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Bettera L, Levante A, Bancalari E, Bottari B, Cirlini M, Neviani E, Gatti M. Lacticaseibacillus Strains Isolated from Raw Milk: Screening Strategy for Their Qualification as Adjunct Culture in Cheesemaking. Foods 2023; 12:3949. [PMID: 37959068 PMCID: PMC10648420 DOI: 10.3390/foods12213949] [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: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The microbial ecology fundamentals of raw milk and long-ripened cheeses consist of a complex interaction between starter lactic acid bacteria (SLAB) and non-starter LAB (NSLAB). Although NSLAB aromatic properties are paramount, other phenotypic traits need to be considered for their use as adjunct cultures, such as the capability to endure technological parameters encountered during cheesemaking. The present study focused on the isolation and characterization of NSLAB from spontaneously fermented raw cow's milk coming from 20 dairies that produce Grana Padano PDO cheese. From 122 isolates, the screening process selected the 10 most diverse strains belonging to Lacticaseibacillus spp. to be phenotypically characterized. The strains were tested for their growth performance in milk in combination with the application of technological stresses, for their ability to produce volatile compounds after their growth in milk, and for their ability to use different nutrient sources and resist chemicals. The complex characterization qualified the strains 5959_Lbparacasei and 5296_Lbparacasei as the best candidates to be used as adjunct strains in the production of raw milk and long-ripened cheeses, provided that antibiotic resistance is measured before their employment. Other strains with interesting aromatic capabilities but lower heat resistance were 5293_Lbparacasei, 5649_Lbparacasei and 5780_Lbparacasei, which could be candidates as adjunct strains for uncooked cheese production.
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Affiliation(s)
| | - Alessia Levante
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (L.B.); (E.B.); (B.B.); (M.C.); (E.N.); (M.G.)
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2
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Rodríguez J, González-Guerra A, Vázquez L, Fernández-López R, Flórez AB, de la Cruz F, Mayo B. Isolation and phenotypic and genomic characterization of Tetragenococcus spp. from two Spanish traditional blue-veined cheeses made of raw milk. Int J Food Microbiol 2022; 371:109670. [DOI: 10.1016/j.ijfoodmicro.2022.109670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/28/2022] [Accepted: 04/02/2022] [Indexed: 11/27/2022]
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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: 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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4
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Levante A, Bertani G, Bottari B, Bernini V, Lazzi C, Gatti M, Neviani E. How new molecular approaches have contributed to shedding light on microbial dynamics in Parmigiano Reggiano cheese. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2020.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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5
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Phenotypic Diversity of Lactobacillus casei Group Isolates as a Selection Criterion for Use as Secondary Adjunct Starters. Microorganisms 2020; 8:microorganisms8010128. [PMID: 31963444 PMCID: PMC7022476 DOI: 10.3390/microorganisms8010128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/15/2022] Open
Abstract
Autochthonous lactic acid bacteria (LAB) play a key role in the development of cheese flavor. As the pasteurization treatment on raw milk causes the elimination of LAB, secondary starter cultures are used in cheese manufacture to obtain cheeses with improved and standardized flavors. In this work, strains of the L. casei group isolated from traditional Italian cheeses were screened for their phenotypic features of technological interest for use as secondary starters. Their milk acidifying performance and the production of volatile compounds when grown in milk were evaluated. Simultaneously, the acetoin metabolic pathway presence was screened in the strains and assessed for its transcriptional activation. The results showed that the analyzed strains, despite belonging to taxonomically-related species, vary greatly according to the measured phenotypes. Four strains among the fourteen screened could be potentially used as adjunct cultures for cheese-making processes. The strain that showed the highest production of acetoin upregulated the aspartate pathway. An increased knowledge of volatile compounds’ production and acidifying properties of LAB strains isolated from traditional dairy products might guide the selection of strains for industrial applications.
