Use of autochthonous mesophilic lactic acid bacteria as starter cultures for making Pecorino Crotonese cheese: Effect on compositional, microbiological and biochemical attributes

Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation

With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.

Influence of Cheese Composition on Aroma Content, Release, and Perception

The quality of a cheese is determined by the balance of aroma compounds primarily produced by microorganisms during the transformation of milk into ripened cheese. The microorganisms, along with the technological parameters used in cheese production, influence aroma formation. The perception of these compounds is further influenced by the composition and structure of the cheese. This study aimed to characterize how cheese composition affects aroma compound production, release, and perception. Sixteen cheeses were produced under controlled conditions, followed by a quantitative descriptive analysis post ripening. Aroma composition was analyzed using HS-SPME-GC-MS, and a dynamic sensory evaluation (TCATA) was combined with nosespace analysis using PTR-ToF-MS. Image analysis was also conducted to characterize cheese structure. Cheese fat and whey lactose contents were identified as key factors in the variability of sensory attributes. GC-MS analyses identified 27 compounds correlated with sensory attributes. In terms of aroma compound release, 23 ions were monitored, with fat, salt, and lactose levels significantly affecting the release of most compounds. Therefore, cheese fat, salt, and whey lactose levels, as well as the types of microbial strains, play a role in influencing the composition, structure, release of aroma compounds, and sensory perception.

Apple Blossom Agricultural Residues as a Sustainable Source of Bioactive Peptides through Microbial Fermentation Bioprocessing

This study explored the impact of starter-assisted fermentation on apple blossoms to enhance their potential as a source of antioxidant and antifungal molecules. Fructobacillus fructosus PL22 and Wickerhamomyces anomalus GY1 were chosen as starters owing to their origin and promising ability to modify plant secondary metabolites. An initial assessment through microbiological and physicochemical analyses showed superior outcomes for starter-assisted fermentation compared to the spontaneous process. Enzymatic hydrolysis of proteins, primarily controlled by starters, orchestrated the generation of new low-molecular-weight peptides. W. anomalus GY1 also induced modifications in the phenolic profile, generating a diverse array of bioactive metabolites. These metabolic changes, particularly the release of potentially bioactive peptides, were associated with significant antioxidant activity and marked antifungal efficacy against three common mold species. Our results shed light on the potential of microbial starters to valorize agricultural wastes and convert them into a valuable resource for industry.

Autochthonous cultures to improve the quality of PGI Castellano cheese: Impact on proteolysis, microstructure and texture during ripening

The aim of this research was to find out the effect of different combinations of starter and non-starter cultures on the proteolysis of Castellano cheese during ripening. Four cheese batches were prepared, each containing autochthonous lactobacilli and or Leuconostoc, and were compared with each other and with a control batch, that used only a commercial starter. To achieve this, nitrogen fractions (pH 4.4-soluble nitrogen and 12 % trichloroacetic acid soluble nitrogen, polypeptide nitrogen and casein nitrogen), levels of free amino acids and biogenic amines were assessed. Texture and microstructure of cheeses were also evaluated. Significant differences in nitrogen fractions were observed between batches at different stages of ripening. The free amino acid content increased throughout the cheese ripening process, with a more significant increase occurring after the first 30 days. Cheeses containing non-starter lactic acid bacteria exhibited the highest values at the end of the ripening period. Among the main amino acids, GABA was particularly abundant, especially in three of the cheese batches at the end of ripening. The autochthonous lactic acid bacteria were previously selected as non-producers of biogenic amines and this resulted in the absence of these compounds in the cheeses. Analysis of the microstructure of the cheese reflected the impact of proteolysis. Additionally, the texture profile analysis demonstrated that the cheese's hardness intensified as the ripening period progressed. The inclusion of autochthonous non-starter lactic acid bacteria in Castellano cheese production accelerated the proteolysis process, increasing significantly the free amino acids levels and improving the sensory quality of the cheeses.

