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Magliulo R, Valentino V, Balivo A, Esposito A, Genovese A, Ercolini D, De Filippis F. Microbiome signatures associated with flavor development differentiate Protected Designation of origin water Buffalo Mozzarella cheese from different production areas. Food Res Int 2024; 192:114798. [PMID: 39147499 DOI: 10.1016/j.foodres.2024.114798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/17/2024]
Abstract
Water Buffalo Mozzarella (BM) is a typical cheese from Southern Italy with unique flavor profile and texture. It is produced following a traditional back-slopping procedure and received the Protected Designation of Origin (PDO) label. To better understand the link between the production area, the microbiome composition and the flavor profile of the products, we performed a multiomic characterization of PDO BM collected from 57 different dairies located in the two main PDO production area, i.e. Caserta (n = 35) and Salerno (n = 22). Thus, we assessed the microbiome by high-throughput shotgun metagenomic sequencing and the Volatile Organic Compounds (VOCs) by gas chromatography/mass spectrometry (GC/MS). Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. delbrueckii were identified as the core microbiome present in all samples. However, the microbiome taxonomic profiles resulted in a clustering of the samples based on their geographical origin, also showing that BM from Caserta had a greater microbial diversity. Consistently, Caserta and Salerno samples also showed different VOC profiles. These results suggest that the microbiome and its specific metabolic activity are part of the terroir that shape BM specific features, linking this traditional product with the area of production, thus opening new clues for improving traceability and fraud protection of traditional products.
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Affiliation(s)
- Raffaele Magliulo
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy; NBFC - National Biodiversity Future Center, Palermo, Italy
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy
| | - Andrea Balivo
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy
| | - Alessia Esposito
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy
| | - Alessandro Genovese
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy; NBFC - National Biodiversity Future Center, Palermo, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
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Fusco V, Fanelli F, Chieffi D. Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages. Foods 2023; 12:3782. [PMID: 37893675 PMCID: PMC10606304 DOI: 10.3390/foods12203782] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.
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Affiliation(s)
- Vincenzina Fusco
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), 70126 Bari, Italy; (F.F.); (D.C.)
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Fusco V, Chieffi D, De Angelis M. Invited review: Fresh pasta filata cheeses: Composition, role, and evolution of the microbiota in their quality and safety. J Dairy Sci 2022; 105:9347-9366. [DOI: 10.3168/jds.2022-22254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
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Isolation and Identification of Lactic Acid Bacteria from Natural Whey Cultures of Buffalo and Cow Milk. Foods 2022; 11:foods11020233. [PMID: 35053966 PMCID: PMC8774387 DOI: 10.3390/foods11020233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/24/2021] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
In southern Italy, some artisanal farms produce mozzarella and caciocavallo cheeses by using natural whey starter (NWS), whose microbial diversity is responsible for the characteristic flavor and texture of the final product. We studied the microbial community of NWS cultures of cow’s milk (NWSc) for the production of caciocavallo and buffalo’s milk (NWSb) for the production of mozzarella, both from artisanal farms. Bacterial identification at species and strain level was based on an integrative strategy, combining culture-dependent (sequencing of the 16S rDNA, species/subspecies-specific Polymerase Chain Reaction (PCR) and clustering by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) and culture-independent (next-generation sequencing analysis, NGS) approaches. Results obtained with both approaches showed the occurrence of five species of lactic acid bacteria in NWSb (Lactococcus lactis subsp. lactis, Lactobacillus fermentum, Streptococcus thermophilus, Lactobacillus delbrueckii, and Lactobacillus helveticus) and five species in NWSc (Lc. lactis subsp. lactis, Enterococcus faecium, and S. thermophilus, Lb. helveticus, and Lb. delbrueckii), with the last two found only by the NGS analysis. Moreover, RAPD profiles, performed on Lc. lactis subsp. lactis different isolates from both NWSs, showed nine strains in NWSb and seven strains in NWSc, showing a microbial diversity also at strain level. Characterization of the microbiota of natural whey starters aims to collect new starter bacteria to use for tracing microbial community during the production of artisanal cheeses, in order to preserve their quality and authenticity, and to select new Lactic Acid Bacteria (LAB) strains for the production of functional foods.
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Dimitrakopoulou ME, Panteleli E, Vantarakis A. Improved PCR-DGGE analysis by emulsion-PCR for the determination of food geographical origin: A case study on Greek PDO "avgotaracho Mesolonghiou". Curr Res Food Sci 2021; 4:746-751. [PMID: 34746808 PMCID: PMC8554341 DOI: 10.1016/j.crfs.2021.10.005] [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: 05/19/2021] [Revised: 09/29/2021] [Accepted: 10/11/2021] [Indexed: 11/15/2022] Open
Abstract
Greek avgotaracho Mesolonghiou (fish eggs from Flathead Mullet) is a highly valuable food product which holds Protected Destination of Origin status. The aim of this work was to use PCR-DGGE technique to examine whether there is a correlation between bacteria population in fish eggs and geographical origin. Cluster analysis of fish eggs from three geographical locations (Mesolonghi, Australia and Mauritania) discriminated samples according to their provenance. Moreover, we utilized emulsion-PCR amplification in DGGE analysis in order to investigate whether we could obtain further information about food products’ bacteria communities. PCR-DGGE proved to be a suitable method for fish eggs traceability, moreover emulsion PCR-DGGE provides better results. Emulsion-PCR can face up the existing limitations of conventional PCR and thus can be demonstrated as alternative molecular technique for complex and processed matrices, regarding food traceability and authentication. Traceability of Greek PDO “avgotaracho Mesolonghiou” by PCR-DGGE is presented. Emulsion PCR for DGGE” improves analysis of microbial communities. Emulsion PCR for DGGE improves geographical traceability of food. Emulsion PCR as an alternative molecular method for food traceability and authentication.
