Cheese peptidomics: a detailed study on the evolution of the oligopeptide fraction in Parmigiano-Reggiano cheese from curd to 24 months of aging

Untargeted metabolomics and machine learning unveil quality and authenticity interactions in grated Parmigiano Reggiano PDO cheese

The chemical composition of Parmigiano Reggiano (PR) hard cheese can be significantly affected by different factors across the dairy supply chain, including ripening, altimetric zone, and rind inclusion levels in grated hard cheeses. The present study proposes an untargeted metabolomics approach combined with machine learning chemometrics to evaluate the combined effect of these three critical parameters. Specifically, ripening was found to exert a pivotal role in defining the signature of PR cheeses, with amino acids and lipid derivatives that exhibited their role as key discriminant compounds. In parallel, a random forest classifier was used to predict the rind inclusion levels (> 18%) in grated cheeses and to authenticate the specific effect of altimetry dairy production, achieving a high prediction ability in both model performances (i.e., ∼60% and > 90%, respectively). Overall, these results open a novel perspective to identifying quality and authenticity markers metabolites in cheese.

Physicochemical and Sensory Characterization of Whey Protein-Enriched Semihard Cheese

In view of potential future changes of German food legislation with regard to cheese product quality parameters, this study aimed to evaluate the quality of whey protein-enriched semihard cheese (WPEC). Model WPEC was produced in a pilot plant and on an industrial scale by adding defined amounts of high-heat (HH) milk to the cheese milk and comprehensively analyzed during cheese processing. The dry matter, total protein, pure protein, fat, and sodium chloride content of six-week ripened cheese samples were not significantly different (p < 0.05) when the technologically necessary heating of the curd was adapted to the amount of HH milk. However, the ripening, firmness, and melting behavior of WPEC was different compared to cheese without HH milk. During ripening, no formation of whey protein peptides was observed, but differences in the amount of some bitter peptides deriving from the casein fraction were found. Sensory data suggested a slightly more bitter taste perception by the panelists for the WPEC. Further technological adjustments are recommended to obtain marketable WPEC.

Cultivable microbial diversity, peptide profiles, and bio-functional properties in Parmigiano Reggiano cheese

Introduction

Lactic acid bacteria (LAB) communities shape the sensorial and functional properties of artisanal hard-cooked and long-ripened cheeses made with raw bovine milk like Parmigiano Reggiano (PR) cheese. While patterns of microbial evolution have been well studied in PR cheese, there is a lack of information about how this microbial diversity affects the metabolic and functional properties of PR cheese.

Methods

To fill this information gap, we characterized the cultivable fraction of natural whey starter (NWS) and PR cheeses at different ripening times, both at the species and strain level, and investigated the possible correlation between microbial composition and the evolution of peptide profiles over cheese ripening.

Results and discussion

The results showed that NWS was a complex community of several biotypes belonging to a few species, namely, Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. lactis. A new species-specific PCR assay was successful in discriminating the cheese-associated species Lacticaseibacillus casei, Lacticaseibacillus paracasei, Lacticaseibacillus rhamnosus, and Lacticaseibacillus zeae. Based on the resolved patterns of species and biotype distribution, Lcb. paracasei and Lcb. zeae were most frequently isolated after 24 and 30 months of ripening, while the number of biotypes was inversely related to the ripening time. Peptidomics analysis revealed more than 520 peptides in cheese samples. To the best of our knowledge, this is the most comprehensive survey of peptides in PR cheese. Most of them were from β-caseins, which represent the best substrate for LAB cell-envelope proteases. The abundance of peptides from β-casein 38-88 region continuously increased during ripening. Remarkably, this region contains precursors for the anti-hypertensive lactotripeptides VPP and IPP, as well as for β-casomorphins. We found that the ripening time strongly affects bioactive peptide profiles and that the occurrence of Lcb. zeae species is positively linked to the incidence of eight anti-hypertensive peptides. This result highlighted how the presence of specific LAB species is likely a pivotal factor in determining PR functional properties.

Milk Antiviral Proteins and Derived Peptides against Zoonoses

Milk is renowned for its nutritional richness but also serves as a remarkable reservoir of bioactive compounds, particularly milk proteins and their derived peptides. Recent studies have showcased several robust antiviral activities of these proteins, evidencing promising potential within zoonotic viral diseases. While several publications focus on milk's bioactivities, antiviral peptides remain largely neglected in reviews. This knowledge is critical for identifying novel research directions and analyzing potential nutraceuticals within the One Health context. Our review aims to gather the existing scientific information on milk-derived antiviral proteins and peptides against several zoonotic viral diseases, and their possible mechanisms. Overall, in-depth research has increasingly revealed them as a promising and novel strategy against viruses, principally for those constituting a plausible pandemic threat. The underlying mechanisms of the bioactivity of milk's proteins include inhibiting viral entry and attachment to the host cells, blocking replication, or even viral inactivation via peptide-membrane interactions. Their marked versatility and effectiveness stand out compared to other antiviral peptides and can support future research and development in the post-COVID-19 era. Overall, our review helps to emphasize the importance of potentially effective milk-derived peptides, and their significance for veterinary and human medicines, along with the pharmaceutical, nutraceutical, and dairy industry.

