Microbial population profile during ripening of Protected Designation of Origin (PDO) Silter cheese, produced with and without autochthonous starter culture

Influence of Autochthonous Lactic Acid Bacteria Cultures on the Microbiota and Biogenic Amine Production in Medium-Ripened Artisan Goat Cheese

This study evaluated the effects of adding the autochthonous cultures Limosilactobacillus mucosae CNPC007 (LM) and Lactiplantibacillus plantarum CNPC003 (LP), originally isolated from goat milk and goat cheese, respectively, on microbiological safety, microbiota composition (analyzed through 16S rRNA gene metataxonomic sequencing), and biogenic amine (BA) production in artisanal goat (coalho) cheese made from raw or pasteurized milk during 60 days of ripening at 10 °C. Six types of cheese were produced, varying in milk treatment (raw or pasteurized) and the presence or absence of LP or LM cultures. Adding either LP or LM significantly modulated the microbiota, favoring Streptococcus dominance and reducing overall bacterial diversity compared to non-inoculated cheeses. Raw milk cheeses with added autochthonous cultures exhibited a microbial profile like pasteurized cheeses, suggesting a homogenizing effect on the microbiome. Both cultures effectively reduced microbial load in raw milk cheeses after 20 days, reaching levels comparable to pasteurized cheeses by the end of ripening. Although BA concentrations increased over time, all samples remained within safe limits. Cheeses with LP addition exhibited lower BA levels, suggesting a modulating effect on their biosynthesis. Histamine concentrations were higher in raw milk cheeses with added cultures but remained well below hazardous levels. These findings suggest that incorporating either LP or LM strains is a promising strategy for enhancing the microbial safety and standardization of artisanal goat cheese while preserving its traditional characteristics.

Investigation of Microbial Community of Korean Soy Sauce (Ganjang) Using Shotgun Metagenomic Sequencing and Its Relationship with Sensory Characteristics

The microbial community of a soy sauce is one of the most important factors in determining the sensory characteristics of that soy sauce. In this study, the microbial communities and sensory characteristics of twenty samples of Korean soy sauce (ganjang) were investigated using shotgun metagenome sequencing and descriptive sensory analysis, and their correlations were explored by partial least square (PLS) regression analysis. The metagenome analysis identified 1332 species of bacteria, yeasts, molds, and viruses across 278 genera, of which Tetragenococcus, Bacillus, and Enterococcus accounted for more than 80% of the total community. In the fungal community, Zygosaccharomyces rouxii, Candida versatilis, Rhodotorula taiwanensis, Debaryomyces hansenii, and Aspergillus oryzae were dominant, while the viral community consisted entirely of bacteriophages, with Bacillus phages SIOphi accounting for 93%. According to the results of the PLS analysis, desirable sensory characteristics, such as umami, sweet, and roasted soybean, as well as preference, were associated with Tetragenococcus, Lysinibacillus, Enterococcus, Staphylococcus, Lactobacillus, Pediococcus, and Weissella. The musty flavor, which is a typical property of traditional fermented foods, was related to Halomonas and Psychrobacte, while the bitter, acrid taste and sour smell were closely associated with Chromohalobacter. The results of this study provide comprehensive information on the microbial community of ganjang and may be used to select starter cultures for soy sauces.

Biodiversity and antibiotic resistance profile provide new evidence for a different origin of enterococci in bovine raw milk and feces

Enterococci are widely distributed in dairy sector. They are commensals of the gastrointestinal tract of animals, thus, via fecal contamination, could reach raw milk and dairy products. The aims of this study were: 1) to investigate the enterococcal diversity in cow feces and milk samples and 2) to evaluate the antibiotic resistance (AR) of dairy-related enterococci and their ability to transfer resistance genes. E. faecalis (59.9%), E. faecium (18.6%) and E. lactis (12.4%) were prevalent in milk, while E. faecium (84.2%) and E. hirae (15.0%) were dominant in bovine feces. RAPD-PCR highlighted a high number of Enterococcus biotypes (45 from milk and 37 from feces) and none of the milk strains exhibited genetic profiles similar to those of feces biotypes. A high percentage of enterococci isolated from milk (71%) were identified as multidrug resistant and resistance against streptomycin and tetracycline were widespread among milk strains while enterococci from feces were commonly resistant to linezolid and quinupristin/dalfopristin. Only E. faecalis strains were able to transfer horizontally the tetM gene to Lb. delbrueckii subsp. lactis. Our results indicated that Enterococcus biotypes from milk and bovine feces belong to different community and the ability of these microorganisms to transfer AR genes is strain-dependent.

