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Martini S, Sola L, Cattivelli A, Cristofolini M, Pizzamiglio V, Tagliazucchi D, Solieri L. Cultivable microbial diversity, peptide profiles, and bio-functional properties in Parmigiano Reggiano cheese. Front Microbiol 2024; 15:1342180. [PMID: 38567075 PMCID: PMC10985727 DOI: 10.3389/fmicb.2024.1342180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Lactic acid bacteria (LAB) communities shape the sensorial and functional properties of artisanal hard-cooked and long-ripened cheeses made with raw bovine milk like Parmigiano Reggiano (PR) cheese. While patterns of microbial evolution have been well studied in PR cheese, there is a lack of information about how this microbial diversity affects the metabolic and functional properties of PR cheese. Methods To fill this information gap, we characterized the cultivable fraction of natural whey starter (NWS) and PR cheeses at different ripening times, both at the species and strain level, and investigated the possible correlation between microbial composition and the evolution of peptide profiles over cheese ripening. Results and discussion The results showed that NWS was a complex community of several biotypes belonging to a few species, namely, Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. lactis. A new species-specific PCR assay was successful in discriminating the cheese-associated species Lacticaseibacillus casei, Lacticaseibacillus paracasei, Lacticaseibacillus rhamnosus, and Lacticaseibacillus zeae. Based on the resolved patterns of species and biotype distribution, Lcb. paracasei and Lcb. zeae were most frequently isolated after 24 and 30 months of ripening, while the number of biotypes was inversely related to the ripening time. Peptidomics analysis revealed more than 520 peptides in cheese samples. To the best of our knowledge, this is the most comprehensive survey of peptides in PR cheese. Most of them were from β-caseins, which represent the best substrate for LAB cell-envelope proteases. The abundance of peptides from β-casein 38-88 region continuously increased during ripening. Remarkably, this region contains precursors for the anti-hypertensive lactotripeptides VPP and IPP, as well as for β-casomorphins. We found that the ripening time strongly affects bioactive peptide profiles and that the occurrence of Lcb. zeae species is positively linked to the incidence of eight anti-hypertensive peptides. This result highlighted how the presence of specific LAB species is likely a pivotal factor in determining PR functional properties.
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Affiliation(s)
- Serena Martini
- Nutritional Biochemistry, Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Laura Sola
- Microbial Biotechnologies and Fermentation Technologies, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alice Cattivelli
- Nutritional Biochemistry, Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Marianna Cristofolini
- Lactic Acid Bacteria and Yeast Biotechnology, Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | | | - Davide Tagliazucchi
- Nutritional Biochemistry, Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Lisa Solieri
- Lactic Acid Bacteria and Yeast Biotechnology, Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
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Cocconcelli PS, Gatti M, Giraffa G, Gobbetti M, Lanciotti R, Morelli L, Neviani E, Parente E. Should the microbiota of raw milk cheeses play a role in the definition of geographical indications and quality schemes within the European Union? mSystems 2023; 8:e0052023. [PMID: 37916828 PMCID: PMC10734520 DOI: 10.1128/msystems.00520-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Affiliation(s)
| | | | | | | | | | - Lorenzo Morelli
- Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
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3
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Pozzi A, Nazzicari N, Capoferri R, Radovic S, Bongioni G. Assessment of residual plant DNA in bulk milk for Grana Padano PDO production by a metabarcoding approach. PLoS One 2023; 18:e0289108. [PMID: 37490502 PMCID: PMC10368264 DOI: 10.1371/journal.pone.0289108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/11/2023] [Indexed: 07/27/2023] Open
Abstract
The aim of this study was to evaluate the ability of DNA metabarcoding, by rbcl as barcode marker, to identify and classify the small traces of plant DNA isolated from raw milk used to produce Grana Padano (GP) cheese. GP is one of the most popular Italian PDO (Protected Designation of Origin) produced in Italy in accordance with the GP PDO specification rules that define which forage can be used for feeding cows. A total of 42 GP bulk tank milk samples were collected from 14 dairies located in the Grana Padano production area. For the taxonomic classification, a local database with the rbcL sequences available in NCBI on September 2020/March 2021 for the Italian flora was generated. A total of 8,399,591 reads were produced with an average of 204,868 per sample (range 37,002-408,724) resulting in 16, 31 and 28 dominant OTUs at family, genus and species level, respectively. The taxonomic analysis of plant species in milk samples identified 7 families, 14 genera and 14 species, the statistical analysis conducted using alpha and beta diversity approaches, did not highlight differences among the investigated samples. However, the milk samples are featured by a high plant variability and the lack of differences at multiple taxonomic levels could be due to the standardisation of the feed rationing, as requested by the GP rules. The results suggest that DNA metabarcoding is a valuable resource to explore plant DNA traces in a complex matrix such as milk.
