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Quantitative PCR assays as a monitoring tool for bacterial genera in fresh fish fillets

2024-12Journal article Open access
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dc.contributor.authorPinto, Patricia IS
dc.contributor.authorNAJAFPOUR, BABAK
dc.contributor.authorLima, Pedro
dc.contributor.authorP. Machado
dc.contributor.authorAires, Tania
dc.contributor.authorEngelen, Aschwin
dc.contributor.authorTsironi, T.
dc.contributor.authorAnjos Guerreiro, Liliana Isabel Tomé
dc.contributor.authorPower, Deborah Mary
dc.date.accessioned2024-10-08T09:35:38Z
dc.date.available2024-10-08T09:35:38Z
dc.date.issued2024-12
dc.description.abstractFresh fish fillets are a valuable but highly perishable food, and their rapid microbial deterioration is a drawback for food safety and sustainability of aquaculture, food and retail industries. Quantitative PCR (qPCR) assays based on 16S rRNA gene (16S) sequences were developed for the most abundant bacteria genera detected by metagenomics in fresh or processed fish fillets. The efficiency and specificity of six qPCR assays (for 16S of all bacteria or genera Shewanella, Pseudomonas, Carnobacterium, Janthinobacterium and Massilia) was verified using in silico predictions, cloning, sequencing and phylogenetic analyses of amplicons obtained from refrigerated control or high-pressure processed (HPP) European sea bass (Dicentrarchus labrax) fillets. In HPP sea bass fillets, significant decreases in total bacteria 16S and of Shewanella, Pseudomonas, Carnobacterium and Janthinobacterium 16S compared to control fillets were confirmed by qPCR, after 11 days of refrigerated storage. The qPCR assays were successfully applied to monitor microbial contamination during refrigerated storage of fresh fillets from commercial (retail) sea bass and gilthead sea bream (Sparus aurata). Significant increases in total bacterial and Shewanella, Pseudomonas, Carnobacterium and Janthinobacterium contamination were detected after 7-14 days. 16S copy number for total bacteria and the four target genera positively correlated with total viable counts using culture enumeration. 16S of Massilia, that is abundant in fresh fish fillets, did not significantly change during storage. The six validated qPCR assays developed are proposed as specific, sensitive, culture-independent methods for monitoring quality or processing outcomes for fish fillets during cold chain storage.eng
dc.description.sponsorshipMAR-01.03.01-FEAMP-0050; CCMAR/BINCGA/09/2021; EMBRC.PT ALG-01-0145-FEDER-022121; BIODATA.PT ALG-01-0145-FEDER-022231; CCMAR/ID/16/2018
dc.identifier.doi10.1016/j.fbio.2024.104928
dc.identifier.issn2212-4292
dc.identifier.urihttp://hdl.handle.net/10400.1/26013
dc.language.isoeng
dc.peerreviewedyes
dc.publisherElsevier
dc.relationStrengthening cooperation in European research on sustainable exploitation of marine resources in the seafood chains- ERANET
dc.relationOptImization of novel value CHains for fish and seafood by developing an integraTed sustainable approacH for improved qualitY, safety and waSte reduction
dc.relationEuropean Marine Biological Research Infrastructure Cluster to promote the Blue Bioeconomy
dc.relationAlgarve Centre for Marine Sciences
dc.relationAlgarve Centre for Marine Sciences
dc.relationCentre for Marine and Environmental Research
dc.relationMarine macrophytes holobionts: Acclimation and adaptation mechanisms across oceans in a global change scenario
dc.relation.ispartofFood Bioscience
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject16S ribosomal RNA gene
dc.subjectFood spoilage
dc.subjectHigh-pressure processing
dc.subjectSea bass
dc.subjectSea bream
dc.subjectShelf life
dc.titleQuantitative PCR assays as a monitoring tool for bacterial genera in fresh fish filletseng
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleStrengthening cooperation in European research on sustainable exploitation of marine resources in the seafood chains- ERANET
oaire.awardTitleOptImization of novel value CHains for fish and seafood by developing an integraTed sustainable approacH for improved qualitY, safety and waSte reduction
oaire.awardTitleEuropean Marine Biological Research Infrastructure Cluster to promote the Blue Bioeconomy
oaire.awardTitleAlgarve Centre for Marine Sciences
oaire.awardTitleAlgarve Centre for Marine Sciences
oaire.awardTitleCentre for Marine and Environmental Research
oaire.awardTitleMarine macrophytes holobionts: Acclimation and adaptation mechanisms across oceans in a global change scenario
oaire.awardURIinfo:eu-repo/grantAgreement/EC/FP7/321553/EU
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/872217/EU
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/654008/EU
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04326%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F04326%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/LA%2FP%2F0101%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/OE/SFRH%2FBPD%2F116774%2F2016/PT
oaire.citation.startPage104928
oaire.citation.titleFood Bioscience
oaire.citation.volume62
oaire.fundingStreamFP7
oaire.fundingStreamH2020
oaire.fundingStreamH2020
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStreamOE
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
person.familyNamePinto
person.familyNameNAJAFPOUR
person.familyNameAires
person.familyNameEngelen
person.familyNameAnjos Guerreiro
person.familyNamePower
person.givenNamePatricia IS
person.givenNameBABAK
person.givenNameTania
person.givenNameAschwin
person.givenNameLiliana Isabel Tomé
person.givenNameDeborah Mary
person.identifier643457
person.identifier282868
person.identifierAAK-3800-2020
person.identifier.ciencia-idE51D-5CCB-B1C6
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person.identifier.ciencia-id911A-9A0C-744D
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person.identifier.ciencia-id891A-8A44-3CAE
person.identifier.orcid0000-0001-7854-3898
person.identifier.orcid0000-0003-2977-482X
person.identifier.orcid0000-0002-1964-6819
person.identifier.orcid0000-0002-9579-9606
person.identifier.orcid0000-0001-9474-522X
person.identifier.orcid0000-0003-1366-0246
person.identifier.ridM-3817-2013
person.identifier.ridM-8306-2013
person.identifier.ridM-3432-2013
person.identifier.scopus-author-id10240774300
person.identifier.scopus-author-id6701622770
person.identifier.scopus-author-id8575757700
person.identifier.scopus-author-id7101806760
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameEuropean Commission
project.funder.nameEuropean Commission
project.funder.nameEuropean Commission
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
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