The Metagenomic in the Service of the Food Microbiology.

Introduction: Food products represent great biotopes for bacteria. The optimisation of foodstuffs conservation, mattering so economically as from the point of view of the public health, pass by a better understanding of those biotopes and their spoilage. Microbiologists had already tried to resolve this problem throughout several approaches. Studies based on classical microbiology cultures were completed by strategies centred on approaches independent from the microbiological culture.
Purpose: The current techniques of new generation sequencing give a new dimension to the microbial ecology, through the metagenomic analysis of individuals' large number, within a mixed microbial population. Our aim is to demonstrate that this methodology can be successfully applied to the study of foodstuffs microbial flora, and can be adapted to the specific requirements of food microbiology.
Methods: This study was carried out on pork's minced meat and white sausage, with shelf-life tests in various conditions of preservation (temperature and packaging). The rDNA 16S was extracted from the original products and samples in the best-before date and, after standardization, hypervariable regions V5 were sequenced.
Results: A total about 130.000 sequences were obtained and a metagenomic analysis succeeded in the taxonomic classification to the genus level for 80 % of this population. The subsequent analysis of microbial populations shows that the majority microbial populations at the expiration date are the same ones which are generally observed during microbiological analysis of these meat products. However, the population subdominants and especially several populations of not cultivable germs were able to be identified. These groups of bacteria, more difficult to obtain by the other methods, must be studied because they participate in the spoilage process of food products.
Significance: The sensibility of this technology makes possible the analysis of foodstuffs presenting a very low microbial rate and, thus, allows the identification of the microbial contaminants before they grow the levels detected by cultural methods.