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Sant'Anna FM, Wetzels SU, Cicco SHS, Figueiredo RC, Sales GA, Figueiredo NC, Nunes CA, Schmitz-Esser S, Mann E, Wagner M, Souza MR. Microbial shifts in Minas artisanal cheeses from the Serra do Salitre region of Minas Gerais, Brazil throughout ripening time. Food Microbiol 2019; 82:349-362. [PMID: 31027793 DOI: 10.1016/j.fm.2019.02.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/12/2019] [Accepted: 02/28/2019] [Indexed: 01/01/2023]
Abstract
The Minas artisanal cheese is a traditional product in its way of producing. Produced in the Minas Gerais state, Brazil, this cheese is made using raw cow's milk with the addition of an endogenous starter culture called "pingo", responsible for inoculating specific microorganisms that could enhance flavor and sensorial aspects. There are seven regions able to produce and commercialize this product - Araxá, Campo das Vertentes, Canastra Cerrado, Serra do Salitre, Serro and Triângulo Mineiro. This study aimed to assess the bacterial community of raw milk, endogenous starter culture and to uncover possible shifts in the bacterial community of the rind and core of cheeses at sixty days of ripening located in the Serra do Salitre region by Illumina MiSeq 16S rRNA gene amplicon sequencing. Raw milk and starter culture are responsible for inoculating specific bacteria into the cheese, with Planococcaceae and Streptococcaceae being prevalent throughout ripening time. The Planococcaceae family seems to develop strong interactions with the Leuconostocaceae family on the surface of these cheeses, and is associated with environmental aspects of the region, probably leading to a microbial signature of these products. Additionally, abiotic factors such as geographical location, moisture and acidity are major drivers in the microbial shift.
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Affiliation(s)
- Felipe Machado Sant'Anna
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil.
| | - Stefanie Urimarie Wetzels
- Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Veterinaerplatz 1, 1210, Vienna, Austria; Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Sávio Henrique Sandes Cicco
- Department of General Biology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Ranier Chaves Figueiredo
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Gilson Assis Sales
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Naiara Chaves Figueiredo
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Cantini Alvaro Nunes
- Department of General Biology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, 3222 NSRIC, 1029 North University Boulevard, 50011, Ames, IA, USA
| | - Evelyne Mann
- Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Veterinaerplatz 1, 1210, Vienna, Austria; Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Marcelo Resende Souza
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
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Bottari B, Levante A, Neviani E, Gatti M. How the Fewest Become the Greatest. L. casei's Impact on Long Ripened Cheeses. Front Microbiol 2018; 9:2866. [PMID: 30524419 PMCID: PMC6262004 DOI: 10.3389/fmicb.2018.02866] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/07/2018] [Indexed: 12/23/2022] Open
Abstract
Members of the Lactobacillus casei group, including species classified currently as L. casei, L. paracasei, and L. rhamnosus, are among the most frequently found species in raw milk, hard cooked, long-ripened cheeses. Starting from very low numbers in raw milk, they become dominant in the cheese during ripening, selected by physical and chemical changes produced by cheese making and ripening. Their presence at different stages of cheese making and ripening is crucial in defining product features. For these reasons, the scientific community has been more and more interested in studying these “tiny but mighty microbes” and their implications during cheese making and ripening. The present paper reviews the current literature on the effect of L. casei in cheeses, with particular reference to the case of Parmigiano Reggiano and Grana Padano, two of the most famous PDO (Protected Designation of Origin) Italian cheeses. Recent advances regarding the selection of new wild strains able to persist until the end of ripening and carrying out slow but crucial activities resulting in specific aromatic features, are also presented.
