Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing
Serra da Estrela PDO cheese is the oldest traditional cheese manufactured in Portugal. In this work, its microbiome as well as the main raw materials used in cheese production, raw ewes’ milk and thistle flowers (<i>Cynara cardunculus</i> L.), were characterized using next generation seq...
| Hauptverfasser: | , , , |
|---|---|
| Format: | Artikel |
| Sprache: | English |
| Veröffentlicht: |
MDPI AG
2021-09-01
|
| Schriftenreihe: | Microorganisms |
| Schlagworte: | |
| Online Zugang: | https://www.mdpi.com/2076-2607/9/10/2007 |
| _version_ | 1827679129780092928 |
|---|---|
| author | Rui Rocha Manuela Vaz Velho Joana Santos Paulo Fernandes |
| author_facet | Rui Rocha Manuela Vaz Velho Joana Santos Paulo Fernandes |
| author_sort | Rui Rocha |
| collection | DOAJ |
| description | Serra da Estrela PDO cheese is the oldest traditional cheese manufactured in Portugal. In this work, its microbiome as well as the main raw materials used in cheese production, raw ewes’ milk and thistle flowers (<i>Cynara cardunculus</i> L.), were characterized using next generation sequencing. Samples were accordingly retrieved from a local producer over two consecutive production campaigns and at different time periods within each campaign. The bacterial and fungi communities associated with each matrix were accessed through sequencing of V3–V4 and Internal Transcribed Spacer 2 regions of rRNA gene amplicons, respectively. A high microbial diversity was found associated to each matrix, differing significantly (<i>p</i> < 0.05) from each other. Over 500 taxa were identified in each analyzed matrix, ranging from dominant (relative abundance > 1%), sub-dominant (0.01–1%) and rare taxa (<0.01%). Specifically, in cheese, 30 taxa were present in all analyzed samples (core taxa), including species of <i>Leuconostoc</i> spp. and <i>Lactococcus</i> spp. for bacteria and <i>Candida</i> spp., <i>Debaryomyces</i> spp. and <i>Yarrowia</i> spp. for fungi, that were cumulatively the most prevalent genera in Serra da Estrela PDO cheese (average relative abundance ≥10%). Ultimately, this characterization study may contribute to a better understanding of the microbial dynamics of this traditional PDO product, namely the influence of raw materials on cheese microbiome, and could assist producers interested in preserving the identity, quality and safety of Serra da Estrela PDO cheese. |
| first_indexed | 2024-03-10T06:22:26Z |
| format | Article |
| id | doaj.art-ca567d769ea5430393d5d0f39b9e7ddf |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T06:22:26Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-ca567d769ea5430393d5d0f39b9e7ddf2023-11-22T19:12:42ZengMDPI AGMicroorganisms2076-26072021-09-01910200710.3390/microorganisms9102007Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation SequencingRui Rocha0Manuela Vaz Velho1Joana Santos2Paulo Fernandes3CISAS—Centre for Research and Development in Agrifood Systems and Sustainability, Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun’Álvares, 4900-347 Viana do Castelo, PortugalCISAS—Centre for Research and Development in Agrifood Systems and Sustainability, Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun’Álvares, 4900-347 Viana do Castelo, PortugalCISAS—Centre for Research and Development in Agrifood Systems and Sustainability, Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun’Álvares, 4900-347 Viana do Castelo, PortugalCISAS—Centre for Research and Development in Agrifood Systems and Sustainability, Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun’Álvares, 4900-347 Viana do Castelo, PortugalSerra da Estrela PDO cheese is the oldest traditional cheese manufactured in Portugal. In this work, its microbiome as well as the main raw materials used in cheese production, raw ewes’ milk and thistle flowers (<i>Cynara cardunculus</i> L.), were characterized using next generation sequencing. Samples were accordingly retrieved from a local producer over two consecutive production campaigns and at different time periods within each campaign. The bacterial and fungi communities associated with each matrix were accessed through sequencing of V3–V4 and Internal Transcribed Spacer 2 regions of rRNA gene amplicons, respectively. A high microbial diversity was found associated to each matrix, differing significantly (<i>p</i> < 0.05) from each other. Over 500 taxa were identified in each analyzed matrix, ranging from dominant (relative abundance > 1%), sub-dominant (0.01–1%) and rare taxa (<0.01%). Specifically, in cheese, 30 taxa were present in all analyzed samples (core taxa), including species of <i>Leuconostoc</i> spp. and <i>Lactococcus</i> spp. for bacteria and <i>Candida</i> spp., <i>Debaryomyces</i> spp. and <i>Yarrowia</i> spp. for fungi, that were cumulatively the most prevalent genera in Serra da Estrela PDO cheese (average relative abundance ≥10%). Ultimately, this characterization study may contribute to a better understanding of the microbial dynamics of this traditional PDO product, namely the influence of raw materials on cheese microbiome, and could assist producers interested in preserving the identity, quality and safety of Serra da Estrela PDO cheese.https://www.mdpi.com/2076-2607/9/10/2007traditional cheesesSerra da Estrela cheeseprotected designation of origin foodsnext generation sequencingmicrobiomeraw ewes’ milk |
| spellingShingle | Rui Rocha Manuela Vaz Velho Joana Santos Paulo Fernandes Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing Microorganisms traditional cheeses Serra da Estrela cheese protected designation of origin foods next generation sequencing microbiome raw ewes’ milk |
| title | Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing |
| title_full | Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing |
| title_fullStr | Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing |
| title_full_unstemmed | Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing |
| title_short | Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing |
| title_sort | serra da estrela pdo cheese microbiome as revealed by next generation sequencing |
| topic | traditional cheeses Serra da Estrela cheese protected designation of origin foods next generation sequencing microbiome raw ewes’ milk |
| url | https://www.mdpi.com/2076-2607/9/10/2007 |
| work_keys_str_mv | AT ruirocha serradaestrelapdocheesemicrobiomeasrevealedbynextgenerationsequencing AT manuelavazvelho serradaestrelapdocheesemicrobiomeasrevealedbynextgenerationsequencing AT joanasantos serradaestrelapdocheesemicrobiomeasrevealedbynextgenerationsequencing AT paulofernandes serradaestrelapdocheesemicrobiomeasrevealedbynextgenerationsequencing |