Tracking microbial quality, safety and environmental contamination sources in artisanal goat cheesemaking factories

A harmonised microbiological survey was performed in two artisanal factories of raw goat milk cheeses (A and B) located in the Andalusian region (Spain). A total of 165 different control points or samples (raw materials, final products, food-contact surfaces [FCS], and air) were examined as microbial and pathogen sources of contamination of artisanal goat raw milk cheeses. For raw milk samples analysed from both producers, the concentrations of aerobic-mesophilic bacteria (AMB), total coliforms, coagulase-positive Staphylococcus spp. (CPS), lactic-acid bacteria (LAB) and moulds and yeasts ranged between 3.48 and 8.59, 2.45-5.48, 3.42-4.81, 4.99-8.59 and 3.35-6.85 log cfu/mL respectively. For the same microbial groups, the analysis of raw milk cheeses revealed concentrations ranging from 7.82 to 8.88, 2.00-6.82, 2.00-5.28, 8.11-9.57 and 2.00-5.76 log cfu/g, respectively. Although the raw material analysed from producer A presented higher microbial loads and between-batch variability, it was B the producer with the most loaded final products. Regarding the microbial air quality, the fermentation area, storage room, milk reception and packaging room were the most AMB loaded places, while the ripening chamber was the area with higher fungal loads in bioareosol from both producers. Conveyor belts, cutting machine, storage boxes and brine tank were highlighted as the most contaminated FCS evaluated. Staphylococcus aureus was the only pathogen detected within the set of 51 isolates from samples as revealed by MALDI-TOF and molecular PCR, with a prevalence of 12.5% for samples from the producer B. The public health risk attributed to the consumption of artisanal goat cheese should not be neglected, and may consider the whole cheesemaking processing chain, from microbiological quality of raw milk to the ready-to-eat final product, especially concerning the presence of S. aureus.

Characterization of Physicochemical, Biological, and Chemical Changes Associated with Coconut Milk Fermentation and Correlation Revealed by 1H NMR-Based Metabolomics

Fermentation of milk enhances its nutritional and biological activity through the improvement of the bioavailability of nutrients and the production of bioactive compounds. Coconut milk was fermented with Lactiplantibacillus plantarum ngue16. The aim of this study was to evaluate the effect of fermentation and cold storage for 28 days on physicochemical characteristics, shelf life, and antioxidant and antibacterial activities of coconut milk as well as its proximate and chemical compositions. The pH of fermented milk decreased from 4.26 to 3.92 on the 28^th day during cold storage. The viable cell count of lactic acid bacteria (LAB) in fermented coconut milk was significantly increased during fermentation and cold storage period (1 to 14 days), reaching 6.4 × 10⁸ CFU/mL, and then decreased significantly after 14 days to 1.6 × 10⁸ CFU/mL at 28 days. Yeast and molds in fermented coconut milk were only detected on the 21^st and 28^th days of cold storage, which ranged from 1.7 × 10² to 1.2 × 10⁴ CFU/mL, respectively. However, the growth of coliforms and E. coli was observed on the 14^th until the 28^th day of cold storage. The fermented coconut milk demonstrated strong antibacterial activity against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Cronobacter sakazakii, Bacillus cereus, and Salmonella typhimurium compared to fresh coconut milk. Fermented coconut milk had the greatest 1,1-diphenyl-2-picrylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP) values, with 67.1% and 61.961 mmol/g at day 14 of cold storage, respectively. Forty metabolites were detected in fermented and pasteurized coconut milk by proton nuclear magnetic resonance (¹H NMR) metabolomics. The principal component analysis (PCA) showed clear difference between the fermented and pasteurized coconut milk as well as the studied cold storage days. The metabolites responsible for this variation were ethanol, valine, GABA, arginine, lactic acid, acetoin, alanine, phenylalanine, acetic acid, methionine, acetone, pyruvate, succinic acid, malic acid, tryptophan, uridine, uracil, and cytosin, which were higher in fermented coconut milk. However, sugars and other identified compounds were higher in fresh coconut milk. The findings of this study show that fermentation of coconut milk with L. plantarum ngue16 had high potential benefits to extending its shelf life and improved biological activities as well as other beneficial nutrients.

