The Changes of the Endophytic Bacterial Community from Pepper Varieties with Different Capsaicinoids

Capsaicinoids, the key compounds responsible for pepper pungency, have significant commercial and health value, yet the role of endophytic bacteria in their biosynthesis remains unclear. This study investigated the relationship between endophytic bacterial communities and capsaicinoid content across 100 Capsicum annuum varieties. Two high-capsaicinoid (35.0 and 24.8 mg/g) and two low-capsaicinoid (0.8 and 0.9 mg/g) varieties were selected for 16S rRNA sequencing and microbial analysis. High-capsaicinoid varieties exhibited greater bacterial richness and diversity compared to low-capsaicinoid varieties. Taxonomic profiling revealed distinct community compositions: <i>Enterobacter</i>, <i>Bacteroides</i>, and <i>Escherichia_Shigella</i> were enriched in high-capsaicinoid fruits and positively correlated with capsaicinoid levels, while <i>Chujaibacter</i> and <i>Brochothrix</i> dominated the low-capsaicinoid varieties. Functional annotation highlighted nitrogen-fixing bacteria as more abundant in high-capsaicinoid varieties. Inoculating peppers with isolated <i>Enterobacter</i> strains significantly increased capsaicinoid content, confirming its role in biosynthesis. These findings demonstrate that the pepper genotype shapes endophytic bacterial communities, which in turn influence capsaicinoid production through metabolic- and nitrogen-associated pathways. This study provides foundational insights into microbiome-mediated enhancement of pepper pungency, offering potential strategies for agricultural and industrial applications.