antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

TLDR

Secondary metabolites from bacteria and fungi are key sources of antimicrobials, and genome mining—particularly via the widely used antiSMASH platform—has become essential for identifying and characterizing biosynthetic gene clusters in microbial genomes. This work introduces a completely redesigned and expanded version 5 of the antiSMASH pipeline. Version 5 incorporates new detection rules for diverse compound classes, refines predictions for type II polyketide synthase clusters, redesigns the HTML visualization, and adds a JSON output format for programmatic use. These enhancements reduce analysis runtime, enabling comprehensive bacterial genome annotations in only a few minutes.

Abstract

Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.