A Strategy for the Recovery of Raw Ewe's Milk Microbiodiversity to Develop Natural Starter Cultures for Traditional Foods

Commercial starter cultures, composed of high concentrations of a few species/strains of lactic acid bacteria (LAB), selected based on their strong technological aptitudes, have been developed to easily and safely carry out food fermentations. Frequently applied to industrial productions, selected starter LAB easily become the dominant microbiota of products, causing a dramatic decrease in biodiversity. On the contrary, natural starter cultures, which usually characterize the most typical and Protected Designation of Origin (PDO) food products, are constituted by a multitude and an indefinite number of LAB species and strains, both starter and nonstarter, thus contributing to preserving microbial biodiversity. However, their use is not risk-free since, if obtained without heat treatment application, natural cultures can contain, together with useful, also spoilage microorganisms or pathogens that could be allowed to multiply during fermentation. In the present study, an innovative method for the production of a natural starter culture directly from raw ewe's milk, inhibiting the growth of spoilage and potentially pathogenic bacteria without applying any heat treatment, was described. The culture developed show a good degree of microbial biodiversity and could be applied to both artisanal and industrial scales, guaranteeing safety, quality constancy, technological performance reproducibility, preserving biodiversity and peculiar sensory characteristics, usually linked to traditional products, while overcoming the problems associated with the daily propagation of natural cultures.

Universal drivers of cheese microbiomes

The culinary value, quality, and safety of cheese are largely driven by the resident bacteria, but comparative analyses of the cheese microbiota across cheese types are scarce. We present the first global synthesis of cheese microbiomes. Following a systematic literature review of cheese microbiology research, we collected 16S rRNA gene amplicon sequence data from 824 cheese samples spanning 58 cheese types and 16 countries. We found a consistent, positive relationship between microbiome richness and pH, and a higher microbial richness in cheeses derived from goat milk. In contrast, we found no relationship between pasteurization, geographic location, or salinity and richness. Milk and cheese type, geographic location, and pasteurization collectively explained 65% of the variation in microbial community composition. Importantly, we identified four universal cheese microbiome types, driven by distinct dominant taxa. Our study reveals notable diversity patterns among the cheese microbiota, which are driven by geography and local environmental variables.

Relationship between the Dynamics of Gross Composition, Free Fatty Acids and Biogenic Amines, and Microbial Shifts during the Ripening of Raw Ewe Milk-Derived Idiazabal Cheese

This study reports for the first time the relationship between bacterial succession, characterized by high-throughput sequencing (sequencing of V3-V4 16S rRNA regions), and the evolution of gross composition, free fatty acids (FFAs) and biogenic amines (BAs) during cheese ripening. Specifically, Idiazabal PDO cheese, a raw ewe milk-derived semi-hard o hard cheese, was analysed. Altogether, 8 gross parameters were monitored (pH, dry matter, protein, fat, Ca, Mg, P and NaCl) and 21 FFAs and 8 BAs were detected. The ripening time influenced the concentration of most physico-chemical parameters, whereas the producer mainly affected the gross composition and FFAs. Through an O2PLS approach, the non-starter lactic acid bacteria Lactobacillus, Enterococcus and Streptococcus were reported as positively related to the evolution of gross composition and FFAs release, while only Lactobacillus was positively related to BAs production. Several environmental or non-desirable bacteria showed negative correlations, which could indicate the negative impact of gross composition on their growth, the antimicrobial effect of FFAs and/or the metabolic use of FFAs by these genera, and their ability to degrade BAs. Nonetheless, Obesumbacterium and Chromohalobacter were positively associated with the synthesis of FFAs and BAs, respectively. This research work provides novel information that may contribute to the understanding of possible functional relationships between bacterial communities and the evolution of several cheese quality and safety parameters.

