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Food Molecular Identification and Characterization: Towards Geographical Traceability SCUOLA DI DOTTORATO UNIVERSITÀ DEGLI STUDI DI MILANO-BICOCCA Department of Biotechnology and Biosciences PhD program in BIOLOGY AND BIOTECHNOLOGY - Cycle XXX Curriculum in MORPHO-FUNCTIONAL BIOLOGY FOOD MOLECULAR IDENTIFICATION AND CHARACTERIZATION: TOWARDS GEOGRAPHICAL TRACEABILITY MEZZASALMA VALERIO 031134 Tutor: Prof. Labra Massimo Coordinator: Prof. Vanoni Marco Ercole ACADEMIC YEAR 2016/2017 INDEX Index 1. Summary 1 2. Introduction 5 2.1 Genomics and Metagenomics and Food Quality 6 2.1.1 DNA Analyses for Food Quality, Authentication and 6 Traceability 2.1.2 DNA Barcoding 8 2.1.3 Other DNA Markers 11 2.1.4 DNA Analysis for Processed Food: the Case of Food 13 Fermented Products 2.2 Vitis vinifera L. and Wine Production 19 2.2.1 Vitis vinifera L.: Origin and Domestication 19 2.2.2 The Process of Domestication 21 2.2.3 The Domestication of the Vitis vinifera L. 22 2.2.4 Grapevine Biodiversity in the Sardinia Region 26 2.3 Discovering the Terroir Secrets 27 2.3.1 The Terroir Concept 27 2.3.2 The Study of Terroir 29 2.3.3 The Microbiome: an Element of Relationship Between 31 Environment and Plant. 2.4 Project Aims 36 2.5 References 37 3. Chapter 1: Emerging DNA-based Technologies to 45 Characterize Food Ecosystems 3.1 Abstract 46 3.2 DNA Barcoding to Characterize Food Raw Material and 47 Derived Products 3.3 The Complex Ecosystem of Food Biotransformation 52 Processes 3.4 Novel Molecular Approaches to Investigate Food Ecosystems 58 3.5 Microbiota Composition and Dynamics in Plant Fermentation 63 Processes 3.6 The Evolution of Microbial Community in Artisanal and 68 Industrial Dairy Production 3.7 Conclusions 74 3.8 References 75 ii Index 4. Chapter 2: Towards a Universal Approach Based on 86 Omics Technologies for the Quality Control of Food 4.1 Abstract 87 4.2 The Demand for Universal Analytical Tools to Characterize 87 Foodstuffs 4.3 DNA Barcoding: A Universal Approach for Food 91 Characterization 4.4 Innovative Applications of Metabolomics Tools for an 97 Exhaustive Food Labelling 4.5 From Omics to Foodomics 105 4.6 References 108 5. Chapter 3: Grape Microbiome as a Reliable and 121 Persistent Signature of Field Origin and Environmental Conditions in Cannonau Wine Production 5.1 Abstract 122 5.2 Introduction 123 5.3 Materials and Methods 126 5.3.1 Samples Collection and Wine Production 126 5.3.2 DNA Extraction 128 5.3.3 Library Preparation and Sequencing 129 5.3.4 Microbial Composition and Community Structure Analysis 130 5.4. Results and Discussion 132 5.4.1 Sequence Analysis 132 5.4.2 Bacteria and Fungi OTU Diversity 132 5.4.3 Microbial Taxonomy Diversity 137 5.4.4 From Field to Wine Cellar 145 5.5 Conclusions 148 5.6 Supporting Information 150 5.7 References 165 6. Chapter 4: Soil and Vineyard Biodiversity Shape Grape 170 Microbiome Regardless of Cultivar 6.1 Abstract 171 6.2 Introduction 172 6.3 Materials and methods 175 6.3.1 Plant and soil sampling 175 iii Index 6.3.2 DNA extraction 176 6.3.3 Library preparation and sequencing 177 6.3.4 Microbial composition and community structure analysis 178 6.4 Results 180 6.4.1 Sequence analysis 180 6.4.2 Grape microbiome diversity and distribution 180 6.4.3 The origin of the grape microbiome 183 6.4.4 Machine learning analysis 187 6.5 Discussion 188 6.5.1 Vineyards as a complex and dynamic ecosystem 188 6.5.2 The passive role of the grapevine in the selection of the fruit 191 microbiome 6.6 Conclusions 192 6.7 Supporting Information 193 6.8 References 194 7. Discussion and Conclusions 198 7.1 Vitis vinifera L. microbiome: from grape to wine. 199 7.2 Effects of vineyard environmental features and cultivar on 203 grape microbiome. 7.3 Grapevine as holobiont. 206 7.4 References 209 8. Other Scientific Contributions 213 9. Acknowledgements 218 iv 1. SUMMARY 1. Summary Food safety and quality depend on raw material characteristics and on the chemical, physical and biotechnological approaches adopted during manufacturing and transformation processes. Since a huge number of microorganisms are involved in food production, most products should be considered as complex matrices where any microbial component has a precise role and evolves in response to changes in physical and chemical features of the whole system. So, understanding the dynamics of microbial community involved in a food supply chain is useful to reduce food spoilage outbreaks, enhance industrial processes and extend product’s shelf-life. The analysis of food microbiota is also pivotal to improve biotransformation processes, like winemaking. From time immemorial, the wine industry has been selectively growing grapevine cultivars showing different traits (e.g., grape size, color and flavor), and small variations in soil composition, irrigation and climate, have long been associated with shifts in these traits. The microbial flora