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Reuben RC, Langer D, Eisenhauer N, Jurburg SD. Universal drivers of cheese microbiomes. iScience 2023; 26:105744. [PMID: 36582819 PMCID: PMC9792889 DOI: 10.1016/j.isci.2022.105744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/25/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
The culinary value, quality, and safety of cheese are largely driven by the resident bacteria, but comparative analyses of the cheese microbiota across cheese types are scarce. We present the first global synthesis of cheese microbiomes. Following a systematic literature review of cheese microbiology research, we collected 16S rRNA gene amplicon sequence data from 824 cheese samples spanning 58 cheese types and 16 countries. We found a consistent, positive relationship between microbiome richness and pH, and a higher microbial richness in cheeses derived from goat milk. In contrast, we found no relationship between pasteurization, geographic location, or salinity and richness. Milk and cheese type, geographic location, and pasteurization collectively explained 65% of the variation in microbial community composition. Importantly, we identified four universal cheese microbiome types, driven by distinct dominant taxa. Our study reveals notable diversity patterns among the cheese microbiota, which are driven by geography and local environmental variables.
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Affiliation(s)
- Rine Christopher Reuben
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103 Leipzig, Germany
| | - Désirée Langer
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Nico Eisenhauer
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103 Leipzig, Germany
| | - Stephanie D. Jurburg
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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2
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Santamarina-García G, Amores G, López de Armentia E, Hernández I, Virto M. Relationship between the Dynamics of Gross Composition, Free Fatty Acids and Biogenic Amines, and Microbial Shifts during the Ripening of Raw Ewe Milk-Derived Idiazabal Cheese. Animals (Basel) 2022; 12:3224. [PMID: 36428451 PMCID: PMC9686631 DOI: 10.3390/ani12223224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
This study reports for the first time the relationship between bacterial succession, characterized by high-throughput sequencing (sequencing of V3-V4 16S rRNA regions), and the evolution of gross composition, free fatty acids (FFAs) and biogenic amines (BAs) during cheese ripening. Specifically, Idiazabal PDO cheese, a raw ewe milk-derived semi-hard o hard cheese, was analysed. Altogether, 8 gross parameters were monitored (pH, dry matter, protein, fat, Ca, Mg, P and NaCl) and 21 FFAs and 8 BAs were detected. The ripening time influenced the concentration of most physico-chemical parameters, whereas the producer mainly affected the gross composition and FFAs. Through an O2PLS approach, the non-starter lactic acid bacteria Lactobacillus, Enterococcus and Streptococcus were reported as positively related to the evolution of gross composition and FFAs release, while only Lactobacillus was positively related to BAs production. Several environmental or non-desirable bacteria showed negative correlations, which could indicate the negative impact of gross composition on their growth, the antimicrobial effect of FFAs and/or the metabolic use of FFAs by these genera, and their ability to degrade BAs. Nonetheless, Obesumbacterium and Chromohalobacter were positively associated with the synthesis of FFAs and BAs, respectively. This research work provides novel information that may contribute to the understanding of possible functional relationships between bacterial communities and the evolution of several cheese quality and safety parameters.
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Affiliation(s)
- Gorka Santamarina-García
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Unibertsitate Ibilbidea 7, 01006 Vitoria-Gasteiz, Basque Country, Spain
| | - Gustavo Amores
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Unibertsitate Ibilbidea 7, 01006 Vitoria-Gasteiz, Basque Country, Spain
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Grape Pomace in Ewes Diet Affects Metagenomic Profile, Volatile Compounds and Biogenic Amines Contents of Ripened Cheese. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The main objective of this research was to evaluate the development of volatile organic compounds (VOCs) and the accumulation of biogenic amines (BAs) in relation to the dynamic of microbial population composition in fresh and ripened cheese produced from raw milk of ewes fed a diet containing grape pomace (GP+) and fed a standard diet (Ctrl). Genomic DNA was extracted from the cheeses at 2 (T2), 60 (T60), 90 (T90) and 120 (T120) days of ripening and prepared for 16S rRNA-gene sequencing to characterize the cheese microbiota; furthermore, VOCs were determined via solid-phase microextraction combined with gas chromatography-mass spectrometry and biogenic amines by HPLC analyses. Diet did not affect the relative abundance of the main phyla identified, Proteobacteria characterized T2 samples, but the scenario changed during the ripening. At genus level, Pseudomonas, Chryseobacterium and Acinetobacter were the dominant taxa, however, a lower percentage of Pseudomonas was detected in GP+ cheeses. Enterococcus became dominant in ripened cheeses followed in Ctrl cheeses by Lactobacillus and in GP+ cheeses by Lactococcus. The diet affected the development of carboxylic acids and ketones but not of aldehydes. Low levels of esters were identified in all the samples. In total, four biogenic amines were determined in cheeses samples and their levels differed between the two groups and during ripening time. In 60, T90 and T120 GP+ cheeses, a lower amount of 2-phenylethylamine was found compared to Ctrl. Putrescine was detected only in GP+ samples and reached the highest level at 120 days. Conversely, the amount of cadaverine in GP+ samples was invariable during the ripening. The concentration of tyramine in GP+ samples was compared to Ctrl during the ripening. Overall, significant positive correlations between some families of bacteria and the formation of VOCs and BAs were found.