Distinctive Traits of Four Apulian Traditional Agri-Food Product (TAP) Cheeses Manufactured at the Same Dairy Plant

This study aimed to highlight the distinctive features of four Traditional Agri-food Products (TAP), namely, Caprino, Pecorino, Vaccino, and Cacioricotta cheeses produced at the same dairy plant to reveal any possible relationships between their microbiological and biochemical characteristics. Two distinct natural whey starter (NWS) cultures were used during Caprino and Vaccino cheesemaking, whereas no starter was used for the other cheeses. Cacioricotta retained the highest concentrations of salt and residual carbohydrates. Lactic acid bacteria dominated the microbiota of the cheeses. Furthermore, staphylococci represented an additional dominant microbial population in Cacioricotta. Although culture-dependent analysis showed that the use of NWS cultures only slightly affected the microbial community of cheeses, 16S metagenetic analysis showed that Lactobacillus helveticus dominated both the NWS cultures and the corresponding Caprino and Vaccino cheeses. This analysis indicated that Staphylococcus equorum and Streptococcus thermophilus dominated Cacioricotta and Pecorino cheeses, respectively. The highest peptidase activities were found in either Caprino or Vaccino. Enzymes involved in the catabolism of free amino acids and esterase showed the highest activity in Pecorino cheese. Each cheese showed a distinct profile of volatile organic compounds, with Pecorino being the richest cheese in carboxylic acids, ketones, and esters, related to lipolysis. The results of this study contribute to valorizing and safeguarding these TAP cheeses, sustaining local farming.

Advantages and disadvantages of non-starter lactic acid bacteria from traditional fermented foods: Potential use as starters or probiotics

Traditional fermented foods are a significant source of starter and/or non-starter lactic acid bacteria (nsLAB). Moreover, these microorganisms are also known for their role as probiotics. The potential of nsLAB is huge; however, there are still challenges to be overcome with respect to characterization and application. In the present review, the most important steps that autochthonous lactic acid bacteria isolated from fermented foods need to overcome, to qualify as novel starter cultures, or as probiotics, in food technology and biotechnology, are considered. These different characterization steps include precise identification, detection of health-promoting properties, and safety evaluation. Each of these features is strain specific and needs to be accurately determined. This review highlights the advantages and disadvantages of nsLAB, isolated from traditional fermented foods, discussing safety aspects and sensory impact.

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.

Modelling the biphasic growth of non-starter lactic acid bacteria on starter-lysate as a substrate

Since cheese is poor in energy for bacterial growth, it is believed that non-starter lactic acid bacteria growth and flavour development are supported by the nutrients from lysis of the starter culture. This study was performed to investigate the dynamics of interaction between starter and non-starter strains from cheese. A starter culture lysate was prepared by enzymatic digestion and tested as a growth substrate for Lactobacillus sp. strains. The two starter culture strains of Lactococcus lactis were also tested on the starter-lysate. All seventeen strains were individually inoculated at the level of 5.0 log₁₀ cfu mL^-1 in M17 broth, with or without 10% starter-lysate, and incubated at 30 °C for 140 h. The optical density_{600 nm} was modelled with the primary log-transformed Logistic model with delay and lag phase duration, maximum specific growth rate as well as maximum population density obtained. Biphasic growth was mainly observed when the strains were able to utilize the starter-lysate as an energy source. To deal with the lack-of-fit related to the biphasic growth, the observed data points of the curve were divided after graphic evaluation and according to deviation of the residuals from the range ±0.05. Modelling was then performed in two phases by applying the same primary Logistic model in each of the two parts of the growth curve. Values of root-mean-square error and graphic evaluation indicated the good fitting of the data with the suggested approach. The growth of the two Lactococcus lactis strains was not affected by the starter-lysate. However, thirteen of the non-starter strains had their growth rates increased. The increase was greatest for Lactobacillus rhamnosus KU-LbR1, which reached maximum optical densities of 0.23 and 0.58 in the absence and the presence of starter-lysate, respectively. No effect of the starter-lysate was shown for the growth of Lactobacillus curvatus strains. The extend of the growth of non-starter strains on the starter-lysate was shown to be species and strain dependent.

