1
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Bellassi P, Fontana A, Morelli L. Application of flow cytometry for rapid bacterial enumeration and cells physiological state detection to predict acidification capacity of natural whey starters. Heliyon 2023; 9:e19146. [PMID: 37636441 PMCID: PMC10458327 DOI: 10.1016/j.heliyon.2023.e19146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/07/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
Natural whey starter cultures are undefined microbial communities mainly consisting of thermophilic lactic acid bacteria (LAB). The technological pressure that shapes the natural whey starter community before and during the back-slopping procedure can impact the amount and viability of the different thermophilic LAB. Traditional culture-dependent analytical methods are useful for evaluating natural whey cultures based on plate enumeration with various culture media and are commonly used as self-control procedures in dairy items. These methods have high variability and require days to obtain results. As the dairy industry has been searching for a solution to this problem for a long time, researchers must explore alternative methods for the technological evaluation of natural whey and assessment of the health status of the thermophilic acidifying bacteria community in the cheesemaking process. The flow cytometry approach has been considered an alternative to classical methods in this work sector. This study compared bacterial enumeration by plate counting and flow cytometry on natural whey samples. Flow cytometry results showed positive agreement with a tendency to overestimate, linearity, and correlation with plate counting. Other parameters have also been introduced for evaluating a natural whey starter, measuring the physiological state of the cells. Specifically, cell-wall damage and metabolic activity were also evaluated, allowing us to quantify the number of cells even in sub-optimal physiological conditions.
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Affiliation(s)
- Paolo Bellassi
- Department for Sustainable Food Process (DISTAS), Università Cattolica Del Sacro Cuore, Italy
| | - Alessandra Fontana
- Department for Sustainable Food Process (DISTAS), Università Cattolica Del Sacro Cuore, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process (DISTAS), Università Cattolica Del Sacro Cuore, Italy
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2
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Sola L, Quadu E, Bortolazzo E, Bertoldi L, Randazzo CL, Pizzamiglio V, Solieri L. Insights on the bacterial composition of Parmigiano Reggiano Natural Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait. Sci Rep 2022; 12:17322. [PMID: 36243881 PMCID: PMC9569347 DOI: 10.1038/s41598-022-22207-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/11/2022] [Indexed: 01/10/2023] Open
Abstract
Natural whey starters (NWS) are undefined bacterial communities produced daily from whey of the previous cheese-making round, by application of high temperature. As a result, in any dairy plant, NWS are continuously evolving, undefined mixtures of several strains and/or species of lactic acid bacteria, whose composition and performance strongly depend on the selective pressure acting during incubation. While NWS is critical to assure consistency to cheese-making process, little is known about the composition, functional features, and plant-to-plant fluctuations. Here, we integrated 16S rRNA metabarcoding and culture-dependent methods to profile bacterial communities of 10 NWS sampled in the production area of Parmigiano Reggiano cheese. 16S rRNA metabarcoding analysis revealed two main NWS community types, namely NWS type-H and NWS type-D. Lactobacillus helveticus was more abundant in NWS type-H, whilst Lactobacillus delbrueckii/St. thermophilus in NWS type-D, respectively. Based on the prediction of metagenome functions, NWS type-H samples were enriched in functional pathways related to galactose catabolism and purine metabolism, while NWS type-D in pathways related to aromatic and branched chain amino acid biosynthesis, which are flavor compound precursors. Culture-dependent approaches revealed low cultivability of individual colonies as axenic cultures and high genetic diversity in the pool of cultivable survivors. Co-culturing experiments showed that fermentative performance decreases by reducing the bacterial complexity of inoculum, suggesting that biotic interactions and cross-feeding relationships could take place in NWS communities, assuring phenotypic robustness. Even though our data cannot directly predict these ecological interactions, this study provides the basis for experiments targeted at understanding how selective regime affects composition, bacterial interaction, and fermentative performance in NWS.
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Affiliation(s)
- Laura Sola
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Emanuele Quadu
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Elena Bortolazzo
- grid.423913.eCentro Ricerche Produzioni Animali, 42121 Reggio Emilia, Italy
| | | | - Cinzia L. Randazzo
- grid.8158.40000 0004 1757 1969Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy ,ProBioEtna Srl, 95123 Catania, Italy
| | - Valentina Pizzamiglio
- grid.433295.aConsorzio del Formaggio Parmigiano Reggiano, 42124 Reggio Emilia, Italy
| | - Lisa Solieri
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy ,NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
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3
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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: 4] [Impact Index Per Article: 1.3] [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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4
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Chessa L, Paba A, Daga E, Dupré I, Comunian R. Biodiversity and Safety Assessment of Half-Century Preserved Natural Starter Cultures for Pecorino Romano PDO Cheese. Microorganisms 2021; 9:microorganisms9071363. [PMID: 34201694 PMCID: PMC8305336 DOI: 10.3390/microorganisms9071363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
The use of biodiverse autochthonous natural starter cultures to produce typical and PDO cheeses contributes to establishing a link between products and territory of production, which commercial starters, constituted by few species and strains, are not able to. The purpose of this work was the assessment of biodiversity, at strain level, and safety of natural scotta-innesto cultures whose use is mandatory for the Pecorino Romano PDO cheese manufacturing, according to its product specification. The biodiversity of three scotta-innesto, collected in the 1960s and preserved in lyophilised form, was assessed by molecular biotyping using both PFGE and (GTG)5 rep-PCR profiling on 209 isolates belonging to Streptococcus thermophilus (30), Lactobacillus delbrueckii subsp. lactis (72), Enterococcus faecium (87), and Limosilactobacillus reuteri (20), revealing high biodiversity, at the strain level, in the cultures. The cultures’ safety was proved through a new approach assessing phenotypic and molecular antibiotic resistance of the cultures in toto, instead of single strains, while the safety of Enterococcus faecium isolates was investigated according to EFSA guidelines. The use of natural biodiverse cultures for the production of microbial starters for typical and PDO cheeses, such as Pecorino Romano, could be an opportunity for recovering the cheese microbiota biodiversity lost during years of commercial starters use.
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5
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Wang X, Lin X, Zheng Z, Lu B, Wang J, Tan AHM, Zhao M, Loh JT, Ng SW, Chen Q, Xiao F, Huang E, Ko KH, Huang Z, Li J, Kok KH, Lu G, Liu X, Lam KP, Liu W, Zhang Y, Yuen KY, Mak TW, Lu L. Host-derived lipids orchestrate pulmonary γδ T cell response to provide early protection against influenza virus infection. Nat Commun 2021; 12:1914. [PMID: 33772013 PMCID: PMC7997921 DOI: 10.1038/s41467-021-22242-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/06/2021] [Indexed: 01/01/2023] Open
Abstract
Innate immunity is important for host defense by eliciting rapid anti-viral responses and bridging adaptive immunity. Here, we show that endogenous lipids released from virus-infected host cells activate lung γδ T cells to produce interleukin 17 A (IL-17A) for early protection against H1N1 influenza infection. During infection, the lung γδ T cell pool is constantly supplemented by thymic output, with recent emigrants infiltrating into the lung parenchyma and airway to acquire tissue-resident feature. Single-cell studies identify IL-17A-producing γδ T (Tγδ17) cells with a phenotype of TCRγδhiCD3hiAQP3hiCXCR6hi in both infected mice and patients with pneumonia. Mechanistically, host cell-released lipids during viral infection are presented by lung infiltrating CD1d+ B-1a cells to activate IL-17A production in γδ T cells via γδTCR-mediated IRF4-dependent transcription. Reduced IL-17A production in γδ T cells is detected in mice either lacking B-1a cells or with ablated CD1d in B cells. Our findings identify a local host-immune crosstalk and define important cellular and molecular mediators for early innate defense against lung viral infection.
