Biodiversity in Lactobacillus helveticus strains present in natural whey starter used for Parmigiano Reggiano cheese

Application of flow cytometry for rapid bacterial enumeration and cells physiological state detection to predict acidification capacity of natural whey starters

Natural whey starter cultures are undefined microbial communities mainly consisting of thermophilic lactic acid bacteria (LAB). The technological pressure that shapes the natural whey starter community before and during the back-slopping procedure can impact the amount and viability of the different thermophilic LAB. Traditional culture-dependent analytical methods are useful for evaluating natural whey cultures based on plate enumeration with various culture media and are commonly used as self-control procedures in dairy items. These methods have high variability and require days to obtain results. As the dairy industry has been searching for a solution to this problem for a long time, researchers must explore alternative methods for the technological evaluation of natural whey and assessment of the health status of the thermophilic acidifying bacteria community in the cheesemaking process. The flow cytometry approach has been considered an alternative to classical methods in this work sector. This study compared bacterial enumeration by plate counting and flow cytometry on natural whey samples. Flow cytometry results showed positive agreement with a tendency to overestimate, linearity, and correlation with plate counting. Other parameters have also been introduced for evaluating a natural whey starter, measuring the physiological state of the cells. Specifically, cell-wall damage and metabolic activity were also evaluated, allowing us to quantify the number of cells even in sub-optimal physiological conditions.

Impact of Spontaneous Fermentation and Inoculum with Natural Whey Starter on Peptidomic Profile and Biological Activities of Cheese Whey: A Comparative Study

Fermentation is a promising solution to valorize cheese whey, the main by-product of the dairy industry. In Parmigiano Reggiano cheese production, natural whey starter (NWS), an undefined community of thermophilic lactic acid bacteria, is obtained from the previous day residual whey through incubation at gradually decreasing temperature after curd cooking. The aim of this study was to investigate the effect of fermentation regime (spontaneous (S) and NWS-inoculated (I-NWS)) on biofunctionalities and release of bioactive peptides during whey fermentation. In S and I-NWS trials proteolysis reached a peak after 24 h, which corresponded to the drop out in pH and the maximum increase in lactic acid. Biological activities increased as a function of fermentation time. NWS inoculum positively affected antioxidant activity, whilst S overcame I-NWS in angiotensin-converting enzyme (ACE) and DPP-IV (dipeptidyl peptidase IV) inhibitory activities. Peptidomics revealed more than 400 peptides, mainly derived from β-casein, κ-casein, and α-lactalbumin. Among them, 49 were bioactive and 21 were ACE-inhibitors. Semi-quantitative analysis strongly correlated ACE-inhibitory activity with the sum of the peptide abundance of ACE-inhibitory peptides. In both samples, lactotripeptide isoleucine-proline-proline (IPP) was higher than valine-proline-proline (VPP), with the highest content in S after 24 h of fermentation. In conclusion, we demonstrated the ability of whey endogenous microbiota and NWS to extensively hydrolyze whey proteins, promoting the release of bioactive peptides and improving protein digestibility.

Lactic acid bacteria in cow raw milk for cheese production: Which and how many?

Lactic Acid Bacteria (LAB) exert a fundamental activity in cheese production, as starter LAB in curd acidification, or non-starter LAB (NSLAB) during ripening, in particular in flavor formation. NSLAB originate from the farm and dairy environment, becoming natural contaminants of raw milk where they are present in very low concentrations. Afterward, throughout the different cheesemaking processes, they withstand chemical and physical stresses becoming dominant in ripened cheeses. However, despite a great body of knowledge is available in the literature about NSLAB effect on cheese ripening, the investigations regarding their presence and abundance in raw milk are still poor. With the aim to answer the initial question: "which and how many LAB are present in cow raw milk used for cheese production?," this review has been divided in two main parts. The first one gives an overview of LAB presence in the complex microbiota of raw milk through the meta-analysis of recent taxonomic studies. In the second part, we present a collection of data about LAB quantification in raw milk by culture-dependent analysis, retrieved through a systematic review. Essentially, the revision of data obtained by plate counts on selective agar media showed an average higher concentration of coccoid LAB than lactobacilli, which was found to be consistent with meta-taxonomic analysis. The advantages of the impedometric technique applied to the quantification of LAB in raw milk were also briefly discussed with a focus on the statistical significance of the obtainable data. Furthermore, this approach was also found to be more accurate in highlighting that microorganisms other than LAB are the major component of raw milk. Nevertheless, the variability of the results observed in the studies based on the same counting methodology, highlights that different sampling methods, as well as the "history" of milk before analysis, are variables of great importance that need to be considered in raw milk analysis.

