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

1
Department of Physics and Astronomy, University of Bologna, 40127 Bologna, Italy
2
Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs, 2800 Lyngby, Denmark
3
German Federal Institute for Risk Assessment, Department of Biological Safety, 12277 Berlin, Germany
4
Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany
5
Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and Vistamilk, T12 YN60 Co. Cork, Ireland
6
Surveillance and Laboratory Services Department, Animal and Plant Health Agency, APHA Weybridge, Addlestone, Surrey, KT15 3NB, UK
7
Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40127 Bologna, Italy
8
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
9
National Veterinary Institute, Ulls väg 2B, 75189 Uppsala, Sweden
10
Laboratoire de Microbiologie, CEDEX 03, 44311 Nantes, France
11
Department of Agricultural and Food Sciences, University of Bologna, 40064 Ozzano dell’Emilia, Italy
12
Epidemiology and Microbial Genomics, Laboratoire National de Santé, L-3555 Dudelange, Luxembourg
13
Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), 62 Nanyang Dr, Singapore 637459, Singapore
14
Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano dell’Emilia, Italy
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(12), 1861; https://doi.org/10.3390/microorganisms8121861
Received: 28 October 2020 / Revised: 17 November 2020 / Accepted: 23 November 2020 / Published: 25 November 2020
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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. View Full-Text
Keywords: shotgun metagenomics; smoked salmon; proficiency test; experimentally spiked samples; wet-lab protocols shotgun metagenomics; smoked salmon; proficiency test; experimentally spiked samples; wet-lab protocols
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MDPI and ACS Style

Sala, C.; Mordhorst, H.; Grützke, J.; Brinkmann, A.; Petersen, T.N.; Poulsen, C.; Cotter, P.D.; Crispie, F.; Ellis, R.J.; Castellani, G.; Amid, C.; Hakhverdyan, M.; Guyader, S.L.; Manfreda, G.; Mossong, J.; Nitsche, A.; Ragimbeau, C.; Schaeffer, J.; Schlundt, J.; Tay, M.Y.F.; Aarestrup, F.M.; Hendriksen, R.S.; Pamp, S.J.; De Cesare, A. Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community. Microorganisms 2020, 8, 1861. https://doi.org/10.3390/microorganisms8121861

AMA Style

Sala C, Mordhorst H, Grützke J, Brinkmann A, Petersen TN, Poulsen C, Cotter PD, Crispie F, Ellis RJ, Castellani G, Amid C, Hakhverdyan M, Guyader SL, Manfreda G, Mossong J, Nitsche A, Ragimbeau C, Schaeffer J, Schlundt J, Tay MYF, Aarestrup FM, Hendriksen RS, Pamp SJ, De Cesare A. Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community. Microorganisms. 2020; 8(12):1861. https://doi.org/10.3390/microorganisms8121861

Chicago/Turabian Style

Sala, Claudia; Mordhorst, Hanne; Grützke, Josephine; Brinkmann, Annika; Petersen, Thomas N.; Poulsen, Casper; Cotter, Paul D.; Crispie, Fiona; Ellis, Richard J.; Castellani, Gastone; Amid, Clara; Hakhverdyan, Mikhayil; Guyader, Soizick L.; Manfreda, Gerardo; Mossong, Joël; Nitsche, Andreas; Ragimbeau, Catherine; Schaeffer, Julien; Schlundt, Joergen; Tay, Moon Y.F.; Aarestrup, Frank M.; Hendriksen, Rene S.; Pamp, Sünje J.; De Cesare, Alessandra. 2020. "Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community" Microorganisms 8, no. 12: 1861. https://doi.org/10.3390/microorganisms8121861

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