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Affiliation(s)
- Anna Pozzi
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| | - Nelson Nazzicari
- CREA-Council for Agricultural Research and Analysis of Agricultural Economics, Research Centre for Animal Production and Aquaculture, Viale Piacenza, Lodi, Italy
| | - Rossana Capoferri
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| | | | - Graziella Bongioni
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
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4
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Carminati D, Bonvini B, Francolino S, Ghiglietti R, Locci F, Tidona F, Mariut M, Abeni F, Zago M, Giraffa G. Low-Level Clostridial Spores' Milk to Limit the Onset of Late Blowing Defect in Lysozyme-Free, Grana-Type Cheese. Foods 2023; 12:foods12091880. [PMID: 37174418 PMCID: PMC10177814 DOI: 10.3390/foods12091880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
The growth of clostridial spores during ripening leads to late blowing (LB), which is the main cause of spoilage in Grana Padano Protected Designation of Origin (PDO) cheese and other hard, long-ripened cheeses such as Provolone, Comté, and similar cheeses. This study aimed to verify the cause-effect relationship between the level of clostridial butyric spores (BCS) in milk and the onset of the LB defect. To this end, experimental Grana-type cheeses were produced without lysozyme, using bulk milk with different average BCS content. The vat milk from the so-called "virtuous" farms (L1) contained average levels of BCS of 1.93 ± 0.61 log most probable number (MPN) L-1, while the vat milk from farms with the highest load of spores (L2), were in the order of 2.99 ± 0.69 log MPN L-1. Cheeses after seven months of ripening evidenced a strong connection between BCS level in vat milk and the occurrence of LB defect. In L2 cheeses, which showed an average BCS content of 3.53 ± 1.44 log MPN g-1 (range 1.36-5.04 log MPN g-1), significantly higher than that found in L1 cheeses (p < 0.01), the defect of LB was always present, with Clostridium tyrobutyricum as the only clostridial species identified by species-specific PCR from MPN-positive samples. The L1 cheeses produced in the cold season (C-L1) were free of defects whereas those produced in the warm season (W-L1) showed textural defects, such as slits and cracks, rather than irregular eyes. A further analysis of the data, considering the subset of the cheesemaking trials (W-L1 and W-L2), carried out in the warm season, confirmed the presence of a climate effect that, often in addition to the BCS load in the respective bulk milks (L1 vs. L2), may contribute to explain the significant differences in the chemical composition and some technological parameters between the two series of cheeses. Metagenomic analysis showed that it is not the overall structure of the microbial community that differentiates L1 from L2 cheeses but rather the relative distribution of the species between them. The results of our trials on experimental cheeses suggest that a low-level BCS in vat milk (<200 L-1) could prevent, or limit, the onset of LB in Grana-type and similar cheeses produced without lysozyme.
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Affiliation(s)
- Domenico Carminati
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
| | - Barbara Bonvini
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
| | - Salvatore Francolino
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
| | - Roberta Ghiglietti
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
| | - Francesco Locci
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
| | - Flavio Tidona
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
| | - Monica Mariut
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
| | - Fabio Abeni
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
| | - Miriam Zago
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
| | - Giorgio Giraffa
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
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5
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Decadt H, Weckx S, De Vuyst L. The rotation of primary starter culture mixtures results in batch-to-batch variations during Gouda cheese production. Front Microbiol 2023; 14:1128394. [PMID: 36876114 PMCID: PMC9978159 DOI: 10.3389/fmicb.2023.1128394] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023] Open
Abstract
Industrial production of Gouda cheeses mostly relies on a rotated use of different mixed-strain lactic acid bacteria starter cultures to avoid phage infections. However, it is unknown how the application of these different starter culture mixtures affect the organoleptic properties of the final cheeses. Therefore, the present study assessed the impact of three different starter culture mixtures on the batch-to-batch variations among Gouda cheeses from 23 different batch productions in the same dairy company. Both the cores and rinds of all these cheeses were investigated after 36, 45, 75, and 100 weeks of ripening by metagenetics based on high-throughput full-length 16S rRNA gene sequencing accompanied with an amplicon sequence variant (ASV) approach as well as metabolite target analysis of non-volatile and volatile organic compounds. Up to 75 weeks of ripening, the acidifying Lactococcus cremoris and Lactococcus lactis were the most abundant bacterial species in the cheese cores. The relative abundance of Leuconostoc pseudomesenteroides was significantly different for each starter culture mixture. This impacted the concentrations of some key metabolites, such as acetoin produced from citrate, and the relative abundance of non-starter lactic acid bacteria (NSLAB). Cheeses with the least Leuc. pseudomesenteroides contained more NSLAB, such as Lacticaseibacillus paracasei that was taken over by Tetragenococcus halophilus and Loigolactobacillus rennini upon ripening time. Taken together, the results indicated a minor role of leuconostocs in aroma formation but a major impact on the growth of NSLAB. The relative abundance of T. halophilus (high) and Loil. rennini (low) increased with ripening time from rind to core. Two main ASV clusters of T. halophilus could be distinguished, which were differently correlated with some metabolites, both beneficial (regarding aroma formation) and undesirable ones (biogenic amines). A well-chosen T. halophilus strain could be a candidate adjunct culture for Gouda cheese production.