Insights on the bacterial composition of Parmigiano Reggiano Natural Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait

Natural whey starters (NWS) are undefined bacterial communities produced daily from whey of the previous cheese-making round, by application of high temperature. As a result, in any dairy plant, NWS are continuously evolving, undefined mixtures of several strains and/or species of lactic acid bacteria, whose composition and performance strongly depend on the selective pressure acting during incubation. While NWS is critical to assure consistency to cheese-making process, little is known about the composition, functional features, and plant-to-plant fluctuations. Here, we integrated 16S rRNA metabarcoding and culture-dependent methods to profile bacterial communities of 10 NWS sampled in the production area of Parmigiano Reggiano cheese. 16S rRNA metabarcoding analysis revealed two main NWS community types, namely NWS type-H and NWS type-D. Lactobacillus helveticus was more abundant in NWS type-H, whilst Lactobacillus delbrueckii/St. thermophilus in NWS type-D, respectively. Based on the prediction of metagenome functions, NWS type-H samples were enriched in functional pathways related to galactose catabolism and purine metabolism, while NWS type-D in pathways related to aromatic and branched chain amino acid biosynthesis, which are flavor compound precursors. Culture-dependent approaches revealed low cultivability of individual colonies as axenic cultures and high genetic diversity in the pool of cultivable survivors. Co-culturing experiments showed that fermentative performance decreases by reducing the bacterial complexity of inoculum, suggesting that biotic interactions and cross-feeding relationships could take place in NWS communities, assuring phenotypic robustness. Even though our data cannot directly predict these ecological interactions, this study provides the basis for experiments targeted at understanding how selective regime affects composition, bacterial interaction, and fermentative performance in NWS.

Antihypertensive Peptides from Ultrafiltration and Fermentation of the Ricotta Cheese Exhausted Whey: Design and Characterization of a Functional Ricotta Cheese

Aiming at valorizing the ricotta cheese exhausted whey (RCEW), one of the most abundant by-products from the dairy industry, a biotechnological protocol to obtain bioactive peptides with angiotensin-I-converting enzyme (ACE)—inhibitory activity was set up. The approach was based on the combination of membrane filtration and fermentation. A Lactobacillus helveticus strain selected to be used as starter for the fermentation of the ultrafiltration protein-rich retentate (R-UF) obtained from RCEW. The fermented R-UF was characterized by a high anti-ACE activity. Peptides responsible for the bioactivity were purified and identified through nano-LC–ESI–MS/MS. The sequences identified in the purified active fractions of the fermented R-UF showed partial or complete overlapping with previously reported κ-casein antihypertensive fragments. The fermented R-UF was spray-dried and used to enrich ricotta cheese at different fortification level (1 and 5% w/w). An integrated approach including the assessment of the microbiological, chemical, functional, textural, and sensory properties was used to characterize the fortified products. A significantly higher anti-ACE activity was found in the ricotta cheese fortified with fermented R-UF as compared to the control and to the samples obtained with the unfermented R-UF fraction at the same levels of fortification. In particular, a 100 g portion of the ricotta cheese produced at 5% fortification level contained circa 30 mg of bioactive peptides. The fortification led to a moderate acidification, increased hardness and chewiness, and decreased the milk odor and taste of the ricotta cheese as compared to the control, while flavor persistence and sapidity improved.

Agricultural-Heritage-Oriented Rural Revitalization: Experiences from the Ancient Tea Town of Xiping

The Anxi Tieguanyin Tea Culture System, as the proposed location of a globally important agricultural heritage system (GIAHS), has demonstrated the great significance of a network of heritage settlements and landscapes and supported rural revitalization and the participation and empowerment of women, based on agricultural heritage. Through fieldwork, participant observation, and in-depth interviews, this study attempts to analyze the experience of rural revitalization in Xiping. Firstly, the unique cultural heritage found within the agricultural landscape, formed by the multi-party linkage and dynamic adaptation of the surrounding natural environment by local residents, has shaped the Anxi Tieguanyin tea culture system of Xiping. Secondly, local residents actively participate in tea competitions and tea associations, so that the implementation process of agricultural cultural heritage preservation and development can be from the perspective of a shared experience. Thirdly, intangible cultural heritage features, such as the Female Tea Master Training Institute, have played a vital role in the development of tea towns and have proved conducive to women’s participation and empowerment. The results show that the agricultural heritage of the area, based on the Tea Manor and its multi-functional resources, has helped Xiping to move toward a more sustainable future, while eventually supporting a local society with a more distinctive rural landscape of which people can be proud. This system meets the need for local socio-economic and cultural development, and the promotion of the sustainable development of the entire region.