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MESH Headings
- Animals
- Antigens, CD1d/immunology
- Antigens, CD1d/metabolism
- Female
- Host-Pathogen Interactions/immunology
- Humans
- Immunity, Innate/immunology
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza, Human/immunology
- Influenza, Human/metabolism
- Influenza, Human/virology
- Interferon Regulatory Factors/immunology
- Interferon Regulatory Factors/metabolism
- Interleukin-17/immunology
- Interleukin-17/metabolism
- Lipids/immunology
- Lung/immunology
- Lung/metabolism
- Lung/virology
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/metabolism
- Orthomyxoviridae Infections/virology
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Mice
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Affiliation(s)
- Xiaohui Wang
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, China.
- Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
| | - Xiang Lin
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, China
| | - Zihan Zheng
- Chongqing International Institute for Immunology, Chongqing, China
| | - Bingtai Lu
- Department of Respiratory Medicine and Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jun Wang
- Department of Respiratory Medicine and Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Andy Hee-Meng Tan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Meng Zhao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Life Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Institute for Immunology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jia Tong Loh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sze Wai Ng
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Qian Chen
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, China
| | - Fan Xiao
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, China
| | - Enyu Huang
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, China
| | - King-Hung Ko
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, China
| | - Zhong Huang
- Department of Pathogen Biology and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Jingyi Li
- Chongqing International Institute for Immunology, Chongqing, China
| | - Kin-Hang Kok
- Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Gen Lu
- Department of Respiratory Medicine and Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaohui Liu
- National Protein Science Facility, Tsinghua University, Beijing, China
| | - Kong-Peng Lam
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wanli Liu
- Ministry of Education Key Laboratory of Protein Sciences, Center for Life Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Institute for Immunology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuxia Zhang
- Department of Respiratory Medicine and Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Kwok-Yung Yuen
- Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Tak Wah Mak
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, China
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Liwei Lu
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, China.
- Chongqing International Institute for Immunology, Chongqing, China.
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6
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Bottari B, Levante A, Bancalari E, Sforza S, Bottesini C, Prandi B, De Filippis F, Ercolini D, Nocetti M, Gatti M. The Interrelationship Between Microbiota and Peptides During Ripening as a Driver for Parmigiano Reggiano Cheese Quality. Front Microbiol 2020; 11:581658. [PMID: 33133050 PMCID: PMC7561718 DOI: 10.3389/fmicb.2020.581658] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/15/2020] [Indexed: 02/02/2023] Open
Abstract
Cheese microbiota contribute significantly to the final characteristics of cheeses due to the growth and interaction between cheese microorganisms during processing and ripening. For raw milk cheeses, such as Parmigiano Reggiano (PR), the microbiota derive from the raw milk itself, the dairy environment, and the starter. The process of cheese making and time of ripening shape this complex ecosystem through the selection of different species and biotypes that will drive the quality of the final product by performing functions of their metabolism such as proteolysis. The diversity in the final peptide and amino acid composition of the cheese is thus mostly linked to the diversity of this microbiota. The purpose of this study was to get more insight into the factors affecting PR cheese diversity and, more specifically, to evaluate whether the composition of the bacterial community of cheeses along with the specific peptide composition are more affected by the ripening times or by the cheese making process. To this end, the microbiota and the peptide fractions of 69 cheese samples (from curd to cheese ripened 24 months) were analyzed during 6 complete PR production cycles, which were performed in six different dairies located in the PR production area. The relation among microbial dynamics, peptide evolution, and ripening times were investigated in this unique and tightly controlled production and sampling set up. The study of microbial and peptide moieties in products from different dairies – from curd to at least 12 months, the earliest time from which the cheese can be sold, and up to a maximum of 24 months of ripening – highlighted the presence of differences between samples coming from different dairies, probably due to small differences in the cheese making process. Besides these differences, however, ripening time had by far the greatest impact on microbial dynamics and, consequently, on peptide composition.
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Affiliation(s)
| | - Alessia Levante
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Elena Bancalari
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Stefano Sforza
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Barbara Prandi
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Marco Nocetti
- Consorzio del Formaggio Parmigiano-Reggiano, Reggio Emilia, Italy
| | - Monica Gatti
- Department of Food and Drug, University of Parma, Parma, Italy
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7
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Bardelli T, Rossetti L, Zago M, Carminati D, Giraffa G, Tidona F. Extracellular and intracellular DNA for bacterial profiling of long-ripened cheeses. FEMS Microbiol Lett 2020; 367:5862581. [PMID: 32584987 DOI: 10.1093/femsle/fnaa095] [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: 04/02/2020] [Accepted: 06/24/2020] [Indexed: 12/29/2022] Open
Abstract
A novel approach was developed to extract the extracellular DNA (eDNA), i.e. the free DNA outside the microbial cell, compared to the intracellular DNA (iDNA). The two DNA fractions were investigated in seven long-ripened cheeses. Among different buffer solutions tested, EDTA 0.5 M at pH 8 enabled a mild homogenization of cheese samples and the highest eDNA recovery. The extraction protocol was tested on single strains of lactic acid bacteria characterizing many Italian long-ripened cheeses, such as Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus rhamnosus. The method resulted suitable for eDNA extraction because it minimized cell-lysis, avoiding the leakage of iDNA from the cells. The yields of eDNA, ranging from 0.01 to 0.36 µg g-1 cheese, were generally higher than the iDNA, indicating that autolytic phenomena prevailed over intact cells after 8-12 months of ripening. In four of the seven cheeses, the same LAB species were detected in the eDNA and iDNA fractions by length-heterogeneity PCR, while in the remaining three samples, a higher number of species was highlighted in the eDNA compared to the corresponding iDNA. The sequential extraction of eDNA and iDNA can be applied to obtain additional information on the composition of the bacterial community in long-aged cheeses.
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Affiliation(s)
- Tommaso Bardelli
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via A. Lombardo 11, 26900 Lodi, Italy
| | - Lia Rossetti
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via A. Lombardo 11, 26900 Lodi, Italy
| | - Miriam Zago
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via A. Lombardo 11, 26900 Lodi, Italy
| | - Domenico Carminati
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via A. Lombardo 11, 26900 Lodi, Italy
| | - Giorgio Giraffa
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via A. Lombardo 11, 26900 Lodi, Italy
| | - Flavio Tidona
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), Via A. Lombardo 11, 26900 Lodi, Italy
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8
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Kamilari E, Tomazou M, Antoniades A, Tsaltas D. High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses? INTERNATIONAL JOURNAL OF FOOD SCIENCE 2019; 2019:5837301. [PMID: 31886165 PMCID: PMC6925717 DOI: 10.1155/2019/5837301] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/08/2019] [Accepted: 09/28/2019] [Indexed: 12/17/2022]
Abstract
Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.