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Characterization of Microbial Shifts during the Production and Ripening of Raw Ewe Milk-Derived Idiazabal Cheese by High-Throughput Sequencing. BIOLOGY 2022; 11:biology11050769. [PMID: 35625497 PMCID: PMC9138791 DOI: 10.3390/biology11050769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Idiazabal is a traditional cheese produced from raw ewe milk in the Basque Country (Southwestern Europe). The sensory properties of raw milk cheeses have been attributed, among other factors, to microbial shifts that occur during the production and ripening processes. In this study, we used high-throughput sequencing technologies to investigate the microbiota of Latxa ewe raw milk and the dynamics during cheese production and ripening processes. The microbiota of raw milk was composed of lactic acid bacteria (LAB), environmental bacteria and non-desirable bacteria. Throughout the cheese making and ripening processes, the growth of LAB was promoted, whereas that of non-desirable and environmental bacteria was inhibited. Moreover, some genera not reported previously in raw ewe milk were detected and clear differences were observed in the bacterial composition of raw milk and cheese among producers, in relation to LAB and environmental or non-desirable bacteria, some of which could be attributed to the production of flavour related compounds. Abstract In this study, we used high-throughput sequencing technologies (sequencing of V3–V4 hypervariable regions of 16S rRNA gene) to investigate for the first time the microbiota of Latxa ewe raw milk and the bacterial shifts that occur during the production and ripening of Idiazabal cheese. Results revealed several bacterial genera not reported previously in raw ewe milk and cheese, such as Buttiauxella and Obesumbacterium. Both the cheese making and ripening processes had a significant impact on bacterial communities. Overall, the growth of lactic acid bacteria (LAB) (Lactococcus, Lactobacillus, Leuconostoc, Enterococcus, Streptococcus and Carnobacterium) was promoted, whereas that of non-desirable and environmental bacteria was inhibited (such as Pseudomonas and Clostridium). However, considerable differences were observed among producers. It is noteworthy that the starter LAB (Lactococcus) predominated up to 30 or 60 days of ripening and then, the growth of non-starter LAB (Lactobacillus, Leuconostoc, Enterococcus and Streptococcus) was promoted. Moreover, in some cases, bacteria related to the production of volatile compounds (such as Hafnia, Brevibacterium and Psychrobacter) also showed notable abundance during the first few weeks of ripening. Overall, the results of this study enhance our understanding of microbial shifts that occur during the production and ripening of a raw ewe milk-derived cheese (Idiazabal), and could indicate that the practices adopted by producers have a great impact on the microbiota and final quality of this cheese.
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A review of methods for the inference and experimental confirmation of microbial association networks in cheese. Int J Food Microbiol 2022; 368:109618. [DOI: 10.1016/j.ijfoodmicro.2022.109618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/21/2022] [Accepted: 03/06/2022] [Indexed: 12/15/2022]
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Tsigkrimani M, Bakogianni M, Paramithiotis S, Bosnea L, Pappa E, Drosinos EH, Skandamis PN, Mataragas M. Microbial Ecology of Artisanal Feta and Kefalograviera Cheeses, Part I: Bacterial Community and Its Functional Characteristics with Focus on Lactic Acid Bacteria as Determined by Culture-Dependent Methods and Phenotype Microarrays. Microorganisms 2022; 10:microorganisms10010161. [PMID: 35056609 PMCID: PMC8780491 DOI: 10.3390/microorganisms10010161] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/17/2022] Open
Abstract
Artisanal cheesemaking is still performed using practices and conditions derived from tradition. Feta and Kefalograviera cheeses are very popular in Greece and have met worldwide commercial success. However, there is a lack of knowledge regarding their lactic acid microecosystem composition and species dynamics during ripening. Thus, the aim of the present study was to assess the microecosystem as well as the autochthonous lactic acid microbiota during the ripening of artisanal Feta and Kefalograviera cheeses. For that purpose, raw sheep’s milk intended for cheesemaking, as well as Feta and Kefalograviera cheeses during early and late ripening were analyzed, and the lactic acid microbiota was identified using the classical phenotypic approach, clustering with PCR-RAPD and identification with sequencing of the 16S-rRNA gene, as well as with the Biolog GEN III microplates. In addition, the functional properties of the bacterial community were evaluated using the Biolog EcoPlates, which consists of 31 different carbon sources. In general, concordance between the techniques used was achieved. The most frequently isolated species from raw sheep’s milk were Enteroroccus faecium, Lactiplantibacillus plantarum and Pediococcus pentosaceus. The microecosystem of Feta cheese in the early ripening stage was dominated by Lp. plantarum and E. faecium, whereas, in late ripening, the microecosystem was dominated by Weissella paramesenteroides. The microecosystem of Kefalograviera cheese in the early ripening stage was dominated by Levilactobacillus brevis and E. faecium, and in late ripening by W. paramesenteroides and E. faecium. Finally, Carbohydrates was the main carbon source category that metabolized by all microbial communities, but the extent of their utilization was varied. Kefalograviera samples, especially at early ripening, demonstrated higher metabolic activity compared to Feta cheese. However, dominating species within microbial communities of the cheese samples were not significantly different.
