Cheesomics: the future pathway to understanding cheese flavour and quality

Iron-based microbial interactions: the role of iron metabolism in the cheese ecosystem

Iron is involved in various microbial metabolisms and interactions and is an essential micronutrient for most microorganisms. This review focuses on the cheese ecosystem, in which iron is sparse (median concentration of 2.9 mg/kg based on a literature survey) and of limited bioavailability due to the presence of various metal-binding agents in the cheese matrix. Cheese microorganisms overcome this low bioavailability of iron by producing and/or importing ferric iron-specific chelators called siderophores. We introduce these siderophores and their specific transporters, which play a key role in ecological interactions and microbial metabolism. We discuss the impact of iron on all the major taxa (fungi, bacteria, and viruses) and functional groups (starters, ripening microorganisms, and pathogens) present and interacting in cheese, from the community to individual levels. We describe the ways in which cheese-ripening microorganisms use iron and the effects of iron limitation on major metabolic pathways, including the tricarboxylic acid (TCA) cycle and amino-acid biosynthesis. The cheese ecosystem is a relevant in situ model for improving our understanding of iron biochemistry and its putative role in microbe-microbe interactions. Yet, this review highlights critical gaps in our understanding of iron's role in cheese from fundamental ecological and biochemical perspectives to applied microbiology, with broader implications for the quality, safety, and organoleptic properties of cheese.

Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses

Metagenomic studies of the Gouda cheese microbiota and starter cultures are scarce. During the present study, short-read metagenomic sequencing (Illumina) was applied on 89 Gouda cheese and processed milk samples, which have been investigated before concerning their metabolite and taxonomic composition, the latter applying amplicon-based, high-throughput sequencing (HTS) of the full-length 16S rRNA gene. Selected samples were additionally investigated using long-read metagenomic sequencing (Oxford Nanopore Technologies, ONT). Whereas the species identified by amplicon-based HTS and metagenomic sequencing were identical, the relative abundances of the major species differed significantly. Lactococcus cremoris was more abundant in the metagenomics-based taxonomic analysis compared to the amplicon-based one, whereas the opposite was true for the non-starter lactic acid bacteria (NSLAB). This discrepancy was related to a higher fragmentation of the lactococcal DNA compared with the DNA of other species when applying ONT. Possibly, a higher fragmentation was linked with a higher percentage of dead or metabolically inactive cells, suggesting that full-length 16S rRNA gene amplicon-based HTS might give a more accurate view on active cells. Further, fungi were not abundantly present in the Gouda cheeses examined, whereas about 2% of the metagenomic sequence reads was related to phages, with higher relative abundances in the cheese rinds and long-ripened cheeses. Intraspecies differences found by short-read metagenomic sequencing were in agreement with the amplicon sequence variants obtained previously, confirming the ability of full-length 16S rRNA gene amplicon-based HTS to reach a taxonomic assignment below species level. Metagenome-assembled genomes (MAGs) were retrieved for 15 species, among which the starter cultures Lc. cremoris and Lactococcus lactis and the NSLAB Lacticaseibacillus paracasei, Loigolactobacillus rennini, and Tetragenococcus halophilus, although obtaining MAGs from Lc. cremoris and Lc. lactis was more challenging because of a high intraspecies diversity and high similarity between these species. Long-read metagenomic sequencing could not improve the retrieval of lactococcal MAGs, but, overall, MAGs obtained by long-read metagenomic sequencing solely were superior compared with those obtained by short-read metagenomic sequencing solely, reaching a high-quality draft status of the genomes.

Metabolomics and (craft) beers - recent advances

Craft beers have encountered a steady rise in popularity over the years, as these artisanal beers produced by microbreweries have responded to consumer preferences for added novelty in such beverages. With this gain in appeal and interest for the beverage, craft beers have also become a growing industry in many parts of the world, and the same can be said for research within the field. This also extends to the chemistry of craft beers, where one method of exploration involves that of metabolomics, appropriately addressing the multi-faceted aspects of craft beer development and chemistry. Alongside advances in metabolomics in general beer and brewing research, the field also mirrors potential in growth. This review touches on relevant aspects of the beer industry and brewing process as preliminaries for discussions on advances in the field of beer metabolomics, leading to the application of metabolomics in pursuit of studying craft beers; future directions, challenges, and opportunities are also presented.

Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking

This review contributes to the knowledge on the complex and adaptive microbial ecosystems within cheese, emphasizing their critical role in determining cheese quality, flavor, and safety. This review synthesizes the current knowledge on the microbial interactions and the dynamics of lactic acid bacteria (LAB), encompassing both starter (SLAB) and non-starter (NSLAB) strains, which are pivotal to the curd fermentation and ripening processes. The adaptability of these microbial consortia to environmental and technological stressors is explored, highlighting their contributions to acidification, proteolysis, and the development of distinctive organoleptic characteristics. Historical and technological perspectives on cheesemaking are also discussed, detailing the impact of milk treatment, starter culture selection, and post-renneting procedures on microbial activity and biochemical transformations. This review underscores the importance of microbial diversity and cooperative interactions in fostering ecosystem resilience and metabolic functionality, and it addresses the challenges in mimicking the technological performance of natural starters using selected cultures. By understanding the ecological roles and interactions of cheese microbiota, this review aims to guide improvements in cheese production practices. Additionally, these insights could spark the development of innovative strategies for microbial community management.

Iron fortification modifies the microbial community structure and metabolome of a model surface-ripened cheese

Iron is a vital micronutrient for nearly all microorganisms, serving as a co-factor in critical metabolic pathways. However, cheese is an iron-restricted environment. Furthermore, it has been demonstrated that iron represents a growth-limiting factor for many microorganisms involved in cheese ripening and that this element is central to many microbial interactions occurring in this ecosystem. This study explores the impact of iron fortification on the growth and activity of a reduced microbial community composed of nine strains representative of the microbial community of surface-ripened cheeses. Three different iron compounds (ferrous sulfate, ferric chloride, ferric citrate) were used at three different concentrations, i.e., 18, 36, and 72 μM, to fortify cheese curd after inoculation with the consortium. This treatment significantly enhanced the growth of certain cheese-ripening bacteria in curd, resulting in substantial changes in the volatilome and metabolome profiles. These observations were dose-dependent, with more pronounced effects detected with higher iron concentrations. No statistically significant difference was observed in the microbial composition based on the iron compounds used for fortification, but this factor had an impact on the volatilome and amino acids profile. These findings highlight the importance of iron availability for the behavior of cheese microbial communities. They also open novel perspectives on cheesemakers' use of iron fortification to control microbial growth and improve cheese quality.