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Affiliation(s)
- Elena Kamilari
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
| | | | | | - Dimitrios Tsaltas
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
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9
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Somerville V, Lutz S, Schmid M, Frei D, Moser A, Irmler S, Frey JE, Ahrens CH. Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. BMC Microbiol 2019; 19:143. [PMID: 31238873 PMCID: PMC6593500 DOI: 10.1186/s12866-019-1500-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/31/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruyère and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. RESULTS Two NWCs from Swiss Gruyère producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats. CONCLUSIONS Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.
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Affiliation(s)
- Vincent Somerville
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Michael Schmid
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Daniel Frei
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Aline Moser
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, CH-3003 Bern, Switzerland
| | - Stefan Irmler
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, CH-3003 Bern, Switzerland
| | - Jürg E. Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Christian H. Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
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10
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AFLP protocol comparison for microbial diversity fingerprinting. J Appl Genet 2019; 60:217-223. [PMID: 30989627 DOI: 10.1007/s13353-019-00492-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/20/2019] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
Abstract
Over the last decade, several methods based on genomic DNA have been developed for the identification and genotyping of prokaryotic and eukaryotic organisms. These genomic methods differ regarding taxonomic range, discriminatory power, reproducibility, and ease of interpretation and standardization. The amplified fragment length polymorphism (AFLP) technique is a very powerful DNA fingerprinting technique for DNA of any source or complexity, varying in both size and base composition. In addition, this method shows high discriminatory power and good reproducibility allowing it to be efficient in discriminating at both the species and strain levels. The development and application of AFLP have allowed significant progress in the study of biodiversity and taxonomy of microorganisms. In the last years, the Applied Biosystems AFLP Microbial Fingerprinting Kit, now out of production, was widely used in various studies to perform AFLP characterization of selected bacteria strains (described by Vos et al. (Nucleic Acids Res 23(21):4407-4414, 1995)). Its replacement gives the possibility for laboratories to continue the use of the previous AFLP data as a reference for bacteria genetic fingerprinting analysis in biodiversity studies. To overcome this issue a result comparison, by using an improved AFLP protocol and the AFLP commercial kit, was performed. In particular, previous results on different species (Listeria monocytogenes, Lactobacillus plantarum, and Streptococcus thermophilus) obtained with the commercial kit were compared with the improved AFLP procedure to validate the protocol. When compared with the AFLP Microbial Fingerprinting Kit, the improved protocol shows high reproducibility, resolution, and overall, is a faster method with lower costs.
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11
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Chessa L, Paba A, Daga E, Comunian R. Effect of growth media on natural starter culture composition and performance evaluated with a polyphasic approach. INT J DAIRY TECHNOL 2018. [DOI: 10.1111/1471-0307.12571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luigi Chessa
- Agris Sardegna; Loc. Bonassai, km 18.600 SS291 07100 Sassari Italy
| | - Antonio Paba
- Agris Sardegna; Loc. Bonassai, km 18.600 SS291 07100 Sassari Italy
| | - Elisabetta Daga
- Agris Sardegna; Loc. Bonassai, km 18.600 SS291 07100 Sassari Italy
| | - Roberta Comunian
- Agris Sardegna; Loc. Bonassai, km 18.600 SS291 07100 Sassari Italy
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Mataragas M, Alessandria V, Ferrocino I, Rantsiou K, Cocolin L. A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods. Food Microbiol 2018; 76:279-286. [PMID: 30166151 DOI: 10.1016/j.fm.2018.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 05/18/2018] [Accepted: 05/23/2018] [Indexed: 11/29/2022]
Abstract
The recent advances in molecular biology, such as the advent of next-generation sequencing (NGS) platforms, have paved the way to new exciting tools which rapidly transform food microbiology. Nowadays, NGS methods such as 16S rDNA/rRNA metagenomics or amplicon sequencing are used for the taxonomic profiling of the food microbial communities. Although 16S rDNA/rRNA NGS-based microbial data are not suited for the investigation of the functional potential of the identified operational taxonomic units as compared to shotgun metagenomics, advances in the bioinformatics discipline allow now the performance of such studies. In this paper, a bioinformatics workflow is described integrating predictive metagenomics profiling with specific application to food microbiology data. Bioinformatics tools pertinent to each sub-module of the pipeline are suggested as well. The published 16S rDNA/rRNA amplicon data originated from an Italian Grana-type cheese, using an NGS platform, was employed to demonstrate the predictive metagenomics profiling approach. The pipeline identified the microbial community and the changes that occurred in the microbial profile during manufacture of the food product studied (taxonomic profiling). The workflow also indicated significant changes in the functional profiling of the community. The tool may help to investigate the functional potential, alterations, and interactions of a microbial community. The proposed workflow may also find an application in the investigation of the ecology of foodborne pathogens encountered in various food products.
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Affiliation(s)
- Marios Mataragas
- Hellenic Agricultural Organization "DEMETER", Institute of Technology of Agricultural Products, Department of Dairy Research, Ethnikis Antistaseos 3, 45221, Ioannina, Greece.
| | - Valentina Alessandria
- University of Turin, Department of Agricultural, Forest and Food Sciences, Laboratory of Food Microbiology, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Ilario Ferrocino
- University of Turin, Department of Agricultural, Forest and Food Sciences, Laboratory of Food Microbiology, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Kalliopi Rantsiou
- University of Turin, Department of Agricultural, Forest and Food Sciences, Laboratory of Food Microbiology, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Luca Cocolin
- University of Turin, Department of Agricultural, Forest and Food Sciences, Laboratory of Food Microbiology, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
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Savo Sardaro ML, Perin LM, Bancalari E, Neviani E, Gatti M. Advancement in LH-PCR methodology for multiple microbial species detections in fermented foods. Food Microbiol 2018; 74:113-119. [PMID: 29706326 DOI: 10.1016/j.fm.2018.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/31/2022]
Abstract
The length-heterogeneity PCR is a low throughput molecular biology methods explored to monitor bacteria populations in different environments. It could be more used in food microbiology analysis, not only for fingerprinting analysis, but it has been hampered until now by a limiting factor which relates to the high percentage of secondary peaks. With the aim to overcome this problem, different experiments were performed focusing on changing PCR parameters in order to obtain more specific amplicon patterns and also to reduce the complexity of community patterns. With this purpose, different annealing temperatures were tested on complex fermented food matrices taken from both animal and vegetable origin and also on the bacteria isolated from the same food source. In particular, the optimal annealing temperature identified for the fermented food samples is 59 °C and the optimal for bacterial strains varied between 63 °C and 65 °C. The approach allowed the modification of the LH-PCR protocol increasing the amplification efficiency and therefore the bacteria species discrimination. These temperatures also allowed the implementation of the previous LH-PCR published database. The modification in the level of accuracy of the LH-PCR technique could also allow an improvement in the relative species quantification by the peak area evaluation.