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Affiliation(s)
- Markella Tsigkrimani
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece; (M.T.); (M.B.); (S.P.); (E.H.D.); (P.N.S.)
| | - Magdalini Bakogianni
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece; (M.T.); (M.B.); (S.P.); (E.H.D.); (P.N.S.)
| | - Spiros Paramithiotis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece; (M.T.); (M.B.); (S.P.); (E.H.D.); (P.N.S.)
| | - Loulouda Bosnea
- Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3 Ethnikis Antistaseos Str., 45221 Ioannina, Greece; (L.B.); (E.P.)
| | - Eleni Pappa
- Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3 Ethnikis Antistaseos Str., 45221 Ioannina, Greece; (L.B.); (E.P.)
| | - Eleftherios H. Drosinos
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece; (M.T.); (M.B.); (S.P.); (E.H.D.); (P.N.S.)
| | - Panagiotis N. Skandamis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece; (M.T.); (M.B.); (S.P.); (E.H.D.); (P.N.S.)
| | - Marios Mataragas
- Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3 Ethnikis Antistaseos Str., 45221 Ioannina, Greece; (L.B.); (E.P.)
- Correspondence:
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Mladenović KG, Grujović MŽ, Kiš M, Furmeg S, Tkalec VJ, Stefanović OD, Kocić-Tanackov SD. Enterobacteriaceae in food safety with an emphasis on raw milk and meat. Appl Microbiol Biotechnol 2021; 105:8615-8627. [PMID: 34731280 DOI: 10.1007/s00253-021-11655-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 10/19/2022]
Abstract
There has been a growing interest in traditional dairy (such as raw milk cheeses) and meat products, in recent years. However, these products are suitable and nutrient medium and may be easily contaminated by microorganisms such as Enterobacteriaceae. Enterobacteriaceae are considered to be the indicator bacteria for microbiological quality of food and hygiene status of a production process. Additionally, the food contaminated by Enterobacteriaceae poses a microbiological risk for consumers. In fact, the contamination of raw milk and meat by Enterobacteriaceae amid manufacturing may easily occur from various environmental sources, and this group of bacteria is frequently detected in dairy and meat products. Therefore, monitoring the microbiological quality of the used raw material and maintaining high standards of hygiene in the production process are mandatory for a high quality of traditional products and the safety of the potential consumers. The goal of this review is to present the most recent survey on Enterobacteriaceae growth, number, and distribution in raw milk cheeses and meat, as well as to discuss the sources of contamination and methods of control. KEY POINTS: • Enterobacteriaceae: role and importance in milk and meat products, EU legal regulations • Dynamics, distribution, and survival of Enterobacteriaceae in milk and meat • Mechanisms of control of Enterobacteriaceae in dairy products.
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Affiliation(s)
- K G Mladenović
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Radoja Domanovića 12, 34000, Kragujevac, Republic of Serbia. .,Institute for Information Technologies, Department of Science, University of Kragujevac, JovanaCvijica Bb, 34000, Kragujevac, Republic of Serbia.
| | - M Ž Grujović
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Radoja Domanovića 12, 34000, Kragujevac, Republic of Serbia.,Institute for Information Technologies, Department of Science, University of Kragujevac, JovanaCvijica Bb, 34000, Kragujevac, Republic of Serbia
| | - M Kiš
- Laboratory for Food and Feed Microbiology, Croatian Veterinary Institute, Veterinary Institute Križevci, Zakmardijeva 10, 48260, Križevci, Croatia
| | - S Furmeg
- Laboratory for Food and Feed Microbiology, Croatian Veterinary Institute, Veterinary Institute Križevci, Zakmardijeva 10, 48260, Križevci, Croatia
| | - V Jaki Tkalec
- Laboratory for Food and Feed Microbiology, Croatian Veterinary Institute, Veterinary Institute Križevci, Zakmardijeva 10, 48260, Križevci, Croatia
| | - O D Stefanović
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Radoja Domanovića 12, 34000, Kragujevac, Republic of Serbia
| | - S D Kocić-Tanackov
- Faculty of Technology, University in Novi Sad, Cara Lazara 1, 21000, Novi Sad, Republic of Serbia
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Mayo B, Rodríguez J, Vázquez L, Flórez AB. Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety. Foods 2021; 10:602. [PMID: 33809159 PMCID: PMC8000492 DOI: 10.3390/foods10030602] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 12/26/2022] Open
Abstract
The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.