The Natural Whey Starter Used in the Production of Grana Padano and Parmigiano Reggiano PDO Cheeses: A Complex Microbial Community

Natural whey starter (NWS) is an undefined complex culture used in the production of Grana Padano and Parmigiano Reggiano PDO cheeses. The aim of this review is to discuss, in light of the latest research results, the role of NWS as a primary player in the cheese-making process, considering the microbial community scenario. NWS is traditionally produced by fermenting part of the whey collected at the end of a previous cheese-making process. The method used to produce NWS, based on the back-slopping principle, favors the selection of a microbiota composed mainly of thermophilic lactic acid bacteria. This method of preparation induces the survival of several different species and biotypes. The presence of such a mixture of strains facilitates the development of a natural starter characterized by a remarkable ability to adapt to non-standardized cheese-making parameters. NWS is a microbial community whose activity is not simply the result of the sum of the activities of individual microorganisms, but rather the activity of the community as a whole, in which each individual bacterial cell responds to the presence of the others. According to this traditional protocol, the NWS becomes the 'microbiological bond' between cheeses over time.

Beyond Harmful: Exploring Biofilm Formation by Enterococci Isolated from Portuguese Traditional Cheeses

This study investigated the biofilm-forming capabilities of Enterococcus isolates from Portuguese traditional cheeses with protected designation of origin (PDO) status, specifically Azeitão and Nisa. Given the absence of added starter cultures in the cheesemaking process, the characteristics of these cheeses are intrinsically linked to the autochthonous microbiota present in the raw materials and the production environment. Our findings demonstrate that all isolates possess biofilm production abilities, which are crucial for their colonization and persistence within cheese factories, thereby maintaining factory-specific microbial heritage. Through an integrated analysis utilizing principal component analysis (PCA), a direct correlation between biofilm formation and cell viability was established. Notably, these results underscore the adaptive capacity of enterococci to survive environmental fluctuations and their role in the unique characteristics of Portuguese traditional cheeses. Overall, this research enhances our understanding of the microbial dynamics in cheese production and highlights the importance of enterococci in preserving cheese quality and heritage.

Microbiome signatures associated with flavor development differentiate Protected Designation of origin water Buffalo Mozzarella cheese from different production areas

Water Buffalo Mozzarella (BM) is a typical cheese from Southern Italy with unique flavor profile and texture. It is produced following a traditional back-slopping procedure and received the Protected Designation of Origin (PDO) label. To better understand the link between the production area, the microbiome composition and the flavor profile of the products, we performed a multiomic characterization of PDO BM collected from 57 different dairies located in the two main PDO production area, i.e. Caserta (n = 35) and Salerno (n = 22). Thus, we assessed the microbiome by high-throughput shotgun metagenomic sequencing and the Volatile Organic Compounds (VOCs) by gas chromatography/mass spectrometry (GC/MS). Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. delbrueckii were identified as the core microbiome present in all samples. However, the microbiome taxonomic profiles resulted in a clustering of the samples based on their geographical origin, also showing that BM from Caserta had a greater microbial diversity. Consistently, Caserta and Salerno samples also showed different VOC profiles. These results suggest that the microbiome and its specific metabolic activity are part of the terroir that shape BM specific features, linking this traditional product with the area of production, thus opening new clues for improving traceability and fraud protection of traditional products.

Sustainability implications and relevance of using omics sciences to investigate cheeses with protected designation of origin

Cheese, a fundamental component of the human diet and a cornerstone of the global food economy, has a significance beyond its role as a commodity, playing a crucial part in the cultural identity of various communities. The intricate natural aging process known as maturation involves a series of reactions that induce changes in the cheese's physical, biochemical, microbiological, and particularly sensory characteristics, making it a complex aspect of cheese production. Recently, the adoption of omics sciences (e.g., metagenomics, metabolomics, proteomics) has emerged as a new trend in studies related to protected designation of origin (PDO) cheese. This mini-summary aims to outline the relationship between omics studies in these food matrices and all the sustainability facets of the production chain in general, and to discuss and recognize that the importance of these studies goes beyond comprehending the cheese biome and extends to fostering and ensuring the sustainability of the production chain. In this context, numerous studies in recent years have linked the identification of intrinsic characteristics of PDO cheeses through omics sciences to crucial sustainability themes such as territoriality, biodiversity, and the preservation of product authenticity. The trajectory suggests that, increasingly, multidisciplinary studies spanning various omics sciences will not only contribute to the characterization of these products but will also address sustainability aspects directly related to the production chain (e.g., authenticity, microbial biodiversity, functionality). This expansion underscores the multidisciplinary nature of these studies, broadening their social impact beyond the academic realm. Consequently, these pivotal studies play a crucial role in advancing discussions on PDO products and sustainability. © 2024 Society of Chemical Industry.

Qu-omics elucidates the formation and spatio-temporal differentiation mechanism underlying the microecology of high temperature Daqu

Even if fermented in the same qu-room, Daqu will form various microecologies. A gradual differentiation of microbial population niches was observed within different qu-layers, manifesting as variations in the abundance of dominant microorganisms including Bacillus, Saccharopolyspora, Weissella, Kroppenstedtia, Thermoascus, Thermomyces, Saccharomycopsis, and Rasamsonia. Moreover, distinctions were observed in the functional expression of microorganisms, including Aspergillus, Virgibacillus, Oceanobacillus, and Neurospora. The community in middle layer Daqu exhibited characteristics of high compactness and niche diversity, which facilitated efficient substrate utilization. During the initial phase, the upper Daqu community demonstrated heightened activity. However, in the middle and lower layers, fungi and bacteria respectively exhibited greater functional expression. The key environmental factors regulating the assembly of communities in the upper and middle layers were pH and temperature, respectively, and the lower was moisture and acidity. Notably, deterministic assembly exerted a stronger influence on fungi.