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Affiliation(s)
| | - Alessia Levante
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Erasmo Neviani
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Monica Gatti
- Department of Food and Drug, University of Parma, Parma, Italy
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8
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Bianco A, Fancello F, Balmas V, Zara G, Dettori M, Budroni M. The microbiome of Sardinian barley and malt. JOURNAL OF THE INSTITUTE OF BREWING 2018. [DOI: 10.1002/jib.522] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Angela Bianco
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
| | - Francesco Fancello
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
| | - Virgilio Balmas
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
| | - Giacomo Zara
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
| | - Marco Dettori
- Agricultural Research Agency of Sardinia (Agris); Cagliari Sardinia Italy
| | - Marilena Budroni
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
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9
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Toward the identification of a type I toxin-antitoxin system in the plasmid DNA of dairy Lactobacillus rhamnosus. Sci Rep 2017; 7:12051. [PMID: 28935987 PMCID: PMC5608710 DOI: 10.1038/s41598-017-12218-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 09/06/2017] [Indexed: 12/27/2022] Open
Abstract
Plasmids carry genes that give bacteria beneficial traits and allow them to survive in competitive environments. In many cases, they also harbor toxin-antitoxin (TA) systems necessary for plasmid maintenance. TA systems are generally characterized by a stable “toxin”, a protein or peptide capable of killing the cell upon plasmid loss and by an unstable “antitoxin”, a protein or a non-coding RNA that inhibits toxin activity. Here we report data toward the identification of a RNA-regulated TA system in the plasmid DNA of L. rhamnosus isolated from cheese. The proposed TA system comprises two convergently transcribed RNAs: a toxin RNA encoding a 29 amino acid peptide named Lpt and an antitoxin non-coding RNA. Both toxin and antitoxin RNAs resulted upregulated under conditions mimicking cheese ripening. The toxicity of the Lpt peptide was demonstrated in E. coli by cloning the Lpt ORF under the control of an inducible promoter. Bioinformatics screening of the bacterial nucleotide database, shows that regions homologous to the Lpt TA locus are widely distributed in the Lactobacillus genus, particularly within the L. casei group, suggesting a relevant role of TA systems in plasmid maintenance of cheese microbiota.
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10
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Levante A, De Filippis F, La Storia A, Gatti M, Neviani E, Ercolini D, Lazzi C. Metabolic gene-targeted monitoring of non-starter lactic acid bacteria during cheese ripening. Int J Food Microbiol 2017; 257:276-284. [PMID: 28735145 DOI: 10.1016/j.ijfoodmicro.2017.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 06/23/2017] [Accepted: 07/02/2017] [Indexed: 02/04/2023]
Abstract
Long ripened cheeses, such as Grana Padano (GP), a Protected Designation of Origin (PDO) Italian cheese, harbor a viable microbiota mainly composed of non-starter lactic acid bacteria (NSLAB), which contribute to the final characteristics of cheese. The NSLAB species Lactobacillus rhamnosus, Lb. casei and Lb. paracasei are frequently found in GP, and form a closely related taxonomic group (Lb. casei group), making it difficult to distinguish the three species through 16S rRNA sequencing. SpxB, a metabolic gene coding for pyruvate oxidase in Lb. casei group, was recently used to distinguish the species within this bacterial group, both in pure cultures and in cheese, where it could provide an alternative energy source through the conversion of pyruvate to acetate. The aim of this work was to study the evolution of the metabolically active microbiota during different stages of GP ripening, targeting 16S rRNA to describe the whole microbiota composition, and spxB gene to monitor the biodiversity within the Lb. casei group. Furthermore, activation of pyruvate oxidase pathway was measured directly in cheese by reverse transcription real time PCR (RT-qPCR). The results showed that Lb. casei group dominates throughout the ripening and high-throughput sequencing of spxB allowed to identify four clusters inside the Lb. casei group. The dynamics of the sequence types forming the clusters were followed during ripening. Pyruvate oxidase pathway was expressed in cheese, showing a decreasing trend over ripening time. This work highlights how the composition of the microbiota in the early manufacturing stages influences the microbial dynamics throughout ripening, and how targeting of a metabolic gene can provide an insight into the activity of strains relevant for dairy products.
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Affiliation(s)
- Alessia Levante
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, 43124 Parma, Italy.
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, 80055 Portici, Italy.
