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PhD thesis of Amélie Rouger

Amélie Rouger
Improvement of the quality and safety of poultry meat by studying bacterial interactions within the ecosystem to control spoilage and pathogenic flora, especially Campylobacter (M. Zagorec, H.Prévost, B. Remenant)

Abstract:

Controlling spoilage bacteria in food, especially raw meat products, is a major challenge for the food industry. The conditions of meat storage in different atmospheres exert selection pressure and modify the behavior and development of the bacterial communities initially present. High throughput sequencing methods, used to characterize different microbial ecosystems, have been applied to study the dynamics of bacterial communities in chicken meat during storage.We have developed a method to constitute standard microbial ecosystems whose composition was determined by pyrosequencing the 16S rRNA gene. The presence of Brochothrix thermosphacta and Pseudomonas among the dominant species was confirmed and we showed that Shewanella and Carnobacterium were under dominant. We have selected two ecosystems to perform reproducible challenge tests on chicken meat stored under 3 commonly used atmospheres. A metatranscriptomic and metagenomic analysis was performed to find out “What bacteria were present?”, “What were they able to do?” and “What were they saying?” depending on the conditions. We were thus able to assess the impact of gas mixtures on bacterial dynamics and the functions expressed by bacteria according to the initial contaminants. This gives us clues to provide indications for optimizing the preservation of meat by controlling microbial ecosystems.

Valorisation :

  • Rouger, A., O. Tresse and M. Zagorec 2017. Bacterial contaminants of poultry meat: sources, species, and dynamics. Microorganisms 5(3): 50. Ranking du JCR: Q2 (JCR® 2018).https://doi.org/10.3390/microorganisms5030050
  • Rouger, A., B. Remenant, H. Prévost and M. Zagorec 2017. A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model. International Journal of Food Microbiology 247: 38-47. Ranking du JCR: Q1. http://dx.doi.org/10.1016/j.ijfoodmicro.2016.04.028.
  • Rouger, A., N. Moriceau, H. Prévost, B. Remenant and M. Zagorec 2018. Diversity of bacterial communities in French chicken cuts stored under modified atmosphere packaging. Food Microbiology 70: 7-16. Ranking du JCR: Q1. http://dx.doi.org/10.1016/j.fm.2017.08.013.
Bacteria & chicken

Bacteria of the chicken meat

High throughput sequencing to describe the microbial communities.
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