Microbiome and Physicochemical Features Associated with Differential Listeria monocytogenes Growth in Soft, Surface-Ripened Cheeses

Soft-ripened cheeses (SRCs) are at a higher risk for the growth of the foodborne pathogen Listeria monocytogenes due to favorable moisture content and pH compared to other cheeses. L. monocytogenes growth is not consistent across SRCs, however, and may be affected by physicochemical and/or microbiome characteristics of the cheeses. Therefore, the purpose of this study was to investigate how the physicochemical and microbiome profiles of SRCs may affect L. monocytogenes growth. Forty-three SRCs produced from raw (n = 12) or pasteurized (n = 31) milk were inoculated with L. monocytogenes (103 CFU/g), and the pathogen growth was monitored over 12 days at 8°C. In parallel, the pH, water activity (aw), microbial plate counts, and organic acid content of cheeses were measured, and the taxonomic profiles of the cheese microbiomes were measured using 16S rRNA gene targeted amplicon sequencing and shotgun metagenomic sequencing. L. monocytogenes growth differed significantly between cheeses (analysis of variance [ANOVA]; P < 0.001), with increases ranging from 0 to 5.4 log CFU (mean of 2.5 ± 1.2 log CFU), and was negatively correlated with aw. Raw milk cheeses showed significantly lower L. monocytogenes growth than pasteurized-milk cheeses (t test; P = 0.008), possibly due to an increase in microbial competition. L. monocytogenes growth in cheeses was positively correlated with the relative abundance of Streptococcus thermophilus (Spearman correlation; P < 0.0001) and negatively correlated with the relative abundances of Brevibacterium aurantiacum (Spearman correlation; P = 0.0002) and two Lactococcus spp. (Spearman correlation; P < 0.01). These results suggest that the cheese microbiome may influence the food safety in SRCs. IMPORTANCE Previous studies have identified differences in L. monocytogenes growth between SRCs, but no clear mechanism has yet been elucidated. To the best of our knowledge, this is the first study to collect a wide range of SRCs from retail sources and attempt to identify key factors associated with pathogen growth. A key finding in this research was the positive correlation between the relative abundance of S. thermophilus and the growth of L. monocytogenes. The inclusion of S. thermophilus as a starter culture is more common in industrialized SRC production, suggesting that industrial production of SRC may increase the risk of L. monocytogenes growth. Overall, the results of this study further our understanding of the impact of aw and the cheese microbiome on the growth of L. monocytogenes in SRCs, hopefully leading toward the development of SRC starter/ripening cultures that can prevent L. monocytogenes growth.

Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods

Fermented foods are important components of the human diet. There is increasing awareness of abundant nutritional and functional properties present in fermented foods that arise from the transformation of substrates by microbial communities. Thus, it is significant to unravel the microbial communities and mechanisms of characteristic flavor formation occurring during fermentation. There has been rapid development of high-throughput and other omics technologies, such as metaproteomics and metabolomics, and as a result, there is growing recognition of the importance of integrating these approaches. The successful applications of multi-omics approaches and bioinformatics analyses have provided a solid foundation for exploring the fermentation process. Compared with single-omics, multi-omics analyses more accurately delineate microbial and molecular features, thus they are more apt to reveal the mechanisms of fermentation. This review introduces fermented foods and an overview of single-omics technologies - including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. We also discuss integrated multi-omics and bioinformatic analyses and their role in recent research progress related to fermented foods, as well as summarize the main potential pathways involved in certain fermented foods. In the future, multilayered analyses of multi-omics data should be conducted to enable better understanding of flavor formation mechanisms in fermented foods.

Distinct Bacterial Communities in São Jorge Cheese with Protected Designation of Origin (PDO)

São Jorge cheese is an iconic product of the Azores, produced from raw cow's milk and natural whey starter (NWS). Although it is produced according to Protected Designation of Origin (PDO) specifications, the granting of the PDO label depends crucially on sensory evaluation by trained tasters. The aim of this work was to characterize the bacterial diversity of this cheese using next-generation sequencing (NGS) and to identify the specific microbiota that contributes most to its uniqueness as a PDO by distinguishing the bacterial communities of PDO and non-PDO cheeses. The NWS and curd microbiota was dominated by Streptococcus and Lactococcus, whereas Lactobacillus and Leuconostoc were also present in the core microbiota of the cheese along with these genera. Significant differences (p < 0.05) in bacterial community composition were found between PDO cheese and non-certified cheese; Leuconostoc was found to play the chief role in this regard. Certified cheeses were richer in Leuconostoc, Lactobacillus and Enterococcus, but had fewer Streptococcus (p < 0.05). A negative correlation was found between contaminating bacteria, e.g., Staphylococcus and Acinetobacter, and the development of PDO-associated bacteria such as Leuconostoc, Lactobacillus and Enterococcus. A reduction in contaminating bacteria was found to be crucial for the development of a bacterial community rich in Leuconostoc and Lactobacillus, thus justifying the PDO seal of quality. This study has helped to clearly distinguish between cheeses with and without PDO based on the composition of the bacterial community. The characterization of the NWS and the cheese microbiota can contribute to a better understanding of the microbial dynamics of this traditional PDO cheese and can help producers interested in maintaining the identity and quality of São Jorge PDO cheese.

An Insight into Goat Cheese: The Tales of Artisanal and Industrial Gidotyri Microbiota

The purpose of this study was to determine for the first time the microbiota in artisanal-type and industrial-type Gidotyri cheeses and investigate the influence of the cheese-making practices on their composition using culture-independent techniques. The microbiota present in artisanal with commercial starters (Artisanal_CS, n = 15), artisanal with in-house starters (Artisanal_IHS, n = 10) and industrial (Ind., n = 9) Gidotyri cheese samples were analyzed using a targeted metagenomic approach (16S rRNA gene). The Ind. Gidotyri cheese microbiota were less complex, dominated by the Streptococcaceae family (91%) that was more abundant compared to the artisanal Gidotyri cheeses (p < 0.05). Artisanal cheeses were more diverse compositionally with specific bacterial species being prevalent to each subtype. Particularly, Loigolactobacillus coryniformis (OTU 175), Secundilactobacillus malefermentans (OTU 48), and Streptococcus parauberis (OTU 50) were more prevalent in Artisanal_IHS cheeses compared to Artisanal_CS (p ≤ 0.001) and Ind. (p < 0.01) Gidotyri cheeses. Carnobacterium maltaromaticum (OTU 23) and Enterobacter hormaechei subsp. hoffmannii (OTU 268) were more prevalent in Artisanal_CS cheeses compared to Artisanal_IHS cheeses (p < 0.05) and Ind. cheeses (p < 0.05). Hafnia alvei (OTU 13) and Acinetobacter colistiniresistens (OTU 111) tended to be more prevalent in Artisanal_CS compared to the other two cheese groups (p < 0.10). In conclusion, higher microbial diversity was observed in the artisanal-type Gidotyri cheeses, with possible bacterial markers specific to each subtype identified with potential application to traceability of the manufacturing processes’ authenticity and cheese quality.

