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dc.contributor.authorSala, Claudia
dc.contributor.authorMordhorst, Hanne
dc.contributor.authorGrützke, Josephine
dc.contributor.authorBrinkmann, Annika
dc.contributor.authorPetersen, Thomas N.
dc.contributor.authorPoulsen, Casper
dc.contributor.authorCotter, Paul D.
dc.contributor.authorCrispie, Fiona
dc.contributor.authorEllis, Richard J.
dc.contributor.authorCastellani, Gastone
dc.contributor.authorAmid, Clara
dc.contributor.authorHakhverdyan, Mikhayil
dc.contributor.authorGuyader, Soizick Le
dc.contributor.authorManfreda, Gerardo
dc.contributor.authorMossong, Joël
dc.contributor.authorNitsche, Andreas
dc.contributor.authorRagimbeau, Catherine
dc.contributor.authorSchaeffer, Julien
dc.contributor.authorSchlundt, Joergen
dc.contributor.authorTay, Moon Y. F.
dc.contributor.authorAarestrup, Frank M.
dc.contributor.authorHendriksen, Rene S.
dc.contributor.authorPamp, Sünje Johanna
dc.contributor.authorDe Cesare, Alessandra
dc.date.accessioned2021-11-16T16:07:13Z
dc.date.available2021-11-16T16:07:13Z
dc.date.issued2020-11-25
dc.identifier.citationSala C, Mordhorst H, Grützke J, et al. Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community. Microorganisms 2020;8(12):1861. doi: https://doi.org/10.3390/microorganisms8121861en_US
dc.identifier.urihttp://hdl.handle.net/11019/2625
dc.descriptionpeer revieweden_US
dc.description.abstractAn 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.en_US
dc.language.isoenen_US
dc.publisherMDPIen_US
dc.relation.ispartofseriesMicroorganisms;Vol. 8
dc.rightsAttribution-NonCommercial-ShareAlike 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subjectshotgun metagenomicsen_US
dc.subjectsmoked salmonen_US
dc.subjectproficiency testen_US
dc.subjectexperimentally spiked samplesen_US
dc.subjectwet-lab protocolsen_US
dc.titleMetagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Communityen_US
dc.typeArticleen_US
dc.identifier.doihttps://doi.org/10.3390/microorganisms8121861
dc.identifier.piimicroorganisms8121861
dc.contributor.sponsorEuropean Unionen_US
dc.contributor.sponsorGerman Federal Ministry of Educationen_US
dc.contributor.sponsorGrantNumberN 643476en_US
dc.contributor.sponsorGrantNumberFKZ 13N13982en_US
dc.source.volume8
dc.source.issue12
dc.source.beginpage1861
refterms.dateFOA2021-11-16T16:07:14Z
dc.source.journaltitleMicroorganisms
dc.identifier.eissn2076-2607


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