The integrated metabolomics and sensory analyses unravel the peculiarities of mountain grassland-based cheese production: The case of Parmigiano Reggiano PDO

Untargeted metabolomics based on ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry was combined with sensory analysis to provide new insights into the impact of the feeding system from mountain regions (grassland deriving from permanent meadows) on the chemical fingerprint of Parmigiano Reggiano PDO hard cheese. In the framework of a representative investigation, two different ripening times (12 and 24 months) were also considered. Multivariate statistics allowed discriminating cheese samples from different feeding regimens according to their metabolomics signatures. Interestingly, mountain grassland-based cheese samples were characterized by a more favourable fatty acid profile, recording also feed-derived compounds (such as terpenoids and linoleic acid derivatives) potentially associated with both beneficial effects on human health and sensory properties. According to the sensory analysis, the impact of herbs and grass enhanced the colour and retro-olfactive complexity of Parmigiano Reggiano PDO cheese, with spicy, umami and intense vegetal aromatic notes representing distinctive features.

Peptide profile of Parmigiano Reggiano cheese after simulated gastrointestinal digestion: From quality drivers to functional compounds

Time of ripening has a strong impact on shaping the valuable and recognizable characteristics of long-ripened types of cheese such as Parmigiano Reggiano (PR) due to the interrelationship between microbiota and proteolysis that occurs during ripening. The derived peptide profile is linked to cheese quality and represents the canvas for enzymes upon digestion, which could be responsible for the release of potentially bioactive peptides (BPs). In this study, we aimed at investigating the presence of BP in 72 PR cheese samples of different ripening times, from curd to 24 months of ripening, produced in six different dairies, and following their fate after simulated gastrointestinal digestion. A small number of peptide sequences sharing 100% similarity with known antimicrobial, antioxidant, and ACE-inhibitor sequences were found in PR cheeses, while a higher number of potential BPs were found after their simulated gastrointestinal digestion, in different amounts according to ripening time. Taking advantage of the complex organization of the sampling plan, we were able to follow the fate of peptides considered quality drivers during cheese ripening to their release as functional compounds upon digestion.

Biochemical and technological properties of moose (<i>Alces alces</i>) recombinant chymosin

Recombinant chymosins (rСhns) of the cow and the camel are currently considered as standard milk coagulants for cheese-making. The search for a new type of milk-clotting enzymes that may exist in nature and can surpass the existing “cheese-making” standards is an urgent biotechnological task. Within this study, we for the first time constructed an expression vector allowing production of a recombinant analog of moose chymosin in the expression system of Escherichia coli (strain SHuffle express). We built a model of the spatial structure of moose chymosin and compared the topography of positive and negative surface charges with the correspondent structures of cow and camel chymosins. We found that the distribution of charges on the surface of moose chymosin has common features with that of cow and camel chymosins. However, the moose enzyme carries a unique positively charged patch, which is likely to affect its interaction with the substrate. Biochemical and technological properties of the moose rChn were studied. Commercial rСhns of cow and camel were used as comparison enzymes. In some technological parameters, the moose rChn proved to be superior to the reference enzymes. Сompared with the cow and camel rСhns, the moose chymosin specific activity is less dependent on the changes in CaCl2 concentration in the range of 1–5 mM and pH in the range of 6–7, which is an attractive technological property. The total proteolytic activity of the moose rСhn occupies an intermediate position between the rСhns of cow and camel. The combination of biochemical and technological properties of the moose rСhn argues for further study of this enzyme.

Effect of Parmigiano Reggiano Consumption on Blood Pressure of Spontaneous Hypertensive Rats

In recent years, due to the significant increase in hypertension, peptides which are able to reduce blood pressure have gained special interest by scientific research and food industry. Several bioactive peptides with ascertained ACE-inhibitory activity have been found in Parmigiano Reggiano (PR) cheese and/or mixtures deriving from its digestion in vitro, and this may be predictive of itspotential antihypertensive effect in vivo. This study investigated the long-term effect of feeding (PR) cheese on blood pressure (BP) of spontaneously hypertensive rats (SHRs). A total of 30 male SHRs, 13 weeks old, were subdivided into 6 groups balanced for body weight and BP, to receive dailydietary supplementation with: 0.1–0.2–0.4–0.6 g PR/rat, captopril, and water. Systolic and diastolic BP were recorded every two weeks, for 10 weeks. Blood samples were collected at the end of the trial. Dietary integration with PR led to a transitory reduction in rats’ pressure in the first 35 days of treatment and pressure decreased in a dose-dependent manner. In the second part of the study, the beneficial effect of PR antihypertensive peptides may have been masked and reduced by the increase in BP of rats linked to the rise in age of animals. No PR derived peptides were detected in rats’ serum. Highlights: Parmigiano Reggiano (PR) cheese led to a transitory reduction in rats’ pressure in the first 35 days of treatment. This effect was PR dose dependent. The highest amounts of PR tested did not increase both systolic and diastolic blood pressures of hypertensive rats.