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Affiliation(s)
| | | | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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6
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Kazou M, Gavriil A, Kalagkatsi O, Paschos T, Tsakalidou E. The Impact of Different Inoculation Schemes on the Microbiota, Physicochemical and Sensory Characteristics of Greek Kopanisti Cheese throughout Production and Ripening. Microorganisms 2022; 11:66. [PMID: 36677358 PMCID: PMC9863000 DOI: 10.3390/microorganisms11010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Kopanisti is a Greek PDO cheese, which is traditionally produced by the addition of an amount of over-mature Kopanisti, called Mana Kopanisti, to initiate cheese ripening. The aim of this study was the production of four types of Kopanisti cheese (A-D) using pasteurized cow milk, and a combination of the following starters/adjuncts in order to test their ability to be used in Kopanisti cheese production: A: Lactococcus lactis subsp. lactis and Lacticaseibacillus paracasei, B: L. lactis and Lc. paracasei/Mana Kopanisti, C: L. lactis and Lc. paracasei/Ligilactobacillus acidipiscis and Loigolactobacillus rennini, D: Lig. acidipiscis and Loig. rennini. Throughout production and ripening, classical microbiological, metataxonomics and physicochemical analyses were employed, while the final products (Day 35) were subjected to sensory analysis as well. Most interestingly, beta-diversity analysis of the metataxonomics data revealed the clusters constructed among the Kopanisti types based on the different inoculation schemes. On day 35, Kopanisti A-C types clustered together due to their similar 16S microbiota, while Kopanisti D was highly differentiated. On the contrary, ITS data clustered Kopanisti B and C together, while Kopanisti A and D were grouped seperately. Finally, based on the sensory evaluation, Kopanisti C appeared to have the most suitable bacteria cocktail for the Kopanisti cheese production. Therefore, not only were the conventional starters used, but also the Lig. acidipiscis and Loig. rennini strains could be used in a standardized Kopanisti cheese production that could lead to final products of high quality and safety.
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Affiliation(s)
- Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece
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7
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Abi Khalil R, Couderc C, Yvon S, Jard G, Sicard D, Bigey F, El Rammouz R, Abi Nakhoul P, Eutamène H, Tormo H, Ayoub MJ. Artisanal Household Milk Pasteurization Is Not a Determining Factor in Structuring the Microbial Communities of Labneh Ambaris: A Pilot Study. Foods 2022; 11:3874. [PMID: 36496682 PMCID: PMC9740543 DOI: 10.3390/foods11233874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/10/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Labneh Ambaris is a traditional Lebanese dairy product traditionally made using raw goat's milk in earthenware jars, but recently the use of artisanally pasteurized milk was introduced for safety reasons. In this study, 12 samples of labneh Ambaris were studied, six made using raw goat's milk and six others using artisanally pasteurized goat's milk. These samples were collected during fermentation and their microbial compositions were analyzed. The 16S V3-V4 and the ITS2 regions of the rDNA were sequenced by DNA metabarcoding analyses for the identification and comparison of bacterial and fungal communities, respectively. The samples had high microbial diversity but differences in samples microbiota were unrelated to whether or not milk was pasteurized. The samples were consequently clustered on the basis of their dominant bacterial or fungal species, regardless of the milk used. Concerning bacterial communities, samples were clustered into 3 groups, one with a higher abundance of Lactobacillus helveticus, another with Lactobacillus kefiranofaciens as the dominant bacterial species, and the third with Lentilactobacillus sp. as the most abundant species. Species belonging to the Enterobacteriaceae family were detected in higher abundance in all raw milk samples than in artisanally pasteurized milk samples. As for fungal communities, the samples were clustered into two groups, one dominated by Geotrichum candidum and the other by Pichia kudriavzevii.
