Discriminating organic and conventional foods by analysis of their microbial ecology: An application on fruits Céline Bigot * , Jean-Christophe Meile, André Kapitan, Didier Montet CIRAD-UMR Qualisud, TA B-95/16, 73, rue Jean-François Breton, 34398 Montpellier Cedex 5, France article info Article history: Received 2 December 2013 Received in revised form 19 March 2014 Accepted 22 March 2014 Available online xxx Keywords: Biological bare code Food microbiology Organic foods PCR-DGGE Traceability Microbial ecology abstract 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. Ó 2014 Elsevier Ltd. All rights reserved. 1. Introduction Following various food crises such as the mad cow disease or the recent fraud in the beef meat market, European consumers are more and more perceptible to the quality and the origin of food- stuffs they buy, and food safety became one of their main concerns (Lairon, 2010). As a response to these safety, sociologic and eco- nomic problems and within the framework of the globalization, the European regulation relative to the sanitary quality of foodstuffs had to be strengthened. The Food Law (European regulation CE No. 178/2002), applied on the 1st of January 2005, imposes to all food- processing companies of the European Union (EU) to keep con- sumers informed about the nature of the product and any sanitary problems. Moreover, it imposes the traceability of foodstuffs at all steps of the food production. This regulation applies also to organic food industry. Organic farming is a method of sustainable production which contributes to the environmental and animal protection by a set of specific agricultural practices. According to the French Agency for Food Safety (Anses, http://www.anses.fr), organic farming is char- acterized by the use of a positive list of chemicals and Genetically Modified Organisms are prohibited. This mode of production is supervised by a European regulation No. 834/2007 which defines the principles of production, preparation and importation to be respected, the lists of usable products, the practices for every type of breeding and the principles of control, certification, penalty and labelling. The “organic farming” mention is obtained after a period of land conversion of two or three years and a variable period of animal conversion according to species. During this period, organic farmers respect a rigorous specification which favours the respect of the ecosystem (Lairon, 2010). The strong consumer demand led to the fast increase of the number of farmers committed to this farming type. Academic literature concerning organic farming is very scarce, even if some papers dealing with quality and safety were published these last years (Dangour et al., 2010; Lairon, 2010). Moreover, there are no published results on the agricultural productions from organic farming, in comparison with products from conventional farming. In other words, similar sanitary standards are applied to both ag- ricultures, particularly regarding pesticide residues for example. The recent crisis of “horse meat” puts in evidence the necessity of better food traceability. In spite of the current European regu- lation, the administrative documents accompanying foodstuffs (organic or conventional farming) only inform about the country of expedition and the identity of the exporter while the country or region of production or the origins of ingredients remain unknown. * Corresponding author. Tel.: þ33 4 67 61 57 28; fax: þ33 4 67 61 44 33. E-mail address: celine.bigot@cirad.fr (C. Bigot). Contents lists available at ScienceDirect Food Control journal homepage: www.elsevier.com/locate/foodcont http://dx.doi.org/10.1016/j.foodcont.2014.03.035 0956-7135/Ó 2014 Elsevier Ltd. All rights reserved. Food Control xxx (2014) 1e7 Please cite this article in press as: Bigot, C., et al., Discriminating organic and conventional foods by analysis of their microbial ecology: An application on fruits, Food Control (2014), http://dx.doi.org/10.1016/j.foodcont.2014.03.035