| | - Antonietta La Storia
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Monica Gatti
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, 43124 Parma, Italy
| | - Erasmo Neviani
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, 43124 Parma, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Camilla Lazzi
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, 43124 Parma, Italy
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11
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Bruno LM, Briggiler Marcó M, Capra ML, Carvalho JDG, Meinardi C, Quiberoni A. Wild Lactobacillus
strains: Technological characterisation and design of Coalho cheese lactic culture. INT J DAIRY TECHNOL 2017. [DOI: 10.1111/1471-0307.12360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Laura Maria Bruno
- Embrapa Agroindústria Tropical; Rua Dra. Sara Mesquita, 2270 Fortaleza Ceará 60511-110 Brasil
| | - Mariángeles Briggiler Marcó
- Instituto de Lactología Industrial (UNL-CONICET); Facultad de Ingeniería Química; Universidad Nacional del Litoral; Santiago del Estero 2829 Santa Fe 3000 Argentina
| | - Maria Luján Capra
- Instituto de Lactología Industrial (UNL-CONICET); Facultad de Ingeniería Química; Universidad Nacional del Litoral; Santiago del Estero 2829 Santa Fe 3000 Argentina
| | - Juliane Döering Gasparin Carvalho
- Departamento de Tecnologia de Alimentos; Universidade Federal do Ceará; Av. Mister Hull, 2977 Bloco 858, Campus do Pici Fortaleza Ceará 60536-000 Brasil
| | - Carlos Meinardi
- Instituto de Lactología Industrial (UNL-CONICET); Facultad de Ingeniería Química; Universidad Nacional del Litoral; Santiago del Estero 2829 Santa Fe 3000 Argentina
| | - Andrea Quiberoni
- Instituto de Lactología Industrial (UNL-CONICET); Facultad de Ingeniería Química; Universidad Nacional del Litoral; Santiago del Estero 2829 Santa Fe 3000 Argentina
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12
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Mangia NP, Fancello F, Deiana P. Microbiological characterization using combined culture dependent and independent approaches of Casizolu pasta filata cheese. J Appl Microbiol 2016; 120:329-45. [PMID: 26551888 DOI: 10.1111/jam.13001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 09/22/2015] [Accepted: 11/02/2015] [Indexed: 12/30/2022]
Abstract
AIMS Casizolu is a traditional Sardinian (Italy) pasta filata cheese made with cow raw milk belonging to Sardo-Modicana and/or Bruno-Sarda breeds added with natural whey starter. This work aims to describe the traditional technology of this product and to evaluate the microbial groups/species involved in the first month of ripening. METHODS AND RESULTS Raw milk, curd after stretching and Casizolu cheese samples from two different farmsteads were subjected to enumeration of microbial groups, isolation and genotypic characterization of isolates and PCR temporal temperature gel electrophoresis (TTGE) analysis. The counts of lactobacilli and lactococci groups in raw milk were about 5-6 log UFC ml(-1) of milk. These counts tended to increase in curd and cheeses, reaching values higher than 8 log UFC g(-1) of cheese. Culture dependent and independent approaches employed in this work highlighted the fundamental role of Lactococcus lactis subsp. lactis, Streptococcus thermophilus and Lactobacillus paracasei in the manufacture and ripening of Casizolu cheese. Other species frequently isolated were Enterococcus durans, Enterococcus faecium, Enterococcus italicus while Enterococcus lactis, Streptococcus parauberis, Lactobacillus plantarum, Lactobacillus pentosus, Lactobacillus brevis, Lactobacillus fermentum and Lactococcus raffinolactis were isolated occasionally. CONCLUSIONS Lactococcus lactis subsp. lactis, Strep. thermophilus and Lact. paracasei were the principal bacterial species involved in the Casizolu cheese manufacturing and ripening. For the first time, Ent. italicus and Ent. lactis were isolated in the pasta filata cheese. SIGNIFICANCE AND IMPACT OF THE STUDY This study shows the first data on microbial groups and species involved in the manufacture of Casizolu cheese and highlights the role of Lact. paracasei and Enterococcus spp. from the earliest stages of ripening cheese; furthermore, provides evidence that raw milk cheese is a source of new strains and therefore a reservoir of microbial biodiversity.
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Affiliation(s)
- N P Mangia
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - F Fancello
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - P Deiana
- Department of Agriculture, University of Sassari, Sassari, Italy
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13
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Ceapa C, Davids M, Ritari J, Lambert J, Wels M, Douillard FP, Smokvina T, de Vos WM, Knol J, Kleerebezem M. The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires. Genome Biol Evol 2016; 8:1889-905. [PMID: 27358423 PMCID: PMC4943194 DOI: 10.1093/gbe/evw123] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence–absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains’ core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.
