Metagenomics-based proficiency test of smoked salmon spiked with a mock community
| Autor: | Gerardo Manfreda, Hanne Mordhorst, Richard J. Ellis, Thomas Nordahl Petersen, Frank Møller Aarestrup, Rene S. Hendriksen, Fiona Crispie, Claudia Sala, Alessandra De Cesare, Josephine Grützke, Paul D. Cotter, Mikhayil Hakhverdyan, Annika Brinkmann, Andreas Nitsche, Moon Y. F. Tay, Catherine Ragimbeau, Joël Mossong, Julien Schaeffer, Gastone Castellani, Joergen Schlundt, Soizick Le Guyader, Sünje Johanna Pamp, Casper Sahl Poulsen, Clara Amid |
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| Přispěvatelé: | School of Chemical and Biomedical Engineering, NTU Food Technology Centre, Sala C., Mordhorst H., Grutzke J., Brinkmann A., Petersen T.N., Poulsen C., Cotter P.D., Crispie F., Ellis R.J., Castellani G., Amid C., Hakhverdyan M., Le Guyader S., 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. |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Microbiology (medical)
proficiency test Library preparation Shotgun Proficiency test Computational biology wet-lab protocols Biology Microbiology Article 03 medical and health sciences Smoked Salmon food Experimentally spiked sample Virology experimentally spiked samples ddc:610 lcsh:QH301-705.5 030304 developmental biology 0303 health sciences 030306 microbiology Biological sciences [Science] Food sample Smoked salmon DNA extraction food.food Wet-lab protocols Shotgun Metagenomics lcsh:Biology (General) Shotgun metagenomic Metagenomics 610 Medizin und Gesundheit Shotgun metagenomics shotgun metagenomics |
| Zdroj: | Sala, C, Mordhorst, H, Grützke, J, Brinkmann, A, Petersen, T N, Poulsen, C S, 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 2020, ' Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community ', Microorganisms, vol. 8, no. 12, 1861 . https://doi.org/10.3390/microorganisms8121861 Microorganisms Microorganisms (2076-2607) (Multidisciplinary Digital Publishing Institute), 2020-12, Vol. 8, N. 12, P. 1861 (16p.) Volume 8 Issue 12 Microorganisms, Vol 8, Iss 1861, p 1861 (2020) |
| DOI: | 10.3390/microorganisms8121861 |
| Popis: | 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. Published version |
| Databáze: | OpenAIRE |
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