Phenotypic and Safety Assessment of the Cheese Strain Lactiplantibacillus plantarum LL441, and Sequence Analysis of its Complete Genome and Plasmidome

This work describes the phenotypic typing and complete genome analysis of LL441, a dairy Lactiplantibacillus plantarum strain. LL441 utilized a large range of carbohydrates and showed strong activity of some carbohydrate-degrading enzymes. The strain grew slowly in milk and produced acids and ketones along with other volatile compounds. The genome of LL441 included eight circular molecules, the bacterial chromosome, and seven plasmids (pLL441-1 through pLL441-7), ranging in size from 8.7 to 53.3 kbp. Genome analysis revealed vast arrays of genes involved in carbohydrate utilization and flavor formation in milk, as well as genes providing acid and bile resistance. No genes coding for virulence traits or pathogenicity factors were detected. Chromosome and plasmids were packed with insertion sequence (IS) elements. Plasmids were also abundant in genes encoding heavy metal resistance traits and plasmid maintenance functions. Technologically relevant phenotypes linked to plasmids, such as the production of plantaricin C (pLL441-1), lactose utilization (pLL441-2), and bacteriophage resistance (pLL441-4), were also identified. The absence of acquired antibiotic resistance and of phenotypes and genes of concern suggests L. plantarum LL441 be safe. The strain might therefore have a use as a starter or starter component in dairy and other food fermentations or as a probiotic.

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses

Flavor characteristics of ripened cheese are established by various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, which spontaneously develop during the cheese-manufacturing process. We previously revealed the relationship between bacterial microbiota and flavor components in soft-type ripened cheeses by using a multiomics approach that combined metagenomics and metabolomics; however, we could not establish a causal relationship. This study aimed to substantiate the causal nature of the correlations revealed by the multiomics approach by using cheese-ripening tests with single isolate inoculation. The bacterial diversity and composition in surface mold-ripened cheeses from Japan and France varied, depending on the differences between the milks (pasteurized or raw), cheese positions (core or rind), and manufacturers. Although the volatile compounds did not clearly reflect the distinctive characteristics of the cheese samples, nonstarter lactic acid bacteria, Actinobacteria, and Proteobacteria positively correlated with ketones and sulfur compounds, as evidenced by a Spearman's correlation analysis. Cheese-ripening tests conducted after inoculation with single bacterial strains belonging to the above-mentioned taxa confirmed that these bacteria formed volatile compounds, in agreement with the correlations observed. In particular, various flavor compounds, such as acids, esters, ketones, and sulfur compounds, were detected in cheese inoculated with Pseudoalteromonas sp. TS-4-4 strain. These findings provide important insights into the role of nonstarter bacteria in the development of cheese flavor and into the effectiveness of the multiomics approach in screening for bacteria that can improve the quality of cheese products. IMPORTANCE Our previous study revealed that the existence of various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, clearly correlated with the abundance of flavor components, such as volatile compounds, in soft-type ripened cheeses via a multiomics approach that used 16S rRNA gene amplicon sequencing and headspace gas chromatography-mass spectrometry. However, this approach only showed correlations derived from statistical analyses rather than causal relationships. Therefore, in the present study, we performed cheese-ripening tests using nonstarter bacteria to substantiate the correlations revealed by the multiomics approach in soft-type ripened cheese. Our results suggest the capability of nonstarter bacteria, such as Proteobacteria, to impart flavor to cheese and the effectiveness of the multiomics approach in screening for microbial isolates that can improve the quality of cheese. Overall, our research provides new insights into the importance of bacteria in cheese production.

Advances in fermented foods revealed by multi-omics: A new direction toward precisely clarifying the roles of microorganisms

Fermented foods generally comprise a complex micro-ecosystem with beneficial microbiota, functional products, and special flavors and qualities that are welcomed globally. Single-omics analysis allows for a comprehensive characterization of the main microbial factors influencing the function, flavor, and quality of fermented foods. However, the species, relative abundance, viability, growth patterns, and metabolic processes of microorganisms vary with changes in processing and environmental conditions during fermentation. Furthermore, the mechanisms underlying the complex interaction among microorganisms are still difficult to completely understand and analyze. Recently, multi-omics analysis and the integration of multiple types of omics data allowed researchers to more comprehensively explore microbial communities and understand the precise relationship between fermented foods and their functions, flavors, and qualities. Multi-omics approaches might help clarify the mechanisms underpinning the fermentation processes, metabolites, and functional components of these communities. This review clarified the recent advances in the roles of microorganisms in fermented foods based on multi-omics data. Current research achievements may allow for the precise control of the whole industrial processing technology of fermented foods, meeting consumers' expectations of healthy products.

Grape Pomace in Ewes Diet Affects Metagenomic Profile, Volatile Compounds and Biogenic Amines Contents of Ripened Cheese

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.

FDF-DB: A Database of Traditional Fermented Dairy Foods and Their Associated Microbiota

BACKGROUND

Fermented foods are attracting increasing interest due to their nutritional and health benefits, including a positive impact on gut microbiota exerted by their associated microbes. However, information relative to traditional fermented dairy products, along with their autochthonous microbiota, is still fragmented and poorly standardized. Therefore, our aim was to collect and aggregate data useful for obtaining a comprehensive overview translated in a classical database interface that can be easily handled by users.

METHODS

a preliminary inventory was built up by systematically collecting data from publicly available resources for the creation of a list of traditional dairy foods produced worldwide, including additional metadata useful for stratifying, and collapsing subgroups.

RESULTS

we developed the Fermented Dairy Food Database (FDF-DB), a feasible resource comprising 1852 traditional dairy foods (cheeses, fermented milks, and yogurt) for which microbial content and other associated metadata such as geographical indication label, country/region of origin, technological aspects were gathered.

CONCLUSIONS

FDF-DB is a useful and user-friendly resource where taxonomic information and processing production details converge. This resource will be of great aid for researchers, food industries, stakeholders and any user interested in the identification of technological and microbiological features characterizing traditional fermented dairy products.