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.

Impact of LAB from Serpa PDO Cheese in Cheese Models: Towards the Development of an Autochthonous Starter Culture

Serpa is a protected designation of origin (PDO) cheese produced with raw ewes' milk and coagulated with Cynara cardunculus. Legislation does not allow for milk pasteurization and starter culture inoculation. Although natural Serpa's rich microbiota allows for the development of a unique organoleptic profile, it also suggests high heterogeneity. This raises issues in the final sensory and safety properties, leading to several losses in the sector. A possible solution to overcoming these issues is the development of an autochthonous starter culture. In the present work, some Serpa cheese Lactic acid bacteria (LAB)-isolated microorganisms, previously selected based on their safety, technological and protective performance, were tested in laboratory-scale cheeses. Their acidification, proteolysis (protein and peptide profile, nitrogen fractions, free amino acids (FAA)), and volatiles generation (volatile fatty acids (VFA) and esters) potential was investigated. Significant differences were found in all parameters analyzed, showing a considerable strain effect. Successive statistical analyses were performed to compare cheese models and Serpa PDO cheese. The strains L. plantarum PL1 and PL2 and the PL1 and L. paracasei PC mix were selected as the most promising, resulting in a closer lipolytic and proteolytic profile of Serpa PDO cheese. In future work, these inocula will be produced at a pilot scale and tested at the cheese level to validate their application.

Organoleptic Chemical Markers of Serpa PDO Cheese Specificity

Serpa is a protected designation of origin cheese produced with a vegetable coagulant (Cynara cardunculus L.) and raw ovine milk. Despite the unique sensory profile of raw milk cheeses, numerous parameters influence their sensory properties and safety. To protect the Serpa cheese quality and contribute to unifying their distinctive features, some rheologic and physicochemical parameters of cheeses from four PDO producers, in distinct seasons and with different sensory scores, were monitored. The results suggested a high chemical diversity and variation according to the dairy, month and season, which corroborates the significant heterogeneity. However, a higher incidence of some compounds was found: a group of free amino acids (Glu, Ala, Leu, Val and Phe), lactic and acetic acids, some volatile fatty acids (e.g., iC4, iC5, C6 and C12) and esters (e.g., ethyl butanoate, decanoate and dodecanoate). Through the successive statistical analysis, 13 variables were selected as chemical markers of Serpa cheese specificity: C3, C4, iC5, C12, Tyr, Trp, Ile, 2-undecanone, ethyl isovalerate, moisture content on a fat-free basis, the nitrogen-fractions (maturation index and non-protein and total nitrogen ratio) and G’ 1 Hz. These sensory markers’ identification will be essential to guide the selection and development of an autochthonous starter culture to improve cheese quality and safety issues and maintain some of the Serpa authenticity.

Bovine Milk Microbiota: Comparison among Three Different DNA Extraction Protocols To Identify a Better Approach for Bacterial Analysis

The bovine udder is colonized by a huge quantity of microorganisms that constitute the intramammary ecosystem, with a specific role in modulating not only udder homeostasis and mastitis susceptibility, but also the quality of the dairy products. However, generating high-quality bacterial DNA can be critical, especially starting from a complex biological matrix like milk, characterized by high fat, protein, and calcium contents. Here, bacterial DNA was recovered from a commercial ultra-high-temperature (UHT) milk sample artificially spiked with a predetermined mock community composition and from three bulk tank milk (raw milk) samples. The DNA was isolated using three different protocols to evaluate the effect of the extraction procedures on the milk microbiota composition. In the mock community experiment, the bacterial profiles generated by the three DNA extraction protocols were profoundly different, with the genera Staphylococcus, Lactobacillus, Listeria, and Salmonella underestimated by all the protocols. Only one protocol revealed values close to the expected abundances for Escherichia/Shigella spp., Bacillus spp., Enterococcus spp., and Pseudomonas spp. On the other hand, the nonspiked UHT milk sample exhibited a similar microbiota composition, revealing the prevalence of Acinetobacter spp., for all the DNA extraction protocols. For the raw milk samples, the three DNA extraction kits performed differently, revealing significant separations in both the microbial richness (alpha diversity) and composition (beta diversity). Our study highlights the presence of significant differences among these procedures, probably due to the different DNA extracting capacities and to the different properties of the milk samples, revealing that the selection of DNA extraction protocol is a critical point.

