Publication
Metagenomic analysis of the bacterial microbiome, resistome and virulome distinguishes Portuguese Serra da Estrela PDO cheeses from similar non-PDO cheeses: An exploratory approach
| dc.contributor.author | Salamandane, Acácio | |
| dc.contributor.author | Leech, John | |
| dc.contributor.author | Almeida, Rita | |
| dc.contributor.author | Silva, Carolina | |
| dc.contributor.author | Crispie, Fiona | |
| dc.contributor.author | Cotter, Paul D. | |
| dc.contributor.author | Malfeito-Ferreira, Manuel | |
| dc.contributor.author | Brito, Luísa | |
| dc.date.accessioned | 2025-07-29T13:09:44Z | |
| dc.date.available | 2025-07-29T13:09:44Z | |
| dc.date.issued | 2024-08 | |
| dc.description.abstract | This study aimed to evaluate the microbiome, resistome and virulome of two types of Portuguese cheese using high throughput sequencing (HTS). Culture-dependent chromogenic methods were also used for certain groups/ microorganisms. Eight samples of raw ewe’s milk cheese were obtained from four producers: two producers with cheeses with a PDO (Protected Designation of Origin) label and the other two producers with cheeses without a PDO label. Agar-based culture methods were used to quantify total mesophiles, Enterobacteriaceae, Escherichia coli, Staphylococcus, Enterococcus and lactic acid bacteria. The presence of Listeria monocytogenes and Salmonella was also investigated. The selected isolates were identified by 16S rRNA gene sequencing and evaluated to determine antibiotic resistance and the presence of virulence genes. The eight cheese samples analyzed broadly complied with EC regulations in terms of the microbiological safety criteria. The HTS results demonstrated that Leuconostoc mesenteroides, Lactococcus lactis, Lactobacillus plantarum, Lacticaseibacillus rhamnosus, Enterococcus durans and Lactobacillus coryniformis were the most prevalent bacterial species in cheeses. The composition of the bacterial community varied, not only between PDO and non-PDO cheeses, but also between producers, partic- ularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bac- terial diversity than non-PDO cheeses, demonstrating that the diversity of spontaneously fermented foods is significantly higher in cheeses produced without the addition of food preservatives and dairy ferments. Despite complying with microbiological regulations, both PDO and non-PDO cheeses harbored potential virulence genes as well as antibiotic resistance genes. However, PDO cheeses exhibited fewer of these virulence and antibiotic resistance genes compared to non-PDO cheeses. Therefore, the combination of conventional microbiological methods and the metagenomic approach could contribute to improving the attribution of the PDO label to this type of cheese. | pt_PT |
| dc.description.version | info:eu-repo/semantics/publishedVersion | pt_PT |
| dc.identifier.citation | Salamandane, Acácio, et al. «Metagenomic Analysis of the Bacterial Microbiome, Resistome and Virulome Distinguishes Portuguese Serra Da Estrela PDO Cheeses from Similar Non-PDO Cheeses: An Exploratory Approach». Food Research International, vol. 189, agosto de 2024, p. 114556. https://doi.org/10.1016/j.foodres.2024.114556 | pt_PT |
| dc.identifier.doi | 10.1016/j.foodres.2024.114556 | pt_PT |
| dc.identifier.uri | http://hdl.handle.net/10400.5/102508 | |
| dc.language.iso | eng | pt_PT |
| dc.peerreviewed | yes | pt_PT |
| dc.publisher | Elsevier | pt_PT |
| dc.relation | Looking for antibiotic resistance genes in food systems | |
| dc.relation.publisherversion | https://www.elsevier.com/locate/foodres | pt_PT |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | pt_PT |
| dc.subject | Raw ewe’s milk cheese | pt_PT |
| dc.subject | Protected Designation of Origin PDO | pt_PT |
| dc.subject | High Throughput Sequencing (HTS) | pt_PT |
| dc.subject | Shotgun metagenomic sequencing | pt_PT |
| dc.title | Metagenomic analysis of the bacterial microbiome, resistome and virulome distinguishes Portuguese Serra da Estrela PDO cheeses from similar non-PDO cheeses: An exploratory approach | pt_PT |
| dc.type | journal article | |
| dspace.entity.type | Publication | |
| oaire.awardTitle | Looking for antibiotic resistance genes in food systems | |
| oaire.awardURI | info:eu-repo/grantAgreement/FCT/Concurso de Projetos de I&D em Todos os Domínios Científicos - 2022/2022.04881.PTDC/PT | |
| oaire.awardURI | info:eu-repo/grantAgreement/FCT/OE/PRT%2FBD%2F151521%2F2021/PT | |
| oaire.awardURI | info:eu-repo/grantAgreement/FCT/Concurso de avaliação no âmbito do Programa Plurianual de Financiamento de Unidades de I&D (2017%2F2018) - Financiamento Base/UIDB%2F04129%2F2020/PT | |
| oaire.citation.startPage | 114556 | pt_PT |
| oaire.citation.title | Food Research International | pt_PT |
| oaire.citation.volume | 189 | pt_PT |
| oaire.fundingStream | Concurso de Projetos de I&D em Todos os Domínios Científicos - 2022 | |
| oaire.fundingStream | OE | |
| oaire.fundingStream | Concurso de avaliação no âmbito do Programa Plurianual de Financiamento de Unidades de I&D (2017/2018) - Financiamento Base | |
| person.familyName | Salamandane | |
| person.familyName | Malfeito-Ferreira | |
| person.givenName | Acácio | |
| person.givenName | Manuel | |
| person.identifier.ciencia-id | B21A-DC37-6D8F | |
| person.identifier.ciencia-id | 7313-2302-AAB5 | |
| person.identifier.orcid | 0000-0003-0822-5549 | |
| person.identifier.orcid | 0000-0002-7985-963X | |
| person.identifier.rid | B-3215-2019 | |
| person.identifier.scopus-author-id | 6602549195 | |
| project.funder.identifier | http://doi.org/10.13039/501100001871 | |
| project.funder.identifier | http://doi.org/10.13039/501100001871 | |
| project.funder.identifier | http://doi.org/10.13039/501100001871 | |
| project.funder.name | Fundação para a Ciência e a Tecnologia | |
| project.funder.name | Fundação para a Ciência e a Tecnologia | |
| project.funder.name | Fundação para a Ciência e a Tecnologia | |
| rcaap.rights | openAccess | pt_PT |
| rcaap.type | article | pt_PT |
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