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2020-11-25Zeitschriftenartikel DOI: 10.3390/microorganisms8121861
Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community
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.authorLe Guyader, Soizick
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.accessioned2021-02-18T07:36:17Z
dc.date.available2021-02-18T07:36:17Z
dc.date.issued2020-11-25none
dc.identifier.other10.3390/microorganisms8121861
dc.identifier.urihttp://edoc.rki.de/176904/7803
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.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subjectshotgun metagenomicseng
dc.subjectsmoked salmoneng
dc.subjectproficiency testeng
dc.subjectexperimentally spiked sampleseng
dc.subjectwet-lab protocolseng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleMetagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Communitynone
dc.typearticle
dc.identifier.urnurn:nbn:de:kobv:0257-176904/7803-6
dc.identifier.doihttps://doi.org/10.3390/microorganisms8121861
dc.identifier.doihttp://dx.doi.org/10.25646/8034
dc.type.versionpublishedVersionnone
local.edoc.container-titlemicroorganismsnone
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://www.mdpi.com/2076-2607/8/12/1861none
local.edoc.container-publisher-nameMDPInone
local.edoc.container-volume8none
local.edoc.container-issue12none
local.edoc.container-reportyear2020none
local.edoc.container-firstpage1none
local.edoc.container-lastpage16none
local.edoc.rki-departmentZentrum für Biologische Gefahren und Spezielle Pathogenenone
dc.description.versionPeer Reviewednone

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