Preparation and Taste Characteristics of Kokumi N-Lactoyl Phenylalanine in the Presence of Phenylalanine and Lactate

N-l-Lactoyl phenylalanine (N-l-lactoyl-Phe) has been identified as a taste-active contributor in many fermented foods. However, its preparation, taste property, and content in foodstuffs are little known to date. In the current study, two preparation technologies of N-l-lactoyl-Phe including heating and enzymatic methods were investigated. Other investigations include its taste property and quantification in several fermented foods. The results indicated that the heating preparation and enzymatic preparation only produced N-l-lactoyl-Phe instead of N-d-lactoyl-Phe in the presence of l-lactate/d-lactate and l-phenylalanine (Phe). A high yield (58.0% ± 0.7%) of N-l-lactoyl-Phe was achieved under the following conditions: Phe, lactate, CaO, and water at molar ratios of 1:8:0.3:9 kept at 100 °C for 3 h. With nine enzymes, a maximum yield of 21.2% ± 0.3% was achieved in the aqueous solution under mild operating conditions: 0.18 M Phe, 0.90 M lactate, 5 g/L Debitrase HYW 20, pH 8, and 55 °C for 24 h. The sensory evaluation revealed that N-l-lactoyl-Phe in water enhanced the salty and umami intensity. It also enhanced the thickness, mouthfulness, and continuity of salt solution, model broth, and chicken broth, revealing that N-l-lactoyl-Phe was a kokumi-active compound. The kokumi thresholds of N-l-lactoyl-Phe in these solutions were 50, 50, and 25 mg/L, respectively. N-l-Lactoyl-Phe was quantified in traditional Chinese fermented foods as 30.12 ± 0.28 mg/kg in preserved pickles, 14.11 ± 0.14 mg/kg in soybean paste, 4.87 ± 0.16 mg/kg in fermented bean, 0.71 ± 0.11 mg/kg in rice vinegar, and 20.34 ± 0.18 mg/kg in soy sauce. These results revealed the potential of N-l-lactoyl-Phe as a taste enhancer, presenting a new opportunity for the food industry.

A combined metabolomics and peptidomics approach to discriminate anomalous rind inclusion levels in Parmigiano Reggiano PDO grated hard cheese from different ripening stages

Parmigiano Reggiano is a hard cheese with a Protected Designation of Origin (PDO) certification that also applies to the grated product. The percentage of rind in grated Parmigiano Reggiano is regulated by the PDO production Specification and must not exceed the limit of 18% (w/w). The present study evaluates the potential of an untargeted foodomics approach to detect anomalous inclusions of rind in grated Parmigiano Reggiano cheese. In particular, a combined metabolomics and peptidomics approach was used to detect potential markers of counterfeits (rind > 18%). In the framework of realistic food integrity purposes, non-Parmigiano Reggiano grated samples and different ripening times were also considered. Untargeted metabolomics allowed detecting 347 compounds, with a prevalence of amino acids and peptide derivatives, followed by fatty acyls and other compounds (such as lactones, ketones, and aldehydes) typically related to proteolysis and lipolysis events. Overall, the unsupervised multivariate statistics showed that the ripening time plays a hierarchically higher impact than rind inclusion in determining the main differences in the chemical profiles detected. Interestingly, supervised statistics highlighted distinctive markers for ripening time and rind inclusion, with only 16 common discriminant compounds being shared between the two conditions. The best markers of rind inclusion > 18% were 2-hydroxyadenine (VIP score = 1.937; AUC value = 0.83) and the amino acid derivatives argininic acid (VIP score = 1.462; AUC value = 0.75) and 5-hydroxyindole acetaldehyde (VIP score = 1.710; AUC value = 0.86). Interestingly, the medium-chain aldehyde 4-hydroperoxy-2-nonenal was a common marker of both ripening time and anomalous rind inclusion (>18%), likely arising from the lipid oxidation processes. Finally, among potential marker peptides of rind inclusion, the alpha-S1 casein proteolytic product (F)FVAPFPEVFGK(E) could be identified.

Authenticity assessment of dairy products by capillary electrophoresis

Milk and derivatives are a very important part in the diet of the world population. Products from goat, buffalo, and sheep species have a greater economic value than the cow ones, therefore, authenticity frauds by improperly adding cow's milk occur frequently: dairy products are among the seven more attractive foods for adulteration. Milk from each of the above-cited animal species has its own definite profile of whey proteins (variants of α-lactalbumin and β-lactoglobulin) and its definite profile of caseins (variants of α_S1 -, α_S2 -, β-, and κ-casein). Such proteins can be usefully exploited as markers of authenticity by using capillary electrophoresis which is the technique of choice for the analysis of proteins. Due to the multiple adjustable parameters that are unknown to other analytical techniques, capillary electrophoresis is able to detect frauds in milk mixtures and cheese with little use of solvents, fast analysis time, and ease of operation. This makes it attractive and competitive for routine checks that are very important to fight the adulteration market. Advantages and limitations are discussed.