Authenticity and Typicity of Traditional Cheeses: A Review on Geographical Origin Authentication Methods

Food fraud, corresponding to any intentional action to deceive purchasers and gain an undue economical advantage, is estimated to result in a 10 to 65 billion US dollars/year economical cost worldwide. Dairy products, such as cheese, in particular cheeses with protected land- and tradition-related labels, have been listed as among the most impacted as consumers are ready to pay a premium price for traditional and typical products. In this context, efficient food authentication methods are needed to counteract current and emerging frauds. This review reports the available authentication methods, either chemical, physical, or DNA-based methods, currently used for origin authentication, highlighting their principle, reported application to cheese geographical origin authentication, performance, and respective advantages and limits. Isotope and elemental fingerprinting showed consistent accuracy in origin authentication. Other chemical and physical methods, such as near-infrared spectroscopy and nuclear magnetic resonance, require more studies and larger sampling to assess their discriminative power. Emerging DNA-based methods, such as metabarcoding, showed good potential for origin authentication. However, metagenomics, providing a more in-depth view of the cheese microbiota (up to the strain level), but also the combination of methods relying on different targets, can be of interest for this field.

The "Crosstalk" between Microbiota and Metabolomic Profile of Kefalograviera Cheese after the Innovative Feeding Strategy of Dairy Sheep by Omega-3 Fatty Acids

The purpose of this study was to examine the effects of two different feeding systems, a control or a flaxseed and lupin diet (experimental), for a sheep flock, on the microbiota and metabolome of Kefalograviera cheese samples produced by their milk. In particular, the microbiota present in Kefalograviera cheese samples was analyzed using 16S rRNA gene sequencing, while ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) was applied to investigate the chemical profile of the cheeses, considering the different feeding systems applied. The metagenomic profile was found to be altered by the experimental feeding system and significantly correlated to specific cheese metabolites, with Streptococcaceae and Lactobacillaceae establishing positive and negative correlations with the discriminant metabolites. Overall, more than 120 features were annotated and identified with high confidence level across the samples while most of them belonged to specific chemical classes. Characteristic analytes detected in different concentrations in the experimental cheese samples including arabinose, dulcitol, hypoxanthine, itaconic acid, L-arginine, L-glutamine and succinic acid. Therefore, taken together, our results provide an extensive foodomics approach for Kefalograviera cheese samples from different feeding regimes, investigating the metabolomic and metagenomic biomarkers that could be used to foresee, improve, and control cheese ripening outcomes, demonstrating the quality of the experimental Kefalograviera cheese.

Phenotype testing, genome analysis, and metabolic interactions of three lactic acid bacteria strains existing as a consortium in a naturally fermented milk

This work reports the characterization of three lactic acid bacteria (LAB) strains -Lactococcus lactis LA1, Lactococcus cremoris LA10, and Lactiplantibacillus plantarum LA30- existing as a stable consortium in a backslopping-inoculated, naturally fermented milk (NFM). This study aimed at uncovering the biochemical and genetic basis of the stability of the consortium and the cooperativity among the strains during milk fermentation. All three strains were subjected to phenotyping, covering the utilization of carbohydrates, enzyme activity, and antibiotic resistance. The strains were grown in milk individually, as well as in all possible combinations, and the resulting fermented product was analyzed for sugars, organic acids, and volatile compounds. Finally, the genomes of the three strains were sequenced and analyzed for genes associated with technological and safety properties. As expected, wide phenotypic diversity was seen between the strains. Lactococcus cremoris LA10 was the only strain to reach high cell densities and coagulate milk alone after incubation at 22°C for 24 h; congruently, it possessed a gene coding for a PrtP type II caseinolytic protease. Compared to any other fermentation, acetaldehyde concentrations were greater by a factor of six when all three strains grew together in milk, suggesting that its production might be the result of an interaction between them. Lactococcus lactis LA1, which carried a plasmid-encoded citQRP operon, was able to utilize milk citrate producing diacetyl and acetoin. No genes encoding virulence traits or pathogenicity factors were identified in any of the strains, and none produced biogenic amines from amino acid precursors, suggesting them to be safe. Lactiplantibacillus plantarum LA30 was susceptible to tetracycline, although it harbors a disrupted antibiotic resistance gene belonging to the tetM/tetW/tetO/tetS family. All three strains contained large numbers of pseudogenes, suggesting that they are well adapted ("domesticated") to the milk environment. The consortium as a whole or its individual strains might have a use as a starter or as starter components for dairy fermentations. The study of simple consortia, such as that existing in this NFM, can help reveal how microorganisms interact with one another, and what influence they may have on the sensorial properties of fermented products.

Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity-the backbone of the regulation of ecosystem services and "soil health" maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.

Comparison of the Microbiome of Artisanal Homemade and Industrial Feta Cheese through Amplicon Sequencing and Shotgun Metagenomics

Feta is the most renowned protected designation of origin (PDO) white brined cheese produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on, among other factors, its overall microbial ecosystem. In this study, we employed 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing, as well as shotgun metagenomics, to investigate the microbiome of artisanal homemade and industrial Feta cheese samples from different regions of Greece, which has very rarely been investigated. 16S rDNA data suggested the prevalence of the Lactococcus genus in the homemade samples, while Streptococcus and Lactobacillus genera prevailed in the industrial control samples. Species identification deriving from shotgun metagenomics corroborated these findings, as Lactococcus lactis dominated two homemade samples while Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were found to be dominating one industrial sample. ITS data revealed a complex diversity of the yeast population among the samples analyzed. Debaryomyces, Kluyveromyces, Cutaneotrichosporon, Pichia, Candida, and Rhodotorula were the major genera identified, which were distributed in a rather arbitrary manner among the different samples. Furthermore, a number of potential metagenome-assembled genomes (MAGs) could be detected among assembled shotgun bins. The overall analysis of the shotgun metagenomics supported the presence of different foodborne pathogens in homemade samples (e.g., Staphylococcus aureus, Listeria monocytogenes, Enterobacter cloacae, and Streptococcus suis), but with low to very low abundances. Concluding, the combination of both amplicon sequencing and shotgun metagenomics allowed us to obtain an in-depth profile of the artisanal homemade Feta cheese microbiome.