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Affiliation(s)
- Maria Luisa Savo Sardaro
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy; San Raffaele University, Department of Nutrition and Gastronomy, Via Val Cannuta 247, Rome, Italy.
| | - Luana Martins Perin
- Universidade Federal de Viçosa, Departamento de Veterinaria, Campus Universitario, Centro, 36570-900 Viçosa, MG, Brazil
| | - Elena Bancalari
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy
| | - Erasmo Neviani
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy
| | - Monica Gatti
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy
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Silvetti T, Capra E, Morandi S, Cremonesi P, Decimo M, Gavazzi F, Giannico R, De Noni I, Brasca M. Microbial population profile during ripening of Protected Designation of Origin (PDO) Silter cheese, produced with and without autochthonous starter culture. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.06.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Perin LM, Savo Sardaro ML, Nero LA, Neviani E, Gatti M. Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods. Food Microbiol 2017; 65:160-169. [PMID: 28399998 DOI: 10.1016/j.fm.2017.02.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 01/10/2017] [Accepted: 02/09/2017] [Indexed: 10/20/2022]
Abstract
Artisanal Minas cheese is produced in Minas Gerais state, Brazil and its varieties are named according to their geographical origin (Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes). The cheese is produced with raw cow's milk and the whey from the previous cheese production ("pingo"). The high economic and cultural importance of artisanal cheese in Brazil justifies the efforts to ensure its safety, quality and provenance. This study aimed to characterize the microbial diversity composition, and geographical distribution of artisanal Minas cheese, focusing on the characterization of its autochthonous lactic acid bacteria (LAB) microbiota. Artisanal Minas cheese varieties from Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes were analyzed by culture-dependent (culturing and LAB sequencing) and -independent (repetitive extragenic palindromic-PCR (rep-PCR) and length heterogeneity-PCR, LH-PCR) methods to characterize the microbiota. The microbial counts were variable between cheese samples, and some samples presented high number of coagulase positive bacteria and coliforms that may be associated with hygienic issues. In all samples was observed a prevalence of LAB. 16S rRNA sequencing and rep-PCR of the LAB strains identified four genus (Lactobacillus, Lactococcus, Enterococcus and Weissella), ten species and more than one strain per species. Lactobacillus was the most prevalent genera in all the cheeses. LH-PCR revealed a further six genera and ten species that were not identified by culturing, highlighting the importance of combining both culture-dependent and -independent methods to fully characterize microbiota diversity. Principal component analysis of the LH-PCR data and cluster analysis of rep-PCR data revealed that the artisanal Minas cheese microbiota was influenced not only by their geographical origin but also by the cheese farm. The lack of standardization in the milking and cheese manufacturing procedures between artisanal cheese farms could explain the microbial diversity.
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Affiliation(s)
- Luana Martins Perin
- University of Parma, Department of Food Science, Parco Area delle Scienze 49/A, 43124 Parma, Italy.
| | - Maria Luisa Savo Sardaro
- University of Parma, Department of Food Science, Parco Area delle Scienze 49/A, 43124 Parma, Italy
| | - Luís Augusto Nero
- Universidade Federal de Viçosa, Departamento de Veterinária, Campus Universitário, Centro, 36570-900 Viçosa, MG, Brazil
| | - Erasmo Neviani
- University of Parma, Department of Food Science, Parco Area delle Scienze 49/A, 43124 Parma, Italy
| | - Monica Gatti
- University of Parma, Department of Food Science, Parco Area delle Scienze 49/A, 43124 Parma, Italy.
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Study of the bacterial diversity of foods: PCR-DGGE versus LH-PCR. Int J Food Microbiol 2017; 242:24-36. [DOI: 10.1016/j.ijfoodmicro.2016.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/08/2016] [Accepted: 11/09/2016] [Indexed: 12/27/2022]
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17
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Can the development and autolysis of lactic acid bacteria influence the cheese volatile fraction? The case of Grana Padano. Int J Food Microbiol 2016; 233:20-28. [DOI: 10.1016/j.ijfoodmicro.2016.06.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/23/2016] [Accepted: 06/07/2016] [Indexed: 11/16/2022]
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18
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Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches. Appl Environ Microbiol 2016; 82:3988-3995. [PMID: 27107125 DOI: 10.1128/aem.00999-16] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/19/2016] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED The microbial ecology of cheese involves a rich and complex interaction between starter lactic acid bacteria and nonstarter lactic acid bacteria (NSLAB), mainly originating from raw milk and/or from the environment, that can contribute to the final characteristics of cheese. The aim of the present research was the exploration of the active microbiota by RNA-based approaches during the manufacturing and ripening of a Grana-like cheese. Reverse transcriptase PCR (RT-PCR)-denaturing gradient gel electrophoresis (DGGE) and RNA-based high-throughput sequencing were applied to profile microbial populations, while the enumeration of active bacteria was carried out by using quantitative PCR (qPCR). Three different cheese productions (named D, E, and F) collected in the same month from the same dairy plant were analyzed. The application of the qPCR protocol revealed the presence of 7 log CFU/ml of bacterial load in raw milk, while, during ripening, active bacterial populations ranged from <4 to 8 log CFU/ml. The natural whey starters used in the three productions showed the same microbiota composition, characterized by the presence of Lactobacillus helveticus and Lactobacillus delbrueckii Nevertheless, beta-diversity analysis of the 16S rRNA sequencing data and RT-PCR-DGGE showed a clear clustering of the samples according to the three productions, probably driven by the different milks used. Milk samples were found to be characterized by the presence of several contaminants, such as Propionibacterium acnes, Acidovorax, Acinetobacter, Pseudomonas, and NSLAB. The core genera of the starter tended to limit the development of the spoilage bacteria only in two of the three batches. This study underlines the influence of different factors that can affect the final microbiota composition of the artisanal cheese. IMPORTANCE This study highlights the importance of the quality of the raw milk in the production of a hard cheese. Independent from the use of a starter culture, raw milk with low microbiological quality can negatively affect the populations of lactic acid bacteria and, as a consequence, impact the quality of the final product due to metabolic processes associated with spoilage bacteria.