IMPORTANCE The advance of high-throughput technologies has increased our knowledge of the world of microorganisms, especially of microbial populations inhabiting living animals. This study provides evidence that milk, as other complex sources, could be critical for generating high-quality DNA for microbiota analysis. In addition, it demonstrates that the microbial population highlighted by metagenomic studies changes in relation to different DNA extraction procedures, revealing that attention should be paid especially when comparing different studies.

Bacterial Community of Grana Padano PDO Cheese and Generical Hard Cheeses: DNA Metabarcoding and DNA Metafingerprinting Analysis to Assess Similarities and Differences

The microbiota of Protected Designation of Origin (PDO) cheeses plays an essential role in defining their quality and typicity and could be applied to protect these products from counterfeiting. To study the possible role of cheese microbiota in distinguishing Grana Padano (GP) cheese from generical hard cheeses (HC), the microbial structure of 119 GP cheese samples was studied by DNA metabarcoding and DNA metafingerprinting and compared with 49 samples of generical hard cheeses taken from retail. DNA metabarcoding highlighted the presence, as dominant taxa, of Lacticaseibacillus rhamnosus, Lactobacillus helveticus, Streptococcus thermophilus, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus spp., and Lactococcus spp. in both GP cheese and HC. Differential multivariate statistical analysis of metataxonomic and metafingerprinting data highlighted significant differences in the Shannon index, bacterial composition, and species abundance within both dominant and subdominant taxa between the two cheese groups. A supervised Neural Network (NN) classification tool, trained by metagenotypic data, was implemented, allowing to correctly classify GP cheese and HC samples. Further implementation and validation to increase the robustness and improve the predictive capacity of the NN classifier will be needed. Nonetheless, the proposed tool opens interesting perspectives in helping protection and valorization of GP and other PDO cheeses.

Lactic Starter Dose Shapes S. aureus and STEC O26:H11 Growth, and Bacterial Community Patterns in Raw Milk Uncooked Pressed Cheeses

Adding massive amounts of lactic starters to raw milk to manage the sanitary risk in the cheese-making process could be detrimental to microbial diversity. Adjusting the amount of the lactic starter used could be a key to manage these adverse impacts. In uncooked pressed cheeses, we investigated the impacts of varying the doses of a lactic starter (the recommended one, 1×, a 0.1× lower and a 2× higher) on acidification, growth of Staphylococcus aureus SA15 and Shiga-toxin-producing Escherichia coli (STEC) O26:H11 F43368, as well as on the bacterial community patterns. We observed a delayed acidification and an increase in the levels of pathogens with the 0.1× dose. This dose was associated with increased richness and evenness of cheese bacterial community and higher relative abundance of potential opportunistic bacteria or desirable species involved in cheese production. No effect of the increased lactic starter dose was observed. Given that sanitary criteria were paramount to our study, the increase in the pathogen levels observed at the 0.1× dose justified proscribing such a reduction in the tested cheese-making process. Despite this, the effects of adjusting the lactic starter dose on the balance of microbial populations of potential interest for cheese production deserve an in-depth evaluation.

High biodiversity in a limited mountain area revealed in the traditional production of Historic Rebel cheese by an integrated microbiota-lipidomic approach

Historic Rebel (HR) cheese is an Italian heritage cheese, produced from raw milk during the summer grazing period in the Alps. The aim of this work was (i) to characterize the cheese microbiota, by 16S rRNA gene amplicons sequencing, and the volatile and non-volatile lipophilic fraction, by Gas Chromatography and Dynamic Headspace Extraction-Gas Chromatography-Mass Spectrometry, and (ii) to evaluate their respective associations. HR cheese was dominated by Firmicutes phylum (99% of the entire abundance). The core microbiota was formed by Streptococcus, Lactobacillus, Lactococcus, Leuconostoc and Pediococcus genera together representing 87.2–99.6% of the total abundance. The polyunsaturated fatty acids composition showed a high PUFA n-3, PUFA n-6 and CLA content, two fold higher than typical plain cheeses, positively correlated with pasture altitude. A complex volatilome was detected, dominated in terms of abundance by ketones, fatty acids and alcohols. Total terpene levels increased at higher altitudes, being the main terpenes compounds α-pinene, camphene and β-pinene. The HR cheese showed a great diversity of bacterial taxa and lipophilic fractions among producers, despite belonging to a small alpine area, revealing a scarce cheese standardization and a chemical fingerprint of a typical mountain cheese produced during the grazing period. A deeper knowledge of the variability of HR cheese due to its composition in microbial community and volatile compounds will be appreciated, in particular, by elite consumers looking for niche products, adding economic value to farming in these alpine areas.