Massive Survey on Bacterial-Bacteriophages Biodiversity and Quality of Natural Whey Starter Cultures in Trentingrana Cheese Production

This study focused on the microbial and bacteriophages identification and characterization in cheese-production facilities that use natural whey starter (NWS) cultures for Trentingrana production. Bacterial and phage screening was carried out on cooked not acidified whey and NWS samples isolated from six dairy factories, for 4 consecutive days in four different months. By means of a combined approach, using plate counts, bacterial isolation, and metataxonomic analysis Lactobacillus helveticus was found occurring as the dominant species in NWS cultures and Levilactobacillus brevis as codominant in the cheese factories where the temperature of NWS production was mainly lower than 40°C, suggesting that the variability in the parameters of the NWS culture preparation could differently modulate the bacterial species in NWS cultures. Using turbidity test approach on 303 bacterial isolates from the NWS cultures, 120 distinct phages were identified. L. helveticus phage contamination of NWS cultures was revealed in most of the analyzed samples, but despite the great recovery of bacteriophage contamination cases, the microbial quality of NWS cultures was high. Our results support the presence of natural bacteriophage resistance mechanisms in L. helveticus. The use of NWS cultures probably creates an ideal environment for the proliferation of different L. helveticus strains balanced with their phages without a clear dominance. It is evident, from this study, that the presence of a high biodiversity of NWS bacterial strains is relevant to avoid phages dominance in NWS cultures and consequently to keep a good acidification ability.

Biodiversity of Lactobacillus helveticus isolates from dairy and cereal fermentations reveals habitat-adapted biotypes

For the present study, we collected 22 Lactobacillus helveticus strains from different dairy (n = 10) and cereal (n  = 12) fermentations to investigate their biodiversity and to uncover habitat-specific traits. Biodiversity was assessed by comparison of genetic fingerprints, low-molecular-weight subproteomes, metabolic and enzymatic activities, growth characteristics and acidification kinetics in food matrices. A clear distinction between the dairy and cereal strains was observed in almost all examined features suggesting that the different habitats are domiciled by different L. helveticus biotypes that are adapted to the specific environmental conditions. Analysis of the low-molecular-weight subproteome divided the cereal isolates into two clusters, while the dairy isolates formed a separate homogeneous cluster. Differences regarding carbohydrate utilization were observed for lactose, galactose, sucrose and cellobiose as well as for plant-derived glucosides. Enzymatic differences were observed mainly for ß-galactosidase and ß-glucosidase activities. Further, growth temperature was optimal in the range from 33 to 37°C for the cereal strains, whereas the dairy strains showed optimal growth at 40°C. Taken together, adaptation of the various biotypes results in a growth benefit in the particular environment. Acidification and growth tests using either sterile skim milk or a wheat flour extract confirmed these results. Differentiation of these biotypes and their physiological characteristics enables knowledge-based starter culture development for cereal versus dairy products within one species.

Draft Genome Sequence of Lactobacillus helveticus Lh 23, Isolated from Natural Whey Starter

Lactobacillus helveticus is a thermophilic lactic acid bacterium that is widely employed as a starter culture for manufacturing several Swiss and Italian hard-cooked cheeses. The sequencing of L. helveticus Lh 23, which consists of 2,100,230 bp with a GC content of 36.5%, reveals industrially useful traits and interesting metabolic pathways.

Lactobacillus helveticus is a thermophilic lactic acid bacterium that is widely employed as a starter culture for manufacturing several Swiss and Italian hard-cooked cheeses. The sequencing of L. helveticus Lh 23, which consists of 2,100,230 bp with a GC content of 36.5%, reveals industrially useful traits and interesting metabolic pathways.

Cultivable non-starter lactobacilli from ripened Parmigiano Reggiano cheeses with different salt content and their potential to release anti-hypertensive peptides