Functional bacterial cultures for dairy applications: towards improving safety, quality, nutritional and health benefit aspects

Traditionally, fermentation was used to preserve the shelf life of food. Currently, in addition to favouring food preservation, well standardized and controlled industrial processes are also aimed at improving the functional characteristics of the final product. In this regard, starter cultures have become an essential cornerstone of food production. The selection of robust microorganisms, well adapted to the food environment, has been followed by the development of microbial consortia that provide some functional characteristics, beyond their acidifying capacity, achieving safer, high‐quality foods with improved nutritional and health‐promoting properties. In addition to starters, adjunct cultures and probiotics, which normally do not have a relevant role in fermentation, are added to the food in order to provide some beneficial characteristics. This review focuses on highlighting the functional characteristics of food starters, as well as adjunct and probiotic cultures (mainly lactic acid bacteria and bifidobacteria), with a specific focus on the synthesis of metabolites for preservation and safety aspects (e.g. bacteriocins), organoleptic properties (e.g. exopolysaccharides), nutritional (e.g. vitamins) and health improvement (e.g. neuroactive molecules). Literature reporting the application of these functional cultures in the manufacture of foods, mainly those related to dairy production, such as cheeses and fermented milks, has also been updated.

High-Performance Thin-Layer Chromatography-Immunostaining as a Technique for the Characterization of Whey Protein Enrichment in Edam Cheese

Whey protein-enriched cheese can be produced by means of a high-temperature treatment of a part of the cheese milk. In this way, the nutritional quality of the resulting cheeses can be increased while resources are conserved. High-performance thin-layer chromatography-immunostaining (HPTLC-IS) using specific β-lactoglobulin (β-LG) antibodies was applied to study the implementation and stability of β-LG in two different sample sets of whey protein-enriched Edam model cheeses, including industrial-scale ones. Two methods were compared for the extraction of the proteins/peptides from the cheese samples. By applying tryptic hydrolysis directly from a suspended cheese sample instead of a supernatant of a centrifuged suspension, a better yield was obtained for the extraction of β-LG. When applying this method, it was found that selected epitopes in the tryptic β-LG peptides remain stable over the ripening period of the cheese. For four of the tryptic β-LG peptides detected by immunostaining, the amino acid sequence was identified using MALDI-TOF-MS/MS. One of the peptides identified was the semi-tryptic peptide VYVEELKPTP. A linear relationship was found between the content of this peptide in cheese and the proportion of high-heated milk in the cheese milk. β-LG enrichment factors of 1.72 (n = 3, sample set I) and 1.33 ± 0.19 (n = 1, sample set II) were determined for the cheese samples containing 30% high-heated milk compared to the non-enriched samples. The relative β-LG contents in the cheese samples with 30% high-heated milk were calculated to be 4.35% ± 0.39% (sample set I) and 9.11% ± 0.29% (sample set II) using a one-point calibration. It can be concluded that the HPTLC-IS method used is a suitable tool for the analysis of whey protein accumulation in cheese, being therefore potentially directly applicable on an industrial scale. For more accurate quantification of the whey protein content in cheese, an enhanced calibration curve needs to be applied.

Omics Approaches to Assess Flavor Development in Cheese

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.

Developments in effective use of volatile organic compound analysis to assess flavour formation during cheese ripening

In the burgeoning demand for optimization of cheese production, ascertaining cheese flavour formation during the cheese making process has been the focal point of determining cheese quality. In this research reflection, we have highlighted how valuable volatile organic compound (VOC) analysis has been in assessing contingent cheese flavour compounds arising from non-starter lactic acid bacteria (NSLAB) along with starter lactic acid bacteria (SLAB), and whether VOC analysis associated with other high-throughput data might help provide a better understanding the cheese flavour formation during cheese process. It is widely known that there is a keen interest to merge all omics data to find specific biomarkers and/or to assess aroma formation of cheese. Towards that end, results of VOC analysis have provided valuable insights into the cheese flavour profile. In this review, we are pinpointing the effective use of flavour compound analysis to perceive flavour-forming ability of microbial strains that are convenient for dairy production, intertwining microbiome and metabolome to unveil potential biomarkers that occur during cheese ripening. In doing so, we summarised the functionality and integration of aromatic compound analysis in cheese making and gave reflections on reconsidering what the role of flavour-based analysis might have in the future.

Foodomic-Based Approach for the Control and Quality Improvement of Dairy Products

The food quality assurance before selling is a needed requirement intended for protecting consumer interests. In the same way, it is also indispensable to promote continuous improvement of sensory and nutritional properties. In this regard, food research has recently contributed with studies focused on the use of 'foodomics'. This review focuses on the use of this technology, represented by transcriptomics, proteomics, and metabolomics, for the control and quality improvement of dairy products. The complex matrix of these foods requires sophisticated technology able to extract large amounts of information with which to influence their aptitude for consumption. Thus, throughout the article, different applications of the aforementioned technologies are described and discussed in essential matters related to food quality, such as the detection of fraud and/or adulterations, microbiological safety, and the assessment and improvement of transformation industrial processes (e.g., fermentation and ripening). The magnitude of the reported results may open the door to an in-depth transformation of the most conventional analytical processes, with the introduction of new techniques that allow a greater understanding of the biochemical phenomena occurred in this type of food.

Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.

Shifts in diversity and function of bacterial community during manufacture of Rushan

Rushan is a traditional dairy product consumed by the Bai people in the Yunnan Province of China, and its production still follows the traditional procedure of backslopping. However, how the microbial composition of raw materials and processing shape the microorganisms in Rushan have not been systemically reported. In this study, high-throughput sequencing technique was applied to analyze the microbial compositions of raw milk, fresh Rushan, curd whey, acid whey, and dry Rushan at the phylum, family, genus, and Lactobacillus species levels. The results indicated that Lactobacillus, Lactococcus, and Streptococcus were dominant genera in Rushan, whereas Lactobacillus kefiranofaciens and Lactobacillus helveticus were the 2 abundant species at the Lactobacillus species level. The network analysis indicated that raw milk mainly contributed to the microbial diversity of Rushan, whereas acid whey made a great contribution to shaping the relative abundance of microbes in Rushan and dramatically increased acid-producing genera, such as Lactobacillus and Acetobacter. The variation in microbial composition led to an increase in the relative abundance of pathways related to energy supply, acid production, fatty acid accumulation, cysteine, methionine, and lysine accumulation. The volatile profile of Rushan was rich in esters and acids, and the high relative abundance of Lactobacillus might be associated with reduction of amino acid metabolism, degradation of unpleasant flavored xylene, and accumulation of decanoic, dodecanoic, and tetradecanoic acids in the products. The accumulation of medium long-chain fatty acids might result from the relative abundance of FabF, FabZ, and FabI, particularly from Lactobacillus amylolyticus and Lacticaseibacillus paracasei.

