Brevibacillus brevis is one of the most common biocontrol strains with broad applications in the prevention and control of plant diseases and insect pests. In order to deepen our understanding of B. brevis genomes, describe their characteristics comprehensively, and mine secondary metabolites, we retrieved the genomic sequences of nine B. brevis strains that had been assembled into complete genomes from the NCBI database. These genomic sequences were analyzed using phylogenetic analysis software, pan-genome analysis software, and secondary metabolite mining software. Results revealed that the genome size of B. brevis strains ranged from 6.16 to 6.73 Mb, with GC content ranging from 47.0% to 54.0%. Phylogenetic analysis classified the nine B. brevis strains into three branches. The analyses of ANI and dDDH showed that B. brevis NEB573 had the potential to become a new species of Brevibacillus and needed further research in the future. The pan-genome analysis identified 10032 gene families, including 3257 core gene families, 3112 accessory gene families, and 3663 unique gene families. In addition, 123 secondary metabolite biosynthetic gene clusters of 20 classes were identified in the genomes of nine B. brevis strains. The major types of biosynthetic gene clusters were non-ribosomal peptide synthase (NRPS) and transAT polyketide synthase (transAT-PKS). Furthermore, a large number of untapped secondary metabolites were identified in B. brevis. In summary, this study elucidated the pan-genome characteristics of the biocontrol bacterium B. brevis and identified its secondary metabolites, providing valuable insights for its further development and utilization.

Phytopathogenic fungi infect crops, presenting a worldwide threat to agriculture. Polyene macrolides are one of the most effective antifungal agents applied in human therapy and crop protection. In this study, we found a cryptic polyene biosynthetic gene cluster in Actinokineospora spheciospongiae by genome mining. Then, this gene cluster was activated via varying fermentation conditions, leading to the discovery of new polyene actinospene (1), which was subsequently isolated and its structure determined through spectroscopic techniques including UV, HR-MS, and NMR. The absolute configuration was confirmed by comparing the calculated and experimental electronic circular dichroism (ECD) spectra. Unlike known polyene macrolides, actinospene (1) demonstrated more versatile post-assembling decorations including two epoxide groups and an unusual isobutenyl side chain. In bioassays, actinospene (1) showed a broad spectrum of antifungal activity against several plant fungal pathogens as well as pathogenic yeasts with minimum inhibitory concentrations ranging between 2 and 10 μg/mL.

A yellow, Gram-stain-negative, aerobic, non-spore-forming, motile, and rod-shaped bacterial strain designated M6^T was isolated from fully weathered granitic soil. The strain showing the highest 16S rRNA gene sequence similarity to M6^T was Sandaracinobacteroides hominis SZY PN-1^T (96.3%), the only species in the genus Sandaracinobacteroides. The average nucleotide identity and digital DNA-DNA hybridization value between these two strains were 72.6% and 18.0% respectively. Growth was inhibited by NaCl (≥0.1% (w/v)). Strain M6^T contained C_18:1ω7c (33.8%), C_14:0 2-OH (16.6%), summed feature 3 (15.8%), and C_16:0 (12.6%) as the major fatty acids. The polar lipids profile consisted of phosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid, four unidentified phospholipids, and four unidentified lipids. The genome of strain M6^T was 3.4 Mb with 67.7% GC content. Further genomic analysis revealed a biosynthetic gene cluster for zeaxanthin, the production of which was verified by a high-resolution mass spectrum. The existence of multiple genes for aromatic ring-hydroxylating dioxygenases implies the potential ability for organic pollution controlling. The morphological, physiological, chemotaxonomic, and phylogenetic analysis clearly distinguished this strain from its phylogenetic neighbors, thus strain M6^T represents a novel species of the genus Sandaracinobacteroides, for which the name Sandaracinobacteroides saxicola sp. nov. is proposed. The type of strain is M6^T (=CGMCC 1.19164^T=NBRC 115420^T).

Plant specialized metabolites play important roles in plant–microbe interactions. Beyond direct antimicrobial activity, some can attenuate pathogen virulence without markedly inhibiting microbial growth. Many gram-negative phytopathogenic bacteria cause important crop diseases and possess interconnected virulence systems, providing multiple opportunities for intervention by plant-derived anti-virulence metabolites. In this review, we summarize recent advances in these metabolites against gram-negative phytopathogenic bacteria according to three functional levels: virulence signal decision-making, virulence execution, and pathogenic ecological phenotypes. Particular attention is given to the strength of mechanistic evidence, including target engagement, pathway modulation, and disease-related outcomes. We further interpret these activities in the chemical-ecology context of plant–pathogen interactions and discuss the challenges and prospects of developing plant-derived metabolites as anti-virulence agents.