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Better preservation of fresh perishable foods is a key factor in reducing waste and losses. We can help by controlling the development of undesirable bacteria with good bacteria. To achieve this, we need to understand the entire product ecosystem.
Characterization of microbial ecosystem dynamics in meat and seafood products during storage
Meat and seafood products are highly perishable commodities whose preservation is critical. Poorly managed, it can lead to major hygiene problems, resulting in wastage and heavy economic losses. The preservation of these products is the result of a strategy to control their ecosystem, i.e. the bacterial flora present. To this end, the use of protective cultures to limit the development of undesirable bacteria has been envisaged for some years, but has not really come to fruition, partly due to a lack of knowledge about the ecosystems of these products. The aim of the Ecobiopro project is to provide scientific support for the potential benefits of protective cultures for seafood and meat products. The aim of the project is to characterize the ecosystems of 4 meat products and 4 seafood products, to identify the species responsible for spoilage in these ecosystems, and to assess how the addition of protective cultures modifies the development of spoilage bacteria and flora as a whole.
Using a molecular method to analyze microbial diversity
The strategy is to use a molecular approach to identify all the microorganisms present in product ecosystems. This method, 16S DNA pyrosequencing, provides an in-depth qualitative and semi-quantitative view of the species present. Indeed, the 16S DNA sequence is specific to each species, and the most exhaustive sequencing possible of all the 16S DNA sequences present enables relative quantification of each of the species present. The high throughput of the pyrosequencing technique makes it possible to estimate the most abundant bacterial species on a scale of around 10,000. This method is more powerful than other molecular methods, which only detect the species that are really in the majority. In addition, the DNA sequencing zone chosen for this project, together with the use of various bioinformatics tools, should enable finer analysis and more precise identification of species. Finally, since it is based on the extraction of bacterial DNA, it does not require a bacterial culture step, thus avoiding the biases due to the varying degrees of selectivity of the culture media conventionally used.
The approach implemented enabled the characterization of ecosystem diversity at the level of bacterial species, a level rarely achieved by pyrosequencing approaches. Data on the microbial ecology of hitherto unexplored products - cod, diced bacon and poultry sausages - were generated. In particular, it revealed the great diversity of seafood ecosystems and their wealth of previously uncultured bacteria. These results also make it possible to revisit the microbial ecology of flagship products, such as minced steak, for which certain species hitherto not or rarely mentioned as altering these products could be incriminated. These initial results open up new prospects in the field of microbial ecology, with a particular challenge being the characterization of organisms that have not been cultivated to date, and therefore never yet described in these products, and which could play an important role in the alteration of seafood products in particular. In addition, these results will undoubtedly raise questions about the relevance of the culture media used for conventional microbiological analyses of foodstuffs. This first phase of the project, by raising new scientific questions, is encouraging the consortium to structure itself with an international (European) perspective.