Food quality and safety had become an increasing issue for quality authorities, food scientists, manufacturers, producers and consumers as well. In the present work, food quality control using bacterial identification isolated from food samples was performed. Greek olives (raw drupes), currants (dry fruits), roe (fish eggs), bacon and “feta” cheese were collected for this purpose. The aim of this study was to investigate the quality of
traditional Greek food types and to compare bacterial population observed of each food matrix according to analysis method. Therefore, culture based and molecular methods were performed in parallel. Total bacterial DNA isolated from food samples was verified by PCR and PCR-RAPD amplification and then analyzed by Next Generation Sequencing. Results showed that NGS analysis can provide an advanced and detailed look at food microbiota in comparison to culture-dependent techniques. Climate conditions, environmental factors, even production or processing procedures can result an abundant bacterial diversity isolated from each food product, so NGS approaches can be suitable to elucidate the whole picture of bacteria populations. NGS analysis regarding food safety management can be applied in food industries and therefore quality and safety of food products can be reassured.