coexisting with the plant may be one of the key factors influencing these traits. Despite long-time difficulties in analyzing single bacterial strains, the High Throughput Sequencing technologies (HTS) are nowadays an emerging and widely adopted tool for microbial characterization, even in food matrices. To clarify the contribution of the microbiome of grape during wine fermentation steps, I used an HTS-based approach to identify bacteria and fungi communities associated to berries and musts of Cannonau cultivar from four vineyards belonging to different regions in Sardinia. Cannonau is the most important grapevine cultivar of Sardinia (Italy), where most vineyards are cultivated without phytochemical treatments. Bioinformatics analyses suggested that microbiome colonizing berries collected at the four different localities shared a core 2 1. Summary composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales bacteria typical of manure. During vinification processes, performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropological conditions (e.g., farming management), and that fruits’ microorganisms persist during the fermentation process. One of the main open questions about grape microbiome, regards the active role of grapevine cultivars in modelling microbial community. To investigate the relationship between plant genotype, its microbiome and the contribution of field environmental and pedoclimatic conditions, I planned sampling activities to collect 3 different grapevine cultivars Sauvignon Blanc, Syrha, Cabernet Sauvignon and soil samples from 3 different geographical area Pavia (Northern Italy), San Michele all’Adige (Northern Italy, close to the Alps) and Logroño (Spain). The HTS analysis of collected samples allowed to characterize bacterial profiles and the correlation between plant, fruit microbiome and the environment. This is a first step towards the understanding of the role of terroir and plant genotype in shaping the microbiome and quality of grapevine fruit and related products (i.e., must and wine). On the whole, such work provides clear evidence that the biogeographic characteristics of field’s microorganisms may lead to regional properties associated to valuable crops. Human microbiome is 3 1. Summary changing the face of medicine. Similarly, future research efforts should be more and more focused on the analysis of crop and environmental microbial communities to change the face of conventional agriculture. 4 2. INTRODUCTION 2. Introduction 2.1 Genomics, metagenomics and food quality 2.1.1 The application of DNA analysis in the food sector The industrial sector finds a solid support in genetic and biomolecular techniques to develop new analytical tools for improving food quality and safety. The continuous advances in molecular technologies, as well as the increase of information, dissemination and communication about DNA tools efficacy caused a progressive interest on food genetic analysis also by non-specialists stakeholders. The application of molecular techniques was used firstly for raw material identification and subsequently for genetic traceability, especially in the agro-food sector. In this context, DNA markers represent a powerful tool to verify the authenticity of products and to protect both producers and consumers, ensuring freedom of choice, accuracy of labelling and avoiding the fraudulent food alterations, such as the partial or complete replacement of a certain food item with cheaper components. Today, DNA extraction can be successfully and reliably achieved in several kinds of foodstuffs and therefore molecular authentication of raw material and processed food can be routinely used at different steps of the food supply chain. In this way, DNA-based characterization and traceability of food components can improve the transparency and the protection of local and industrial food production systems. Moreover, this trend meets the consumer’s demand. Consumers are more and more aware and informed about food quality and safety; they read products’ label carefully and prefer those items having a well-declared origin and composition. In addition, increased human intolerances and allergies and the healthy lifestyles have been contributing to increase the public 6 2. Introduction attention towards a critic selection of food products. Taking advantage of the modern traceability systems, it is nowadays easier to trace each single step of an articulated food supply chain, thus allowing consumers to have accurate information and control on the product, but also facilitating the withdrawal of foodstuffs in case of problems. All food products must comply with the description provided by the manufacturers or processors, with reference to the origin of the ingredients, details of the transformation process, the geographic origin and the identity of the species, breeds or varieties used.
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