Discriminating organic and conventional foods by analysis of their microbial ecology: An application on fruits

•Yeast 26S rDNA and bacterial 16S rDNA profiles of nectarines and peaches were generated by PCR-DGGE.•Yeast and bacterial ecologies of nectarines and peaches from the same geographical origin are specific for each farming type.•PCR-DGGE is a suitable tool for farming types discrimination of fruits.

Traceability of foods is mainly done at the administrative level, and the use of analytical tools is rare. Previous studies have demonstrated that microbial ecology analyses at the molecular level (such as PCR-DGGE) could be used to provide food with a unique biological signature that could be linked to the geographical origin of food. The present study aimed at testing this approach to differentiate farming types by analyzing organic and conventional food products. To this end, the microbial ecology of organic and conventional nectarines was analyzed and statistically compared.Our results show that yeast and bacterial communities were specific of the farming type allowing organic fruits to be discriminated from conventional ones. Several microbial species were identified as potential, biological markers which detection could be used to certify the origin as well as the mode of production of foodstuff. We proposed this analytical tool as a first step to control and authentify organic foods.