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Quantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genusā€specific primers

2022Journal article Open access
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dc.contributor.authorNajafpour, Babak
dc.contributor.authorCanario, Adelino
dc.contributor.authorPower, Deborah
dc.contributor.authorPinto, Patricia IS
dc.date.accessioned2022-09-19T12:34:24Z
dc.date.available2022-09-19T12:34:24Z
dc.date.issued2022
dc.description.abstractThe goal of this study was to design genus-specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon-based sequencing of the 16S rRNA gene in fish-related samples and surrounding water. Efficient genus-specific primers were designed for 11 bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus-specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus-specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus-specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus-specific primers are proposed as rapid and cost-effective tools to evaluate the most abundant bacterial genera in fish-related or potentially other metagenomics samples.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.doi10.1002/mbo3.1274pt_PT
dc.identifier.issn2045-8827
dc.identifier.urihttp://hdl.handle.net/10400.1/18262
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherWileypt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subject16S rRNA genept_PT
dc.subjectAquaculture sitept_PT
dc.subjectAbundant microbiotapt_PT
dc.subjectEggspt_PT
dc.subjectGenus-specific primerspt_PT
dc.subjectLarvaept_PT
dc.subjectqPCRpt_PT
dc.titleQuantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genusā€specific primerspt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.issue3pt_PT
oaire.citation.titleMicrobiologyOpenpt_PT
oaire.citation.volume11pt_PT
person.familyNameNAJAFPOUR
person.familyNameCanario
person.familyNamePower
person.familyNamePinto
person.givenNameBABAK
person.givenNameAdelino
person.givenNameDeborah Mary
person.givenNamePatricia IS
person.identifier143624
person.identifier643457
person.identifier.ciencia-id1F1E-D3B3-F804
person.identifier.ciencia-id891A-8A44-3CAE
person.identifier.ciencia-idE51D-5CCB-B1C6
person.identifier.orcid0000-0003-2977-482X
person.identifier.orcid0000-0002-6244-6468
person.identifier.orcid0000-0003-1366-0246
person.identifier.orcid0000-0001-7854-3898
person.identifier.ridC-7942-2009
person.identifier.ridM-3817-2013
person.identifier.scopus-author-id56568523700
person.identifier.scopus-author-id7101806760
person.identifier.scopus-author-id10240774300
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication8f1689bd-f300-49d5-9d7a-5ad8ccbe51af
relation.isAuthorOfPublication5f6e51ee-9113-469e-8b9e-f30f2d452521
relation.isAuthorOfPublicationc68f5ffb-63f6-4c70-8957-29e464fb59c0
relation.isAuthorOfPublication64bc526e-5281-44e5-91eb-5743436109f9
relation.isAuthorOfPublication.latestForDiscovery5f6e51ee-9113-469e-8b9e-f30f2d452521

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