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Multi-omics Methods to unravel Microbial Diversity in Fermentation of Riesling Wines

  • Wine and alcoholic fermentations are complex and fascinating ecosystems. Wine aroma is shaped by the wine’s chemical compositions, in which both microbes and grape constituents play crucial roles. Activities of the microbial community impact the sensory properties of the final product, therefore, the characterisation of microbial diversity is essential in understanding and predicting sensory properties of wine. Characterisation has been challenging with traditional approaches, where microbes are isolated and therefore analyzed outside from their natural environment. This causes a bias in the observed microbial composition structure. In addition, true community interactions cannot be studied using isolates. Furthermore, the multiplex ties between wine chemical and sensory compositions remain evasive due to their multivariate and nonlinear nature. Therefore, the sensorial outcome arising from different microbial communities has remained inconclusive. In this thesis, microbial diversity during Riesling wine fermentations is investigated with the aim to understand the roles of microbial communities during fermentations and their links to sensory properties. With the advancement of high-throughput tools based ‘omic methods, such as next-generation sequencing (NGS) technologies, it is now possible to study microbial communities and their functions without isolation by culturing. This developing field and its potential to wine community is reviewed in Chapter 1. The standardisation of methods remains challenging in the field. DNA extraction is a key step in capturing the microbial diversity in samples for generating NGS data, therefore, DNA extraction methods are evaluated in Chapter 2. In Chapter 3, machine learning is utilized in guiding raw data mining generated by the untargeted GC-MS analysis. This step is crucial in order to take full advantages of the large scope of data generated by ‘omic methods. These lay a solid foundation for Chapters 4 and 5 where microbial community structures and their outputs - chemical and sensory compositions are studied by using approaches and tools based on multiple ‘omics methods. The results of this thesis show first that by using novel statistical approaches, it is possible to extract meaningful information from heterogeneous biological, chemical and sensorial data. Secondly, results suggest that the variation in wine aroma, might be related to microbial interactions taking place not only inside a single community, but also the IV interactions between communities, such as vineyard and winery communities. Therefore, the true sensory expression of terroir might be masked by the interaction between two microbial communities, although more work is needed to uncover this potential relationship. Such potential interaction mechanisms were uncovered between non- Saccharomyces yeast and bacteria in this work and unexpected novel bacterial growth was observed during alcohol fermentation. This suggests new layers in understanding of wine fermentations. In the future, multi-omic approaches could be applied to identify biological pathways leading to specific wine aroma as well as investigate the effects upon specific winemaking conditions. These results are relevant not just for the wine industry, but also to other industries where complex microbial networks are important. As such, the approaches presented in this thesis might find widely use in the food industry. 

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Author:Kimmo Siren
URN (permanent link):urn:nbn:de:hbz:386-kluedo-55965
Advisor:Ulrich Fischer
Document Type:Doctoral Thesis
Language of publication:English
Publication Date:2019/06/01
Year of Publication:2019
Publishing Institute:Technische Universität Kaiserslautern
Granting Institute:Technische Universität Kaiserslautern
Acceptance Date of the Thesis:2019/03/08
Date of the Publication (Server):2019/04/17
Number of page:VIII, 294
Faculties / Organisational entities:Fachbereich Chemie
DDC-Cassification:5 Naturwissenschaften und Mathematik / 540 Chemie
Licence (German):Creative Commons 4.0 - Namensnennung, nicht kommerziell (CC BY-NC 4.0)