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Affiliation(s)
- Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (J.R.); (L.V.); (A.B.F.)
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10
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Use of indicator bacteria for monitoring sanitary quality of raw milk cheeses – A literature review. Food Microbiol 2020; 85:103283. [DOI: 10.1016/j.fm.2019.103283] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 06/06/2019] [Accepted: 07/30/2019] [Indexed: 11/17/2022]
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Tilocca B, Costanzo N, Morittu VM, Spina AA, Soggiu A, Britti D, Roncada P, Piras C. Milk microbiota: Characterization methods and role in cheese production. J Proteomics 2019; 210:103534. [PMID: 31629058 DOI: 10.1016/j.jprot.2019.103534] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/04/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
Milk is a complex body fluid aimed at addressing the nutritional and defensive needs of the mammal's newborns. Harbored microbiota plays a pivotal role throughout the cheesemaking process and contributes to the development of flavor and texture typical of different type of cheeses. Understanding the dairy microbiota dynamics is of paramount importance for controlling the qualitative, sensorial and biosafety features of the dairy products. Although many studies investigated the contribution of single or few microorganisms, still there is some information lacking about microbial communities. The widespread of the omics platforms and bioinformatic tools enable the investigation of the cheese-associated microbial community in both phylogenetical and functional terms, highlighting the effects of the diverse cheesemaking variables. In this review, the most relevant literature is revised to provide an introduction of the milk- and cheese-associated microbiota, along with their structural and functional dynamics in relation to the diverse cheesemaking technologies and influencing variables. Also, we focus our attention on the latest omics technologies adopted in dairy microbiota investigation. Discussion on the key-steps and major drawbacks of each omics discipline is provided along with a collection of results from the latest research studies performed to unravel the fascinating world of the dairy-associated microbiota. SIGNIFICANCE: Understanding the milk- and cheese- associated microbial community is nowadays considered a key factor in the dairy industry, since it allows a comprehensive knowledge on how all phases of the cheesemaking process impact the harbored microflora; thus, predict the consequences in the finished products in terms of texture, organoleptic characteristics, palatability and biosafety. This review, collect the pioneering and milestones works so far performed in the field of dairy microbiota, and provide the basic guidance to whom approaching the cheese microbiota investigation by means of the latest omics technologies. Also, the review emphasizes the benefits and drawbacks of the omics disciplines, and underline how the integration of diverse omics sciences enhance a comprehensive depiction of the cheese microbiota. In turn, a better consciousness of the dairy microbiota might results in the application of improved starter cultures, cheesemaking practices and technologies; supporting a bio-safe and standardized production of cheese, with a strong economic benefit for both large-scale industries and local traditional dairy farms.
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Affiliation(s)
- Bruno Tilocca
- Department of Health Sciences, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Nicola Costanzo
- Department of Health Sciences, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Valeria Maria Morittu
- Department of Health Sciences, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Anna Antonella Spina
- Department of Health Sciences, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Alessio Soggiu
- Department of Veterinary Sciences, University of Milano, Milano, Italy
| | - Domenico Britti
- Department of Health Sciences, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Paola Roncada
- Department of Health Sciences, University Magna Græcia of Catanzaro, Catanzaro, Italy.
| | - Cristian Piras
- Department of Chemistry, University of Reading, Reading, United Kingdom
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Kamimura BA, De Filippis F, Sant’Ana AS, Ercolini D. Large-scale mapping of microbial diversity in artisanal Brazilian cheeses. Food Microbiol 2019; 80:40-49. [DOI: 10.1016/j.fm.2018.12.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/12/2018] [Accepted: 12/22/2018] [Indexed: 11/28/2022]
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13
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Milk and Dairy Products. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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De Pasquale I, Di Cagno R, Buchin S, De Angelis M, Gobbetti M. Use of autochthonous mesophilic lactic acid bacteria as starter cultures for making Pecorino Crotonese cheese: Effect on compositional, microbiological and biochemical attributes. Food Res Int 2018; 116:1344-1356. [PMID: 30716924 DOI: 10.1016/j.foodres.2018.10.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/05/2018] [Accepted: 10/07/2018] [Indexed: 11/16/2022]
Abstract
The use of selected autochthonous mesophilic lactic acid bacteria as starter cultures was investigated according to the traditional protocol for making Pecorino Crotonose (PC). Leuconostoc mesenteroides subsp. mesenteroides 2A, Lactobacillus casei 23C and Lactobacillus plantarum 18C (Autochthonous Starter, AS1) and Leuc. mesenteroides subsp. mesenteroides 2A, and L. casei 25D and 16A (AS2) were isolated and identified from aged ewes' milk PC cheeses, selected based on several enzymatic activities, and used as starter cultures. As shown by the in vitro kinetic of acidification, selected starter cultures had suitable capabilities to acidify. The manufacture of PC cheeses was carried out at an industrial plant scale. A control cheese (CC) was also made, using commercial starters consisting of mesophilic and thermophilic species. Ripening lasted 105 days at 10 °C. A poly-phasic approach was used to compare cheeses during manufacture and ripening, mainly based on pyrosequencing of the 16S rRNA targeting DNA, proteolysis and volatile component analyses. Compared to CC, both autochthonous starter cultures slightly affected the gross chemical composition of PC cheese. The cell density of thermophilic starters of CC progressively decreased throughout ripening. Plate count and RAPD-PCR showed that the cell number of autochthonous lactobacilli cultures of PC cheeses, made with AS1 and AS2, was almost constant throughout ripening and abundantly higher than that observed in CC. As shown by culture-independent analysis, the OTUs found during ripening varied depending on the manufacture with or without autochthonous starter cultures. The major chemical differences among cheeses were the concentration of free amino acids and the synthesis of some key volatile components (e.g., 2-methyl-1-propanol, 2-methyl-1-butanol, isobutyric, isovaleric, and isocaproic acids). Compared to CC, the use of AS1 positively affected the overall cheese quality.