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Affiliation(s)
- Reine Abi Khalil
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
| | - Christel Couderc
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
| | - Sophie Yvon
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
- Toxalim, UMR 1331, INRA, INP-ENVT, INP-PURPAN, Université de Toulouse, 31027 Toulouse, France
| | - Gwenaelle Jard
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
| | - Delphine Sicard
- INRAE, Institute Agro Montpellier, SPO, University Montpellier, 34060 Montpellier, France
| | - Frédéric Bigey
- INRAE, Institute Agro Montpellier, SPO, University Montpellier, 34060 Montpellier, France
| | - Rabih El Rammouz
- Department of Animal Production, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon
| | - Pierre Abi Nakhoul
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon
| | - Hélène Eutamène
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
- Toxalim, UMR 1331, INRA, INP-ENVT, INP-PURPAN, Université de Toulouse, 31027 Toulouse, France
| | - Hélène Tormo
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
| | - Marie-José Ayoub
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon
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Cardin M, Cardazzo B, Mounier J, Novelli E, Coton M, Coton E. Authenticity and Typicity of Traditional Cheeses: A Review on Geographical Origin Authentication Methods. Foods 2022; 11:3379. [PMID: 36359992 PMCID: PMC9653732 DOI: 10.3390/foods11213379] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 08/13/2023] Open
Abstract
Food fraud, corresponding to any intentional action to deceive purchasers and gain an undue economical advantage, is estimated to result in a 10 to 65 billion US dollars/year economical cost worldwide. Dairy products, such as cheese, in particular cheeses with protected land- and tradition-related labels, have been listed as among the most impacted as consumers are ready to pay a premium price for traditional and typical products. In this context, efficient food authentication methods are needed to counteract current and emerging frauds. This review reports the available authentication methods, either chemical, physical, or DNA-based methods, currently used for origin authentication, highlighting their principle, reported application to cheese geographical origin authentication, performance, and respective advantages and limits. Isotope and elemental fingerprinting showed consistent accuracy in origin authentication. Other chemical and physical methods, such as near-infrared spectroscopy and nuclear magnetic resonance, require more studies and larger sampling to assess their discriminative power. Emerging DNA-based methods, such as metabarcoding, showed good potential for origin authentication. However, metagenomics, providing a more in-depth view of the cheese microbiota (up to the strain level), but also the combination of methods relying on different targets, can be of interest for this field.
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Affiliation(s)
- Marco Cardin
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Jérôme Mounier
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - Enrico Novelli
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Monika Coton
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - Emmanuel Coton
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
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Kamilari E, Tsaltas D, Stanton C, Ross RP. Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses. Foods 2022; 11:2483. [PMID: 36010485 PMCID: PMC9407514 DOI: 10.3390/foods11162483] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
The distinct sensorial characteristics of local cheeses influence consumer preferences, and make an essential contribution to the local economy. Microbial diversity in cheese is among the fundamental contributors to sensorial and qualitative characteristics. However, knowledge regarding the existence of microbial patterns associated with regional production practices in ripened cheeses remains limited. The present research was conducted to test the hypothesis that the background metagenome of cheeses could be used as a marker of their origin. We compared Irish versus Eastern Mediterranean cheeses-namely Greek and Cypriot-using High Throughput Sequencing (HTS). The study identified a significantly distinct separation among cheeses originating from the three different countries, in terms of the total microbial community composition. The use of machine learning and biomarkers discovery algorithms defined key microbes that differentiate each geographic region. Finally, the development of interaction networks revealed that the key species developed mostly negative interactions with the other members of the communities, highlighting their dominance in the community. The findings of the present research demonstrate that metagenome could indeed be used as a biological marker of the origin of mature cheeses, and could provide further insight into the dynamics of microbial community composition in ripened cheeses.
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Affiliation(s)
- Eleni Kamilari
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland or
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - Dimitrios Tsaltas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos 3036, Cyprus
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland or
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- Department of Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co., P61 C996 Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland or
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
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Morandi S, Cremonesi P, Arioli S, Stocco G, Silvetti T, Biscarini F, Castiglioni B, Greco Ç, D'Ascanio V, Mora D, Brasca M. Effect of using mycotoxin-detoxifying agents in dairy cattle feed on natural whey starter biodiversity. J Dairy Sci 2022; 105:6513-6526. [PMID: 35840409 DOI: 10.3168/jds.2022-21793] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/15/2022] [Indexed: 11/19/2022]
Abstract
Natural whey cultures (NWC) are undefined multiple-strain bacterial starter communities that can be affected by even small changes along the entire dairy chain. We applied a multidisciplinary approach to investigate how the addition of 2 mycotoxin-detoxifying agents [sodium smectite and lignocellulose-based material (B1); leonardite and betaine (B2)] to cow diets modified the microbiota of the NWC in manufacture of a Grana-like cheese. Microbiological and flow cytometry analyses showed that the content and viability of lactic acid bacteria (LAB) and the total whey microbiota were not affected by the detoxifying agents, and Streptococcus thermophilus, Lactobacillus helveticus, and Limosilactobacillus fermentum were the dominant taxa. Random amplified polymorphic DNA-PCR fingerprinting and metagenomic analysis highlighted differences in the bacterial community of the NWC and in the relative abundance of Bacteroidetes that increased when B1 and B2 were included in the diet. Two of 6 St. thermophilus biotypes were detected only in control samples; conversely, none of the Lb. helveticus biotypes found in control samples were isolated from B1 and B2. In vitro tests showed that the 2 binders did not significantly affect the development of St. thermophilus, but they stimulated the growth of Lb. helveticus strains recovered only from B1 and B2 NWC. The addition of binders in cow feed can affect the LAB biotypes present in NWC.