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Affiliation(s)
| | - Efstratia Panteleli
- Department of Public Health, Medical School, University of Patras, Patras, Greece
| | - Apostolos Vantarakis
- Department of Public Health, Medical School, University of Patras, Patras, Greece
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Biodiversity and succession of lactic microbiota involved in Brazilian buffalo mozzarella cheese production. Braz J Microbiol 2021; 53:303-316. [PMID: 34661886 DOI: 10.1007/s42770-021-00629-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022] Open
Abstract
The biodiversity and succession of lactic acid bacteria (LAB) involved in the production and storage of Brazilian buffalo mozzarella cheese were evaluated. The isolates were characterized by Gram staining and catalase test, by the ability to grow at different conditions: temperatures, pH, concentrations of NaCl, and production of CO2 from glucose. The biodiversity and succession of 152 LAB isolated during cheese production were evaluated by 16S rRNA gene sequencing, Random Amplified Polymorphic DNA (RAPD-PCR), and Restriction Fragment Length Polymorphism (RFLP-PCR) techniques. Most of the strains grow well at 30 °C and are tolerant to 6.5% of NaCl, and in general, the best pH for growing was 9.6. Leuconostoc mesenteroides, Lacticaseibacillus casei, Limosilactobacillus fermentum, and Enterococcus sp. were prevalent and present in almost all steps of production. The LAB strains are typically found in the traditional Italian cheese, except the Leuconostoc citreum species. Sixty clusters were obtained by RAPD-PCR with 85% of similarity (114 isolates) while most of the LAB was clustered with 100% of similarity by the RFLP-PCR technique. The applied techniques enabled a valuable elucidation of the LAB biodiversity and succession, contributing to a better understanding of the specific microbial cultures with a technological aptitude of this cheese.
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Miragoli F, Patrone V, Romaniello F, Rebecchi A, Callegari ML. Development of an S-layer gene-based PCR-DGGE assay for monitoring dominant Lactobacillus helveticus strains in natural whey starters of Grana Padano cheese. Food Microbiol 2020; 89:103457. [DOI: 10.1016/j.fm.2020.103457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/11/2019] [Accepted: 02/08/2020] [Indexed: 10/25/2022]
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Iacumin L, Cecchini F, Vendrame M, Comi G. Emulsion PCR (ePCR) as a Tool to Improve the Power of DGGE Analysis for Microbial Population Studies. Microorganisms 2020; 8:microorganisms8081099. [PMID: 32717823 PMCID: PMC7465085 DOI: 10.3390/microorganisms8081099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/26/2022] Open
Abstract
To the authors’ knowledge, this is the first report of the use of emulsion-Polymerase chain reaction (e-PCR) coupled with denaturing gradient gel electrophoresis (DGGE) analysis. In the present work the effectiveness of ePCR in improving the power of the DGGE technique for microbial population studies was tested. Our results indicated that ePCR results in uniform amplification of several DNA molecules, overcoming the major limitations of conventional PCR, such as preferential amplification and DNA concentration dependence. Moreover, ePCR-DGGE resulted in higher sensitivity when compared to conventional PCR-DGGE methods used for studying microbial populations in a complex matrix. In fact, compared to conventional PCR, the DGGE profiles of ePCR products permitted the detection of a higher number of the species that were present in the tested sample.
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Biolcati F, Andrighetto C, Bottero MT, Dalmasso A. Microbial characterization of an artisanal production of Robiola di Roccaverano cheese. J Dairy Sci 2020; 103:4056-4067. [DOI: 10.3168/jds.2019-17451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/14/2020] [Indexed: 01/26/2023]
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Safety and technological application of autochthonous Streptococcus thermophilus cultures in the buffalo Mozzarella cheese. Food Microbiol 2019; 87:103383. [PMID: 31948624 DOI: 10.1016/j.fm.2019.103383] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/03/2019] [Accepted: 11/16/2019] [Indexed: 11/20/2022]
Abstract
Thermophilic and mesophilic lactic acid bacteria (LAB), such as Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus helveticus, and Lactococcus lactis, play a crucial role in the technological and sensory quality of Mozzarella cheese. In this study, the safety (genes encoding virulence factors and antibiotic resistance) and acidifying activity of autochthonous S. thermophilus cultures were evaluated in order to choose the most suitable strain for industrial application. The safe and good acidifying culture was tested in two buffalo Mozzarella cheese batches: Mozzarella cheeses produced with autochthonous culture (SJRP107) and commercial culture (STM5). The cultivable LAB was evaluated by culture-dependent method (plate counting) and the quantification of S. thermophilus cultures (commercial and autochthonous) were evaluated by culture-independent method RealT-qPCR (real-time quantitative polymerase chain reaction). The texture, physicochemical and proteolytic properties of the Mozzarella cheeses were similar for both batches. The nonstarter LAB count was higher during manufacture than in the storage, and the RealT-qPCR indicated the presence of S. thermophilus culture until the end of storage. S. thermophilus SJRP107 presented high potential for safety application in the production of Mozzarella cheese. Furthermore, considering the culture characteristics and their relationship with product quality, further studies could be helpful to determine their effect on the sensory characteristics of the cheese.