Study of the microbial diversity of a panel of Belgian artisanal cheeses associated with challenge studies for Listeria monocytogenes

High throughput sequencing could become a powerful tool in food safety. This study was the first to investigate artisanal cheeses from Belgium (31 batches) using metagenetics, in relation to Listeria monocytogenes growth data acquired during a previous project. Five cheese types were considered, namely unripened acid-curd cheeses, smear- and mold-ripened soft cheeses, and Gouda-type and Saint-Paulin-type cheeses. Each batch was analyzed in triplicate the first and the last days of storage at 8 °C. Globally, 2697 OTUs belonging to 277 genera and to 15 phyla were identified. Lactococcus was dominant in all types, but Streptococcus was co-dominant in smear-ripened soft cheeses and Saint-Paulin-type cheeses. The dominant population was not always associated with added starter cultures. Bacterial richness and diversity were significantly higher in both types of soft cheeses than in other categories, including particular genera like Prevotella, Faecalibacterium and Hafnia-Obesumbacterium in mold-ripened cheeses and Brevibacterium, Brachybacterium, Microbacterium, Bacteroides, Corynebacterium, Marinilactibacillus, Fusobacterium, Halomonas and Psychrobacter in smear-ripened soft cheeses. A strong correlation was observed between no growth of L. monocytogenes in a smear-ripened cheese and the presence of an unknown Fusobacterium (relative abundance around 10%). This in silico correlation should be confirmed by further experiments in vitro and in situ.

Evaluation of the Relationships Between Microbiota and Metabolites in Soft-Type Ripened Cheese Using an Integrated Omics Approach

Cheese ripening is effected by various microorganisms and results in the characteristic flavors of cheese. Owing to the complexity of the microbiota involved, the relationship between microorganisms and components during ripening remains unclear. In this study, metagenomics and metabolomics were integrated to reveal these relationships in three kinds of surface mold-ripened cheeses and two kinds of bacterial smear-ripened cheeses. The microbiota is broadly divided into two groups to correspond with different cheese types. Furthermore, surface mold-ripened cheese showed similar microbiota regardless of the cheese variety, whereas bacterial smear-ripened cheese showed specific microbiota characterized by marine bacteria (MB) and halophilic and alkaliphilic lactic acid bacteria for each cheese variety. In the metabolite analysis, volatile compounds suggested differences in cheese types, although organic acids and free amino acids could not determine the cheese characteristics. On the other hand, Spearman correlation analysis revealed that the abundance of specific bacteria was related to the formation of specific organic acids, free amino acids, and volatile compounds. In particular, MB was positively correlated with esters and pyrazines, indicating their contribution to cheese quality. These methodologies and results further our understanding of microorganisms and allow us to select useful strains for cheese ripening.

The occurrence, growth, and biocontrol of Listeria monocytogenes in fresh and surface-ripened soft and semisoft cheeses

Listeria monocytogenes continues to pose a food safety risk in ready-to-eat foods, including fresh and soft/semisoft cheeses. Despite L. monocytogenes being detected regularly along the cheese production continuum, variations in cheese style and intrinsic/extrinsic factors throughout the production process (e.g., pH, water activity, and temperature) affect the potential for L. monocytogenes survival and growth. As novel preservation strategies against the growth of L. monocytogenes in susceptible cheeses, researchers have investigated the use of various biocontrol strategies, including bacteriocins and bacteriocin-producing cultures, bacteriophages, and competition with native microbiota. Bacteriocins produced by lactic acid bacteria (LAB) are of particular interest to the dairy industry since they are often effective against Gram-positive organisms such as L. monocytogenes, and because many LAB are granted Generally Regarded as Safe (GRAS) status by global food safety authorities. Similarly, bacteriophages are also considered a safe form of biocontrol since they have high specificity for their target bacterium. Both bacteriocins and bacteriophages have shown success in reducing L. monocytogenes populations in cheeses in the short term, but regrowth of surviving cells can commonly occur in the finished cheeses. Competition with native microbiota, not mediated by bacteriocin production, has also shown potential to inhibit the growth of L. monocytogenes in cheeses, but the mechanisms are still unclear. Here, we have reviewed the current knowledge on the growth of L. monocytogenes in fresh and surface-ripened soft and semisoft cheeses, as well as the various methods used for biocontrol of this common foodborne pathogen.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

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.

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as "foods made through desired microbial growth and enzymatic conversions of food components". This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.

Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture

Undefined strain starters are used for the production of many traditional and artisanal cheeses. Composition of undefined starters depends on several factors, and the diversity in strains and species significantly affects cheese quality and features. Culture-dependent approaches have long been used for the microbial profiling and functionalities of undefined cultures but underestimate their diversity due to culturability biases. Recently, culture-independent methods, based on high-throughput sequencing (HTS), have been preferred, with a significant boost in resolution power and sensitivity level. Amplicon targeted (AT) metagenomics, based on 16S rRNA sequencing, returned a larger microbiota diversity at genus and, sometimes, at species levels for artisanal starters of several PDO cheeses, but was inappropriate for populations with high strain diversity, and other gene targets were tested in AT approaches. Shotgun metagenomics (total DNA) and metatranscriptomics (total RNA), although are more powerful in depicting diversity and functionality of undefined cultures, have been rarely applied because of some limitations (e.g., high costs and laboriousness, need for bioinformatics skills). The advantages of HTS technologies are undoubted, but some hurdles need to be still overcame (e.g., resolution power, discrepancy between active and inactive cells, robust analytic pipelines, cost and time reduction for integrated approaches) so that HTS become routinary and convenient for defining complexity, microbial interactions (including host-phage relationships) and evolution in cheeses of undefined starters.

Role of lactic acid bacteria in flavor development in traditional Chinese fermented foods: A review

Traditional Chinese fermented foods are favored by consumers due to their unique flavor, texture and nutritional values. A large number of microorganisms participate in the process of fermentation, especially lactic acid bacteria (LAB), which are present in almost all fermented foods and contribute to flavor development. The formation process of flavor is complex and involves the biochemical conversion of various food components. It is very important to fully understand the conversion process to direct the flavor formation in foods. A comprehensive link between the LAB community and the flavor formation in traditional Chinese fermented foods is reviewed. The main mechanisms involved in the flavor formation dominated by LAB are carbohydrate metabolism, proteolysis and amino acid catabolism, and lipolysis and fatty acid metabolism. This review highlights some useful novel approaches for flavor enhancement, including the application of functional starter cultures and metabolic engineering, which may provide significant advances toward improving the flavor of fermented foods for a promising market.