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19
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Lysozyme affects the microbial catabolism of free arginine in raw-milk hard cheeses. Food Microbiol 2016; 57:16-22. [PMID: 27052697 DOI: 10.1016/j.fm.2015.11.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 11/22/2022]
Abstract
Lysozyme (LZ) is used in several cheese varieties to prevent late blowing which results from fermentation of lactate by Clostridium tyrobutyricum. Side effects of LZ on lactic acid bacteria population and free amino acid pattern were studied in 16 raw-milk hard cheeses produced in eight parallel cheese makings conducted at four different dairies using the same milk with (LZ+) or without (LZ-) addition of LZ. The LZ-cheeses were characterized by higher numbers of cultivable microbial population and lower amount of DNA arising from lysed bacterial cells with respect to LZ + cheeses. At both 9 and 16 months of ripening, Lactobacillus delbrueckii and Lactobacillus fermentum proved to be the species mostly affected by LZ. The total content of free amino acids indicated the proteolysis extent to be characteristic of the dairy, regardless to the presence of LZ. In contrast, the relative patterns showed the microbial degradation of arginine to be promoted in LZ + cheeses. The data demonstrated that the arginine-deiminase pathway was only partially adopted since citrulline represented the main product and only trace levels of ornithine were found. Differences in arginine degradation were considered for starter and non-starter lactic acid bacteria, at different cheese ripening stages.
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20
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Parente E, Guidone A, Matera A, De Filippis F, Mauriello G, Ricciardi A. Microbial community dynamics in thermophilic undefined milk starter cultures. Int J Food Microbiol 2016; 217:59-67. [DOI: 10.1016/j.ijfoodmicro.2015.10.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/28/2015] [Accepted: 10/13/2015] [Indexed: 02/08/2023]
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21
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Microbial changes of natural milk cultures for mozzarella cheese during repeated propagation cycles. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2015.08.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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22
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Biodiversity ofLactobacillus helveticusbacteriophages isolated from cheese whey starters. J DAIRY RES 2015; 82:242-7. [DOI: 10.1017/s0022029915000151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Twenty-oneLactobacillus helveticusbacteriophages, 18 isolated from different cheese whey starters and three from CNRZ collection, were phenotypically and genetically characterised. A biodiversity between phages was evidenced both by host range and molecular (RAPD-PCR) typing. A more detailed characterisation of six phages showed similar structural protein profiles and a relevant genetic biodiversity, as shown by restriction enzyme analysis of total DNA. Latent period, burst time and burst size data evidenced that phages were active and virulent. Overall, data highlighted the biodiversity ofLb. helveticusphages isolated from cheese whey starters, which were confirmed to be one of the most common phage contamination source in dairy factories. More research is required to further unravel the ecological role ofLb. helveticusphages and to evaluate their impact on the dairy fermentation processes where whey starter cultures are used.
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23
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High-throughput sequencing reveals microbial community diversity of Tibetan naturally fermented yak milk. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-014-1013-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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24
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De Filippis F, La Storia A, Stellato G, Gatti M, Ercolini D. A selected core microbiome drives the early stages of three popular italian cheese manufactures. PLoS One 2014; 9:e89680. [PMID: 24586960 PMCID: PMC3933672 DOI: 10.1371/journal.pone.0089680] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/22/2014] [Indexed: 02/07/2023] Open
Abstract
Mozzarella (M), Grana Padano (GP) and Parmigiano Reggiano (PR) are three of the most important traditional Italian cheeses. In the three cheese manufactures the initial fermentation is carried out by adding natural whey cultures (NWCs) according to a back-slopping procedure. In this study, NWCs and the corresponding curds from M, GP and PR manufactures were analyzed by culture-independent pyrosequencing of the amplified V1–V3 regions of the 16S rRNA gene, in order to provide insights into the microbiota involved in the curd acidification. Moreover, culture-independent high-throughput sequencing of lacS gene amplicons was carried out to evaluate the biodiversity occurring within the S. thermophilus species. Beta diversity analysis showed a species-based differentiation between GP-PR and M manufactures indicating differences between the preparations. Nevertheless, all the samples shared a naturally-selected core microbiome, that is involved in the curd acidification. Type-level variability within S. thermophilus species was also found and twenty-eight lacS gene sequence types were identified. Although lacS gene did not prove variable enough within S. thermophilus species to be used for quantitative biotype monitoring, the possibility of using non rRNA targets for quantitative biotype identification in food was highlighted.
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Affiliation(s)
- Francesca De Filippis
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Antonietta La Storia
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Giuseppina Stellato
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Monica Gatti
- Department of Food Science, University of Parma, Parma, Italy
- Multidisciplinary Interdepartmental Dairy Center - MILC, University of Parma, Parma, Italy
| | - Danilo Ercolini
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- * E-mail:
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Santarelli M, Bottari B, Lazzi C, Neviani E, Gatti M. Survey on the community and dynamics of lactic acid bacteria in Grana Padano cheese. Syst Appl Microbiol 2013; 36:593-600. [DOI: 10.1016/j.syapm.2013.04.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 04/16/2013] [Indexed: 10/26/2022]
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26
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Pogačić T, Mancini A, Santarelli M, Bottari B, Lazzi C, Neviani E, Gatti M. Diversity and dynamic of lactic acid bacteria strains during aging of a long ripened hard cheese produced from raw milk and undefined natural starter. Food Microbiol 2013; 36:207-15. [DOI: 10.1016/j.fm.2013.05.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/12/2013] [Accepted: 05/28/2013] [Indexed: 12/01/2022]
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Lactobacillus helveticus MIMLh5-specific antibodies for detection of S-layer protein in Grana Padano protected-designation-of-origin cheese. Appl Environ Microbiol 2013; 80:694-703. [PMID: 24242242 DOI: 10.1128/aem.03057-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Single-chain variable-fragment antibodies (scFvs) have considerable potential in immunological detection and localization of bacterial surface structures. In this study, synthetic phage-displayed antibody libraries were used to select scFvs against immunologically active S-layer protein of Lactobacillus helveticus MIMLh5. After three rounds of panning, five relevant phage clones were obtained, of which four were specific for the S-layer protein of L. helveticus MIMLh5 and one was also capable of binding to the S-layer protein of L. helveticus ATCC 15009. All five anti-S-layer scFvs were expressed in Escherichia coli XL1-Blue, and their specificity profiles were characterized by Western blotting. The anti-S-layer scFv PolyH4, with the highest specificity for the S-layer protein of L. helveticus MIMLh5, was used to detect the S-layer protein in Grana Padano protected-designation-of-origin (PDO) cheese extracts by Western blotting. These results showed promising applications of this monoclonal antibody for the detection of immunomodulatory S-layer protein in dairy (and dairy-based) foods.
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Santarelli M, Bottari B, Malacarne M, Lazzi C, Sforza S, Summer A, Neviani E, Gatti M. Variability of lactic acid production, chemical and microbiological characteristics in 24-hour Parmigiano Reggiano cheese. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s13594-013-0135-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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29
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Characterization of the genome of the dairy Lactobacillus helveticus bacteriophage {Phi}AQ113. Appl Environ Microbiol 2013; 79:4712-8. [PMID: 23728811 DOI: 10.1128/aem.00620-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The complete genomic sequence of the dairy Lactobacillus helveticus bacteriophage ΦAQ113 was determined. Phage ΦAQ113 is a Myoviridae bacteriophage with an isometric capsid and a contractile tail. The final assembled consensus sequence revealed a linear, circularly permuted, double-stranded DNA genome with a size of 36,566 bp and a G+C content of 37%. Fifty-six open reading frames (ORFs) were predicted, and a putative function was assigned to approximately 90% of them. The ΦAQ113 genome shows functionally related genes clustered together in a genome structure composed of modules for DNA replication/regulation, DNA packaging, head and tail morphogenesis, cell lysis, and lysogeny. The identification of genes involved in the establishment of lysogeny indicates that it may have originated as a temperate phage, even if it was isolated from natural cheese whey starters as a virulent phage, because it is able to propagate in a sensitive host strain. Additionally, we discovered that the ΦAQ113 phage genome is closely related to Lactobacillus gasseri phage KC5a and Lactobacillus johnsonii phage Lj771 genomes. The phylogenetic similarities between L. helveticus phage ΦAQ113 and two phages that belong to gut species confirm a possible common ancestral origin and support the increasing consideration of L. helveticus as a health-promoting organism.