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.

Functional milk proteome analysis of genetically diverse goats from different agro climatic regions

Goat milk, a choice of substitution to mother's milk for its composition, fulfils nutritional requirement of infants, pregnant mothers and older people. The present study was carried out to unravel the milk proteome profiles from geographically and genetically diverse goat breeds by gel based 2DE and nLC-MS/MS. A total of 1307 functional proteins comprising casein and other low abundance proteins were identified. Gene annotations revealed that the majority of the proteins were involved in binding function, catalytic activity and structural molecules and localised in nucleus and membrane. The distinguished proteins were involved in 144 KEGG pathways in information processing, metabolism, cellular process, organismal systems and diseases. The large number of proteins and peptides including bioactive peptides were reported from goat milk from diverse agro-climatic regions of India indicating their significant potential for human health applications. SIGNIFICANCE: Goat milk in India is used in various Ayurvedic formulations to treat a number of ailments and allergies as well as for nutraceutical formulations. The study identifies milk protein variants both at protein and DNA level and subsequent identification of proteins by 2DE and nLC-MS/MS resulting in a proteome comprising of 1307 proteins. The specific proteins and peptides having significant role in immune regulation, disease pathways, cellular growth and metabolism have been identified. The results contribute to goat milk protein and peptide database which is very limited. We identified proteins for specific functional categories and associated them with different pathways for studying functional diversity of goat milk proteins. The proteins and peptides identified can be used for multiple human health application.

Brazilian artisanal cheeses are rich and diverse sources of nonstarter lactic acid bacteria regarding technological, biopreservative, and safety properties-Insights through multivariate analysis

In this study a total of 220 isolates of lactic acid bacteria (LAB) recovered from 10 types of Brazilian artisanal cheeses marketed in 4 main regions of Brazil were evaluated regarding their safety and ability to produce diacetyl (a precursor of aromatic compounds), exopolysaccharides (EPS; from different sugar sources), and antagonistic activity against Listeria monocytogenes and Staphylococcus aureus. The results indicated that 131 isolates (59.6%) were classified as strong (40.5%) and moderate (19.1%) diacetyl producers; 28 isolates (12.7%) stood out due to their remarkable production of EPS from different sugars, including sucrose (3.2%), fructose (2.3%), lactose (2.3%), and glucose (6%). Furthermore, 94.1% and 95.9% of isolates presented antagonistic activity against S. aureus and L. monocytogenes, respectively, even though only 27 isolates (12.3%) exhibited positive results in the bacteriocin production test. None of the isolates tested presented hemolytic activity, and 117 were classified as safe, due to their intrinsic resistance to a maximum of 4 different antibiotics. The data obtained for assessment of antibiogram profile and technological potential (moderate and high production of diacetyl, EPS, and bacteriocins) were submitted to a multiple correspondence analysis to correlate them with the cheese of isolation. Regarding the antimicrobial profile of LAB strains, it was possible to verify an association between isolates from Minas artisanal cheeses from Araxá and resistance to tetracycline; Minas artisanal cheeses from Serro and resistance to erythromycin; Coalho and Minas artisanal cheese from Cerrado and resistance to penicillin; and isolates from Serrano and Colonial cheeses with clindamycin and ceftazidime resistance. Although the susceptibility of strains to these antibiotics was considered high (71.8-80.5%), these data may be related to the horizontal transfer of genes in the production chain of these cheeses. Results of multiple correspondence analysis also showed that isolates with antagonistic activity were mostly isolated from Manteiga, Colonial, and Coalho cheeses. The isolates with high or moderate EPS-producer ability from sucrose, glucose, and fructose were mainly associated with Minas artisanal cheeses from Cerrado. In contrast, isolates with high or moderate EPS-producer ability from lactose were isolated from Serrano, Minas artisanal cheeses from Canastra, and Campo das Vertentes microregions. Finally, isolates from Minas artisanal cheeses (from Araxá microregion), Coalho, and Caipira cheeses were associated with moderate/high diacetyl production. To the best of the authors' knowledge, this study provides, for the first time, data indicating that the dominant technological, biopreservative, and safety properties of LAB isolates can be correlated with the type of Brazilian artisanal cheeses, which denotes its singularity. This knowledge is of utmost relevance for the development of starter or adjunct cultures with tailored properties.

