FN Archimer Export Format
PT J
TI Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community
BT 
AF Sala, Claudia
   Mordhorst, Hanne
   Grützke, Joesphine
   Brinkmann, Annika
   Petersen, Thomas N
   Poulsen, Casper
   Cotter, Paul D
   Crispie, Fiona
   Ellis, Richard J
   Castellani, Gastone
   Amid, Clara
   Hakhverdyan, Mikhayil
   LE GUYADER, Soizick
   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
AS 1:1;2:2;3:3;4:4;5:2;6:2;7:5;8:5;9:6;10:7;11:8;12:9;13:10;14:11;15:12;16:4;17:12;18:10;19:13;20:13;21:2;22:2;23:2;24:14;
FF 1:;2:;3:;4:;5:;6:;7:;8:;9:;10:;11:;12:;13:PDG-RBE-SGMM-LSEM;14:;15:;16:;17:;18:PDG-RBE-SGMM-LSEM;19:;20:;21:;22:;23:;24:;
C1 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
   Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany
   Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and Vistamilk, T12 YN60 Co. Cork, Ireland
   Surveillance and Laboratory Services Department, Animal and Plant Health Agency, APHA Weybridge, Addlestone, Surrey, KT15 3NB, UK
   Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40127 Bologna, Italy
   European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
   National Veterinary Institute, Ulls väg 2B, 75189 Uppsala, Sweden
   Laboratoire de Microbiologie, CEDEX 03, 44311 Nantes, France
   Department of Agricultural and Food Sciences, University of Bologna, 40064 Ozzano dell’Emilia, Italy
   Epidemiology and Microbial Genomics, Laboratoire National de Santé, L-3555 Dudelange, Luxembourg
   Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), 62 Nanyang Dr, Singapore 637459, Singapore
   Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano dell’Emilia, Italy
C2 UNIV BOLOGNA, ITALY
   UNIV TECH DENMARK, DENMARK
   BFR, GERMANY
   INST ROBERT KOCH, GERMANY
   APC MICROBIOME, IRELAND
   APHA, UK
   UNIV BOLOGNA, ITALY
   EMBL EBI, UK
   NATL VET INST, SWEDEN
   IFREMER, FRANCE
   UNIV BOLOGNA, ITALY
   LNS, LUXEMBOURG
   NAFTEC, SINGAPORE
   UNIV BOLOGNA, ITALY
SI NANTES
SE PDG-RBE-SGMM-LSEM
IN WOS Ifremer UPR
   DOAJ
   copubli-europe
   copubli-int-hors-europe
IF 4.167
TC 6
UR https://archimer.ifremer.fr/doc/00664/77615/79636.pdf
   https://archimer.ifremer.fr/doc/00664/77615/79671.pdf
LA English
DT Article
DE ;shotgun metagenomics;smoked salmon;proficiency test;experimentally spiked samples;wet-lab protocols
AB 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. 
PY 2020
PD DEC
SO Microorganisms
SN 2076-2607
PU Multidisciplinary Digital Publishing Institute
VL 8
IS 12
UT 000602538500001
DI 10.3390/microorganisms8121861
ID 77615
ER

EF