The impact of salt and fat intake on human health drives the consumer's attention towards dairy food with reduced salt and fat contents. How changes in salt and fat content modulate dairy LAB population and the associated proteolytic activities have been poorly studied. Here, non-starter LAB populations from 12 Parmigiano Reggiano (PR) cheeses (12-month ripened), clustered in low salt and fat content (LL-PR) and high salt and fat content (HH-PR) groups, were investigated and identified at specie-level with molecular assays. Lactobacillus rhamnosus was dominant in HH-PR samples, whereas Lactobacillus paracasei in LL-PR samples. (GTG)₅ rep-PCR analysis discriminated 11 and 12 biotypes for L. rhamnosus and L. paracasei isolates, respectively. Screening for proteolytic activity identified L. rhamnosus strains more proteolytic than L. paracasei, and, within L. rhamnosus species, HH-PR strains were generally more proteolytic than LL-PR strains. Two L. rhamnosus representatives, namely strain 0503 from LL-PR and strain 2006 from HH-PR, were functionally characterized in cow milk fermentation assay. HH-PR strain 2006 overcame LL-PR strain 0503 in acidification performance, leading to a fermented milk with higher angiotensin I-converting enzyme inhibitory and antioxidant activities. L. rhamnosus 2006 was more prone to release VPP, while L. rhamnosus 0503 released higher amount of IPP. This study provides evidences that salt/fat content affects NSLAB cultivable fraction and the associated proteolytic ability resulting in a complex occurrence of bioactive peptides featuring health-promoting properties.

Dynamics of a natural bacterial community under technological and environmental pressures: The case of natural whey starter for Parmigiano Reggiano cheese

Natural starter cultures are undefined multiple-strains culture communities of mostly thermophilic lactic acid bacteria (LAB), in association with minor amounts of mesophilic bacteria, which structure could be affected by small changes in the parameters of the cheese/whey-making process. This study aims to investigate the complex microbiota of natural whey starter (NWS) used in Parmigiano Reggiano (PR) cheese-making, focusing on both the absolute and relative abundance of bacterial species and on the modification of the bacterial community under environmental and technological pressures. To reach this purpose a combined approach, using quantitative PCR (qPCR) and High-Throughput Sequencing (HTS), was used to investigate the bacterial dynamics of 91 whey samples collected during different steps of PR cheese-making, in one dairy, through two different lines of production, one Conventional and one Organic, over a 10 weeks period. Our results highlighted that NWS used for the production of PR cheese is a dynamic microbial community, which adapts to the different technological parameters encountered in the cheese/NWS manufacturing process, while retaining a high level of resilience of the thermophilic LAB species mainly involved in the steps of curd acidification and the early maturation process. Differences were also observed in bacterial species diversity between samples from Conventional and Organic line but, in conclusion, NWS resulted to be shaped by technological treatments, regardless of its initial different composition.

The impact of sodium chloride reduction on Grana-type cheese production and quality

With the aim to reduce the Na content, hard cheeses manufactured using the same technology as for Grana cheese (Grana-type) were salted using three brines containing different amounts of KCl (K-brines) and compared with control cheeses, salted with marine NaCl. A lower weight loss was observed in cheeses salted with K-brines (K-cheeses), whereas the yield and dry matter did not differ significantly between K-cheeses and controls. After 3 months of ripening (T3), the distribution of the Na cations (Na) was centripetal, with a higher Na concentration in the outer (0-3 cm of depth) layer, whereas the K cations (K) seemed to diffuse into the cheese more rapidly and homogeneously. Starting from the 6th month (T6), the distribution of both Na and K was stabilized through the different cheese layers. The use of the brine with the highest concentration of potassium (53.8% K) enabled us to successfully halve the Na content compared to the controls whereas, with the other brines, the reduction of Na was below 30%. At the end of ripening (T9), all the cheeses were without defects and the partial substitution of Na with K did not impact on the chemical composition, microbiological characteristics and ripening process. The sensory evaluation did not show any difference between K-salted and control cheeses in discriminant analysis.

Detection of vaginal lactobacilli as probiotic candidates

The vaginal microbiota of healthy women is dominated by lactobacilli, which exerts important health-promoting effects to the host. In the present study, 261 lactobacilli isolated from vagina of healthy women were screened for their potential probiotic characteristics. Safety features (haemolytic activity, antibiotic susceptibility, bile salt hydrolase activity) and functional properties (resistance to low pH and bile salts, lysozyme tolerance, gastrointestinal survival, antagonistic activity against pathogens, hydrophobicity, auto-aggregation, and co-aggregation abilities, hydrogen peroxide production, biofilm formation, exopolysaccharide production, adhesion capacity to both normal human vagina epithelial cells and Caco-2 epithelial cells, and lactic acid production) were in depth evaluated. Seven strains, identified as Lactobacillus rhamnosus, Lactobacillus helveticus and Lactobacillus salivarius fulfilled the criteria described above. Therefore, the vaginal ecosystem represents a suitable source of probiotic candidates that could be used in new functional formulates for both gastrointestinal and vaginal eubiosis.