Lactococcus lactis Diversity Revealed by Targeted Amplicon Sequencing of purR Gene, Metabolic Comparisons and Antimicrobial Properties in an Undefined Mixed Starter Culture Used for Soft-Cheese Manufacture

The undefined mixed starter culture (UMSC) is used in the manufacture of cheeses. Deciphering UMSC microbial diversity is important to optimize industrial processes. The UMSC was studied using culture-dependent and culture-independent based methods. MALDI-TOF MS enabled identification of species primarily from the Lactococcus genus. Comparisons of carbohydrate metabolism profiles allowed to discriminate five phenotypes of Lactococcus (n = 26/1616). The 16S sequences analysis (V1–V3, V3–V4 regions) clustered the UMSC microbial diversity into two Lactococcus operational taxonomic units (OTUs). These clustering results were improved with the DADA2 algorithm on the housekeeping purR sequences. Five L. lactis variants were detected among the UMSC. The whole-genome sequencing of six isolates allowed for the identification of the lactis subspecies using Illumina^® (n = 5) and Pacbio^® (n = 1) technologies. Kegg analysis confirmed the L. lactis species-specific niche adaptations and highlighted a progressive gene pseudogenization. Then, agar spot tests and agar well diffusion assays were used to assess UMSC antimicrobial activities. Of note, isolate supernatants (n = 34/1616) were shown to inhibit the growth of Salmonella ser. Typhimurium CIP 104115, Lactobacillus sakei CIP 104494, Staphylococcus aureus DSMZ 13661, Enterococcus faecalis CIP103015 and Listeria innocua CIP 80.11. Collectively, these results provide insightful information about UMSC L. lactis diversity and revealed a potential application as a bio-protective starter culture.

Microbiome and Functional Analysis of a Traditional Food Process: Isolation of a Novel Species (Vibrio hibernica) With Industrial Potential

Traditional food preservation processes are vital for the food industry. They not only preserve a high-quality protein and nutrient source but can also provide important value-added organoleptic properties. The Wiltshire process is a traditional food curing method applied to meat, and special recognition is given to the maintenance of a live rich microflora within the curing brine. We have previously analyzed a curing brine from this traditional meat process and characterized a unique microbial core signature. The characteristic microbial community is actively maintained and includes the genera, Marinilactibacillus, Carnobacterium, Leuconostoc, and Vibrio. The bacteria present are vital for Wiltshire curing compliance. However, the exact function of this microflora is largely unknown. A microbiome profiling of three curing brines was conducted and investigated for functional traits by the robust bioinformatic tool, Tax4Fun. The key objective was to uncover putative metabolic functions associated with the live brine and to identify changes over time. The functional bioinformatic analysis revealed metabolic enrichments over time, with many of the pathways identified as being involved in organoleptic development. The core bacteria present in the brine are Lactic Acid Bacteria (LAB), with the exception of the Vibrio genus. LAB are known for their positive contribution to food processing, however, little work has been conducted on the use of Vibrio species for beneficial processes. The Vibrio genome was sequenced by Illumina MiSeq technologies and annotated in RAST. A phylogenetic reconstruction was completed using both the 16S rRNA gene and housekeeping genes, gapA, ftsZ, mreB, topA, gyrB, pyrH, recA, and rpoA. The isolated Vibrio species was defined as a unique novel species, named Vibrio hibernica strain B1.19. Metabolic profiling revealed that the bacterium has a unique substrate scope in comparison to other closely related Vibrio species tested. The possible function and industrial potential of the strain was investigated using carbohydrate metabolizing profiling under food processing relevant conditions. Vibrio hibernica is capable of metabolizing a unique carbohydrate profile at low temperatures. This characteristic provides new application options for use in the industrial food sector, as well as highlighting the key role of this bacterium in the Wiltshire curing process.