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Affiliation(s)
- S Morandi
- Institute of Sciences of Food Production (ISPA), Italian National Research Council (CNR), Via Celoria 2, 20133, Milan, Italy.
| | - P Cremonesi
- Institute of Agricultural Biology and Biotechnology (IBBA), Italian National Research Council (CNR), Via Einstein, 26900, Lodi, Italy
| | - S Arioli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - G Stocco
- Department of Veterinary Science, University of Parma, Via del Taglio 10, I-43126 Parma, Italy
| | - T Silvetti
- Institute of Sciences of Food Production (ISPA), Italian National Research Council (CNR), Via Celoria 2, 20133, Milan, Italy
| | - F Biscarini
- Institute of Agricultural Biology and Biotechnology (IBBA), Italian National Research Council (CNR), Via Einstein, 26900, Lodi, Italy
| | - B Castiglioni
- Institute of Agricultural Biology and Biotechnology (IBBA), Italian National Research Council (CNR), Via Einstein, 26900, Lodi, Italy
| | - Ç Greco
- Institute of Sciences of Food Production (ISPA), Italian National Research Council (CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - V D'Ascanio
- Institute of Sciences of Food Production (ISPA), Italian National Research Council (CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - D Mora
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - M Brasca
- Institute of Sciences of Food Production (ISPA), Italian National Research Council (CNR), Via Celoria 2, 20133, Milan, Italy
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11
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Güley Z, Fallico V, Cabrera-Rubio R, Cotter PD, Beresford T. Identification of Streptococcus infantarius subsp. infantarius as the species primarily responsible for acid production in Izmir Brined Tulum Cheese from the Aegean Region of Türkiye. Food Res Int 2022; 160:111707. [DOI: 10.1016/j.foodres.2022.111707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/02/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022]
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12
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Parlindungan E, McDonnell B, Lugli GA, Ventura M, van Sinderen D, Mahony J. Dairy streptococcal cell wall and exopolysaccharide genome diversity. Microb Genom 2022; 8. [PMID: 35442186 PMCID: PMC9453073 DOI: 10.1099/mgen.0.000803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The large-scale and high-intensity application of
Streptococcus thermophilus
species in milk fermentation processes is associated with a persistent threat of (bacterio)phage infection. Phage infection of starter cultures may cause inconsistent, slow or even failed fermentations with consequent diminished product quality and/or output. The phage life cycle commences with the recognition of, and binding to, a specific host-encoded and surface-exposed receptor, which in the case of
S. thermophilus
can be the rhamnose-glucose polysaccharide (RGP; specified by the rgp gene cluster) or exopolysaccharide (EPS; specified by the eps gene cluster). The genomic diversity of 23
S
.
thermophilus
strains isolated from unpasteurized dairy products was evaluated, including a detailed analysis of the rgp and eps loci. In the present study, five novel eps genotypes were identified while variations of currently recognized rgp gene cluster types were also observed. Furthermore, the diversity of rgp genotypes amongst retrieved isolates positively correlated with phage diversity based on phageome analysis of eight representative dairy products. Our findings therefore substantially expand our knowledge on S. thermophilus’ strain and phage diversity in (artisanal) dairy products and highlight the merit of phageome analysis of artisanal and traditional fermented foods as a sensitive marker of dominant microbiota involved in the fermentation.
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Affiliation(s)
- Elvina Parlindungan
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Brian McDonnell
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
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13
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Dreier M, Meola M, Berthoud H, Shani N, Wechsler D, Junier P. High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota. BMC Microbiol 2022; 22:48. [PMID: 35130830 PMCID: PMC8819918 DOI: 10.1186/s12866-022-02451-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/17/2022] [Indexed: 12/31/2022] Open
Abstract
Background Next-generation sequencing (NGS) methods and especially 16S rRNA gene amplicon sequencing have become indispensable tools in microbial ecology. While they have opened up new possibilities for studying microbial communities, they also have one drawback, namely providing only relative abundances and thus compositional data. Quantitative PCR (qPCR) has been used for years for the quantification of bacteria. However, this method requires the development of specific primers and has a low throughput. The constraint of low throughput has recently been overcome by the development of high-throughput qPCR (HT-qPCR), which allows for the simultaneous detection of the most prevalent bacteria in moderately complex systems, such as cheese and other fermented dairy foods. In the present study, the performance of the two approaches, NGS and HT-qPCR, was compared by analyzing the same DNA samples from 21 Raclette du Valais protected designation of origin (PDO) cheeses. Based on the results obtained, the differences, accuracy, and usefulness of the two approaches were studied in detail. Results The results obtained using NGS (non-targeted) and HT-qPCR (targeted) show considerable agreement in determining the microbial composition of the cheese DNA samples studied, albeit the fundamentally different nature of these two approaches. A few inconsistencies in species detection were observed, particularly for less abundant ones. The detailed comparison of the results for 15 bacterial species/groups measured by both methods revealed a considerable bias for certain bacterial species in the measurements of the amplicon sequencing approach. We identified as probable origin to this PCR bias due to primer mismatches, variations in the number of copies for the 16S rRNA gene, and bias introduced in the bioinformatics analysis. Conclusion As the normalized microbial composition results of NGS and HT-qPCR agreed for most of the 21 cheese samples analyzed, both methods can be considered as complementary and reliable for studying the microbial composition of cheese. Their combined application proved to be very helpful in identifying potential biases and overcoming methodological limitations in the quantitative analysis of the cheese microbiota. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02451-y.