Current Trends of Enterococci in Dairy Products: A Comprehensive Review of Their Multiple Roles

As a genus that has evolved for resistance against adverse environmental factors and that readily exchanges genetic elements, enterococci are well adapted to the cheese environment and may reach high numbers in artisanal cheeses. Their metabolites impact cheese flavor, texture, and rheological properties, thus contributing to the development of its typical sensorial properties. Due to their antimicrobial activity, enterococci modulate the cheese microbiota, stimulate autolysis of other lactic acid bacteria (LAB), control pathogens and deterioration microorganisms, and may offer beneficial effects to the health of their hosts. They could in principle be employed as adjunct/protective/probiotic cultures; however, due to their propensity to acquire genetic determinants of virulence and antibiotic resistance, together with the opportunistic character of some of its members, this genus does not possess Qualified Presumption of Safety (QPS) status. It is, however, noteworthy that some putative virulence factors described in foodborne enterococci may simply reflect adaptation to the food environment and to the human host as commensal. Further research is needed to help distinguish friend from foe among enterococci, eventually enabling exploitation of the beneficial aspects of specific cheese-associated strains. This review aims at discussing both beneficial and deleterious roles played by enterococci in artisanal cheeses, while highlighting the need for further research on such a remarkably hardy genus.

Bacterial Succession through the Artisanal Process and Seasonal Effects Defining Bacterial Communities of Raw-Milk Adobera Cheese Revealed by High Throughput DNA Sequencing

The bacterial community of the artisanal Adobera cheese from Los Altos de Jalisco was described through high-throughput sequencing of 16S rRNA gene libraries. Samples were collected in two different seasons (dry and rainy) during four key steps of the manufacturing process (raw milk, fresh curd, matured curd, and cheese). Bacterial diversity was higher in early steps in comparison with the final elaboration stages. Firmicutes and Proteobacteria were the most abundant phyla, strongly represented by the Streptococcaceae, Enterobacteriaceae and Lactobacillaceae families, and core bacteria genera such as Streptococcus spp., Lactococcus spp., and Lactobacillus spp. Undesirable bacteria, including Pseudomonas spp. and Acinetobacter spp., were also detected in raw milk but almost undetectable at the end of the cheese manufacturing process, and seemed to be displaced by lactic-acid bacteria-related genera. Seasonal effects were observed on the community structure but did not define the core microbiota composition. Predictive metabolism was related to membrane transport, and amino-acid, lipid, and carbohydrate metabolism pathways. Our results contribute to deduce the role of bacteria involved in Adobera cheese manufacturing in terms of the metabolism involved, cheese microbial safety, and how undesirable bacterial populations could be regulated by process standardization as a potential tool to improve safety.

Influence of Autochthonous Putative Probiotic Cultures on Microbiota, Lipid Components and Metabolome of Caciotta Cheese

The present study was undertaken to produce probiotic Caciotta cheeses from pasteurized ewes' milk by using different combinations of autochthonous microbial cultures, containing putative probiotic strains, and evaluate their influence on gross composition, lipid components, sensory properties and microbiological and metabolite profiles of the cheeses throughout ripening process. A control cheese was produced using commercial starter cultures. The hydrophilic molecular pools (mainly composed by amino acids, organic acids, and carbohydrates) were characterized by means of 1H NMR spectroscopy, while the cholesterol, α-tocopherol and fatty acid composition by HPLC-DAD/ELSD techniques. Conventional culturing and a PCR-DGGE approach using total cheese DNA extracts were used to analyze cheese microbiota and monitor the presence and viability of starters and probiotic strains. Our findings showed no marked differences for gross composition, total lipids, total cholesterol, and fatty acid levels among all cheeses during ripening. Differently, the multivariate statistical analysis of NMR data highlighted significant variations in the cheese' profiles both in terms of maturation time and strains combination. The use of autochthonous cultures and adjunct probiotic strains did not adversely affect acceptability of the cheeses. Higher levels of lactobacilli (viability of 108-109 cfu/g of cheese) were detected in cheeses made with the addition of probiotic autochthonous strains with respect to control cheese during the whole ripening period, suggesting the adequacy of Caciotta cheese as a carrier for probiotic bacteria delivery.

