Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community

Claudia Sala, Hanne Mordhorst, Josephine Grützke, Annika Brinkmann, Thomas Nordahl Petersen, Casper Sahl Poulsen, Paul D. Cotter, Fiona Crispie, Richard J. Ellis, Gastone Castellani, Clara Amid, Mikhayil Hakhverdyan, Soizick Le Guyader, Gerardo Manfreda, Joël Mossong, Andreas Nitsche, Catherine Ragimbeau, Julien Schaeffer, Jørgen Schlundt, Moon Y. F. TayFrank Møller Aarestrup, Rene S. Hendriksen, Sünje Johanna Pamp, Alessandra De Cesare*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample.
Original languageEnglish
Article number1861
JournalMicroorganisms
Volume8
Issue number12
Number of pages16
ISSN2076-2607
DOIs
Publication statusPublished - 2020

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