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Affiliation(s)
- Corina Ceapa
- Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands Laboratory of Microbiology, Wageningen University, the Netherlands
| | - Mark Davids
- Laboratory of Systems and Synthetic Biology, Wageningen University, the Netherlands
| | - Jarmo Ritari
- RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Finland
| | - Jolanda Lambert
- Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands
| | | | | | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, the Netherlands RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Finland Department of Veterinary Biosciences, University of Helsinki, Finland
| | - Jan Knol
- Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands Laboratory of Microbiology, Wageningen University, the Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands
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Technological, phenotypic and genotypic characterization of lactobacilli from Graviera Kritis PDO Greek cheese, manufactured at two traditional dairies. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Henríquez-Aedo K, Durán D, Garcia A, Hengst MB, Aranda M. Identification of biogenic amines-producing lactic acid bacteria isolated from spontaneous malolactic fermentation of chilean red wines. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2015.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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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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17
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Mei J, Guo Q, Wu Y, Li Y. Microbial diversity of a Camembert-type cheese using freeze-dried Tibetan kefir coculture as starter culture by culture-dependent and culture-independent methods. PLoS One 2014; 9:e111648. [PMID: 25360757 PMCID: PMC4216126 DOI: 10.1371/journal.pone.0111648] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/01/2014] [Indexed: 12/11/2022] Open
Abstract
The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.
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Affiliation(s)
- Jun Mei
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Qizhen Guo
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yan Wu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yunfei Li
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- * E-mail:
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Diversity and functional characterization of Lactobacillus spp. isolated throughout the ripening of a hard cheese. Int J Food Microbiol 2014; 181:60-6. [DOI: 10.1016/j.ijfoodmicro.2014.04.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 04/01/2014] [Accepted: 04/18/2014] [Indexed: 12/24/2022]
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19
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A comparative study of different PCR-based DNA fingerprinting techniques for typing of lactic acid bacteria. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-014-2197-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Lazzi C, Turroni S, Mancini A, Sgarbi E, Neviani E, Brigidi P, Gatti M. Transcriptomic clues to understand the growth of Lactobacillus rhamnosus in cheese. BMC Microbiol 2014; 14:28. [PMID: 24506811 PMCID: PMC3928093 DOI: 10.1186/1471-2180-14-28] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 02/03/2014] [Indexed: 12/25/2022] Open
Abstract
Background Lactobacillus rhamnosus is a non-starter lactic acid bacterium that plays a significant role during cheese ripening, leading to the formation of flavor. In long-ripened cheeses it persists throughout the whole time of ripening due to its capacity to adapt to changing environmental conditions. The versatile adaptability of L. rhamnosus to different ecosystems has been associated with the capacity to use non-conventional energy sources, regulating different metabolic pathways. However, the molecular mechanisms allowing the growth of L. rhamnosus in the cheese dairy environment are still poorly understood. The aim of the present study was to identify genes potentially contributing to the growth ability of L. rhamnosus PR1019 in cheese-like medium (CB) using a transcriptomic approach, based on cDNA-amplified fragment length polymorphism (cDNA-AFLP) and quantitative real-time reverse transcription-PCR (qPCR). Results Using three primer combinations, a total of 89 and 98 transcript-derived fragments were obtained for L. rhamnosus PR1019 grown in commercial MRS medium and CB, respectively. The cDNA-AFLP results were validated on selected regulated genes by qPCR. In order to investigate the main adaptations to growth in a cheese-mimicking system, we focused on 20 transcripts over-expressed in CB with respect to MRS. It is worth noting the presence of transcripts involved in the degradation of pyruvate and ribose. Pyruvate is a intracellular metabolite that can be produced through different metabolic routes starting from the carbon sources present in cheese, and can be released in the cheese matrix with the starter lysis. Similarly the ribonucleosides released with starter lysis could deliver ribose that represents a fermentable carbohydrate in environments, such as cheese, where free carbohydrates are lacking. Both pyruvate degradation and ribose catabolism induce a metabolite flux toward acetate, coupled with ATP production via acetate kinase. Taking into account these considerations, we suggest that the energy produced through these pathways may concur to explain the great ability of L. rhamnosus PR1019 to grow on CB. Conclusions By a transcriptomic approach we identified a set of genes involved in alternative metabolic pathways in L. rhamnosus that could be responsible for L. rhamnosus growth in cheese during ripening.
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Affiliation(s)
- Camilla Lazzi
- Department of Food Science, Parma University, Parco Area delle Scienze 48/A, 43124 Parma, Italy.