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Gong S, Fei P, Ali A, Cai X, Xue W, Jiang W, Guo L. Effect of milk types on the attributes of a glutinous rice wine-fermented yogurt-like product. J Dairy Sci 2019; 103:220-227. [PMID: 31704015 DOI: 10.3168/jds.2019-17091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/17/2019] [Indexed: 01/15/2023]
Abstract
This study was conducted to analyze the effect of milk types on the attributes of the glutinous rice wine-fermented yogurt-like product named Kouwan Lao (KWL). Four types of raw milks were used in this study, including high temperature, long time (HTLT: H milk), HTLT milk supplemented with 3% skim milk powder (S milk), pasteurized milk (P milk), and ultra-high temperature milk (U milk). Microbiological compositions of the fermented glutinous rice and KWL at different stages were analyzed using PCR-denaturing gradient gel electrophoresis and gene sequencing based on 16S rRNA and 26S rRNA. The physicochemical properties of KWL samples were determined, and textural properties of those were analyzed using a texture analyzer (Jiawei Innovation and Technology Co. Ltd., Zhejiang Province, China). The microstructure of KWL samples was observed using scanning electron microscopy. The results showed that the milk types had significant influences on the bacterial composition of KWL. In the curdling process, the predominant bacteria of H, S, P, and U KWL samples were Lactobacillus brevis, Janthinobacterium sp., Lactobacillus casei, and Streptococcus agalactiae, respectively. In the ripening process, the main strains in H KWL were Enterococcus faecium and Pediococcus pentosaceus. Lactobacillus casei and Lactobacillus paracasei were the dominant bacteria of U KWL. Lactobacillus casei was the main strain of P KWL, and no bacteria were detected in S KWL. Saccharomyces cerevisiae was the dominant fungus of KWL, and no significant effect of milk types on fungal composition of KWL was found. The results of physicochemical properties showed that significant differences in protein contents were found in the KWL samples, and P KWL had the highest protein content. The fat content of U KWL was significantly higher than that of samples from the other 3 groups. The U KWL and P KWL showed lower moisture than that of the other 2 KWL samples. In addition, no significant difference in pH value was found in all samples. The results of texture analysis and microstructure showed that compared with other 3 types of KWL samples, the related mass parameters of U KWL were more advantageous and improved significantly with the increase of the heat treatment temperature of raw milk and the addition of skim milk powder. Our findings revealed the effects of milk types on microbial composition, physicochemical properties, textural properties, and microstructure of KWL, and provided a basic theory for the optimization and industrial production of KWL.
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Affiliation(s)
- Shaoying Gong
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Peng Fei
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Aslam Ali
- Department of Agro-Processing, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706, Bangladesh
| | - Xiaolin Cai
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Wei Xue
- Heilongjiang Metrology Institute of Measurement and Verification, No. 99, Situ Street, Xiangfang District, Harbin, Heilongjiang, China 150036
| | - Wen Jiang
- National Agricultural Standardization Monitoring and Research Center (Heilongjiang), No. 1218, Chuangxin'er Road, Songbei District, Harbin, Heilongjiang, China 150028
| | - Ling Guo
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China.
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Sha SP, Suryavanshi MV, Jani K, Sharma A, Shouche Y, Tamang JP. Diversity of Yeasts and Molds by Culture-Dependent and Culture-Independent Methods for Mycobiome Surveillance of Traditionally Prepared Dried Starters for the Production of Indian Alcoholic Beverages. Front Microbiol 2018; 9:2237. [PMID: 30319566 PMCID: PMC6169615 DOI: 10.3389/fmicb.2018.02237] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/03/2018] [Indexed: 12/25/2022] Open
Abstract
Marcha, thiat, dawdim, hamei, humao, khekhrii, chowan, and phut are traditionally prepared dried starters used for production of various ethnic alcoholic beverages in North East states of India. The surveillance of mycobiome associated with these starters have been revealed by culture-dependent methods using phenotypic and molecular tools. We identified Wickerhamomyces anomalus, Pichia anomala, Saccharomycopsis fibuligera, Pichia terricola, Pichia kudriavzevii, and Candida glabrata by ITS-PCR. The diversity of yeasts and molds in all 40 samples was also investigated by culture-independent method using PCR-DGGE analysis. The average distributions of yeasts showed Saccharomyces cerevisiae (16.5%), Saccharomycopsis fibuligera (15.3%), Wickerhamomyces anomalus (11.3%), S. malanga (11.7%), Kluyveromyces marxianus (5.3%), Meyerozyma sp. (2.7%), Candida glabrata (2.7%), and many strains below 2%. About 12 strains of molds were also identified based on PCR-DGGE analysis which included Aspergillus penicillioides (5.0%), Rhizopus oryzae (3.3%), and sub-phylum: Mucoromycotina (2.1%). Different techniques used in this paper revealed the diversity and differences of mycobiome species in starter cultures of India which may be referred as baseline data for further research.
