Abstract
Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.
Highlights
In order to protect traditional products and secure potential economic bene ts for local producers, di erentiating them from potential commercial fraud, the European Union (EU) has established three types of quality labels: Protected Designation of Origin (PDO), Protected Geographical Indication (PGI) and Traditional Speciality Guaranteed (TSG) (European Commission, 2013) [1]
E identification of the microbial communities guiding the fermentation process in different cheeses has been largely attained from traditional culture-dependent, as well as culture-independent molecular methods. e latter methodologies include the analysis of 16S rRNA gene, via denaturing or temperature gradient, gel electrophoresis (DGGE/TGGE) [12,13,14], fluorescent in situ hybridization (FISH) [15], single-stranded conformation polymorphisms (SSCP) [16], terminal-restriction fragment length polymorphism (T-RFLP) [17] or length heterogeneity-PCR (LH-PCR) [18]
Each type of cheese is comprised by a unique pool of microbes. is pool includes the dominant population, favored by the configured microenvironment and colonizing the cheese more successfully, the subdominant, which are microbes found in lower abundance due to the restrictive pressure of the dominant species, and the low abundant species group that exists in the cheese mostly due to contamination from the environment [34]. e initial dominance of Starter Lactic Acid Bacteria (SLAB) is based on their metabolic capacity to successfully ferment lactose
Summary
In order to protect traditional products and secure potential economic bene ts for local producers, di erentiating them from potential commercial fraud, the European Union (EU) has established three types of quality labels: Protected Designation of Origin (PDO), Protected Geographical Indication (PGI) and Traditional Speciality Guaranteed (TSG) (European Commission, 2013) [1]. Several methodologies have been used to characterize PDO cheeses, mainly based on their organic compounds and other basic components, including gas chromatography (GC) [3], high-performance liquid chromatography (HPLC) [4, 5], infrared (IR) spectroscopy [6, 7], solid phase microextraction (SPME) and purge and trap (P&T) [8] and nuclear magnetic resonance (NMR) spectroscopy [9, 10] As it was indicated, the speci c production conditions within the PDO area select for particular microbial populations, which contribute through the fermentation of the available nutrients in the sensorial and safety characteristics of the cheese, introducing. The analysis of the microbial biodiversity has important value, for understanding the contribution of key microbes in the process of ripening, and to comprehend how the technological parameters applied influence the quality and safety of the product [32, 33]. e current review focuses on the application of HTS technologies as a new additional tool for establishing of the authenticity of PDO cheeses. ese technologies may allow the identification of the microbial communities developed in PDO cheeses, to explore the contribution of manufacturing conditions as well as to uncover additional factors that contribute to microbial communities’ formation and to investigate the influence of the metabolically active microbiota in cheese sensorial characteristics development
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