Austrian Raw-Milk Hard-Cheese Ripening Involves Successional Dynamics of Non-Inoculated Bacteria and Fungi

Cheese ripening involves successional changes of the rind microbial composition that harbors a key role on the quality and safety of the final products. In this study, we analyzed the evolution of the rind microbiota (bacteria and fungi) throughout the ripening of Austrian Vorarlberger Bergkäse (VB), an artisanal surface-ripened cheese, by using quantitative and qualitative approaches. The real-time quantitative PCR results revealed that bacteria were more abundant than fungi in VB rinds throughout ripening, although both kingdoms were abundant along the process. The qualitative investigation was performed by high-throughput gene-targeted (amplicon) sequencing. The results showed dynamic changes of the rind microbiota throughout ripening. In the fresh products, VB rinds were dominated by Staphylococcus equorum and Candida. At early ripening times (14–30 days) Psychrobacter and Debaryomyces flourished, although their high abundance was limited to these time points. At the latest ripening times (90–160 days), VB rinds were dominated by S. equorum, Brevibacterium, Corynebacterium, and Scopulariopsis. Strong correlations were shown for specific bacteria and fungi linked to specific ripening periods. This study deepens our understanding of VB ripening and highlights different bacteria and fungi associated to specific ripening periods which may influence the organoleptic properties of the final products.

Microbiota and Metabolite Profiling Combined With Integrative Analysis for Differentiating Cheeses of Varying Ripening Ages

Cheese maturation and flavor development results from complex interactions between milk substrates, cheese microbiota and their metabolites. In this study, bacterial 16S rRNA-gene sequencing, untargeted metabolomics (gas chromatography-mass spectrometry) and data integration analyses were used to characterize and differentiate commercial Cheddar cheeses of varying maturity made by the same and different manufacturers. Microbiota and metabolite compositions varied between cheeses of different ages and brands, and could be used to distinguish the cheeses. Individual amino acids and carboxylic acids were positively correlated with the ripening age for some brands. Integration and Random Forest analyses revealed numerous associations between specific bacteria and metabolites including a previously undescribed positive correlation between Thermus and phenylalanine and a negative correlation between Streptococcus and cholesterol. Together these results suggest that multi-omics analyses has the potential to be used for better understanding the relationships between cheese microbiota and metabolites during ripening and for discovering biomarkers for validating cheese age and brand authenticity.

The Interrelationship Between Microbiota and Peptides During Ripening as a Driver for Parmigiano Reggiano Cheese Quality

Cheese microbiota contribute significantly to the final characteristics of cheeses due to the growth and interaction between cheese microorganisms during processing and ripening. For raw milk cheeses, such as Parmigiano Reggiano (PR), the microbiota derive from the raw milk itself, the dairy environment, and the starter. The process of cheese making and time of ripening shape this complex ecosystem through the selection of different species and biotypes that will drive the quality of the final product by performing functions of their metabolism such as proteolysis. The diversity in the final peptide and amino acid composition of the cheese is thus mostly linked to the diversity of this microbiota. The purpose of this study was to get more insight into the factors affecting PR cheese diversity and, more specifically, to evaluate whether the composition of the bacterial community of cheeses along with the specific peptide composition are more affected by the ripening times or by the cheese making process. To this end, the microbiota and the peptide fractions of 69 cheese samples (from curd to cheese ripened 24 months) were analyzed during 6 complete PR production cycles, which were performed in six different dairies located in the PR production area. The relation among microbial dynamics, peptide evolution, and ripening times were investigated in this unique and tightly controlled production and sampling set up. The study of microbial and peptide moieties in products from different dairies – from curd to at least 12 months, the earliest time from which the cheese can be sold, and up to a maximum of 24 months of ripening – highlighted the presence of differences between samples coming from different dairies, probably due to small differences in the cheese making process. Besides these differences, however, ripening time had by far the greatest impact on microbial dynamics and, consequently, on peptide composition.

Metaproteomics insights into traditional fermented foods and beverages

Traditional fermented foods and beverages (TFFB) are important dietary components. Multi-omics techniques have been applied to all aspects of TFFB research to clarify the composition and nutritional value of TFFB, and to reveal the microbial community, microbial interactions, fermentative kinetics, and metabolic profiles during the fermentation process of TFFB. Because of the advantages of metaproteomics in providing functional information, this technology has increasingly been used in research to assess the functional diversity of microbial communities. Metaproteomics is gradually gaining attention in the field of TFFB research because it can reveal the nature of microorganism function at the protein level. This paper reviews the common methods of metaproteomics applied in TFFB research; systematically summarizes the results of metaproteomics research on TFFB, such as sauces, wines, fermented tea, cheese, and fermented fish; and compares the differences in conclusions reached through metaproteomics versus other omics methods. Metaproteomics has great advantages in revealing the microbial functions in TFFB and the interaction between the materials and microbial community. In the future, metaproteomics should be further applied to the study of functional protein markers and protein interaction in TFFB; multi-omics technology requires further integration to reveal the molecular nature of TFFB fermentation.

New insights into cheddar cheese microbiota-metabolome relationships revealed by integrative analysis of multi-omics data

Cheese microbiota and metabolites and their inter-relationships that underpin specific cheese quality attributes remain poorly understood. Here we report that multi-omics and integrative data analysis (multiple co-inertia analysis, MCIA) can be used to gain deeper insights into these relationships and identify microbiota and metabolite fingerprints that could be used to monitor product quality and authenticity. Our study into different brands of artisanal and industrial cheddar cheeses showed that Streptococcus, Lactococcus and Lactobacillus were the dominant taxa with overall microbial community structures differing not only between industrial and artisanal cheeses but also among different cheese brands. Metabolome analysis also revealed qualitative and semi-quantitative differences in metabolites between different cheeses. This also included the presence of two compounds (3-hydroxy propanoic acid and O-methoxycatechol-O-sulphate) in artisanal cheese that have not been previously reported in any type of cheese. Integrative analysis of multi-omics datasets revealed that highly similar cheeses, identical in age and appearance, could be distinctively clustered according to cheese type and brand. Furthermore, the analysis detected strong relationships, some previously unknown, which existed between the cheese microbiota and metabolome, and uncovered specific taxa and metabolites that contributed to these relationships. These results highlight the potential of this approach for identifying product specific microbe/metabolite signatures that could be used to monitor and control cheese quality and product authenticity.