Impact of DNA extraction and sampling methods on bacterial communities monitored by 16S rDNA metabarcoding in cold-smoked salmon and processing plant surfaces

Amplicon sequencing approaches have been widely used in food bacterial ecology. However, choices regarding the methodology can bias results. In this study, communities associated with cold-smoked salmon products and their processing plant surfaces were monitored via of V3–V4 region 16S rRNA gene. The impact DNA extraction protocols, sampling methods (swabbing or sponging) surface materials on investigated. ? ? diversity analyses revealed that mainly influence observed microbiota composition. Moreover, different significant differences community richness evenness. ?-Proteobacteria: Photobacterium, Serratia Firmicutes: Brochothrix, Carnobacterium Staphylococcus identified as dominant genera. Surface richness, composition affected by cleaning disinfection procedures but not methods. evenness appeared higher when sampled sponging compared to swabbing. ?-diversity highlighted topology, devices seemed affect bacteria Flavobacteriaceae, ?-Proteobacteria ?-Proteobacteria described fish spoilers such Acinetobacter, Pseudomonas Shewanella. an results ecological analysis structures. This study confirmed importance standardization need for analytical validation before rDNA metabarcoding surveys.