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Affiliation(s)
- Shankar Prasad Sha
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Mangesh Vasant Suryavanshi
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India.,National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Jyoti Prakash Tamang
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
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Yunita D, Dodd CE. Microbial community dynamics of a blue-veined raw milk cheese from the United Kingdom. J Dairy Sci 2018; 101:4923-4935. [DOI: 10.3168/jds.2017-14104] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/10/2018] [Indexed: 11/19/2022]
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14
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Attar MA, Yavarmanesh M, Mortazavi A, Edalatian Dovom MR, Habibi Najafi MB. Antibacterial effects of Lactococcus lactis isolated from Lighvan cheese regarding the recognition of Nisin, Lacticin and Lactococcin structural genes. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Cuevas-González PF, Heredia-Castro PY, Méndez-Romero JI, Hernández-Mendoza A, Reyes-Díaz R, Vallejo-Cordoba B, González-Córdova AF. Artisanal Sonoran cheese (Cocido cheese): an exploration of its production process, chemical composition and microbiological quality. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:4459-4466. [PMID: 28295334 DOI: 10.1002/jsfa.8309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 03/05/2017] [Accepted: 03/06/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND The objective of this study was to explore and document the production process of artisanal Cocido cheese and to determine its chemical composition and microbiological quality, considering samples from six dairies and four retailers. RESULTS Cocido cheese is a semi-hard (506-555 g kg-1 of moisture), medium fat (178.3-219.1 g kg-1 ), pasta filata-type cheese made from raw whole cow's milk. The production process is not standardized and therefore the chemical and microbiological components of the sampled cheeses varied. Indicator microorganisms significantly decreased (P < 0.05) during the processing of Cocido cheese. Salmonella spp. were not found during the production process, and both Listeria monocytogenes and staphylococcal enterotoxin were absent in the final cheeses. CONCLUSION This study provides more information on one of the most popular artisanal cheeses with high cultural value and economic impact in northwestern Mexico. In view of the foregoing, good manufacturing practices need to be implemented for the manufacture of Cocido cheese. Also, it is of utmost importance to make sure that the heat treatment applied for cooking the curd ensures a phosphatase-negative test, otherwise it would be necessary to pasteurize milk. Nevertheless, since Cocido cheese is a non-ripened, high-moisture product, it is a highly perishable product that could present a health risk if not properly handled. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Paúl F Cuevas-González
- Laboratorio de Química y Biotecnología de Productos Lácteos, Coordinación de Tecnología de Alimentos de Origen Animal (CTAOA), Centro de Investigación en Alimentación y Desarrollo (CIAD), Hermosillo, Sonora, Mexico
| | - Priscilia Y Heredia-Castro
- Laboratorio de Química y Biotecnología de Productos Lácteos, Coordinación de Tecnología de Alimentos de Origen Animal (CTAOA), Centro de Investigación en Alimentación y Desarrollo (CIAD), Hermosillo, Sonora, Mexico
| | - José I Méndez-Romero
- Laboratorio de Química y Biotecnología de Productos Lácteos, Coordinación de Tecnología de Alimentos de Origen Animal (CTAOA), Centro de Investigación en Alimentación y Desarrollo (CIAD), Hermosillo, Sonora, Mexico
| | - Adrián Hernández-Mendoza
- Laboratorio de Química y Biotecnología de Productos Lácteos, Coordinación de Tecnología de Alimentos de Origen Animal (CTAOA), Centro de Investigación en Alimentación y Desarrollo (CIAD), Hermosillo, Sonora, Mexico
| | - Ricardo Reyes-Díaz
- Laboratorio de Química y Biotecnología de Productos Lácteos, Coordinación de Tecnología de Alimentos de Origen Animal (CTAOA), Centro de Investigación en Alimentación y Desarrollo (CIAD), Hermosillo, Sonora, Mexico
| | - Belinda Vallejo-Cordoba
- Laboratorio de Química y Biotecnología de Productos Lácteos, Coordinación de Tecnología de Alimentos de Origen Animal (CTAOA), Centro de Investigación en Alimentación y Desarrollo (CIAD), Hermosillo, Sonora, Mexico
| | - Aarón F González-Córdova
- Laboratorio de Química y Biotecnología de Productos Lácteos, Coordinación de Tecnología de Alimentos de Origen Animal (CTAOA), Centro de Investigación en Alimentación y Desarrollo (CIAD), Hermosillo, Sonora, Mexico
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Real-time PCR is a potential tool to determine the origin of milk used in cheese production. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2016.11.065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Li J, Zheng Y, Xu H, Xi X, Hou Q, Feng S, Wuri L, Bian Y, Yu Z, Kwok LY, Sun Z, Sun T. Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses. BMC Microbiol 2017; 17:13. [PMID: 28068902 PMCID: PMC5223556 DOI: 10.1186/s12866-016-0911-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 12/10/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial diversity profiles of 6 traditional artisanal cheese samples of Kazakhstan origin, followed by comparatively analyzed the microbiota composition between the current dataset and those from cheeses originated from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy. RESULTS Across the Kazakhstan cheese samples, a total of 238 bacterial species belonging to 14 phyla and 140 genera were identified. Lactococcus lactis (28.93%), Lactobacillus helveticus (26.43%), Streptococcus thermophilus (12.18%) and Lactobacillus delbrueckii (12.15%) were the dominant bacterial species for these samples. To further evaluate the cheese bacterial diversity of Kazakhstan cheeses in comparison with those from other geographic origins, 16S rRNA datasets of 36 artisanal cheeses from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy were retrieved from public databases. The cheese bacterial microbiota communities were largely different across sample origins. By principal coordinate analysis (PCoA) and multivariate analysis of variance (MANOVA), the structure of the Kazakhstan artisanal cheese samples was found to be different from those of the other geographic origins. Furthermore, the redundancy analysis (RDA) identified 16 bacterial OTUs as the key variables responsible for such microbiota structural difference. CONCLUSION Our results together suggest that the diversity of bacterial communities in different groups is stratified by geographic region. This study does not only provide novel information on the bacterial microbiota of traditional artisanal cheese of Kazakhstan at species level, but also interesting insights into the bacterial diversity of artisanal cheeses of various geographical origins.
