Abstract

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

Highlights

  • The history of cheesemaking is lost in the mists of time [1]

  • We focus on studies where individual -omics technologies have been applied, and on integrated multi-omics studies that unravel the composition and functionality of the complex cheese microbiota on flavor formation

  • Volatile analysis by solid phase micro-extraction (SPME) gas chromatography (GC)-mass spectrometry (MS) showed differences between non-starter lactic acid bacteria (LAB) (NSLAB) strains grown in cheese-based medium (CBM) and LCM, providing a better understanding of how NSLABproduced volatile flavor compounds contribute to the development of cheese flavor during ripening, a first step toward the selection of wild NSLAB possessing a specific aromatic profile, for use as adjunct culture [216]

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Summary

Introduction

The history of cheesemaking is lost in the mists of time [1]. Over the years, cheese making has greatly evolved with a remarkable diversity of cheeses produced worldwide, with culture and resources shaping the production in each region. The integration of multiple meta-omics tools, together with powerful statistical analysis methods, has allowed detailed functional characterization of the cheese microbiota and determination of its contribution to the development of characteristic flavor metabolites [23,24,25,26,27,28,29]. This in-depth study of cheese microbiota could result in the application of selected cultures able to enhance or diversify cheese flavor, and leading to cheese making practices and technologies for accelerated or improved ripening with economic benefit for both cheese producers and consumers. Inter-farm variability is wide, while intra-farm variability is generally much lower except from season to season [38]

Factors Affecting the Cheese Microbiota
The Cheese Microbial Pool
Conventional Methods
Cheese Microbiota Metabolic Pathways for Flavor Development
Citrate Catabolism
Lipid Catabolism
44.4. PPrrootteeiinn aanndd AAmmiinnoo AAcidd Catabolism
Metagenomics
Transcriptomics
Metatranscriptomics
Metaproteomics
Metabolomics to Assess Flavor Formation in Cheese
Metabolomics as a Means of Cheese Authentication
Integration
Amplicon Metagenomics-Shotgun Metagenomics
Amplicon Metagenomics-Metabolomics-Metatranscriptomics
Shotgun Metagenomics-Metatranscriptomics
Genomics-Amplicon Metagenomics-Shotgun Metagenomics-Metabolomics
Findings
Conclusions

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