Addition of selected starter/non-starter lactic acid bacterial inoculums to stabilise PDO Pecorino Siciliano cheese production

The present study was carried out to produce Protected Denomination of Origin (PDO) Pecorino Siciliano cheese with a multi-species lactic acid bacteria (LAB) culture, composed of starter and non-starter strains in order to reduce the microbiological variability of the products derived without LAB inoculums. To this end, cheese samples produced in six factories located in five provinces (Agrigento, Catania, Enna, Palermo and Trapani) of Sicily, and previously characterised for physicochemical, microbiological and sensory aspects, have been investigated in this work for bacterial microbiome, fatty acid (FA) composition as well as volatile organic compound (VOC) profiles. Analysis of the cheese microbiomes indicated that streptococci (30.62-77.18% relative abundance) and lactobacilli (on average 25.90% relative abundance) dominated the bacterial communities of control cheeses, produced without exogenous inoculums, whereas the cheeses produced with the selected multi-strain culture saw the dominance of lactococci (in the range 6.49-14.92% relative abundance), streptococci and lactobacilli. After the addition of the selected mixed culture, Shannon index increased in all cheeses, but only the cheeses produced with the selected LAB mixed culture in the factory 2 showed Gini-Simpson diversity index (0.79) closer to the reference value (0.94) for a perfect even community. FA composition, mainly represented by saturated FA (on average 69.60% and 69.39% in control cheeses and experimental cheeses, respectively), was not affected by adding LAB culture. The presence of polyunsaturated FA ranged between 7.93 and 8.03% of FA. VOC profiles were different only for the content of butanoic acid, registered for the experimental cheeses at higher concentrations (on average 662.54 mg/kg) than control cheeses (barely 11.96 mg/kg). This study validated addition of the ad hoc starter/non-starter culture for PDO Pecorino cheese production.

Attenuated Lactococcus lactis and Surface Bacteria as Tools for Conditioning the Microbiota and Driving the Ripening of Semisoft Caciotta Cheese

This study aimed at establishing the effects of attenuated starters and surface bacteria on various features of caciotta cheese. The cheese undergoes a ripening period during which the house microbiota contaminates the surface. Conventional cheese (the control cheese [CC]) is made using only primary starters. Primary starters and attenuated (i.e., unable to grow and synthesize lactic acid) Lactococcus lactis (Lc. lactis) subsp. lactis were used to produce caciotta cheese without (ATT cheese) or with an inoculum of surface bacteria: (i) Leuconostoc lactis (Le. lactis) (LL cheese), (ii) Vibrio casei (VC cheese), (iii) Staphylococcus equorum (SE cheese), (iv) Brochothrix thermosphacta (BX cheese), and (v) a mixture of all four (MIX cheese). Attenuated Lc. lactis increased microbial diversity during cheese ripening. At the core, attenuated starter mainly increased indigenous lactococci and Lactobacillus delbrueckii group bacteria. At the surface, the main effect was on Macrococcus caseolyticus Autochthonous Le. lactis strains took advantage of the attenuated starter, becoming dominant. Adjunct Le. lactis positively affected Lactobacillus sakei group bacteria on the LL cheese surface. Adjunct V. casei, S. equorum, and B. thermosphacta did not become dominant. Surfaces of VC, SE, and BX cheeses mainly harbored Staphylococcus succinus Peptidase activities were higher in cheeses made with attenuated starter than in CC, which had the lowest concentration of free amino acids. Based on the enzymatic activities of adjunct Le. lactis, LL and MIX cheeses exhibited the highest glutamate dehydrogenase, cystathionine-γ-lyase, and esterase activities. As shown by multivariate statistical analyses, LL and MIX cheeses showed the highest similarity for microbiological and biochemical features. LL and MIX cheeses received the highest scores for overall sensory acceptability.IMPORTANCE This study provides in-depth knowledge of the effects of attenuated starters and surface bacterial strains on the microbiota and related metabolic activities during cheese ripening. The use of attenuated Lc. lactis strongly impacted the microbiota assembly of caciotta cheese. This led to improved biochemical and sensory features compared to conventional cheese. Among surface bacterial strains, Le. lactis played a key role in the metabolic activities involved in cheese ripening. This resulted in an improvement of the sensory quality of caciotta cheese. The use of attenuated lactic acid bacteria and the surface adjunct Le. lactis could be a useful biotechnology to improve the flavor formation of caciotta cheese.