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Gatti M, Bottari B, Lazzi C, Neviani E, Mucchetti G. Invited review: Microbial evolution in raw-milk, long-ripened cheeses produced using undefined natural whey starters. J Dairy Sci 2014; 97:573-91. [DOI: 10.3168/jds.2013-7187] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/09/2013] [Indexed: 11/19/2022]
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22
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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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23
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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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Identification of dairy lactic acid bacteria by tRNAAla–23S rDNA-RFLP. J Microbiol Methods 2012; 91:380-90. [DOI: 10.1016/j.mimet.2012.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/08/2012] [Accepted: 10/09/2012] [Indexed: 11/18/2022]
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25
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Bove CG, Angelis MD, Gatti M, Calasso M, Neviani E, Gobbetti M. Metabolic and proteomic adaptation of Lactobacillus rhamnosus
strains during growth under cheese-like environmental conditions compared to de Man, Rogosa, and Sharpe medium. Proteomics 2012; 12:3206-18. [DOI: 10.1002/pmic.201200157] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/20/2012] [Accepted: 08/22/2012] [Indexed: 11/09/2022]
Affiliation(s)
| | - Maria De Angelis
- Department of Soil; Plant and Food Science; University of Bari Aldo Moro; Bari Italy
| | - Monica Gatti
- Department of Food Science; University of Parma; Parma Italy
| | - Maria Calasso
- Department of Soil; Plant and Food Science; University of Bari Aldo Moro; Bari Italy
| | - Erasmo Neviani
- Department of Food Science; University of Parma; Parma Italy
| | - Marco Gobbetti
- Department of Soil; Plant and Food Science; University of Bari Aldo Moro; Bari Italy
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26
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Inventory of non starter lactic acid bacteria from ripened Parmigiano Reggiano cheese as assessed by a culture dependent multiphasic approach. Syst Appl Microbiol 2012; 35:270-7. [DOI: 10.1016/j.syapm.2012.04.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/20/2012] [Accepted: 04/23/2012] [Indexed: 11/23/2022]
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27
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Langford VS, Reed CJ, Milligan DB, McEwan MJ, Barringer SA, Harper WJ. Headspace Analysis of Italian and New Zealand Parmesan Cheeses. J Food Sci 2012; 77:C719-26. [DOI: 10.1111/j.1750-3841.2012.02730.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Bove CG, Lazzi C, Bernini V, Bottari B, Neviani E, Gatti M. cDNA-amplified fragment length polymorphism to study the transcriptional responses of Lactobacillus rhamnosus growing in cheese-like medium. J Appl Microbiol 2011; 111:855-64. [PMID: 21762473 DOI: 10.1111/j.1365-2672.2011.05101.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS Lactobacillus rhamnosus is a dominant species during Parmigiano Reggiano cheese ripening and exhibits a great adaptability to unfavourable growth conditions. Gene expression of a Lact. rhamnosus, isolated from Parmigiano Reggiano cheese, grown in a rich medium (MRS) and in a cheese-like medium (CB) has been compared by a novel cDNA-amplified fragment length polymorphism (cDNA-AFLP) protocol. METHODS AND RESULTS Two techniques, capillary and gel electrophoresis cDNA-AFLP, were applied to generate unique transcript tags from reverse-transcribed messenger RNA using the immobilization of biotinylated 3'-terminal cDNA fragments on streptavidin-coated Dynabeads. The use of three pairs of primers allowed detecting 64 genes expressed in MRS and 96 in CB. Different transcripts were observed when Lact. rhamnosus was cultured on CB and MRS. CONCLUSIONS The cDNA-AFLP approach proved to be able to show that Lact. rhamnosus modifies the expression of a large part of genes when cultivated in CB compared with growth under optimal conditions (MRS). In particular, the profiles of the strain grown in CB were more complex probably because the cells activate different metabolic pathways to generate energy and to respond to the environmental changes. SIGNIFICANCE AND IMPACT OF STUDY This is the first research on Lact. rhamnosus isolated from cheese and represents one of the few concerning bacterial transcriptomic analysis towards cDNA-AFLP approaches.
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Affiliation(s)
- C G Bove
- Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy.
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