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Affiliation(s)
- Jing Li
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Yi Zheng
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Xiaoxia Xi
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Shuzhen Feng
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Laga Wuri
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Yanfei Bian
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Zhongjie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Tiansong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.
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Seasonal variations of Italian Mediterranean Buffalo (Bubalus bubalis) Mozzarella cheese quality. J DAIRY RES 2016; 83:476-478. [PMID: 27845021 DOI: 10.1017/s0022029916000649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Water buffalo Mozzarella cheese is more appreciated in the summer, but milk production is higher during wintertime, as water buffalo are seasonally polyoestrous animals. The aim of the study reported in this Research Communication was to evaluate the effect of the reversing of the calving period on Mozzarella cheese composition and quality traits. Ten batches of Mozzarella cheeses produced during the summer and winter periods were analysed for pH, colour, chemical composition. Seasonal differences were observed for cheese yield (26·66% in winter and 25·61% in summer), moisture content (66·54% in winter and 61·18% in summer) colour and consumer evaluation.
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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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Corsaro C, Cicero N, Mallamace D, Vasi S, Naccari C, Salvo A, Giofrè SV, Dugo G. HR-MAS and NMR towards Foodomics. Food Res Int 2016. [DOI: 10.1016/j.foodres.2016.09.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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21
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Bozoudi D, Torriani S, Zdragas A, Litopoulou-Tzanetaki E. Assessment of microbial diversity of the dominant microbiota in fresh and mature PDO Feta cheese made at three mountainous areas of Greece. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.04.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Aquilanti L, Santarelli S, Babini V, Osimani A, Garofalo C, Polverigiani S, Clementi F. PCR-DGGE for the profiling of cheese bacterial communities: strengths and weaknesses of a poorly explored combined approach. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s13594-016-0296-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Puppo S, Grandoni F, Ferri B, Antonelli S, Chiariotti A, Cuscunä F. Comparison between two hay based diets in buffalo nutrition: microbiological characteristics of milk, curd and mozzarella cheese. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2007.s2.524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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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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25
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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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26
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Guidone A, Zotta T, Matera A, Ricciardi A, De Filippis F, Ercolini D, Parente E. The microbiota of high-moisture mozzarella cheese produced with different acidification methods. Int J Food Microbiol 2016; 216:9-17. [DOI: 10.1016/j.ijfoodmicro.2015.09.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/20/2015] [Accepted: 09/04/2015] [Indexed: 12/17/2022]
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27
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Evolution of microbial counts and chemical and physico-chemical parameters in high-moisture Mozzarella cheese during refrigerated storage. Lebensm Wiss Technol 2015. [DOI: 10.1016/j.lwt.2015.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Garofalo C, Osimani A, Milanović V, Aquilanti L, De Filippis F, Stellato G, Di Mauro S, Turchetti B, Buzzini P, Ercolini D, Clementi F. Bacteria and yeast microbiota in milk kefir grains from different Italian regions. Food Microbiol 2015; 49:123-33. [DOI: 10.1016/j.fm.2015.01.017] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/07/2015] [Accepted: 01/31/2015] [Indexed: 01/23/2023]
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Sardina MT, Tortorici L, Mastrangelo S, Di Gerlando R, Tolone M, Portolano B. Application of microsatellite markers as potential tools for traceability of Girgentana goat breed dairy products. Food Res Int 2015; 74:115-122. [DOI: 10.1016/j.foodres.2015.04.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 04/02/2015] [Accepted: 04/12/2015] [Indexed: 11/29/2022]
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30
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Flórez AB, Mayo B. Diversity and dynamics of antibiotic-resistant bacteria in cheese as determined by PCR denaturing gradient gel electrophoresis. Int J Food Microbiol 2015; 214:63-69. [PMID: 26241491 DOI: 10.1016/j.ijfoodmicro.2015.07.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/14/2015] [Accepted: 07/20/2015] [Indexed: 11/29/2022]
Abstract
