title: The use of 16S rRNA gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: the example of white pudding.
abstract: In order to control food losses and wastage, monitoring the microbial diversity of food products, during processing and storage is important, as studies have highlighted the metabolic activities of some microorganisms which can lead to spoilage. Knowledge of this diversity can be greatly improved by using a metagenetic approach based on high throughput 16S rRNA gene sequencing, which enables a much higher resolution than culture-based methods. Moreover, the Jameson effect, a phenomenon described by Jameson in 1962, is often used to classify bacterial strains within an ecosystem. According to this, we have studied the bacterial microbiota of Belgian white pudding during storage at different temperatures using culture-dependent and independent methods. The product was inoculated with a mix of dominant strains previously isolated from this foodstuff at the end of its shelf life (Carnobacterium maltaromaticum, Lactobacillus fuchuensis, Lactobacillus graminis, Lactobacillus oligofermentans, Lactococcus lactis, Leuconostoc mesenteroides, Raoultella terrigena and Serratia sp.). Daily during 16days, the absolute abundance of inoculated strain was monitored by combining total count on plate agar and metagenetic analysis. The results were confirmed by qPCR analysis. The growth of each species was modelled for each temperature conditions, representative of good or bad storage practices. These data allowed the bacterial strains subdivision into three classes based on criteria of growth parameters for the studied temperature: the "dominant", the "subdominant" and the "inhibited" bacterial species, according to their maximal concentration (Nmax, log CFU/g), growth rate (μmax, 1/h) and time to reach the stationary phase (TRSP, days). Thereby, depending on the storage conditions, these data have permitted to follow intrinsically the evolution of each strain on the bacterial ecosystem of Belgian white pudding. Interestingly, it has shown that the reliability of the Jameson effect can be discussed. For example, at 4°C when Lactococcus lactis and Serratia sp. stopped growth at day 12, at the same time Carnobacterium maltaromaticum reached its maximal concentration and entered its stationary phase. In opposition to this, it can be noticed that in the same condition, the "sub-dominant" organisms continued their growth independently of the "dominant" species behaviour. In this case, the Jameson effect was not illustrated. This pattern is described for all storage conditions with the same strain classifications. These results highlighted the importance of combining metagenetic analysis and classical methods, with modelling, to offer a new tool for studying the evolution of microorganisms present in perishable food within different environmental conditions.
authors.affiliation: University of Liège, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animal & Health (FARAH), Food Science Departement - Food Microbiology, Quartier Vallée 2, Avenue de Cureghem 10, B-4000 Liège, Belgium. Electronic address: ecauchie@ulg.ac.be.
authors.forename: Emilie
authors.initials: E
authors.lastname: Cauchie
authors.affiliation: University of Liège, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animal & Health (FARAH), Food Science Departement - Food Microbiology, Quartier Vallée 2, Avenue de Cureghem 10, B-4000 Liège, Belgium.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Gand
authors.affiliation: University of Liège, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animal & Health (FARAH), Food Science Departement - Food Microbiology, Quartier Vallée 2, Avenue de Cureghem 10, B-4000 Liège, Belgium.
authors.forename: Gilles
authors.initials: G
authors.lastname: Kergourlay
authors.affiliation: University of Liège, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animal & Health (FARAH), Food Science Departement - Food Microbiology, Quartier Vallée 2, Avenue de Cureghem 10, B-4000 Liège, Belgium.
authors.forename: Bernard
authors.initials: B
authors.lastname: Taminiau
authors.affiliation: KeyFood platform, rue Auguste Piccard, 20, Maison de l'Industrie, 6040 Gosselies, Belgium.
authors.forename: Laurent
authors.initials: L
authors.lastname: Delhalle
authors.affiliation: University of Liège, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animal & Health (FARAH), Food Science Departement - Food Microbiology, Quartier Vallée 2, Avenue de Cureghem 10, B-4000 Liège, Belgium.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Korsak
authors.affiliation: University of Liège, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animal & Health (FARAH), Food Science Departement - Food Microbiology, Quartier Vallée 2, Avenue de Cureghem 10, B-4000 Liège, Belgium.
authors.forename: Georges
authors.initials: G
authors.lastname: Daube
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D001530:Belgium; D015169:Colony Count, Microbial; D004269:DNA, Bacterial / Q000235:genetics*; D005516:Food Microbiology; D018857:Food Packaging / Q000379:methods; D061353:Food Storage; D007700:Kinetics; D008461:Meat Products / Q000382:microbiology*; D056186:Metagenomics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D015203:Reproducibility of Results; D013552:Swine; D013696:Temperature
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Jameson effect; Meat product; Metagenetics; Microbial ecosystem; White pudding; qPCR