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Affiliation(s)
- Ilaria De Pasquale
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari 70126, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy.
| | - Solange Buchin
- Technologie et Analyses Laitières, INRA, Poligny UR 342, France
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari 70126, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
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Sánchez-Gamboa C, Hicks-Pérez L, Gutiérrez-Méndez N, Heredia N, García S, Nevárez-Moorillón GV. Microbiological Changes during Ripening of Chihuahua Cheese Manufactured with Raw Milk and Its Seasonal Variations. Foods 2018; 7:foods7090153. [PMID: 30227599 PMCID: PMC6163408 DOI: 10.3390/foods7090153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/03/2018] [Accepted: 09/14/2018] [Indexed: 11/28/2022] Open
Abstract
Chihuahua cheese is a traditional cheese produced in Northwest Mexico that is consumed shortly after production. Cheeses prepared during autumn, winter and summer were collected from five dairies, and analyzed to determine seasonal influence on proximate analysis, texture profile and the microbiological dynamic during a ripening period of 270 days. Coliforms, coagulase-positive staphylococci, molds, yeast, as well as presumptive mesophilic lactobacilli, thermophilic lactobacilli, lactococci, thermophilic cocci and enterococci, were enumerated by plate count on selective agar. Manufacturing dairy had an effect on Chihuahua cheese composition and texture profile. Seasonality influence on the microbial dynamic was observed, since the highest initial counts of coliforms (5.14 log CFU/g), coagulase-positive staphylococci (4.13 log CFU/g) and mesophilic lactobacilli (7.86 log CFU/g) were detected on summer samples. Also, ripening time affected the survival of coliforms and presumptive lactococci after 270 days (1.24 and 5.89 log CFU/g respectively) while from day 90th, coagulase-positive staphylococci were absent. Microbial changes and seasonal influence provide information on the microbiota that can influence the sensorial characteristics of Chihuahua cheese.
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Affiliation(s)
- Cristina Sánchez-Gamboa
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ave. Pedro de Alba s/n cruce con Ave. Manuel L. Barragán, 66450 San Nicolás de los Garza, Nuevo León, México.
| | - Liliana Hicks-Pérez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n Campus Universitario II, 31125 Chihuahua, Chihuahua, México.
| | - Néstor Gutiérrez-Méndez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n Campus Universitario II, 31125 Chihuahua, Chihuahua, México.
| | - Norma Heredia
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ave. Pedro de Alba s/n cruce con Ave. Manuel L. Barragán, 66450 San Nicolás de los Garza, Nuevo León, México.
| | - Santos García
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ave. Pedro de Alba s/n cruce con Ave. Manuel L. Barragán, 66450 San Nicolás de los Garza, Nuevo León, México.
| | - Guadalupe Virginia Nevárez-Moorillón
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n Campus Universitario II, 31125 Chihuahua, Chihuahua, México.
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16
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Gobbetti M, Di Cagno R, Calasso M, Neviani E, Fox PF, De Angelis M. Drivers that establish and assembly the lactic acid bacteria biota in cheeses. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.06.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Yeluri Jonnala BR, McSweeney PLH, Sheehan JJ, Cotter PD. Sequencing of the Cheese Microbiome and Its Relevance to Industry. Front Microbiol 2018; 9:1020. [PMID: 29875744 PMCID: PMC5974213 DOI: 10.3389/fmicb.2018.01020] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/30/2018] [Indexed: 12/28/2022] Open
Abstract
The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.