An Integrated Peptidomics and In Silico Approach to Identify Novel Anti-Diabetic Peptides in Parmigiano-Reggiano Cheese

Simple Summary

Dietary habits and sedentary lifestyle are widely established to be the major risk factors for the development of long-term chronic conditions, such as type-2 diabetes (T2D). In this framework, where consumer’s food choices are even more influenced by an ever-growing awareness on nutritional, environmental, and healthy aspects, the presence and identification of natural bioactive compounds are gaining increasing attention in the scientific community. Pharmacological treatment of T2D is based on the administration of molecules able to inhibit some key enzymes involved in the carbohydrate digestion and insulin secretion. The multiple side-effects of synthetic inhibitors led to an increased demand for natural food-derived anti-diabetic agents. The present work offers a new integrated approach for the identification and selection of new bioactive peptides, able to inhibit the key digestive enzymes implicated in the control of blood glucose level. The novelty lies in the development of a new, quick, and cost-effective integrated methodology supported by confirmed in vitro evidence. In fact, the present work successfully accomplished the identification of two selected candidates with a possible application in the diabetes management. Indeed, the functional and healthy role of Parmigiano-Reggiano cheese in human nutrition was assessed, highlighting its potential anti-diabetic properties.

Abstract

Inhibition of key metabolic enzymes linked to type-2-diabetes (T2D) by food-derived compounds is a preventive emerging strategy in the management of T2D. Here, the impact of Parmigiano-Reggiano (PR) cheese peptide fractions, at four different ripening times (12, 18, 24, and 30 months), on the enzymatic activity of α-glucosidase, α-amylase, and dipeptidyl peptidase-IV (DPP-IV) as well as on the formation of fluorescent advanced glycation end-products (fAGEs) was assessed. The PR peptide fractions were able to inhibit the selected enzymes and fAGEs formation. The 12-month-ripening PR sample was the most active against the three enzymes and fAGEs. Mass spectrometry analysis enabled the identification of 415 unique peptides, 54.9% of them common to the four PR samples. Forty-nine previously identified bioactive peptides were found, mostly characterized as angiotensin-converting enzyme-inhibitors. The application of an integrated approach that combined peptidomics, in silico analysis, and a structure–activity relationship led to an efficient selection of 6 peptides with potential DPP-IV and α-glucosidase inhibitory activities. Peptide APFPE was identified as a potent novel DPP-IV inhibitor (IC₅₀ = 49.5 ± 0.5 μmol/L). In addition, the well-known anti-hypertensive tripeptide, IPP, was the only one able to inhibit the three digestive enzymes, highlighting its possible new and pivotal role in diabetes management.

Rapid Discrimination and Authentication of Korean Farmstead Mozzarella Cheese through MALDI-TOF and Multivariate Statistical Analysis

Geographical origin and authenticity are the two crucial factors that propel overall cheese perception in terms of quality and price; therefore, they are of great importance to consumers and commercial cheese producers. Herein, we demonstrate a rapid, accurate method for discrimination of domestic and import mozzarella cheeses in the Republic of Korea by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The protein profiles' data aided by multivariate statistical analysis successfully differentiated farmstead and import mozzarella cheeses according to their geographical location of origin. A similar investigation within domestic samples (farmsteads/companies) also showed clear discrimination regarding the producer. Using the biomarker discovery tool, we identified seven distinct proteins, of which two (m/z 7407.8 and 11,416.6) were specific in farmstead cheeses, acting as potential markers to ensure authentication and traceability. The outcome of this study can be a good resource in building a database for Korean domestic cheeses. This study also emphasizes the combined utility of MALDI-TOF MS and multivariate analysis in preventing fraudulent practices, thereby ensuring market protection for Korean farmstead cheeses.

Reduction in the Brining Time in Parmigiano Reggiano Cheese Production Minimally Affects Proteolysis, with No Effect on Sensory Properties

Brine soaking is one of the most important steps in the production of Parmigiano Reggiano cheese, since it determines the amount of salt in the final product. Reduction in salt in Parmigiano Reggiano cheese might be important for improving its nutritional profile, but it could affect the manufacturing processes by altering proteolysis and consequently the product quality. In this study, for the first time, salt reduction was explored at the industrial level on real cheese samples manufactured in a local dairy. In particular, 20 wheels were produced with conventional (18 days, 10 wheels) and shorter (12 days, 10 wheels) brining steps. In every group, wheels were studied at two different ripening times, 15 and 30 months. A shorter brining time resulted in an average 12% decrease in salt content. A full characterization of free amino acids and peptides was performed by LC-MS on all samples. Free amino acids and peptides, as expected, increased with ripening, due to proteolysis, with samples having low salt content showing a slightly faster increase when compared to standard ones, hinting to a slightly accelerated proteolytic process. Nonetheless, low-salt and conventional cheeses shared similar sensory profiles at both ripening times.

