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.

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.

Brevibacillus brevis B011 is an endophytic isolate from tobacco roots with significant antifungal activity, yet the metabolites responsible for this phenotype and their biosynthetic mechanisms have not been clearly resolved. Genome mining predicted 13 biosynthetic gene clusters, including nonribosomal peptide clusters for edeine, tyrocidine, and gramicidin. Gene knockout, confrontation assays and High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS) indicated that edeines is the primary determinant of antifungal activity, with tyrocidine contributing secondarily, whereas gramicidin plays a minimal role under the tested conditions. Absolute quantitative shows that the total yield of edeine is 19.2 mg/L. Based on LC–MS total ion chromatogram peak areas, the relative abundances of tyrocidines F, G, H, and I were normalized to the sum of these four derivatives as 100%, giving proportions of 25.6%, 18.4%, 34.4%, and 21.6%, respectively, with tyrocidine H being the most abundant. MS/MS putative the primary structure of edeines and four tyrocidine derivatives (each containing leucine as the third residue). The derivatives and their biosynthetic pathways were further verified through in vitro one-pot system. Comparative analysis revealed that tyrocidine F is a previously unreported derivative, whereas the remaining derivatives are consistent with reported streptocidins. Multiple sequence alignment of the adenylation (A) domains showed that TycB_M3 had only 34.7% identity with the canonical Phe-specific A domain (1AMU), showing higher similarity (39.1–56.9%) to Leu-specific A domains and exclusively recognizing leucine. Molecular docking predicted Leu-specificity-conferring residues (S401, Q404, G424, K427, S429, S591, and D593), with G424 (G301 in 1AMU) likely playing a key role in the substrate shifts from Phe to Leu. This study discovery new antimicrobial peptides through genome mining and established an antifungal phenotype-metabolite-BGC framework for B. brevis B011, providing a stronger experimental basis for its future application in plant disease biocontrol.