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Affiliation(s)
- Bhagya R Yeluri Jonnala
- Food and Nutrition Deptartment, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Fermoy, Ireland
| | | | | | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland
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18
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Alvarenga VO, Campagnollo FB, do Prado-Silva L, Horita CN, Caturla MYR, Pereira EPR, Crucello A, Sant'Ana AS. Impact of Unit Operations From Farm to Fork on Microbial Safety and Quality of Foods. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 85:131-175. [PMID: 29860973 DOI: 10.1016/bs.afnr.2018.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Unit operations modify material properties aiming to produce uniform and high-quality food products with greater acceptance by the increasingly demanding consumers or with longer shelf life and better possibilities of storage and transport. Microorganisms, including bacteria, molds, viruses, and parasites, may have different susceptibilities to unit operations employed during food processing. On-farm (cleaning, selection and classification, cooling, storage, and transport) and on-factory unit operations (heating, refrigeration/freezing, dehydration, modification of atmosphere, irradiation, and physical, chemical, and microbial-based operations) are commonly employed throughout food production chain. The intensity and combination of unit operations along with food composition, packaging, and storage conditions will influence on the dominance of specific microorganisms, which can be pathogenic or responsible for spoilage. Thus, in the context of food safety objective (FSO), the knowledge and the quantification of the effects caused by each step of processing can enable to control and ensure the quality and safety of manufactured products.
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Affiliation(s)
| | | | | | - Claudia N Horita
- Faculty of Food Engineering, University of Campinas, Campinas, Brazil
| | | | | | - Aline Crucello
- Faculty of Food Engineering, University of Campinas, Campinas, Brazil
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19
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Zheng X, Li K, Shi X, Ni Y, Li B, Zhuge B. Potential characterization of yeasts isolated from Kazak artisanal cheese to produce flavoring compounds. Microbiologyopen 2017; 7. [PMID: 29277964 PMCID: PMC5822340 DOI: 10.1002/mbo3.533] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/26/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
Cheese is a typical handcrafted fermented food in Kazak minority from the Uighur Autonomy Region in China and Central Asia. Among the microbial community that is responsible for Kazak cheese fermentation, yeasts play important role in flavor formation during ripening. To develop ripening cultures, we isolated 123 yeasts from 25 cheese products in Kazak, and identified 87 isolates by the D1/D2 domain of the large subunit rRNA gene sequence. Pichia kudriavzevii was the dominant yeast in Kazak cheese, followed by Kluyveromyces marxianus and Kluyveromyces lactis. Of these, the ability to exhibit enzyme of dominant isolates and contribution to the typical flavor of cheeses was assessed. Enzyme producing yeast strains were inoculated in Hazak cheese‐like medium and volatile compounds were identified by head space solid phase micro extraction coupled to gas chromatography and mass spectroscopy. Pichia kudriavzevii N‐X displayed the strongest extracellular proteolytic and activity on skim milk agar and produced a range of aroma compounds (ethanol, ethyl acetate, 3‐methylbutanol, and acetic acid) for Kazak cheese flavor, could be explored as ripening cultures in commercial production of Kazak cheeses.
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Affiliation(s)
- Xiaoji Zheng
- The Key Lab of Industrial Biotechnology of Ministry of Education, Research Centre of Industrial Microorganisms, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, China.,College of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region, China
| | - Kaixiong Li
- College of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region, China
| | - Xuewei Shi
- College of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region, China
| | - Yongqing Ni
- College of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region, China
| | - Baokun Li
- College of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region, China
| | - Bin Zhuge
- The Key Lab of Industrial Biotechnology of Ministry of Education, Research Centre of Industrial Microorganisms, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, China
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20
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Doyle CJ, O'Toole PW, Cotter PD. Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments. Environ Microbiol 2017; 19:4382-4391. [DOI: 10.1111/1462-2920.13859] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/10/2017] [Accepted: 07/17/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Conor J. Doyle
- Teagasc Food Research Centre; Moorepark, Fermoy, Cork Ireland
- School of Microbiology; University College Cork; Cork Ireland
| | - Paul W. O'Toole
- School of Microbiology; University College Cork; Cork Ireland
- APC Microbiome Institute; Cork Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre; Moorepark, Fermoy, Cork Ireland
- APC Microbiome Institute; Cork Ireland
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21
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Calasso M, Mancini L, De Angelis M, Conte A, Costa C, Del Nobile MA, Gobbetti M. Multiple microbial cell-free extracts improve the microbiological, biochemical and sensory features of ewes’ milk cheese. Food Microbiol 2017; 66:129-140. [DOI: 10.1016/j.fm.2017.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/23/2017] [Accepted: 04/23/2017] [Indexed: 11/30/2022]
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22
