# Cross-Platform Evaluation of Established NGS-Based Metabarcoding Methods for Detecting Food Fraud in Pistachio Products

## TL;DR

This study compares Illumina and MinION sequencing platforms for detecting food fraud in processed pistachio products, finding MinION to be a reliable and cost-effective alternative.

## Contribution

The study evaluates the transferability of an Illumina-based metabarcoding method to the MinION platform for food fraud detection in pistachios.

## Key findings

- MinION sequencing provides reliable accuracy for detecting pistachio adulteration in processed foods.
- The MinION platform offers faster processing and lower costs compared to Illumina for routine food authenticity testing.
- Both MinION and Flongle flow cells are suitable for metabarcoding applications in food fraud analysis.

## Abstract

Next Generation Sequencing is a constantly evolving technology whose applicability is increasingly expanding into the field of routine food analysis. In this context, metabarcoding has proven to be a powerful tool for detecting food fraud due to its ability to taxonomically classify even highly fragmented DNA from processed products. While Illumina sequencing platforms, representing second-generation sequencing technologies, are widely used for such applications, fourth-generation sequencing devices such as Oxford Nanopore Technologies’ MinION offer advantages in terms of flexibility, scalability, and simplified handling. In this study, we evaluate the transferability of an established Illumina-based metabarcoding method for the detection of pistachio adulteration in processed foods to the MinION platform of Oxford Nanopore Technology. In more detail, we transferred the established method from Illumina on both MinION and Flongle flow cells to assess sequencing accuracy, quantification potential and practical aspects such as cost-efficiency and workflow. Our results highlight the applicability of the MinION sequencing platform as a reliable and cost-effective alternative to Illumina protocols for routine food authenticity testing, enabling faster processing and broader accessibility without significantly compromising accuracy.