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Article Dans Une Revue Microorganisms Année : 2020

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

Claudia Sala
  • Fonction : Auteur
Hanne Mordhorst
  • Fonction : Auteur
Joesphine Grützke
  • Fonction : Auteur
Annika Brinkmann
  • Fonction : Auteur
Thomas N Petersen
  • Fonction : Auteur
Casper Poulsen
  • Fonction : Auteur
Paul D Cotter
  • Fonction : Auteur
Fiona Crispie
  • Fonction : Auteur
Richard J Ellis
  • Fonction : Auteur
Gastone Castellani
  • Fonction : Auteur
Clara Amid
  • Fonction : Auteur
Mikhayil Hakhverdyan
  • Fonction : Auteur
Gerardo Manfreda
  • Fonction : Auteur
Joël Mossong
  • Fonction : Auteur
Andreas Nitsche
  • Fonction : Auteur
Catherine Ragimbeau
  • Fonction : Auteur
Joergen Schlundt
  • Fonction : Auteur
Moon Y. F. Tay
  • Fonction : Auteur
Frank M. Aarestrup
  • Fonction : Auteur
Rene S. Hendriksen
  • Fonction : Auteur
Sünje Johanna Pamp
  • Fonction : Auteur
Alessandra de Cesare
  • Fonction : Auteur

Résumé

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.

Dates et versions

hal-04203266 , version 1 (11-09-2023)

Identifiants

Citer

Claudia Sala, Hanne Mordhorst, Joesphine Grützke, Annika Brinkmann, Thomas N Petersen, et al.. Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community. Microorganisms, 2020, 8 (12), 1861 (16p.). ⟨10.3390/microorganisms8121861⟩. ⟨hal-04203266⟩
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