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Sánchez-Gamboa C, Hicks-Pérez L, Gutiérrez-Méndez N, Heredia N, García S, Nevárez-Moorillón GV. Seasonal influence on the microbial profile of Chihuahua cheese manufactured from raw milk. INT J DAIRY TECHNOL 2017. [DOI: 10.1111/1471-0307.12423] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Cristina Sánchez-Gamboa
- Facultad de Ciencias Biológicas; Universidad Autónoma de Nuevo León; Ave. Pedro de Alba s/n; Ciudad Universitaria; 66451 San Nicolás de los Garza Nuevo León México
| | - Liliana Hicks-Pérez
- Facultad de Ciencias Químicas; Universidad Autónoma de Chihuahua; Circuito Universitario S/N; Campus Universitario II 31125 Chihuahua Chihuahua México
| | - Néstor Gutiérrez-Méndez
- Facultad de Ciencias Químicas; Universidad Autónoma de Chihuahua; Circuito Universitario S/N; Campus Universitario II 31125 Chihuahua Chihuahua México
| | - Norma Heredia
- Facultad de Ciencias Biológicas; Universidad Autónoma de Nuevo León; Ave. Pedro de Alba s/n; Ciudad Universitaria; 66451 San Nicolás de los Garza Nuevo León México
| | - Santos García
- Facultad de Ciencias Biológicas; Universidad Autónoma de Nuevo León; Ave. Pedro de Alba s/n; Ciudad Universitaria; 66451 San Nicolás de los Garza Nuevo León México
| | - Guadalupe V Nevárez-Moorillón
- Facultad de Ciencias Químicas; Universidad Autónoma de Chihuahua; Circuito Universitario S/N; Campus Universitario II 31125 Chihuahua Chihuahua México
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23
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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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24
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De Filippis F, Parente E, Ercolini D. Metagenomics insights into food fermentations. Microb Biotechnol 2016; 10:91-102. [PMID: 27709807 PMCID: PMC5270737 DOI: 10.1111/1751-7915.12421] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 11/26/2022] Open
Abstract
This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.
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Affiliation(s)
- Francesca De Filippis
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy
| | - Danilo Ercolini
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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25
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26
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De Pasquale I, Di Cagno R, Buchin S, De Angelis M, Gobbetti M. Spatial Distribution of the Metabolically Active Microbiota within Italian PDO Ewes' Milk Cheeses. PLoS One 2016; 11:e0153213. [PMID: 27073835 PMCID: PMC4830609 DOI: 10.1371/journal.pone.0153213] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 03/25/2016] [Indexed: 11/19/2022] Open
Abstract
Italian PDO (Protected Designation of Origin) Fiore Sardo (FS), Pecorino Siciliano (PS) and Pecorino Toscano (PT) ewes' milk cheeses were chosen as hard cheese model systems to investigate the spatial distribution of the metabolically active microbiota and the related effects on proteolysis and synthesis of volatile components (VOC). Cheese slices were divided in nine sub-blocks, each one separately subjected to analysis and compared to whole cheese slice (control). Gradients for moisture, and concentrations of salt, fat and protein distinguished sub-blocks, while the cell density of the main microbial groups did not differ. Secondary proteolysis differed between sub-blocks of each cheese, especially when the number and area of hydrophilic and hydrophobic peptide peaks were assessed. The concentration of free amino acids (FAA) agreed with these data. As determined through Purge and Trap (PT) coupled with Gas Chromatography-Mass Spectrometry (PT-GC/MS), and regardless of the cheese variety, the profile with the lowest level of VOC was restricted to the region identified by the letter E defined as core. As shown through pyrosequencing of the 16S rRNA targeting RNA, the spatial distribution of the metabolically active microbiota agreed with the VOC distribution. Differences were highlighted between core and the rest of the cheese. Top and bottom under rind sub-blocks of all three cheeses harbored the widest biodiversity. The cheese sub-block analysis revealed the presence of a microbiota statistically correlated with secondary proteolysis events and/or synthesis of VOC.
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Affiliation(s)
- Ilaria De Pasquale
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Raffaella Di Cagno
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
- * E-mail:
| | - Solange Buchin
- INRA, UR 342, Technologie et Analyses Laitières, Poligny, France
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Gobbetti
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
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27
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Calasso M, Ercolini D, Mancini L, Stellato G, Minervini F, Di Cagno R, De Angelis M, Gobbetti M. Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant. Food Microbiol 2016. [DOI: 10.1016/j.fm.2015.10.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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28
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Carafa I, Clementi F, Tuohy K, Franciosi E. Microbial evolution of traditional mountain cheese and characterization of early fermentation cocci for selection of autochtonous dairy starter strains. Food Microbiol 2016; 53:94-103. [DOI: 10.1016/j.fm.2015.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/25/2015] [Accepted: 09/03/2015] [Indexed: 11/28/2022]
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29
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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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30
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Parente E, Cocolin L, De Filippis F, Zotta T, Ferrocino I, O'Sullivan O, Neviani E, De Angelis M, Cotter PD, Ercolini D. FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis. Int J Food Microbiol 2015; 219:28-37. [PMID: 26704067 DOI: 10.1016/j.ijfoodmicro.2015.12.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/27/2015] [Accepted: 12/04/2015] [Indexed: 12/12/2022]
Abstract
Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry.