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Affiliation(s)
- Matthias Dreier
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland. .,Laboratory of Microbiology, University of Neuchâtel, Emile-Argand 11, CH-2000, Neuchâtel, Switzerland.
| | - Marco Meola
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland.,Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Hélène Berthoud
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland
| | - Noam Shani
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland
| | - Daniel Wechsler
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
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14
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da Silva Duarte V, Lombardi A, Corich V, Giacomini A. Assessment of the microbiological origin of blowing defects in Grana Padano Protected Designation of Origin cheese. J Dairy Sci 2022; 105:2858-2867. [PMID: 35086714 DOI: 10.3168/jds.2021-21097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022]
Abstract
Recognized worldwide for its history, flavor, and high nutritional quality, Grana Padano (GP) is one of the most traditional Italian raw-milk, hard-cooked, long-ripened cheese. Throughout GP manufacturing, some well-known and undesired bacterial species, such as clostridia, can proliferate and lead to spoilage defects that mischaracterize the final product; however, little is known about the development of late-blowing defects in hard cheese samples without clostridia. Therefore, in this study we aimed to use metataxonomic analysis to identify bacterial taxa associated with the development of late-blowing defect in GP samples. Furthermore, the presence of several heterofermentative lactobacilli species in defective zones were verified by primer-specific PCR assay. Considering α- and β-diversity analyses, no statistically significant differences were detected between cheese samples with and without blowing defect. Following taxonomic assignment, Lactobacillus and Streptococcus were the dominant genera, whereas clostridia-related taxa were not detected in any of the 20 analyzed samples. Using EdgeR, the genera Propionibacterium and Acinetobacter were found to be prevalently more abundant in samples categorized as having "big regular holes." In samples with "small regular holes," multiplex PCR amplification revealed differences in terms of Lactobacillus population composition, mainly obligate homofermentative lactobacilli, between defective and non-defective zones of the same cheese wheel. This study demonstrated that GP samples with blowing defects not caused by clostridial development share similar biodiversity indices with GP collected from control zones, but an imbalance of obligate homofermentative lactobacilli was noticed between samples, which requires further analysis to better comprehend the exact mechanism involved in this process.
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Affiliation(s)
- Vinícius da Silva Duarte
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro (Padua), Italy
| | - Angiolella Lombardi
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro (Padua), Italy
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro (Padua), Italy.
| | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro (Padua), Italy
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15
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Grujović MŽ, Mladenović KG, Semedo-Lemsaddek T, Laranjo M, Stefanović OD, Kocić-Tanackov SD. Advantages and disadvantages of non-starter lactic acid bacteria from traditional fermented foods: Potential use as starters or probiotics. Compr Rev Food Sci Food Saf 2022; 21:1537-1567. [PMID: 35029033 DOI: 10.1111/1541-4337.12897] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
Traditional fermented foods are a significant source of starter and/or non-starter lactic acid bacteria (nsLAB). Moreover, these microorganisms are also known for their role as probiotics. The potential of nsLAB is huge; however, there are still challenges to be overcome with respect to characterization and application. In the present review, the most important steps that autochthonous lactic acid bacteria isolated from fermented foods need to overcome, to qualify as novel starter cultures, or as probiotics, in food technology and biotechnology, are considered. These different characterization steps include precise identification, detection of health-promoting properties, and safety evaluation. Each of these features is strain specific and needs to be accurately determined. This review highlights the advantages and disadvantages of nsLAB, isolated from traditional fermented foods, discussing safety aspects and sensory impact.
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Affiliation(s)
- Mirjana Ž Grujović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Kragujevac, Republic of Serbia.,Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Kragujevac, Republic of Serbia
| | - Katarina G Mladenović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Kragujevac, Republic of Serbia.,Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Kragujevac, Republic of Serbia
| | - Teresa Semedo-Lemsaddek
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Marta Laranjo
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Olgica D Stefanović
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Kragujevac, Republic of Serbia
| | - Sunčica D Kocić-Tanackov
- Department of Food Preservation Engineering, Faculty of Technology, University of Novi Sad, Novi Sad, Republic of Serbia
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16
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Giraffa G. The Microbiota of Grana Padano Cheese. A Review. Foods 2021; 10:2632. [PMID: 34828913 PMCID: PMC8621370 DOI: 10.3390/foods10112632] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/23/2022] Open
Abstract
Grana Padano (GP) is the most appreciated and marketed cheese with Protected Designation of Origin in the world. The use of raw milk, the addition of undefined cultures (defined as 'sieroinnesto naturale'), the peculiar manufacturing proces, and the long ripening make the cheese microbiota play a decisive role in defining the quality and the organoleptic properties of the product. The knowledge on the microbial diversity associated with GP has been the subject, in recent years, of several studies aimed at understanding its composition and characteristics in order, on the one hand, to improve its technological performances and, on the other hand, to indirectly enhance the nutritional quality of the product. This review aims to briefly illustrate the main available knowledge on the composition and properties of the GP microbiota, inferred from dozens of studies carried out by both classical microbiology techniques and metagenomic analysis. The paper will essentially, but not exclusively, be focused on the lactic acid bacteria (LAB) derived from starter (SLAB) and the non-starter bacteria, both lactic (NSLAB) and non-lactic, of milk origin.
