Environmental Microbiota monitoring in food factories. The smoked salmon Case Study

June 21, 2018

Congratulations to Aurélien Maillet (PhD student, Biofortis Mérieux NutriSciences) who has received two Awards from the IAFP (International Association for Food Protection) for the best poster presentation at the European symposium in Stockholm: “Sequencing the Food Factory: Environmental Microbiota Monitoring - the Smoked Salmon Case Study”, and at the MiBioGate congress in Nantes, France.

Aurélien works on the Alterobio project a Research Consortium led by Dr Jérôme COMBRISSON (NGS Industry manager Europe, Mérieux NutriSciences).

To know more about the consortium follow this link




Surface hygiene is considered as a main part of the quality system of food processing plants. However, surfaces bacteria are commonly not identified; their roles for food spoilage and safety are generally unknown. These residential communities persist in food processing plants due to growth at low temperatures, biofilms formation and tolerance to biocides. They may affect food quality through cross-contaminations at each step of a process. NGS technologies like metabarcoding 16S can be used to appreciate the potential implications of surfaces microbiota for food safety and quality.



The aim of this study is to develop a metabarcoding methodology to monitor bacterial communities in food processing plants. This could be useful to characterize microbial reservoir, improve targeted hygiene procedures and lead to shelf life and products quality optimization.



Surfaces samples from a smoked salmon production plant and from products were analyzed using a polyphasic approach. Bacteria were plate counted and identified by MALDI-TOF MS and full 16S rDNA sequencing. DNA was extracted from samples, used to PCR amplify the V3-V4 region of 16S rDNA then sequenced on Illumina MiSeq. Taxonomic classifications were obtained using FROGS pipeline, Silva 16S reference database, RDP classifier.



An environmental surface strain collection was identified. NGS were useful to evaluate bacterial community diversity and dynamics on the environment and on products. From 14 surfaces and product samples, 391 operational taxonomic units could be identified. Beta diversity allowed to identify a core community between the processing environment and products. This core microbiota is mainly composed of Gram positive spoilage bacteria : lactic acid bacteria, Brochothrix and Gram negative : Enterobacteriaceae, Psychrobacter, Pseudomonas and Shewanella.





2. From 14 environment and product samples, 118 strains were isolated and identified by MALDI-TOF MS and full 16S rRNA gene sequencing.
A food processing environment strain collection was developed.


3. A core microbiota common to both the environment and the product was identified.
Spoilage bacteria were shared by the CSS and the processing environment.

  • CSS and environment fraction of community are closely related.

  • CSS spoilage known community could come from the processing environment.





Residential bacteria within the processing environment were identified. A core microbiota mainly composed by spoilage bacteria was highlighted. Contamination hotspots were also detected and suggest that the environment impacts product quality and safety. Microbial ecology knowledge in this complex ecosystem could be useful to characterize microbial reservoirs, improve targeted hygiene procedures, and lead to shelf life and product quality optimization.


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Aurélien MAILLET(1,2), Agnès BOUJU(2), Pauline VAISSIÉ(1), Sébastien LEUILLET(1), Xavier DOUSSET(2), Emmanuel JAFFRÈS(2), Jérôme COMBRISSON(1), Hervé PRÉVOST(2)


1: Biofortis Mérieux NutriSciences, Saint Herblain, France; 2: UMR 1014 Secalim, UBL, INRA, Oniris, Nantes, France


To know more about our expertise and services, please contact  jerome.combrisson@mxns.com










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