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Affiliation(s)
- Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy.
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Science, University of Torino, Grugliasco, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Teresa Zotta
- Istituto di Scienze dell'Alimentazione, CNR, Avellino, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Science, University of Torino, Grugliasco, Italy
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland; APC Microbiome Institute, Cork, Ireland
| | - Erasmo Neviani
- Department of Food Science, Parma University, Parco Area delle Scienze 48, /A, Parma, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland; APC Microbiome Institute, Cork, Ireland
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
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31
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Pros and cons for using non-starter lactic acid bacteria (NSLAB) as secondary/adjunct starters for cheese ripening. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.07.016] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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32
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Calasso M, Mancini L, Di Cagno R, Cardinali G, Gobbetti M. Microbial cell-free extracts as sources of enzyme activities to be used for enhancement flavor development of ewe milk cheese. J Dairy Sci 2015; 98:5874-89. [PMID: 26142846 DOI: 10.3168/jds.2015-9362] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/26/2015] [Indexed: 02/04/2023]
Abstract
Freeze-dried cell-free extracts (CFE) from Lactobacillus casei LC01, Weissella cibaria 1XF5, Hafnia alvei Moller ATCC 51815, and Debaryomyces hansenii LCF-558 were used as sources of enzyme activities for conditioning the ripening of ewe milk cheese. Compared with control cheese (CC), CFE did not affect the gross composition and the growth of the main microbial groups of the cheeses. As shown through urea-PAGE electrophoresis of the pH 4.6-soluble nitrogen fraction and the analysis of free AA, the secondary proteolysis of the cheeses with CFE added was markedly differed from that of the CC. Compared with CC, several enzyme activities were higher in the water-soluble extracts from cheeses made with CFE. In agreement, the levels of 49 volatile compounds significantly differentiated CC from the cheeses made with CFE. The level of some alcohols, ketones, sulfur compounds, and furans were the lowest in the CC, whereas most aldehydes were the highest. Each CFE seemed to affect a specific class of chemical compounds (e.g., the CFE from H. alvei ATCC 51815 mainly influenced the synthesis of sulfur compounds). Apart from the microbial source used, the cheeses with the addition of CFE showed higher score for acceptability than the control cheese. Cheese ripening was accelerated or conditioned using CFE as sources of tailored enzyme activities.
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Affiliation(s)
- Maria Calasso
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Leonardo Mancini
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Raffaella Di Cagno
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy.
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Marco Gobbetti
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
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33
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Cocolin L, Ercolini D. Zooming into food-associated microbial consortia: a ‘cultural’ evolution. Curr Opin Food Sci 2015. [DOI: 10.1016/j.cofs.2015.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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De Pasquale I, Di Cagno R, Buchin S, De Angelis M, Gobbetti M. Microbial ecology dynamics reveal a succession in the core microbiota involved in the ripening of pasta filata caciocavallo pugliese cheese. Appl Environ Microbiol 2014; 80:6243-55. [PMID: 25085486 PMCID: PMC4178672 DOI: 10.1128/aem.02097-14] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 07/28/2014] [Indexed: 11/20/2022] Open
Abstract
Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese. Plate counts revealed that cheese manufacture affected the microbial ecology. The results agreed with those from culture-independent approaches. As shown by urea-PAGE, reverse-phase high pressure liquid chromatography (RP-HPLC), and free-amino-acid (FAA) analyses, the extent of secondary proteolysis mainly increased after 30 to 45 days of ripening. VOCs and volatile free fatty acids (VFFA) were identified by a purge-and-trap method (PT) and solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS), respectively. Except for aldehydes, the levels of most of VOCs and VFFA mainly increased from 30 to 45 days onwards. As shown through pyrosequencing analysis, raw cows' milk was contaminated by Firmicutes (53%), Proteobacteria (39%), Bacteroidetes (7.8%), Actinobacteria (0.06%), and Fusobacteria (0.03%), with heterogeneity at the genus level. The primary starter Streptococcus thermophilus dominated the curd population. Other genera occurred at low incidence or sporadically. The microbial dynamics reflected on the overall physiological diversity. At 30 days, a microbial succession was clearly highlighted. The relative abundance of Streptococcus sp. and especially St. thermophilus decreased, while that of Lactobacillus casei, Lactobacillus sp., and especially Lactobacillus paracasei increased consistently. Despite the lower relative abundance compared to St. thermophilus, mesophilic lactobacilli were the only organisms positively correlated with the concentration of FAAs, area of hydrophilic peptide peaks, and several VOCs (e.g., alcohols, ketones, esters and all furans). This study showed that a core microbiota was naturally selected during middle ripening, which seemed to be the main factor responsible for cheese ripening.
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Affiliation(s)
- Ilaria De Pasquale
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Raffaella Di Cagno
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Solange Buchin
- INRA, UR 342, Technologie et Analyses Laitières, Poligny, France
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Gobbetti
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
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