This work reports the composition and succession of tetracycline- and erythromycin-resistant bacterial communities in a model cheese, monitored by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). Bacterial 16S rRNA genes were examined using this technique to detect structural changes in the cheese microbiota over manufacturing and ripening. Total bacterial genomic DNA, used as a template, was extracted from cultivable bacteria grown without and with tetracycline or erythromycin (both at 25 μg ml(-1)) on a non-selective medium used for enumeration of total and viable cells (Plate Count agar with Milk; PCA-M), and from those grown on selective and/or differential agar media used for counting various bacterial groups; i.e., lactic acid bacteria (de Man, Rogosa and Sharpe agar; MRSA), micrococci and staphylococci (Baird-Parker agar; BPA), and enterobacteria (Violet Red Bile Glucose agar; VRBGA). Large numbers of tetracycline- and erythromycin-resistant bacteria were detected in cheese samples at all stages of ripening. Counts of antibiotic-resistant bacteria varied widely depending on the microbial group and the point of sampling. In general, resistant bacteria were 0.5-1.0 Log10 units fewer in number than the corresponding susceptible bacteria. The PCR-DGGE profiles obtained with DNA isolated from the plates for total bacteria and the different bacterial groups suggested Escherichia coli, Lactococcus lactis, Enterococcus faecalis and Staphylococcus spp. as the microbial types resistant to both antibiotics tested. This study shows the suitability of the PCR-DGGE technique for rapidly identifying and tracking antibiotic resistant populations in cheese and, by extension, in other foods.
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Affiliation(s)
- Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares, s/n, 33300-Villaviciosa, Asturias, Spain.
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares, s/n, 33300-Villaviciosa, Asturias, Spain
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31
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Ricciardi A, Guidone A, Ianniello RG, Cioffi S, Aponte M, Pavlidis D, Tsakalidou E, Zotta T, Parente E. A survey of non-starter lactic acid bacteria in traditional cheeses: Culture dependent identification and survival to simulated gastrointestinal transit. Int Dairy J 2015. [DOI: 10.1016/j.idairyj.2014.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Silva LF, Casella T, Gomes ES, Nogueira MCL, De Dea Lindner J, Penna ALB. Diversity of Lactic Acid Bacteria Isolated from Brazilian Water Buffalo Mozzarella Cheese. J Food Sci 2015; 80:M411-7. [DOI: 10.1111/1750-3841.12771] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 04/12/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Luana Faria Silva
- UNESP-São Paulo State Univ; Food Engineering and Technology Dept; São José do Rio Preto Brazil
| | - Tiago Casella
- FAMERP-Medical School of São José do Rio Preto; Microbiology Laboratory; São José do Rio Preto Brazil
| | | | | | - Juliano De Dea Lindner
- UFSC-Federal Univ. of Santa Catarina; Food Science and Technology Dept; Florianópolis Brazil
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Guidone A, Braghieri A, Cioffi S, Claps S, Genovese F, Morone G, Napolitano F, Parente E. Effect of adjuncts on microbiological and chemical properties of Scamorza cheese. J Dairy Sci 2015; 98:1467-78. [PMID: 25582584 DOI: 10.3168/jds.2014-8554] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/22/2014] [Indexed: 11/19/2022]
Abstract
Scamorza is a semi-hard, pasta filata cheese resembling low-moisture Mozzarella cheese, with a short ripening time (<30d). Scamorza has a bland flavor and, to provide diversification from similar cheeses, it was manufactured using 2 types of milk in the current study: 100% Italian Friesian milk (F) or 90% F and 10% Jersey cow milk (mixed, M), and 2 types of starter: Streptococcus thermophilus or S. thermophilus with peptidolytic Lactococcus lactis, Lactobacillus helveticus, and Lactobacillus paracasei strains as adjuncts). The cheeses were ripened for 30d. The adjunct did not significantly affect acid production or growth of the primary starter; 2 of the species used in the adjunct (Lb. paracasei and Lb. helveticus) rapidly colonized the cheese and persisted until the end of ripening, whereas the counts of nonstarter lactic acid bacteria in the control cheese were low until the end of ripening. The use of adjuncts affected pH, microbial composition (as assessed by both culture-dependent and culture-independent methods), total free amino acid content, and volatile profile (measured using an electronic nose), whereas milk type had only a minor effect. Although differences in primary proteolysis were found, they were probably indirect and related to the effects on pH and moisture. We conclude that, even with a short ripening time (30d), use of a peptidolytic adjunct may significantly affect important features of Scamorza and may be used to create a product that is measurably different from competing products.
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Affiliation(s)
- Angela Guidone
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Ada Braghieri
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Silvia Cioffi
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Salvatore Claps
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Unità di ricerca per la Zootecnia Estensiva, 85054 Muro Lucano (PZ), Italy
| | - Francesco Genovese
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Giuseppe Morone
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Unità di ricerca per la Zootecnia Estensiva, 85054 Muro Lucano (PZ), Italy
| | - Fabio Napolitano
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Eugenio Parente
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy.