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30
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Neviani E, Bottari B, Lazzi C, Gatti M. New developments in the study of the microbiota of raw-milk, long-ripened cheeses by molecular methods: the case of Grana Padano and Parmigiano Reggiano. Front Microbiol 2013; 4:36. [PMID: 23450500 PMCID: PMC3584316 DOI: 10.3389/fmicb.2013.00036] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/09/2013] [Indexed: 12/01/2022] Open
Abstract
Microorganisms are an essential component of cheeses and play important roles during both cheese manufacture and ripening. Both starter and secondary flora modify the physical and chemical properties of cheese, contributing and reacting to changes that occur during the manufacture and ripening of cheese. As the composition of microbial population changes under the influence of continuous shifts in environmental conditions and microorganisms interactions during manufacturing and ripening, the characteristics of a given cheese depend also on microflora dynamics. The microbiota present in cheese is complex and its growth and activity represent the most important, but the least controllable steps. In the past, research in this area was dependent on classical microbiological techniques. However, culture-dependent methods are time-consuming and approaches that include a culturing step can lead to inaccuracies due to species present in low numbers or simply uncultivable. Therefore, they cannot be used as a unique tool to monitor community dynamics. For these reasons approaches to cheese microbiology had to change dramatically. To address this, in recent years the focus on the use of culture-independent methods based on the direct analysis of DNA (or RNA) has rapidly increased. Application of such techniques to the study of cheese microbiology represents a rapid, sound, reliable, and effective way for the detection and identification of the microorganisms present in dairy products, leading to major advances in understanding this complex microbial ecosystem and its impact on cheese ripening and quality. In this article, an overview on the recent advances in the use of molecular methods for thorough analysis of microbial communities in cheeses is given. Furthermore, applications of culture-independent approaches to study the microbiology of two important raw-milk, long-ripened cheeses such as Grana Padano and Parmigiano Reggiano, are presented.
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Affiliation(s)
- Erasmo Neviani
- Department of Food Science, University of ParmaParma, Italy
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31
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Spizzirri UG, Restuccia D, Curcio M, Parisi OI, Iemma F, Picci N. Determination of biogenic amines in different cheese samples by LC with evaporative light scattering detector. J Food Compost Anal 2013. [DOI: 10.1016/j.jfca.2012.09.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bottari B, Agrimonti C, Gatti M, Neviani E, Marmiroli N. Development of a multiplex real time PCR to detect thermophilic lactic acid bacteria in natural whey starters. Int J Food Microbiol 2012; 160:290-7. [PMID: 23290237 DOI: 10.1016/j.ijfoodmicro.2012.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 10/08/2012] [Accepted: 10/19/2012] [Indexed: 10/27/2022]
Abstract
A multiplex real time PCR (mRealT-PCR) useful to rapidly screen microbial composition of thermophilic starter cultures for hard cooked cheeses and to compare samples with potentially different technological properties was developed. Novel primers directed toward pheS gene were designed and optimized for multiple detection of Lactobacillus helveticus, Lactobacillus delbrueckii, Streptococcus thermophilus and Lactobacillus fermentum. The assay was based on SYBR Green chemistry followed by melting curves analysis. The method was then evaluated for applications in the specific detection of the 4 lactic acid bacteria (LAB) in 29 different natural whey starters for Parmigiano Reggiano cheese production. The results obtained by mRealT-PCR were also compared with those obtained on the same samples by Fluorescence in Situ Hybridization (FISH) and Length-Heterogeneity PCR (LH-PCR). The mRealT-PCR developed in this study, was found to be effective for analyzing species present in the samples with an average sensitivity down to less than 600 copies of DNA and therefore sensitive enough to detect even minor LAB community members of thermophilic starter cultures. The assay was able to describe the microbial population of all the different natural whey starter samples analyzed, despite their natural variability. A higher number of whey starter samples with S. thermophilus and L. fermentum present in their microbial community were revealed, suggesting that these species could be more frequent in Parmigiano Reggiano natural whey starter samples than previously shown. The method was more effective than LH-PCR and FISH and, considering that these two techniques have to be used in combination to detect the less abundant species, the mRealT-PCR was also faster. Providing a single step sensitive detection of L. helveticus, L. delbrueckii, S. thermophilus and L. fermentum, the developed mRealT-PCR could be used for screening thermophilic starter cultures and to follow the presence of those species during ripening of derived dairy products. A major increase in understanding the starter culture contribution to cheese ecosystem could be harnessed to control cheese ripening and flavor formation.
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Affiliation(s)
- Benedetta Bottari
- Department of Food Science, University of Parma, Parco Area delle Scienze 95/A, Parma, Italy
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ROSSI FRANCA, GATTO VERONICA, SABATTINI GIANCARLO, TORRIANI SANDRA. An assessment of factors characterising the microbiology of Grana Trentino cheese, a Grana-type cheese. INT J DAIRY TECHNOL 2012. [DOI: 10.1111/j.1471-0307.2012.00844.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Biodiversity in Oscypek, a traditional Polish cheese, determined by culture-dependent and -independent approaches. Appl Environ Microbiol 2012; 78:1890-8. [PMID: 22247135 DOI: 10.1128/aem.06081-11] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Oscypek is a traditional Polish scalded-smoked cheese, with a protected-designation-of-origin (PDO) status, manufactured from raw sheep's milk without starter cultures in the Tatra Mountains region of Poland. This study was undertaken in order to gain insight into the microbiota that develops and evolves during the manufacture and ripening stages of Oscypek. To this end, we made use of both culturing and the culture-independent methods of PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing of 16S rRNA gene amplicons. The culture-dependent technique and PCR-DGGE fingerprinting detected the predominant microorganisms in traditional Oscypek, whereas the next-generation sequencing technique (454 pyrosequencing) revealed greater bacterial diversity. Besides members of the most abundant bacterial genera in dairy products, e.g., Lactococcus, Lactobacillus, Leuconostoc, Streptococcus, and Enterococcus, identified by all three methods, other, subdominant bacteria belonging to the families Bifidobacteriaceae and Moraxellaceae (mostly Enhydrobacter), as well as various minor bacteria, were identified by pyrosequencing. The presence of bifidobacterial sequences in a cheese system is reported for the first time. In addition to bacteria, a great diversity of yeast species was demonstrated in Oscypek by the PCR-DGGE method. Culturing methods enabled the determination of a number of viable microorganisms from different microbial groups and their isolation for potential future applications in specific cheese starter cultures.
