antiSMASH 6.0: improving cluster detection and comparison capabilities

Abstract

Many microorganisms produce natural products that form the basis of antimicrobials, antivirals, and other drugs. Genome mining is routinely used to complement screening-based workflows to discover novel natural products. Since 2011, the "antibiotics and secondary metabolite analysis shell—antiSMASH" (https://antismash.secondarymetabolites.org/) has supported researchers in their microbial genome mining tasks, both as a free-to-use web server and as a standalone tool under an OSI-approved open-source license. It is currently the most widely used tool for detecting and characterising biosynthetic gene clusters (BGCs) in bacteria and fungi. Here, we present the updated version 6 of antiSMASH. antiSMASH 6 increases the number of supported cluster types from 58 to 71, displays the modular structure of multi-modular BGCs, adds a new BGC comparison algorithm, allows for the integration of results from other prediction tools, and more effectively detects tailoring enzymes in RiPP clusters.

Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord

“…CRISPRDetect v2.3 ( Biswas et al, 2016 ) was applied for the detection of CRISPR (clustered regularly interspaced short palindromic repeats) arrays. AntiSMASH version 6.0.0 ( Blin et al, 2021 ) was used to detect presence of biosynthetic gene clusters (BGCs) predicted to produce secondary metabolites.…”

The Ever-Expanding <em>Pseudomonas</em> Genus: Description of 43 New Species and Partition of the <em>Pseudomonas Putida </em>Group

“…Among the 16 type strains of the newly described species within the P. putida group, 4 were already described as CLP producers (WLIP and Xantholysin producers) [30,31]. Consequently, all strains belonging to the P. putida group, with available genome sequences, were subjected to an antiSMASH analysis (antiSMASH 6.0) [34]. Positive hits were then inspected manually to confirm the typical features of Pseudomonas CLP NRPS clusters (i.e.…”

Complete Genome Sequence of the Cytokinin-Producing Biocontrol Strain Pseudomonas fluorescens G20-18

“…The Prokka annotation of the G20-18 genome revealed the presence of 5,917 predicted coding sequences (CDS) and 93 predicted RNA (19 rRNAs, 72 tRNAs, and 2 transfer-messenger RNAs [tmRNAs]) coding sequences. Several potentially relevant secondary metabolite biosynthetic gene clusters were identified using antiSMASH 6.0 ( 12 ), including the lankacidin C, fengycin, pyoverdine, l -2-amino-4-methoxy-trans-3-butenoic acid, and arylpolyene biosynthesis clusters that may help to explain the plant beneficial role of strain G20-18, which will be further explored in future studies. The presence of the previously described cytokinin biosynthetic gene tRNA delta(2)-isopentenylpyrophosphate transferase ( miaA ) ( 1 ) was confirmed.…”