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.

Milk microbiota: Characterization methods and role in cheese production

Milk is a complex body fluid aimed at addressing the nutritional and defensive needs of the mammal's newborns. Harbored microbiota plays a pivotal role throughout the cheesemaking process and contributes to the development of flavor and texture typical of different type of cheeses. Understanding the dairy microbiota dynamics is of paramount importance for controlling the qualitative, sensorial and biosafety features of the dairy products. Although many studies investigated the contribution of single or few microorganisms, still there is some information lacking about microbial communities. The widespread of the omics platforms and bioinformatic tools enable the investigation of the cheese-associated microbial community in both phylogenetical and functional terms, highlighting the effects of the diverse cheesemaking variables. In this review, the most relevant literature is revised to provide an introduction of the milk- and cheese-associated microbiota, along with their structural and functional dynamics in relation to the diverse cheesemaking technologies and influencing variables. Also, we focus our attention on the latest omics technologies adopted in dairy microbiota investigation. Discussion on the key-steps and major drawbacks of each omics discipline is provided along with a collection of results from the latest research studies performed to unravel the fascinating world of the dairy-associated microbiota. SIGNIFICANCE: Understanding the milk- and cheese- associated microbial community is nowadays considered a key factor in the dairy industry, since it allows a comprehensive knowledge on how all phases of the cheesemaking process impact the harbored microflora; thus, predict the consequences in the finished products in terms of texture, organoleptic characteristics, palatability and biosafety. This review, collect the pioneering and milestones works so far performed in the field of dairy microbiota, and provide the basic guidance to whom approaching the cheese microbiota investigation by means of the latest omics technologies. Also, the review emphasizes the benefits and drawbacks of the omics disciplines, and underline how the integration of diverse omics sciences enhance a comprehensive depiction of the cheese microbiota. In turn, a better consciousness of the dairy microbiota might results in the application of improved starter cultures, cheesemaking practices and technologies; supporting a bio-safe and standardized production of cheese, with a strong economic benefit for both large-scale industries and local traditional dairy farms.

Serra da Estrela cheese's free amino acids profiles by UPLC-DAD-MS/MS and their application for cheese origin assessment

Serra da Estrela cheese is a high-value Portuguese Protected Designation of Origin cheese, produced with raw ewe milk. Thus, information regarding its composition is of utmost relevance for both consumers and certified producers. In this work, the chromatographic profiles of free amino acids in cheeses (45 days of maturation, 6 producers located in 5 municipalities and produced from November 2017 to March 2018) were established by UPLC-DAD-MS/MS. The proposed method allowed detecting 19 free amino acids and cystine with overall limits of detection and quantification lower than 44 μmol/L (1.4 mg/100 g cheese, wet matter) and than 134 μmol/L (4.2 mg/100 g cheese, wet matter), respectively. In all cheeses, 17 free amino acids were quantified including 8 essential amino acids (histidine, leucine-isoleucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine) and 9 non-essential amino acids (arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, proline, serine and tyrosine). The amounts of the free amino acids, essential free amino acids, branched chain free amino acids (leucine, isoleucine and valine) plus the free amino acids ratios (mg/g protein) were further used to identify the producer of Serra da Estrela cheeses. Linear discriminant analysis coupled with the simulated annealing variable selection algorithm was used allowing the correct classification of 96% and 90 ± 8% of the samples, for leave-one-out and repeated K-fold cross-validation procedures, respectively. The satisfactory predictive performance pointed out the possibility of using cheeses' amino acids profiles as origin biomarkers for authenticity control, warranting the correctness identification of the cheese producer/brand, which is quite relevant for ensuring the consumer confidence and satisfaction when purchasing this high-value dairy food.