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34
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Wu Q, Cheung CK, Shah NP. Towards galactose accumulation in dairy foods fermented by conventional starter cultures: Challenges and strategies. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2014.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Mayo B, Rachid CTCC, Alegría A, Leite AMO, Peixoto RS, Delgado S. Impact of next generation sequencing techniques in food microbiology. Curr Genomics 2014; 15:293-309. [PMID: 25132799 PMCID: PMC4133952 DOI: 10.2174/1389202915666140616233211] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 06/04/2014] [Accepted: 06/13/2014] [Indexed: 02/07/2023] Open
Abstract
Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.
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Affiliation(s)
- Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
| | - Caio T C C Rachid
- Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Angel Alegría
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
| | - Analy M O Leite
- Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Raquel S Peixoto
- Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Susana Delgado
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
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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: 232] [Impact Index Per Article: 23.2] [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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Lv XC, Huang XL, Zhang W, Rao PF, Ni L. Yeast diversity of traditional alcohol fermentation starters for Hong Qu glutinous rice wine brewing, revealed by culture-dependent and culture-independent methods. Food Control 2013. [DOI: 10.1016/j.foodcont.2013.04.020] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation. Int J Food Microbiol 2013; 167:29-43. [DOI: 10.1016/j.ijfoodmicro.2013.05.008] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 04/29/2013] [Accepted: 05/09/2013] [Indexed: 12/21/2022]
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Quigley L, O'Sullivan O, Stanton C, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. The complex microbiota of raw milk. FEMS Microbiol Rev 2013; 37:664-98. [PMID: 23808865 DOI: 10.1111/1574-6976.12030] [Citation(s) in RCA: 471] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 06/14/2013] [Accepted: 06/18/2013] [Indexed: 12/15/2022] Open
Abstract
Here, we review what is known about the microorganisms present in raw milk, including milk from cows, sheep, goats and humans. Milk, due to its high nutritional content, can support a rich microbiota. These microorganisms enter milk from a variety of sources and, once in milk, can play a number of roles, such as facilitating dairy fermentations (e.g. Lactococcus, Lactobacillus, Streptococcus, Propionibacterium and fungal populations), causing spoilage (e.g. Pseudomonas, Clostridium, Bacillus and other spore-forming or thermoduric microorganisms), promoting health (e.g. lactobacilli and bifidobacteria) or causing disease (e.g. Listeria, Salmonella, Escherichia coli, Campylobacter and mycotoxin-producing fungi). There is also concern that the presence of antibiotic residues in milk leads to the development of resistance, particularly among pathogenic bacteria. Here, we comprehensively review these topics, while comparing the approaches, both culture-dependent and culture-independent, which can be taken to investigate the microbial composition of milk.
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Affiliation(s)
- Lisa Quigley
- Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
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Delgado S, Rachid CTCC, Fernández E, Rychlik T, Alegría A, Peixoto RS, Mayo B. Diversity of thermophilic bacteria in raw, pasteurized and selectively-cultured milk, as assessed by culturing, PCR-DGGE and pyrosequencing. Food Microbiol 2013; 36:103-11. [PMID: 23764225 DOI: 10.1016/j.fm.2013.04.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 04/18/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
Abstract
Thermophilic lactic acid bacteria (LAB) species, such as Streptococcus thermophilus, Lactobacillus delbrueckii and Lactobacillus helveticus, enjoy worldwide economic importance as dairy starters. To assess the diversity of thermophilic bacteria in milk, milk samples were enriched in thermophilic organisms through a stepwise procedure which included pasteurization of milk at 63 °C for 30 min (PM samples) and pasteurization followed by incubation at 42 °C for 24 h (IPM samples). The microbial composition of these samples was analyzed by culture-dependent (at 42 °C) and culture-independent (PCR-DGGE and pyrosequencing of 16S rRNA gene amplicons) microbial techniques. The results were then compared to those obtained for their corresponding starting raw milk counterparts (RM samples). Twenty different species were scored by culturing among 352 isolates purified from the counting plates and identified by molecular methods. Mesophilic LAB species (Lactococcus lactis, Lactococcus garvieae) were dominant (87% of the isolates) among the RM samples. However, S. thermophilus and Lb. delbrueckii were found to be the dominant recoverable organisms in both PM and IPM samples. The DGGE profiles of RM and PM samples were found to be very similar; the most prominent bands belonging to Lactococcus, Leuconostoc and Streptococcus species. In contrast, just three DGGE bands were obtained for IPM samples, two of which were assigned to S. thermophilus. The pyrosequencing results scored 95 operational taxonomic units (OTUs) at 3% sequence divergence in an RM sample, while only 13 were encountered in two IPM samples. This technique identified Leuconostoc citreum as the dominant microorganism in the RM sample, while S. thermophilus constituted more than 98% of the reads in the IPM samples. The procedure followed in this study allowed to estimate the bacterial diversity in milk and afford a suitable strategy for the isolation of new thermophilic LAB strains, among which adequate starters might be selected.
