From soil to market: Microbiome dynamics and food safety implications along Brazilian black pepper production chain

Understanding how the microbiome is influenced throughout food production chains is crucial for advancing microbial ecology and food safety. However, integrative studies tracking microbiome dynamics from field to consumer remain scarce. In this study, we investigated the structure of the bacterial microbiome along the production chain of black pepper ( Piper nigrum L.) produced in Brazil, using 16S rRNA gene metabarcoding combined with culture-dependent and conventional molecular methods (BAX® system and Sanger sequencing). We analyzed 180 samples collected along the production chain in the states of Pará and Espírito Santo, as well as from retail outlets in São Paulo. Enterobacterales counts ranged from <10 to 7.7 × 10 8 CFU/g, with the highest levels observed during storage (intermediary collectors) and persistent detection throughout the entire production chain. Microbiome analysis revealed a clear ecological succession: soil exhibited the highest alpha diversity (Chao1 > 4300; Shannon >10), followed by a progressive reduction in diversity during drying and storage stages, and a partial recovery in retail samples. The stages displayed distinct microbial profiles, with a predominance of oligotrophic taxa in soil, fermentative genera in field samples, and desiccation-tolerant taxa, particularly Bacillus and Enterobacteriaceae, becoming more prevalent in dried and retail samples. Salmonella spp. was detected in only 3.9% of samples, appearing in fresh, dried, and retail pepper, indicating both pre- and post-harvest contamination pathways. Molecular characterization identified Salmonella enterica subsp. salamae and subsp. diarizonae , representing the first report of these subspecies in black pepper. These results provide new insights into microbiome succession and Salmonella ecology along the black pepper supply chain, aiding in the identification of critical control points to improve the quality and safety of this foodstuff.