potential.