Natural Pigment Production by Bacillus velezensis YM–3 Isolated from Traditional Pixian Douban Condiment: Biosynthesis Pathway, Structural Characterization, and Bioactivities

Natural microbial pigments offer important advantages and are widely studied for food applications. We investigated the biosynthetic pathways, characteristics, and bioactivities of the orange–red pigment produced by Bacillus velezensis YM–3, a strain isolated from the traditional Pixian Douban condiment. Whole-genome sequencing revealed complete pathways for melanin, phytoene, and heme biosynthesis. The purified extracellular pigment was characterized using ultraviolet–visible spectroscopy, Fourier-transform infrared spectroscopy, nuclear magnetic resonance spectroscopy, and ultra-performance liquid chromatography–high-resolution mass spectrometry; it was preliminarily characterized as melanin-like pigment. The pigment was highly soluble in alkaline solutions, moderately soluble in water, and insoluble in common organic solvents. It exhibited strong photostability and remained stable at low temperature, precipitated under acidic conditions, and showed high stability under alkaline environments. Furthermore, the pigment demonstrated in vitro free radical scavenging activity. Hence, this study provides a scientific foundation for exploring the potential utility of B. velezensis YM–3 and its pigment metabolites as functional agents.