Analysis of the Bacterial Diversity of Paipa Cheese (a Traditional Raw Cow's Milk Cheese from Colombia) by High-Throughput Sequencing

Background: Paipa cheese is a traditional, semi-ripened cheese made from raw cow’s milk in Colombia. The aim of this work was to gain insights on the microbiota of Paipa cheese by using a culture-independent approach. Method: two batches of Paipa cheese from three formal producers were sampled during ripening for 28 days. Total DNA from the cheese samples was used to obtain 16S rRNA gene sequences by using Illumina technology. Results: Firmicutes was the main phylum found in the cheeses (relative abundances: 59.2–82.0%), followed by Proteobacteria, Actinobacteria and Bacteroidetes. Lactococcus was the main genus, but other lactic acid bacteria (Enterococcus, Leuconostoc and Streptococcus) were also detected. Stapylococcus was also relevant in some cheese samples. The most important Proteobacteria were Enterobacteriaceae, Aeromonadaceae and Moraxellaceae. Enterobacter and Enterobacteriaceae (others) were detected in all cheese samples. Serratia and Citrobacter were detected in some samples. Aeromonas and Acinetobacter were also relevant. Other minor genera detected were Marinomonas, Corynebacterium 1 and Chryseobacterium. The principal coordinates analysis suggested that there were producer-dependent differences in the microbiota of Paipa cheeses. Conclusions: lactic acid bacteria are the main bacterial group in Paipa cheeses. However, other bacterial groups, including spoilage bacteria, potentially toxin producers, and bacteria potentially pathogenic to humans and/or prone to carry antimicrobial resistance genes are also relevant in the cheeses.

High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses?

Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.

Selection of Leuconostoc strains isolated from artisanal Serrano Catarinense cheese for use as adjuncts in cheese manufacture

BACKGROUND

Serrano Catarinense cheese is a raw bovine milk cheese produced in the region of Santa Catarina, Brazil. Twelve representative strains of Leuconostoc isolated from 20 samples of this artisanal cheese were selected and submitted for evaluation of the acidifying, proteolytic, autolytic, aminopeptidase and lipolytic activities, NaCl and acid resistance, production of dextran and biogenic amines and antimicrobial activity. The aim was to genetically and technologically characterize the Leuconostoc strains in order to use them in mixed starter cultures for cheese manufacture.

RESULTS

Leuconostoc mesenteroides subsp. mesenteroides was the species that accounted for the largest proportion of isolates of Leuconostoc genus. Two leuconostoc isolates stood out in the acidifying activity, with reduction in pH of 1.12 and 1.04 units. The isolates showed low proteolytic and autolytic activity. Most of the isolates were dextran producers, presented good resistance to the salt and pH conditions of the cheese and showed antimicrobial activity against cheese pathogen bacteria, and none of them produced biogenic amines.

CONCLUSION

These results allowed the selection of five strains (UEL 04, UEL 12, UEL 18, UEL 21 and UEL 28) as good candidates for use as adjunct cultures for cheese manufacture. © 2018 Society of Chemical Industry.

Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses

Traditional fermented dairy foods including cottage cheese have been major components of the Buryatia diet for centuries. Buryatian cheeses have maintained not only their unique taste and flavor but also their rich natural lactic acid bacteria (LAB) content. However, relatively few studies have described their microbial communities or explored their potential to serve as LAB resources. In this study, the bacterial microbiota community of 7 traditional artisan cheeses produced by local Buryatian families was investigated using single-molecule, real-time sequencing. In addition, we compared the bacterial microbiota of the Buryatian cheese samples with data sets of cheeses from Kazakhstan and Italy. Furthermore, we isolated and preserved several LAB samples from Buryatian cheese. A total of 62 LAB strains (belonging to 6 genera and 14 species or subspecies) were isolated from 7 samples of Buryatian cheese. Full-length 16S rRNA sequencing of the microbiota revealed 145 species of 82 bacterial genera, belonging to 7 phyla. The most dominant species was Lactococcus lactis (43.89%). Data sets of cheeses from Italy and Kazakhstan were retrieved from public databases. Principal component analysis and multivariate ANOVA showed marked differences in the structure of the microbiota communities in the cheese data sets from the 3 regions. Linear discriminant analyses of the effect size identified 48 discriminant bacterial clades among the 3 groups, which might have contributed to the observed structural differences. Our results indicate that the bacterial communities of traditional artisan cheeses vary depending on geographic origin. In addition, we isolated novel and valuable LAB resources for the improvement of cottage cheese production.