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Affiliation(s)
- Susana Delgado
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias-IPLA-CSIC, Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
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Aquilanti L, Santarelli S, Babini V, Osimani A, Clementi F. Quality evaluation and discrimination of semi-hard and hard cheeses from the Marche region (Central Italy) using chemometric tools. Int Dairy J 2013. [DOI: 10.1016/j.idairyj.2012.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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Arcuri EF, El Sheikha AF, Rychlik T, Piro-Métayer I, Montet D. Determination of cheese origin by using 16S rDNA fingerprinting of bacteria communities by PCR–DGGE: Preliminary application to traditional Minas cheese. Food Control 2013. [DOI: 10.1016/j.foodcont.2012.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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43
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"Remake" by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese. Appl Environ Microbiol 2012; 78:8142-5. [PMID: 22941080 DOI: 10.1128/aem.02218-12] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Intermediates of production of two batches of traditional mozzarella cheese were analyzed by culture-independent pyrosequencing. The quantitative distribution of taxa within the samples suggested that thermophilic lactic acid bacteria from the natural starter were mainly responsible for the fermentation, while microorganisms found in raw milk did not develop during fermentation.
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Deperrois-Lafarge V, Meheut T. Use of the rpoB gene as an alternative to the V3 gene for the identification of spoilage and pathogenic bacteria species in milk and milk products. Lett Appl Microbiol 2012; 55:99-108. [DOI: 10.1111/j.1472-765x.2012.03261.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mazzei P, Piccolo A. 1H HRMAS-NMR metabolomic to assess quality and traceability of mozzarella cheese from Campania buffalo milk. Food Chem 2012; 132:1620-1627. [DOI: 10.1016/j.foodchem.2011.11.142] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 10/05/2011] [Accepted: 11/17/2011] [Indexed: 11/25/2022]
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46
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Microbial diversity of the traditional Iranian cheeses Lighvan and Koozeh, as revealed by polyphasic culturing and culture-independent approaches. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s13594-011-0045-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Quigley L, O'Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese. Int J Food Microbiol 2011; 150:81-94. [PMID: 21868118 DOI: 10.1016/j.ijfoodmicro.2011.08.001] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 10/17/2022]
Abstract
The availability and application of culture-independent tools that enable a detailed investigation of the microbiota and microbial biodiversity of food systems has had a major impact on food microbiology. This review focuses on the application of DNA-based technologies, such as denaturing gradient gel electrophoresis (DGGE), temporal temperature gradient gel electrophoresis (TTGE), single stranded conformation polymorphisms (SSCP), the polymerase chain reaction (PCR) and others, to investigate the diversity, dynamics and identity of microbes in dairy products from raw milk. Here, we will highlight the benefits associated with culture-independent methods which include enhanced sensitivity, rapidity and the detection of microorganisms not previously associated with such products.
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Affiliation(s)
- Lisa Quigley
- Teagasc, Moorepark Food Research Centre, Fermoy, Cork, Ireland
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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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49
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Aquilanti L, Babini V, Santarelli S, Osimani A, Petruzzelli A, Clementi F. Bacterial dynamics in a raw cow’s milk Caciotta cheese manufactured with aqueous extract of Cynara cardunculus dried flowers. Lett Appl Microbiol 2011; 52:651-9. [DOI: 10.1111/j.1472-765x.2011.03053.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Devirgiliis C, Barile S, Perozzi G. Antibiotic resistance determinants in the interplay between food and gut microbiota. GENES AND NUTRITION 2011; 6:275-84. [PMID: 21526400 PMCID: PMC3145056 DOI: 10.1007/s12263-011-0226-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 04/07/2011] [Indexed: 01/31/2023]
Abstract
A complex and heterogeneous microflora performs sugar and lactic acid fermentations in food products. Depending on the fermentable food matrix (dairy, meat, vegetable etc.) as well as on the species composition of the microbiota, specific combinations of molecules are produced that confer unique flavor, texture, and taste to each product. Bacterial populations within such “fermented food microbiota” are often of environmental origin, they persist alive in foods ready for consumption, eventually reaching the gastro-intestinal tract where they can interact with the resident gut microbiota of the host. Although this interaction is mostly of transient nature, it can greatly contribute to human health, as several species within the food microbiota also display probiotic properties. Such an interplay between food and gut microbiota underlines the importance of the microbiological quality of fermented foods, as the crowded environment of the gut is also an ideal site for genetic exchanges among bacteria. Selection and spreading of antibiotic resistance genes in foodborne bacteria has gained increasing interest in the past decade, especially in light of the potential transferability of antibiotic resistance determinants to opportunistic pathogens, natural inhabitants of the human gut but capable of acquiring virulence in immunocompromised individuals. This review aims at describing major findings and future prospects in the field, especially after the use of antibiotics as growth promoters was totally banned in Europe, with special emphasis on the application of genomic technologies to improve quality and safety of fermented foods.
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Affiliation(s)
- Chiara Devirgiliis
- INRAN, National Research Institute on Food and Nutrition, Via Ardeatina 546, 00178 Rome, Italy
| | - Simona Barile
- INRAN, National Research Institute on Food and Nutrition, Via Ardeatina 546, 00178 Rome, Italy
| | - Giuditta Perozzi
- INRAN, National Research Institute on Food and Nutrition, Via Ardeatina 546, 00178 Rome, Italy
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