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Culture-independent detection of microorganisms in traditional Slovakian bryndza cheese. Int J Food Microbiol 2011; 150:73-8. [DOI: 10.1016/j.ijfoodmicro.2011.07.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 07/17/2011] [Indexed: 11/22/2022]
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The spatial distribution of bacteria in Grana-cheese during ripening. Syst Appl Microbiol 2011; 35:54-63. [PMID: 21943677 DOI: 10.1016/j.syapm.2011.07.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 06/24/2011] [Accepted: 07/01/2011] [Indexed: 11/22/2022]
Abstract
The microbial composition and its spatial distribution of Grana Trentino, a hard Parmesan-like cheese, was determined, from vat milk to cheese. After cutting along the vertical axis of the cheese wheels, three layers were sampled diagonally across the cheese: under the cheese rind, an intermediate section and the cheese core. After two different ripening periods (9 and 18 months), the cheese samples were analysed using traditional culture dependent and culture independent methods. Milk samples were dominated by mesophilic and psychrophilic bacterial counts. Thermophilic bacteria (Lactobacillus helveticus) were found in high amounts in cooked whey and natural whey starter cultures. After 9 months of ripening, lactic acid bacteria (LAB) counts were higher than those after 18 months. Furthermore, the LAB numbers in the cheese core was lower than those under the rind or in the intermediate section. The main LAB species isolated from milk (Lactococcus lactis, Pediococcus pentosaceus, Streptococcus uberis and Lactococcus garvieae) were not found in the corresponding cheeses. Some differences were observed in the species composition among the three cheese sections. Microbiota under the rind and in the intermediate section was similar and dominated by Lactobacillus paracasei and Lactobacillus rhamnosus. The core, after 18 months of ripening, was characterized by a total absence of LAB. In each sample, all LAB were genotypically grouped and the different biotypes were subjected to several technological tests indicating that some non-starter LAB (NSLAB) displayed technological features that are favorable for the production of Grana Trentino cheese.
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Ndoye B, Rasolofo EA, LaPointe G, Roy D. A review of the molecular approaches to investigate the diversity and activity of cheese microbiota. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s13594-011-0031-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Dynamics of bacterial community exposed to hydrocarbons and oleophilic fertilizer in high-Arctic intertidal beach. Polar Biol 2011. [DOI: 10.1007/s00300-011-1003-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Cremonesi P, Vanoni L, Morandi S, Silvetti T, Castiglioni B, Brasca M. Development of a pentaplex PCR assay for the simultaneous detection of Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. helveticus, L. fermentum in whey starter for Grana Padano cheese. Int J Food Microbiol 2011; 146:207-11. [PMID: 21377750 DOI: 10.1016/j.ijfoodmicro.2011.02.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 01/17/2011] [Accepted: 02/16/2011] [Indexed: 11/29/2022]
Abstract
A pentaplex PCR assay for the rapid, selective and simultaneous detection of Lactobacillus helveticus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and L. fermentum, was developed. The target sequences were a group of genes coding for beta-galactosidase production (S. thermophilus and L. delbrueckii subsp. bulgaricus), for cell-enveloped associated proteinase synthesis (L. helveticus), for dipeptide transport system production (L. delbrueckii subsp. lactis) and for arginine-ornithine antiporter protein production (L. fermentum). The analytical specificity of the assay was evaluated with 5 reference strains and 140 lactic acid bacterial strains derived from raw milk cheeses and belonging to the Lactobacillus, Streptococcus, Lactococcus and Enterococcus genera. The identification limit for each target strain was 10(3)CFU/ml. This new molecular assay was used to investigate the LAB population by direct extraction of DNA from the 12 whey cultures for Grana Padano. The pentaplex PCR assay revealed a good correspondence with microbiological analyses and allowed to identify even minor LAB community members which, can be out-competed in vitro by numerically more abundant microbial species.
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Affiliation(s)
- Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council, Via Bassini 15, Milan, Italy.
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Bottari B, Santarelli M, Neviani E, Gatti M. Natural whey starter for Parmigiano Reggiano: culture-independent approach. J Appl Microbiol 2010; 108:1676-84. [DOI: 10.1111/j.1365-2672.2009.04564.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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COLOMBO E, FRANZETTI L, FRUSCA M, SCARPELLINI M. Phenotypic and Genotypic Characterization of Lactic Acid Bacteria Isolated from Artisanal Italian Goat Cheese. J Food Prot 2010; 73:657-62. [DOI: 10.4315/0362-028x-73.4.657] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The lactic acid bacteria community in traditional goat cheese produced in three dairies in Valsesia (Piemonte, Italy) was studied at different steps of the manufacturing process. These cheeses were produced from raw milk without starter bacteria, and no protocol was followed during the manufacturing process. Three hundred thirty-two isolates were characterized and grouped by results of both morphophysiological tests and random amplification of polymorphic DNA plus PCR analysis. Bacteria were identified by partial sequencing of the 16S rRNA gene. Lactococci were the dominant lactic acid bacteria in raw milk. Their initial numbers ranged from 5 to 7 log CFU ml−1. Their levels increased during manufacturing and decreased during ripening. The growth trend for enterococci was comparable to that of lactococci, although enterococci counts were lower. Lactococcus lactis subsp. cremoris, Lactococcus garviae, and Enterococcus faecalis were the most frequently isolated species during goat cheese manufacturing, whereas the highest numbers of Enterococcus (E. faecium, E. durans, E. gilvus, and E. casseliflavus) were isolated with the greatest frequency from ripened cheese samples. Occasionally, Leuconostoc mesenteroides, Leuconostoc lactis, and Lactobacillus paraplantarum also were isolated.