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Affiliation(s)
- Giorgio Giraffa
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via Lombardo 11, 26900 Lodi, Italy
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17
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Biodiversity and succession of lactic microbiota involved in Brazilian buffalo mozzarella cheese production. Braz J Microbiol 2021; 53:303-316. [PMID: 34661886 DOI: 10.1007/s42770-021-00629-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022] Open
Abstract
The biodiversity and succession of lactic acid bacteria (LAB) involved in the production and storage of Brazilian buffalo mozzarella cheese were evaluated. The isolates were characterized by Gram staining and catalase test, by the ability to grow at different conditions: temperatures, pH, concentrations of NaCl, and production of CO2 from glucose. The biodiversity and succession of 152 LAB isolated during cheese production were evaluated by 16S rRNA gene sequencing, Random Amplified Polymorphic DNA (RAPD-PCR), and Restriction Fragment Length Polymorphism (RFLP-PCR) techniques. Most of the strains grow well at 30 °C and are tolerant to 6.5% of NaCl, and in general, the best pH for growing was 9.6. Leuconostoc mesenteroides, Lacticaseibacillus casei, Limosilactobacillus fermentum, and Enterococcus sp. were prevalent and present in almost all steps of production. The LAB strains are typically found in the traditional Italian cheese, except the Leuconostoc citreum species. Sixty clusters were obtained by RAPD-PCR with 85% of similarity (114 isolates) while most of the LAB was clustered with 100% of similarity by the RFLP-PCR technique. The applied techniques enabled a valuable elucidation of the LAB biodiversity and succession, contributing to a better understanding of the specific microbial cultures with a technological aptitude of this cheese.
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18
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Zago M, Rossetti L, Bardelli T, Carminati D, Nazzicari N, Giraffa G. Bacterial Community of Grana Padano PDO Cheese and Generical Hard Cheeses: DNA Metabarcoding and DNA Metafingerprinting Analysis to Assess Similarities and Differences. Foods 2021; 10:1826. [PMID: 34441603 PMCID: PMC8392751 DOI: 10.3390/foods10081826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
The microbiota of Protected Designation of Origin (PDO) cheeses plays an essential role in defining their quality and typicity and could be applied to protect these products from counterfeiting. To study the possible role of cheese microbiota in distinguishing Grana Padano (GP) cheese from generical hard cheeses (HC), the microbial structure of 119 GP cheese samples was studied by DNA metabarcoding and DNA metafingerprinting and compared with 49 samples of generical hard cheeses taken from retail. DNA metabarcoding highlighted the presence, as dominant taxa, of Lacticaseibacillus rhamnosus, Lactobacillus helveticus, Streptococcus thermophilus, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus spp., and Lactococcus spp. in both GP cheese and HC. Differential multivariate statistical analysis of metataxonomic and metafingerprinting data highlighted significant differences in the Shannon index, bacterial composition, and species abundance within both dominant and subdominant taxa between the two cheese groups. A supervised Neural Network (NN) classification tool, trained by metagenotypic data, was implemented, allowing to correctly classify GP cheese and HC samples. Further implementation and validation to increase the robustness and improve the predictive capacity of the NN classifier will be needed. Nonetheless, the proposed tool opens interesting perspectives in helping protection and valorization of GP and other PDO cheeses.
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Affiliation(s)
- Miriam Zago
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Lia Rossetti
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Tommaso Bardelli
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 26900 Lodi, Italy;
| | - Domenico Carminati
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Giorgio Giraffa
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
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19
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Michailidou S, Pavlou E, Pasentsis K, Rhoades J, Likotrafiti E, Argiriou A. Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding. Food Microbiol 2021; 99:103836. [PMID: 34119120 DOI: 10.1016/j.fm.2021.103836] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/14/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
Greece is a country possessing many cheese products granted with a PDO (Protected Designation of Origin) certificate, with high exporting activities. In this study, we analyzed six popular cheese PDO products purchased from different industries to assess their microbial communities using amplicon metabarcoding analysis. To this end, using Next Generation Sequencing technology, we sequenced the 16S rRNA gene and the ITS spacer for prokaryotes and fungi, respectively. Alpha diversity indices revealed higher bacterial species richness for some cheeses (Kopanisti, Batzos) and poor for others (Feta, Galotiri). Kopanisti, together with Kalathaki and Anevato, also presented increased species diversity concerning fungal populations. Results showed that lactic acid bacteria (LAB) prevailed the bacterial populations in all samples (Lactococcus, Lactobacillus, Streptococcus, Leuconostoc), whereas for fungi, members of the Saccharomycetaceae, Dipodascaceae and Debaryomycetaceae families prevailed the fungal populations. Several other genera were identified that make up each product's microbiome leading to the creation of the unique organoleptic attributes of Greek PDO cheeses. However, the identified species could not be directly linked to certain cheese types, assuming that starter and adjunct cultures, combined with the raw material used during production greatly impact the microbial communities in cheeses. Our data, produced for the first time for six Greek PDO cheeses, can be exploited in the process of creating a core microbial signature within each cheese type, supporting the Greek brand name and valorizing cheese products.
