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PhD thesis of Aurélien Maillet (2017-2020)

Aurélien Maillet
Characterize environmental microbiota in food factories in order to control and anticipate microbiological contamination of products (smoked salmon) (Hervé Prévost et Emmanuel Jaffrès)

Aurélien Maillet's PhD thesis is funded by the inter-regional Brittany - Pays de la Loire ALTEROBIO.

Abstract of the PhD thesis:

Surface hygiene is an essential component of food industries quality system. Non-pathogenic bacteria are able to be resident in food processing factories and are generally unidentified but can be spoilers and contaminate foodstuffs at each processing step. Therefore, they might be a risk that must be controlled to ensure food safety and quality. In this study, cold-smoked salmon was used as a model to characterize the diversity of bacterial communities in food and food processing plants by 16S rDNA metabarcoding. A comparative analysis of different DNA extraction methods and surface sampling techniques has been performed to define their impacts on the results of a 16S metabarcoding analysis.     Therefore, it allowed us to select the study methodological conditions. Analysis of the diversity of bacterial communities in different batches of cold-smoked salmon showed a connection with the production facility in which they were processed. This suggests that the products bore a signature of the processing environment microbiota. Finally, a comparison of the products and processing environment surfaces bacterial communities allowed to identify the environmental sources of contamination. The use of this approach, in an industrial context, could lead to the implementation of targeted corrective measures in order to reduce product spoilage and the global food wastage.


  • Maillet, A., P. Denojean, A. Bouju-Albert, E. Scaon, S. Leuillet, X. Dousset, E. Jaffrès, J. Combrisson and H. Prévost 2021. Characterization of bacterial communities of cold-smoked salmon during storage. Foods 10(2). Ranking du JCR: Q1 (JCR® 2019).
  • Maillet, A., A. Bouju-Albert, S. Roblin, P. Vaissié, S. Leuillet, X. Dousset, E. Jaffrès, J. Combrisson and H. Prévost 2021. Impact of DNA extraction and sampling methods on bacterial communities monitored by 16S rDNA metabarcoding in cold-smoked salmon and processing plant surfaces. Food Microbiology 95.  Ranking du JCR: Q1  (JCR® 2019).
Microbiota & environment

Microbiota of smoked salmon and production surfaces

The need to standardize and validate analysis methods
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Microbial ecology & smoked salmon

Microbial ecology of smoked salmon and effect of the production environment

A microbiological signature associated with the production plant
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PhD defense of Aurélien Maillet

PhD defense of Aurélien Maillet

On June 15, Aurélien Maillet publicly defended his thesis on the study of the microbiota of the agrifood plant environment and its impact on the...
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