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Affiliation(s)
- E. COLOMBO
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche sez, Microbiologia Agraria Alimentare Ecologica, Università degli Studi di Milano, Via Celoria, 2 201333 Milano, Italy
| | - L. FRANZETTI
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche sez, Microbiologia Agraria Alimentare Ecologica, Università degli Studi di Milano, Via Celoria, 2 201333 Milano, Italy
| | - M. FRUSCA
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche sez, Microbiologia Agraria Alimentare Ecologica, Università degli Studi di Milano, Via Celoria, 2 201333 Milano, Italy
| | - M. SCARPELLINI
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche sez, Microbiologia Agraria Alimentare Ecologica, Università degli Studi di Milano, Via Celoria, 2 201333 Milano, Italy
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Application of molecular approaches to study lactic acid bacteria in artisanal cheeses. J Microbiol Methods 2009; 78:1-9. [DOI: 10.1016/j.mimet.2009.04.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 04/03/2009] [Accepted: 04/06/2009] [Indexed: 11/17/2022]
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Polyphasic study of microbial communities of two Spanish farmhouse goats' milk cheeses from Sierra de Aracena. Food Microbiol 2009; 26:294-304. [DOI: 10.1016/j.fm.2008.12.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 12/09/2008] [Accepted: 12/21/2008] [Indexed: 11/17/2022]
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Brusetti L, Malkhazova I, Gtari M, Tamagnini I, Borin S, Merabishvili M, Chanishvili N, Mora D, Cappitelli F, Daffonchio D. Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography. BMC Microbiol 2008; 8:220. [PMID: 19077307 PMCID: PMC2625358 DOI: 10.1186/1471-2180-8-220] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 12/15/2008] [Indexed: 11/30/2022] Open
Abstract
Background BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) is one of the most used techniques in biogeography studies of microbial isolates. However the traditional separation of BOX-PCR patterns by agarose gel electrophoresis suffers many limitations. The aim of this research was to set up a fluorescent BOX-PCR (F-BOX-PCR) assay in which separation of PCR products is automated in a capillary electrophoresis system. F-BOX-PCR was compared with the traditional BOX-PCR using bacterial strains with different G+C content (Bacillus cereus; Escherichia coli; isolates of the family Geodermatophilaceae). Resolution, discriminatory power and reproducibility were evaluated by assaying different electrophoretic runs, PCR reactions and independent DNA extractions. BOX-PCR and F-BOX-PCR were compared for the analysis of 29 strains of Modestobacter multiseptatus isolated from three different microsites in an altered carbonatic wall from Cagliari, Italy, and 45 strains of Streptococcus thermophilus isolated from 34 samples of the hand-made, yogurt-like product Matsoni, collected in different locations in Georgia. Results Fluorophore 6-FAM proved more informative than HEX and BOX-PCR both in agarose gel electrophoresis (p < 0.004 and p < 0.00003) and in capillary electrophoresis (compared only with HEX, p < 2 × 10-7). 6-FAM- and HEX-based F-BOX-PCR respectively detected up to 12.0 and 11.3 times more fragments than BOX-PCR. Replicate separations of F-BOX-PCR showed an accuracy of the size calling of ± 0.5 bp until 500 bp, constantly decreasing to ± 10 bp at 2000 bp. Cluster analysis of F-BOX-PCR profiles grouped M. multiseptatus strains according to the microsite of isolation and S. thermophilus strains according to the geographical origin of Matsoni, but resulted intermixed when a BOX-PCR dataset was used. Conclusion F-BOX-PCR represents an improved method for addressing bacterial biogeography studies both in term of sensitivity, reproducibility and data analysis.
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Affiliation(s)
- Lorenzo Brusetti
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DISTAM), Università degli Studi di Milano, Milan, Italy.
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Grattepanche F, Miescher-Schwenninger S, Meile L, Lacroix C. Recent developments in cheese cultures with protective and probiotic functionalities. ACTA ACUST UNITED AC 2008. [DOI: 10.1051/dst:2008013] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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48
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Dynamics of whole and lysed bacterial cells during Parmigiano-Reggiano cheese production and ripening. Appl Environ Microbiol 2008; 74:6161-7. [PMID: 18689516 DOI: 10.1128/aem.00871-08] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial succession during Parmigiano-Reggiano cheesemaking was monitored by length heterogeneity PCR (LH-PCR), considering the intact and lysed cells at different stages of cheese production and ripening. When starter species underwent autolysis, species coming from milk were able to grow. For the first time, the LH-PCR technique was applied to study a fermented food.
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Polyphasic approach to bacterial dynamics during the ripening of Spanish farmhouse cheese, using culture-dependent and -independent methods. Appl Environ Microbiol 2008; 74:5662-73. [PMID: 18658288 DOI: 10.1128/aem.00418-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the dynamics of the microbial population during ripening of Cueva de la Magahá cheese using a combination of classical and molecular techniques. Samples taken during ripening of this Spanish goat's milk cheese in which Lactococcus lactis and Streptococcus thermophilus were used as starter cultures were analyzed. All bacterial isolates were clustered by using randomly amplified polymorphic DNA (RAPD) and identified by 16S rRNA gene sequencing, species-specific PCR, and multiplex PCR. Our results indicate that the majority of the 225 strains isolated and enumerated on solid media during the ripening period were nonstarter lactic acid bacteria, and Lactobacillus paracasei was the most abundant species. Other Lactobacillus species, such as Lactobacillus plantarum and Lactobacillus parabuchneri, were also detected at the beginning and end of ripening, respectively. Non-lactic-acid bacteria, mainly Kocuria and Staphylococcus strains, were also detected at the end of the ripening period. Microbial community dynamics determined by temporal temperature gradient gel electrophoresis provided a more precise estimate of the distribution of bacteria and enabled us to detect Lactobacillus curvatus and the starter bacteria S. thermophilus and L. lactis, which were not isolated. Surprisingly, the bacterium most frequently found using culture-dependent analysis, L. paracasei, was scarcely detected by this molecular approach. Finally, we studied the composition of the lactobacilli and their evolution by using length heterogeneity PCR.
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Henri-Dubernet S, Desmasures N, Guéguen M. Diversity and dynamics of lactobacilli populations during ripening of RDO Camembert cheese. Can J Microbiol 2008; 54:218-28. [PMID: 18388993 DOI: 10.1139/w07-137] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The diversity and dynamics of Lactobacillus populations in traditional raw milk Camembert cheese were monitored throughout the manufacturing process in 3 dairies. Culture-dependent analysis was carried out on isolates grown on acidified de Man - Rogosa - Sharpe agar and Lactobacillus anaerobic de Man Rogosa Sharpe agar supplemented with vancomycin and bromocresol green media. The isolates were identified by polymerase chain reaction - temperature gradient gel electrophoresis (PCR-TGGE) and (or) species-specific PCR and (or) sequencing, and Lactobacillus paracasei and Lactobacillus plantarum isolates were characterized by pulsed field gel electrophoresis (PFGE). Milk and cheese were subjected to culture-independent analysis by PCR-TGGE. Presumed lactobacilli were detected by plate counts throughout the ripening process. However, molecular analysis of total DNA and DNA of isolates failed to detect Lactobacillus spp. in certain cases. The dominant species in the 3 dairies was L. paracasei. PFGE analysis revealed 21 different profiles among 39 L. paracasei isolates. Lactobacillus plantarum was the second most isolated species, but it occurred nearly exclusively in one dairy. The other species isolated were Lactobacillus parabuchneri, Lactobacillus fermentum, Lactobacillus acidophilus, Lactobacillus helveticus, a Lactobacillus psittaci/delbrueckii subsp. bulgaricus/gallinarum/crispatus group, Lactobacillus rhamnosus, Lactobacillus delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, Lactobacillus brevis, Lactobacillus kefiri, and Lactobacillus perolens. Lactobacilli diversity at the strain level was high. Dynamics varied among dairies, and each cheese exhibited a specific picture of species and strains.
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Affiliation(s)
- Ségolène Henri-Dubernet
- Fromageries BEL S.A, Departement Recherche Appliquee Groupe, 7 bd de l'Industrie, 41100 Vendome, France
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