Peptides in Brewed Wines: Formation, Structure, and Function

The traditional low-alcoholic beverages, such as grape wine, sake, and rice wine, have been consumed all over the world for thousands of years, each with their unique methods of production that have been practiced for centuries. Moderate consumption of wine is generally touted as beneficial for health, although there is ongoing debate for the responsible components in wine. In this review, the structural and functional characteristics, the formation mechanisms, and their health-promoting activities of peptides in three brewed wines, grape wine, Chinese rice wine (also called Chinese Huangjiu or Chinese yellow wine), and Japanese sake, are discussed. The formation of peptides in wine imparts sensorial, technological, and biological attributes. Prospects on future research, with an emphasis on the peptide characterization, formation mechanism, physiological activity, and molecular mechanisms of action, are presented.

Post translational modifications of milk proteins in geographically diverse goat breeds

Goat milk is a source of nutrition in difficult areas and has lesser allerginicity than cow milk. It is leading in the area for nutraceutical formulation and drug development using goat mammary gland as a bioreactor. Post translational modifications of a protein regulate protein function, biological activity, stabilization and interactions. The protein variants of goat milk from 10 breeds were studied for the post translational modifications by combining highly sensitive 2DE and Q-Exactive LC-MS/MS. Here we observed high levels of post translational modifications in 201 peptides of 120 goat milk proteins. The phosphosites observed for CSN2, CSN1S1, CSN1S2, CSN3 were 11P, 13P, 17P and 6P, respectively in 105 casein phosphopeptides. Whey proteins BLG and LALBA showed 19 and 4 phosphosites respectively. Post translational modification was observed in 45 low abundant non-casein milk proteins mainly associated with signal transduction, immune system, developmental biology and metabolism pathways. P_asp is reported for the first time in 47 sites. The rare conserved peptide sequence of (SSSEE) was observed in αS1 and αS2 casein. The functional roles of identified phosphopeptides included anti-microbial, DPP-IV inhibitory, anti-inflammatory and ACE inhibitory. This is first report from tropics, investigating post translational modifications in casein and non-casein goat milk proteins and studies their interactions.

Simulated in vitro gastrointestinal digestion of traditional Chinese Rushan and Naizha cheese: Peptidome profiles and bioactivity elucidation

Chinese Rushan and Naizha, the traditional acid coagulated cheese types produced from cow and yak milk, respectively, have been consumed for more than thousands of years. In this study, we aimed to characterise peptides of Rushan and Naizha in simulated in vitro gastrointestinal digestion using label-free based peptidomic. The identified peptide sequences were subjected to BIOPEP database driven bioactivity search. In total, 309 and 225 peptides were identified from Rushan and Naizha cheese, respectively, corresponding to 20 protein annotations. Analysis of label-free quantification found different protein digestibility, where casein was the primary source of peptides in Rushan, among which 62% represented β-casein by peptide count. The release of peptides was concentrated in specific residues 145-155 of β-casein in Rushan. In contrast, κ-casein and 7 minor milk proteins were dominant in digestion of Naizha cheese (p < 0.05). In particular, there were 11 peptides from digestion that were exact matches in databases to sequences with immunomodulatory, antibacterial, ACE-inhibition, DPP IV inhibition and antioxidant activities. Four novel angiotensin I-converting enzyme inhibitory (ACEI) activities peptides (YPFPGPIH, LKNWGEGW, RELEEIR, and HPHPHLS) were explored using molecular docking, chemically synthesized, and in vitro ACEI activity. The peptides had lower estimated free energy values (-5.34 to -7.66 kcal/mol), and exhibited the lowest IC₅₀ value of 109.5, 77.7, 196.6, and 64.30 μM, respectively. Our study is the most comprehensive peptidomic analysis of Chinese Rushan and Naizha cheese to date.

Can cheese mites, maggots and molds enhance bioactivity? Peptidomic investigation of functional peptides in four traditional cheeses

Aside from their amino acid content, dairy proteins are valuable for their ability to carry encrypted bioactive peptides whose activities are latent until released by digestive enzymes or endogenous enzymes within the food. Peptides can possess a wide variety of functionalities, such as antibacterial, antihypertensive, and antioxidative properties, as demonstrated by in vitro and in vivo studies. This phenomenon raises the question as to what impact various traditional cheese-making processes have on the formation of bioactive peptides in the resulting products. In this study, we have profiled the naturally-occurring peptides in two hard and two soft traditional cheeses and have identified their known bioactive sequences. While past studies have typically identified fewer than 100 peptide sequences in a single cheese, we have used modern instrumentation to identify between 2900 and 4700 sequences per cheese, an increase by a factor of about 50. We demonstrated substantial variations in proteolysis and peptide formation between the interior and rind of each cheese, which we ascribed to the differences in microbial composition between these regions. We identified a total of 111 bioactive sequences among the four cheeses, with the greatest number of sequences, 89, originating from Mimolette. The most common bioactivities identified were antimicrobial and inhibition of the angiotensin-converting enzyme. This work revealed that cheese proteolysis and the resulting peptidomes are more complex than originally thought in terms of the number of peptides released, variation in peptidome across sites within a single cheese, and variation in bioactive peptides among cheese-making techniques.

