Exploration of microbial ecosystems of fish and meat products: effects of bio-protective cultures – ECOBIOPRO

The strategy is to use a molecular method for identifying all microorganisms in the meat and fish products. This method, 16S DNA pyrosequencing, allows qualitative and quantitative information on species. In fact, each species is characterized by its own 16S sequence and sequencing all 16S sequences of a given product allows a relative quantification of each present species. High troughput pyrosequencing allows to evaluate most abundant bacterial species on a range of approximately10000. This method is more powerful than other molecular ones which generally only detect highly represented species. Moreover, the use dedicated bioinformatic tools allows a more accurate identification of species. Finally, based on bacterial DNA extraction, this method does not require cultivation of microorganisms, limiting thus bias due to the lack of specificity of some classical cultural media.

The organized approach allowed the characterization of the diversity of the ecosystems at the level of the bacterial species, a level rarely achieved by pyrosequencing approaches.
New data have been generated for yet unexplored ecosystems such as cod filet, dice cubes or poultry sausages.
It apeared in particular that fish product ecosystems harbour lots of yet uncultured bacteria. Data also provide new insights on the ecology of well known products such as ground beef, for wich some species, rarely cited as spoilage organisms, could in fact be incriminated.
These first results open field for the caracterization of uncultured species which could be involved in fish product spoilage. Moreover, these results will lead to ask questions about the relevance of culture media used within the classical framework of food microbiology.
This first phase of the project, by raising of new scientific questions, incite the consortium to form itself in an (European) international perspective. This run-up is supported by the poles of competitiveness to which the first results were presented.

By providing a new vision of the microbial ecology of food, these results could lead to suggest other criteria to be taken into account for the analysis in laboratory by the usual cultural methods of bacteriology. The continuation of the project will see the contribution of knowledge on the impact of protective cultures on the characterized ecosystems. This will constitute a solid scientific foundation for the legislative debate on the use of protective cultures.

An oral communication has been presented at congress « Ecosystèmes microbiens et bioprotection des aliments» ». co-organised by « société française de microbiologie » (SFM) and RMT FlorePro
A poster will be presented at Food Micro, Istanbul September2012.

Meat and seafood products are highly perishable foodstuffs, the preservation of which is crucial. Indeed, a bad preservation of these products may lead to important hygienic and safety risks as well as considerable economic loss, a situation that is particularly true for novel products. The utilisation of protective cultures in order to limit these risks is proposed since several years but is still not in common use, partially because a lack of knowledge of microbial ecosystems of these products. The partners of the French network FLOREPRO decided to share their know-how and scientific knowledge on one hand, and their various expertise about food on the other hand, in order to increase the knowledge of meat and seafood products and on the impact of protective cultures on these ecosystems and on the quality of the products. Our aim is thus to provide a sound scientific based information on the benefit that the utilisation of protective cultures may represent in the production of meat/fish foodstuffs.
The project is divided into three tasks:
- an as exhaustive as possible characterisation of the ecosystem of height selected products (meat and seafood) by the up to date most performing method, 16S rDNA pyrosequencing of the bacterial DNA present on these products, at the time of production and after the use by date. This task also encompasses the selection of putative spoiler micro-organisms from those products;
- set up and sharing of model matrices and sensory analysis in order to reproduce spoilage and to prove the spoiling properties of the strains selected from the first task;
- evaluation of the impact of already available protective cultures on spoilage, sensorial quality, and global ecosystem of the products we propose to study.
The partners of this project are academics, agro institutes and one SME which was a pioneer in the commercialisation of protective cultures. Other industries, SMEs with no financial support, joined the project to furnish the foodstuffs to be analysed. Know-how, expertise and missions of the partners are complementary and about meat/fish products. The foodstuffs we selected are representative of a large panel of origins (beef, veal, poultry, fish, shellfish) and processes (ground, diced cubes, fillets, peeled) and concern novel products for which knowledge about their ecosystem and sanitary quality is scarce.