Application of Full‐Length 16S rRNA Metabarcoding for Characterization of Food‐Associated Bacterial Communities and Screening of Putative Foodborne Pathogen‐Associated Taxa in Fresh‐ and Processed‐Foods

ABSTRACT Food‐associated bacterial communities may influence food quality, spoilage, and microbiological safety, creating a need for broad culture‐independent screening approaches. This exploratory study characterized bacterial communities in fresh and processed foods and screened for putative foodborne pathogen‐associated taxa using full‐length 16S rRNA metabarcoding. Food products obtained from three independent retail vendors in Semarang City, Indonesia, were combined through a two‐stage pooling procedure into six category‐level composites representing fresh foods (FF1–FF3) and processed foods (PF1–PF3). Oxford Nanopore long‐read sequencing of the nearly full‐length 16S rRNA gene was used for bacterial community profiling. Descriptive alpha‐diversity analysis showed that fresh‐food composites generally had greater taxon richness, whereas processed‐food composites showed higher Shannon and Simpson diversity values and lower taxon dominance. Lactic acid bacteria constituted a major component of both food categories, with higher cumulative relative sequence abundance in fresh‐food composites and substantial variation in dominant genera among food matrices. Low‐abundance sequence assignments corresponding to putative foodborne pathogen‐associated taxa were detected in both fresh‐ and processed‐food composites, with 13 such taxa observed across fresh foods and nine across processed foods. The higher cumulative relative sequence abundance in processed foods was largely concentrated in the fish‐ and seafood‐based PF2 composite and was predominantly associated with Vibrio‐related assignments. Full‐length 16S rRNA metabarcoding therefore shows potential for broad characterization of food‐associated bacterial communities, while suspected pathogen‐associated signals require confirmation using independent samples and targeted molecular or culture‐based methods.