Leveraging Microbiome Analysis to Discriminate between Organic and Non-organic Produce: Apple Case Study

Introduction: With the rise of organic products, authentication becomes important as economically-motivated incidents become more of a risk. Combining the large capacity and robustness of Next Generation Sequencing (NGS) and the accuracy and reliability of barcoding, this study compares the microbial maps of the communities that thrive on the surface of organic and non-organic apples and examines the potential of these maps to be used as an authenticity test for organic products.

Purpose: The objective of the study is to measure the microbial differences between different varieties of organic and non-organic apples.

Methods: 16 organic varieties and 14 non-organic varieties of apples were purchased, and the skins of the apples were sampled for mass DNA extraction. Universally accepted regions, with markers covering 85% of ribosomal 16s region, were amplified in a 96-well format, using multiplex Polymerase Chain Reaction (PCR). PCR products were sequenced on the MiSeq platform to identify the species present in the apples.

Results: A signature profile of the microbial communities between the two categories of apples was established, and a clear trend emerged. The bacterial signatures were quite distinct, with Sphingomonas being the only commonality between organic and non-organic apples. Mycobiome signatures also differed significantly; several genera, such as Comoclathris and Exophiala, were detected only in non-organic products. Further, more species of microorganisms were found in non-organic than organic.

Significance: As the discussion of how different foods’ microbiomes affect consumers becomes more pervasive, creating these signature profiles for organic and non-organic produce will be essential in understanding how certain products, pesticides, and foods are linked to public health. Moreover, consumer access to microbiome and mycobiome data may aid in making confident and healthier dietary choices.