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.

Higher microbial diversity in raw than in pasteurized milk Raclette-type cheese enhances peptide and metabolite diversity after in vitro digestion

Numerous bacteria are responsible for hydrolysis of proteins during cheese ripening. The raw milk flora is a major source of bacterial variety, starter cultures are needed for successful acidification of the cheese and proteolytic strains like Lactobacillus helveticus, are added for flavor improvement or acceleration of ripening processes. To study the impact of higher bacterial diversity in cheese on protein hydrolysis during simulated human digestion, Raclette-type cheeses were produced from raw or heat treated milk, with or without proteolytic L. helveticus and ripened for 120 days. Kinetic processes were studied with a dynamic (DIDGI®) in vitro protocol and endpoints with the static INFOGEST in vitro digestion protocol, allowing a comparison of the two in vitro protocols at the level of gastric and intestinal endpoints. Both digestion protocols resulted in comparable peptide patterns after intestinal digestion and higher microbial diversity in cheeses led to a more diverse peptidome after simulated digestion.

Ripening of Nostrano Valtrompia PDO Cheese in Different Storage Conditions: Influence on Chemical, Physical and Sensory Properties

Nostrano Valtrompia is a hard, long-ripened, Italian Protected Designation of Origin (PDO) cheese typically produced by applying traditional cheesemaking practices in small dairies. Due to the limited production, this cheese is characterized by an important market price. Nostrano Valtrompia physico-chemical and sensory quality can be influenced by the duration and conditions of ripening. The objectives of this work were to characterize the physico-chemical and sensory characteristics of Nostrano Valtrompia cheese ripened for 12 and 16 months and to study the influence of different ripening warehouses: a temperature conditioned warehouse (TCW) and in a traditional, not conditioned warehouse (TNCW). The moisture gradient from the rind to the center of the cheese influenced texture, moisture, aw and color. Ripening in different warehouses did not affect the overall appreciation of the cheese nor other physico-chemical (color, moisture) or sensory traits. TCW cheeses were characterized by a slightly softer texture, slightly different openings distribution, and a different sensory perception than TNCW cheeses. These minor differences were related to the less variable environmental ripening conditions of TCW than TNCW. The results of this study can be useful to support the management of the ripening conditions of Nostrano Valtrompia PDO cheese and to rationally introduce new, suitable ripening sites.

Application of the UHPLC-DIA-HRMS Method for Determination of Cheese Peptides

Until now, cheese peptidomics approaches have been criticised for their lower throughput. Namely, analytical gradients that are most commonly used for mass spectrometric detection are usually over 60 or even 120 min. We developed a cheese peptide mapping method using nano ultra-high-performance chromatography data-independent acquisition high-resolution mass spectrometry (nanoUHPLC-DIA-HRMS) with a chromatographic gradient of 40 min. The 40 min gradient did not show any sign of compromise in milk protein coverage compared to 60 and 120 min methods, providing the next step towards achieving higher-throughput analysis. Top 150 most abundant peptides passing selection criteria across all samples were cross-referenced with work from other publications and a good correlation between the results was found. To achieve even faster sample turnaround enhanced DIA methods should be considered for future peptidomics applications.

Identification and Detection of Bioactive Peptides in Milk and Dairy Products: Remarks about Agro-Foods

Food-based components represent major sources of functional bioactive compounds. Milk is a rich source of multiple bioactive peptides that not only help to fulfill consumers 'nutritional requirements but also play a significant role in preventing several health disorders. Understanding the chemical composition of milk and its products is critical for producing consistent and high-quality dairy products and functional dairy ingredients. Over the last two decades, peptides have gained significant attention by scientific evidence for its beneficial health impacts besides their established nutrient value. Increasing awareness of essential milk proteins has facilitated the development of novel milk protein products that are progressively required for nutritional benefits. The need to better understand the beneficial effects of milk-protein derived peptides has, therefore, led to the development of analytical approaches for the isolation, separation and identification of bioactive peptides in complex dairy products. Continuous emphasis is on the biological function and nutritional characteristics of milk constituents using several powerful techniques, namely omics, model cell lines, gut microbiome analysis and imaging techniques. This review briefly describes the state-of-the-art approach of peptidomics and lipidomics profiling approaches for the identification and detection of milk-derived bioactive peptides while taking into account recent progress in their analysis and emphasizing the difficulty of analysis of these functional and endogenous peptides.