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Affiliation(s)
- Sofia Michailidou
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece.
| | - Eleftherios Pavlou
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece
| | - Konstantinos Pasentsis
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece
| | - Jonathan Rhoades
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400, Thessaloniki, Greece
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece; Department of Food Science and Nutrition, University of the Aegean, Myrina, 81400, Lemnos, Greece
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20
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Syrokou MK, Themeli C, Paramithiotis S, Mataragas M, Bosnea L, Argyri AA, Chorianopoulos NG, Skandamis PN, Drosinos EH. Microbial Ecology of Greek Wheat Sourdoughs, Identified by a Culture-Dependent and a Culture-Independent Approach. Foods 2020; 9:foods9111603. [PMID: 33158141 PMCID: PMC7694216 DOI: 10.3390/foods9111603] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 01/20/2023] Open
Abstract
The aim of the present study was to assess the microecosystem of 13 homemade spontaneously fermented wheat sourdoughs from different regions of Greece, through the combined use of culture-dependent (classical approach; clustering by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) and identification by PCR species-specific for Lactiplantibacillus plantarum, and sequencing of the 16S-rRNA and 26S-rRNA gene, for Lactic Acid Bacteria (LAB) and yeasts, respectively) and independent approaches [DNA- and RNA-based PCR-Denaturing Gradient Gel Electrophoresis (DGGE)]. The pH and Total Titratable Acidity (TTA) values ranged from 3.64–5.05 and from 0.50–1.59% lactic acid, respectively. Yeast and lactic acid bacteria populations ranged within 4.60–6.32 and 6.28–9.20 log CFU/g, respectively. The yeast: LAB ratio varied from 1:23–1:10,000. A total of 207 bacterial and 195 yeast isolates were obtained and a culture-dependent assessment of their taxonomic affiliation revealed dominance of Lb. plantarum in three sourdoughs, Levilactobacillus brevis in four sourdoughs and co-dominance of these species in two sourdoughs. In addition, Companilactobacillusparalimentarius dominated in two sourdoughs and Fructilactobacillussanfranciscensis and Latilactobacillus sakei in one sourdough each. Lactococcus lactis, Lb. curvatus, Leuconostoc citreum, Ln. mesenteroides and Lb. zymae were also recovered from some samples. Regarding the yeast microbiota, it was dominated by Saccharomyces cerevisiae in 11 sourdoughs and Pichia membranifaciens and P. fermentans in one sourdough each. Wickerhamomyces anomalus and Kazachstania humilis were also recovered from one sample. RNA-based PCR-DGGE provided with nearly identical results with DNA-based one; in only one sample the latter provided an additional band. In general, the limitations of this approach, namely co-migration of amplicons from different species to the same electrophoretic position and multiband profile of specific isolates, greatly reduced resolution capacity, which resulted in only partial verification of the microbial ecology detected by culture-dependent approach in the majority of sourdough samples. Our knowledge regarding the microecosystem of spontaneously fermented Greek wheat-based sourdoughs was expanded, through the study of sourdoughs originating from regions of Greece that were not previously assessed.
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Affiliation(s)
- Maria K. Syrokou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece; (M.K.S.); (C.T.); (S.P.); (P.N.S.); (E.H.D.)
| | - Christina Themeli
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece; (M.K.S.); (C.T.); (S.P.); (P.N.S.); (E.H.D.)
| | - Spiros Paramithiotis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece; (M.K.S.); (C.T.); (S.P.); (P.N.S.); (E.H.D.)
| | - Marios Mataragas
- Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “DEMETER”, 3 Ethnikis Antistaseos St., 45221 Ioannina, Greece;
- Correspondence:
| | - Loulouda Bosnea
- Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “DEMETER”, 3 Ethnikis Antistaseos St., 45221 Ioannina, Greece;
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “DEMETER”, 1 Sof. Venizelou St., 14123 Lycovrissi, Greece; (A.A.A.); (N.G.C.)
| | - Nikos G. Chorianopoulos
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “DEMETER”, 1 Sof. Venizelou St., 14123 Lycovrissi, Greece; (A.A.A.); (N.G.C.)
| | - Panagiotis N. Skandamis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece; (M.K.S.); (C.T.); (S.P.); (P.N.S.); (E.H.D.)
| | - Eleftherios H. Drosinos
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece; (M.K.S.); (C.T.); (S.P.); (P.N.S.); (E.H.D.)
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