De-novo assembly of 82 bacterial genomes using Nanopore sequencing and prediction of biosynthetic capacity

Historically, antibiotic development has been driven by research into secondary metabolism which is responsible for the biosynthesis of so-called natural products. This research has been revolutionized by our growing capacity to rapidly generate and analyze prokaryotic genome sequences, facilitating the identification of biosynthetic gene clusters (BGCs) involved in secondary metabolism. We present the genomic analysis of 82 bacterial isolates from our collection, covering a broad taxonomic spectrum. The bulk of analyzed isolates belong to the actinobacterial class of Actinomycetes, known for their remarkable ability to generate antimicrobial compounds with diverse chemistries. Whole genome sequencing was performed using the Oxford Nanopore technology and the majority of assembled sequences exhibit over 90% gene completeness, enabling reliable functional annotation. Genome mining analyses revealed variability in BGC content across different phyla, confirming isolates in the Streptomyces genus as preeminent producers of secondary metabolites. Utilization of the current dataset holds potential not only for the elucidation of the bacterial biosynthetic machinery, but also for phylogenetic comparison and biotechnological exploitation of the isolates under study.