Peptide Profiling and Biological Activities of 12-Month Ripened Parmigiano Reggiano Cheese

Proteolysis degree, biological activities, and water-soluble peptide patterns were evaluated in 12 month-ripened Parmigiano Reggiano (PR) cheeses collected in different dairy farms and showing different salt and fat content. Samples classified in high-salt and high-fat group (HH) generally showed lower proteolysis degree than samples having low-salt and low-fat content (LL). This positive correlation between salt/fat reduction and proteolysis was also confirmed by the analysis of biological activities, as the LL group showed higher average values of angiotensin-converting enzyme (ACE)-inhibitory and antioxidant activities. UHPLC/HR-MS allowed the identification of 805 unique peptides: LL and HH groups shared 59.3% of these peptides, while 20.9% and 19.9% were LL and HH specific, respectively. Frequency analysis of peptides identified a core of 183 peptides typical of 12-month ripened PR cheeses (corresponding to the 22.7% of total peptides), but no significant differences were detected in peptide patterns between LL and HH groups. Forty bioactive peptides, including 18 ACE-inhibitors and 12 anti-microbial peptides, were identified, of which 25 firstly found in PR cheese. Globally, this work contributed to unraveling the potentially healthy benefits of peptides fraction in PR cheese and provided prior evidence that PR with reduced fat/salt content showed the highest antihypertensive and antioxidant activities.

Characterization of Defatted Products Obtained from the Parmigiano-Reggiano Manufacturing Chain: Determination of Peptides and Amino Acids Content and Study of the Digestibility and Bioactive Properties

Parmigiano–Reggiano (PR) is a worldwide known Italian, long ripened, hard cheese. Its inclusion in the list of cheeses bearing the protected designation of origin (PDO, EU regulation 510/2006) poses restrictions to its geographic area of production and its technological characteristics. To innovate the Parmigiano–Reggiano (PR) cheese manufacturing chain from the health and nutritional point of view, the output of defatted PR is addressed. Two defatting procedures (Soxhlet, and supercritical CO₂ extraction) were tested, and the obtained products were compared in the composition of their nitrogen fraction, responsible for their nutritional, organoleptic, and bioactive functions. Free amino acids were quantified, and other nitrogen compounds (peptides, proteins, and non-proteolytic aminoacyl derivatives) were identified in the extracts and the mixtures obtained after simulated gastrointestinal digestion. Moreover, antioxidant and angiotensin converting enzyme (ACE) inhibition capacities of the digests were tested. Results obtained from the molecular and biofunctional characterization of the nitrogen fraction, show that both the defatted products keep the same nutritional properties of the whole cheese.

Impact of Extending Hard-Cheese Ripening: A Multiparameter Characterization of Parmigiano Reggiano Cheese Ripened up to 50 Months

Extending ripening of hard cheeses well beyond the traditional ripening period is becoming increasingly popular, although little is known about the actual evolution of their characteristics. The present work aimed at investigating selected traits of Parmigiano Reggiano cheese ripened for 12, 18, 24, 30, 40 and 50 months. Two cheeses per each ripening period were sampled. Although moisture constantly decreased and was close to 25% in 50-month cheeses, with a parallel increase in cheese hardness, several biochemical changes occurred involving the activity of both native and microbial enzymes. Capillary electrophoresis demonstrated degradation of α_s1- and β-casein, indicating residual activity of both chymosin and plasmin. Similarly, continuous release of free amino acids supported the activity of peptidases deriving from lysed bacterial cells. Volatile flavor compounds, such as short-chain fatty acids and some derived ketones, alcohols and esters, evaluated by gas chromatography with solid-phase micro-extraction, accumulated as well. Cheese microstructure was characterized by free fat trapped in irregularly shaped areas within a protein network, with native fat globules being no longer visible. This study showed for the first time that numerous biochemical and structural variations still occur in a hard cheese at up to 50 months of aging, proving that the ripening extension deserves to be highlighted to the consumer and may justify a premium price.

Origins, Technological Development, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.

Milk Peptidomics to Identify Functional Peptides and for Quality Control of Dairy Products

Human milk and dairy products are important parts of human nutrition. In addition to supplying nutrients, milk proteins contain fragments-peptides-with important biological functions that are released during processing or digestion. Besides their potential functional relevance, peptides released during processing can be used as markers of ripening stage or product deterioration. Hence, identification and quantification of peptides in milk can be used to assay potential health benefits or product quality. This chapter describes how to extract, identify, and analyze peptides within breast milk, dairy products, and dairy digestive samples. We describe how to analyze extracted peptides with liquid chromatography-mass spectrometry, to use software to identify peptides based on database searching, and to extract peak areas for relative quantification of each peptide. We describe methods for data analysis, including predicting which enzymes are responsible for protein cleavage, identifying the site specificity of protein breakdown, mapping identified peptides to known bioactive peptides, and applying models to predict novel functional peptides.

