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

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 Le; Manfreda, Gerardo; Mossong, Joël; Nitsche, Andreas; Ragimbeau, Catherine; Schaeffer, Julien; Schlundt, Joergen; Tay, Moon Y. F.; Aarestrup, Frank M.; Hendriksen, Rene S.; Pamp, Sünje Johanna; De Cesare, Alessandra

doi:10.3390/microorganisms8121861

Submit to this Journal Review for this Journal Edit a Special Issue

Article Menu

...

Open AccessArticle

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

²,

⁴,

²,

⁵,

⁵,

⁶,

⁷,

⁸

⁹

¹⁰,

¹¹,

¹²,

⁴,

¹²

¹⁰,

¹³,

¹³,

²,

²,

and

^14,* Show full author list Hide full author list

Department of Physics and Astronomy, University of Bologna, 40127 Bologna, Italy

Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs, 2800 Lyngby, Denmark

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

Show full affiliation list

Hide full affiliation list

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)

View Full-Text Download PDF

Browse Figures

Review Reports Citation Export

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. View Full-Text

Keywords: shotgun metagenomics; smoked salmon; proficiency test; experimentally spiked samples; wet-lab protocols

▼ Show Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Supplementary Material

Supplementary File 1:
PDF-Document (PDF, 1072 KiB)

Share and Cite

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

Find Other Styles

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Metrics

Abstract views Pdf views Html views

Article Menu

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

Abstract

Supplementary Material

Share and Cite

Article Metrics

Article Access Statistics

Article Access Map by Country/Region

Further Information

Guidelines

MDPI Initiatives

Follow MDPI