Detection Of Biosynthetic Gene Clusters From Metagenome Of Natural Honey Collected In Vietnam

The antimicrobial properties of natural honey are partly attributed to bioactive secondary metabolites produced by its associated microbial communities, yet the biosynthetic capacity of these communities remains poorly characterized. Here, we applied a metagenomic approach to investigate the biosynthetic gene cluster (BGC) diversity of bacteria associated with Apis cerana honey from the Northwest mountainous region of Vietnam - a biogeographically distinct and underexplored ecosystem. A total of 366 BGCs spanning 38 compound classes were identified, with terpenes, nonribosomal peptide synthetases (NRPS), and ribosomally synthesized and post-translationally modified peptides (RiPPs) being the most prevalent. Strikingly, 304 BGCs (>83%) lacked close matches in the MIBiG reference database, indicating a high degree of biosynthetic novelty relative to previously characterized natural product repertoires. Among the identified clusters, an azole-containing RiPP BGC recovered from a metagenome-assembled genome (MAG) assigned to Atlantibacter hermannii was predicted to exhibit strong antibacterial activity, with a probability score of 74.5%, representing a prioritized target for heterologous expression and bioactivity validation. These findings establish the Apis cerana honey microbiome as a tractable and largely untapped reservoir for applied microbial research, with direct implications for the discovery of novel antimicrobial agents from underexplored environmental niches. ImportanceAntimicrobial resistance represents one of the most pressing challenges in modern medicine, driving urgent demand for novel bioactive compounds from underexplored microbial sources. Honey-associated bacterial communities are recognized contributors to the antimicrobial properties of natural honey, yet their biosynthetic capacity remains poorly characterized at the metagenomic level. This study demonstrates that the microbiome of Apis cerana honey from a biogeographically distinct region of Vietnam harbors extensive and largely novel biosynthetic gene cluster diversity, with over 83% (304/366) of identified BGCs lacking database references. These findings position honey microbiomes as a tractable and underutilized reservoir for applied microbial research, with direct relevance to the discovery of new antimicrobial agents. The identification of a candidate antibacterial RiPP BGC in Atlantibacter hermannii provides a concrete target for future cultivation-based and heterologous expression studies, bridging metagenomic discovery with applied biotechnological pipelines.