Comprehensive analysis of proteolysis during 8 months of ripening of high-cooked Old Saare cheese

We applied capillary electrophoresis, liquid chromatography coupled with tandem mass-spectrometry (MS/MS), and ultra-performance liquid chromatography to determine the composition of water-insoluble and water-soluble proteinaceous fractions of the cheese and to study in detail the degradation of caseins during 8 mo of ripening of Estonian high-temperature cooked hard cheese Old Saare. The application of high-resolution and high-accuracy MS/MS enabled identification of more than 3,000 small peptides, representing a fairly full casein peptidome containing peptides of 4 to 25 AA in length: 1,049 from β-casein (CN), 944 from α_S1-CN, 813 from α_S2-CN, and 234 from κ-CN. The majority of β-CN- and α_S1-CN-derived peptides originated from the N-terminal parts of the molecule, f6-93 and f1-124, respectively; peptides from α_S2-CN arose predominantly from the C-terminal end f100-162. At the beginning of ripening, we found a relatively high amount of peptides originating from the glycomacropeptide part of κ-CN, whereas peptides from para-κ-CN prevailed during the later stages of ripening of the cheese. The cleavage patterns of β-CN, α_S2-CN, as well as α_S1-CN, showed that primary proteolysis was started mainly by plasmin, although a low proteolytic activity of chymosin was also evident. Based on the analysis of cleavage sites, we observed a significant participation of proteolytic enzymes, including amino- and carboxypeptidases, of both mesophilic and thermophilic starter bacteria in further hydrolysis of oligopeptides during the ripening. Several new phosphopeptides were detected in the result of MS/MS data analysis. The profiles of the estimated concentrations of phosphopeptides revealed that those originating from β-CN and α_S1-CN accumulated during cheese maturation. In contrast, we did not notice any generation of phosphopeptides from the highly phosphorylated part of α_S2-CN, f25-80, presumably due to the inaccessibility of this region to the action of plasmin and chymosin. The analysis of cleavage sites and the combination of principal component and clustering analyses provided a characterization of the complex dynamics of formation and degradation of peptides during cheese maturation. We made an attempt to obtain a comprehensive picture of proteolysis during Old Saare cheese ripening on the basis of the detailed peptidomic data, including also the less abundant peptides determined by MS/MS, and complemented by the data on intact caseins and free AA and reported the results in the paper.

Characterization of the peptide fraction from digested Parmigiano Reggiano cheese and its effect on growth of lactobacilli and bifidobacteria

Parmigiano Reggiano (PR) is a raw-milk, hard cooked, long-ripened cheese of high quality and nutritional value. Long ripening times allow for extensive proteolysis of milk proteins to yield a number of peptides, some of which have potential healthy bioactive properties. This study aimed to: i) determine the peptide profile of PR cheese subjected to simulated gastrointestinal transit; ii) evaluate in vitro whether the peptides could support growth of beneficial microbial groups of the gut microbiota. PR samples were subjected to in vitro digestion, simulating oral, gastric, and duodenal transit. Liquid chromatography coupled with tandem mass spectrometry revealed that digestion caused the disappearance of the serum proteins and most of the original peptides, while 71 new peptides were found, all ranging from 2 to 24 residues. The digests were given as sole nitrogen source to pure cultures of Bifidobacterium (27 strains) and Lactobacillus (30 strains), and to bioreactor batch cultures of human gut microbiota. Most of bifidobacteria and lactobacilli grew more abundantly on PR digests than on the control peptone, and exhibited strain- or species-specific peptide preferences, as evidenced by principal component analysis. Bifidobacteria generally consumed a greater amount of peptides than lactobacilli, in terms of both the mean peptide consumption and the number of peptides consumed. For bifidobacteria, peptide preferences were very diverse, but a core of 10 peptides with 4 or 5 residues were consumed by all the strains. Lactobacilli behaved more homogenously and consumed nearly only the same 6 peptides, mostly dipeptides. The peptide preferences of the different groups of bifidobacteria and lactobacilli could not be ascribed to features such as the length of the peptide or the abundance of residues with peculiar properties (hydrophobicity, polarity, charge) and likely depend on specific proteases and/or peptide transporters preferentially recognizing specific sequence motifs. The cultures of human colonic microbiota confirmed that PR digest promoted the growth of commensal bifidobacteria. This study demonstrated that peptides derived from simulated gastrointestinal digestion of PR supported the growth of most lactobacilli and bifidobacteria.

Cheese as Functional Food: The Example of Parmigiano Reggiano and Grana Padano

Italian hard cooked types of cheese, like Parmigiano Reggiano and Grana Padano, are characterised by positive nutritional qualities. In fact, they contain substances that have particular biological activities, and therefore they can be fully considered, according to the definition given by the European Unit, as 'functional' foods. This short review concisely describes these components and the beneficial effects related to their activities. The description of the biologically active components has been organised in the following paragraphs: protein and peptides, fat and lipids, carbohydrates and prebiotics, probiotic bacteria, vitamins, mineral salts, and components of dairy products active in disease prevention. In particular, several known bioactive peptides were found in Parmigiano Reggiano cheese samples: for example, phosphopeptides, which are known for their mineral-binding capacity and vehiculation activity, peptides with immunomodulatory activity, and angiotensin-converting enzyme-inhibitory peptides with anti-hypertensive effects. Among lipids, the role of conjugated linoleic acid and other fatty acids present in these cheese types was taken into consideration. The presence of oligosaccharides with prebiotic properties and probiotic bacteria was also described. Finally, particular emphasis was given to highly available calcium and its impact on bone health.