Genome-guided screening of bacterial isolates to identify potential antibiotic producers

Abstract

The urgent need for new antibiotics cannot be overemphasized. Bacterial secondary metabolites remain a relatively untapped source of new therapies. The ability to produce these bioactive compounds is however not universal to all bacterial species. Two key indicators are bacterial genome size (>3 Mb), and the presence of antibiotic-encoding biosynthetic gene cluster (BGCs) within the genomes. BGC distribution is largely determined by phylogeny. Another attribute of some antibiotic producers is the ability to withstand nutritional stress. We exploited these attributes to isolate and identify potential antibiotic producers. A minimal substrate medium was used to isolate nutritionally versatile bacterial strains from topsoil collected from the rhizosphere. The genera of isolates were identified by 16S rRNA gene sequence comparison as Pseudomonas, Hafnia and Obesumbacterium. The typical genome size of species in these genera are 6.2 Mb, 4.7 Mb and 5.0 Mb respectively. The antiSMASH database was browsed by phylogeny to determine the distribution pattern of BGCs in these genera. Pseudomonas strains have an average of 7 BGCs within their genomes that may encode antibiotics, whilst Hafnia and Obesumbacterium strains have 2 and 0 respectively. Therefore, the isolated Pseudomonas strain has the greatest potential to biosynthesis antibiotics. However, the biosynthetic potential of other isolates may be understated given the typical genome size of species in their genera, and their ecological origin. Consequently, all isolates are prime candidates for the next stage of the project which involves genome mining for cryptic or silent genes that may encode novel compounds with antibiotic properties. More isolates are also being recovered.