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Amplicon sequencing approaches are widely used to analyze the bacterial ecology of food products. These methodologies, based on the sequencing of a specific region of bacterial DNA (for example the V3-V4 region of 16S rDNA), allow the taxonomic identification (determination of the genus or even of the bacterial species) of the bacteria analyzed. as well as their relative abundance. Prior to sequencing, samples should be taken and DNA extracted.
In this study, bacteria were collected from two types of matrix: an end-product (smoked salmon) as well as surfaces of the production plant. In order to assess the influence of the methodology on the characterization of the microbiota of smoked salmon and the surfaces in contact with it during processing, Secalim evaluated the efficiency of different DNA extraction protocols as well as compared different methods of microbiological sampling (swab / sponge) from surfaces of various materials.
Ecology analyzes revealed that DNA extraction methods had an effect on the microbiota compositional results of smoked salmon, especially on the diversity of bacteria identified. The dominant bacterial genera on this matrix were Photobacterium, Serratia, Brochothrix, Carnobacterium and Staphylococcus. Conversely, the extraction methods did not influence the microbiota of surfaces, the composition of which as well as the richness and diversity were mainly affected by the cleaning and disinfection procedures applied in the plant. Regarding the sampling methods, sponge sampling allowed the collection of richer and more uniform surface bacterial communities than by swabbing.

Ecology analyzes have shown that the type of material, cleaning and disinfection, and sampling devices seem to affect the composition of the bacterial communities, mainly composed of bacteria responsible for spoilage of fish.
Methods of microbiological sampling as well as DNA extraction are likely to influence the results of the sequencing and therefore the ecological analysis of the structure of bacterial communities. This study thus confirmed the importance of the standardization of the methodology and the need for analytical validation before undertaking studies based on amplicon sequencing of 16S rDNA.

Partners:

This study was carried out by the UMR INRAE ​​SECALIM of the Center Pays de la Loire, as part of the ALTEROBIO project, funded by the Pays de la Loire Region, as part of a Cifre thesis funded by the National Association of research and technology (ANRT) and Biofortis Mérieux Nutrisciences.

Associated publication:

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. https://doi.org/10.1016/j.fm.2020.103705