Population Dynamics of Lactobacillus helveticus in Swiss Gruyère-Type Cheese Manufactured With Natural Whey Cultures

Lactobacillus helveticus, a ubiquitous bacterial species in natural whey cultures (NWCs) used for Swiss Gruyère cheese production, is considered to have crucial functions for cheese ripening such as enhancing proteolysis. We tracked the diversity and abundance of L. helveticus strains during 6 months of ripening in eight Swiss Gruyère-type cheeses using a culture-independent typing method. The study showed that the L. helveticus population present in NWCs persisted in cheese and demonstrated a stable multi-strain coexistence during cheese ripening. With regard to proteolysis, one of the eight L. helveticus populations exhibited less protein degradation during ripening.

Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods

Artisanal Minas cheese is produced in Minas Gerais state, Brazil and its varieties are named according to their geographical origin (Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes). The cheese is produced with raw cow's milk and the whey from the previous cheese production ("pingo"). The high economic and cultural importance of artisanal cheese in Brazil justifies the efforts to ensure its safety, quality and provenance. This study aimed to characterize the microbial diversity composition, and geographical distribution of artisanal Minas cheese, focusing on the characterization of its autochthonous lactic acid bacteria (LAB) microbiota. Artisanal Minas cheese varieties from Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes were analyzed by culture-dependent (culturing and LAB sequencing) and -independent (repetitive extragenic palindromic-PCR (rep-PCR) and length heterogeneity-PCR, LH-PCR) methods to characterize the microbiota. The microbial counts were variable between cheese samples, and some samples presented high number of coagulase positive bacteria and coliforms that may be associated with hygienic issues. In all samples was observed a prevalence of LAB. 16S rRNA sequencing and rep-PCR of the LAB strains identified four genus (Lactobacillus, Lactococcus, Enterococcus and Weissella), ten species and more than one strain per species. Lactobacillus was the most prevalent genera in all the cheeses. LH-PCR revealed a further six genera and ten species that were not identified by culturing, highlighting the importance of combining both culture-dependent and -independent methods to fully characterize microbiota diversity. Principal component analysis of the LH-PCR data and cluster analysis of rep-PCR data revealed that the artisanal Minas cheese microbiota was influenced not only by their geographical origin but also by the cheese farm. The lack of standardization in the milking and cheese manufacturing procedures between artisanal cheese farms could explain the microbial diversity.

Application of Impedance Microbiology for Evaluating Potential Acidifying Performances of Starter Lactic Acid Bacteria to Employ in Milk Transformation

Impedance microbiology is a method that enables tracing microbial growth by measuring the change in the electrical conductivity. Different systems, able to perform this measurement, are available in commerce and are commonly used for food control analysis by mean of measuring a point of the impedance curve, defined "time of detection." With this work we wanted to find an objective way to interpret the metabolic significance of impedance curves and propose it as a valid approach to evaluate the potential acidifying performances of starter lactic acid bacteria to be employed in milk transformation. To do this it was firstly investigated the possibility to use the Gompertz equation to describe the data coming from the impedance curve obtained by mean of BacTrac 4300®. Lag time (λ), maximum specific M% rate (μmax), and maximum value of M% (Yend) have been calculated and, given the similarity of the impedance fitted curve to the bacterial growth curve, their meaning has been interpreted. Potential acidifying performances of eighty strains belonging to Lactobacillus helveticus, Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis, and Streptococcus thermophilus species have been evaluated by using the kinetics parameters, obtained from Excel add-in DMFit version 2.1. The novelty and importance of our findings, obtained by means of BacTrac 4300®, is that they can also be applied to data obtained from other devices. Moreover, the meaning of λ, μmax, and Yend that we have extrapolated from Modified Gompertz equation and discussed for lactic acid bacteria in milk, can be exploited also to other food environment or other bacteria, assuming that they can give a curve and that curve is properly fitted with Gompertz equation.

Traditional cheeses: rich and diverse microbiota with associated benefits

The risks and benefits of traditional cheeses, mainly raw milk cheeses, are rarely set out objectively, whence the recurrent confused debate over their pros and cons. This review starts by emphasizing the particularities of the microbiota in traditional cheeses. It then describes the sensory, hygiene, and possible health benefits associated with traditional cheeses. The microbial diversity underlying the benefits of raw milk cheese depends on both the milk microbiota and on traditional practices, including inoculation practices. Traditional know-how from farming to cheese processing helps to maintain both the richness of the microbiota in individual cheeses and the diversity between cheeses throughout processing. All in all more than 400 species of lactic acid bacteria, Gram and catalase-positive bacteria, Gram-negative bacteria, yeasts and moulds have been detected in raw milk. This biodiversity decreases in cheese cores, where a small number of lactic acid bacteria species are numerically dominant, but persists on the cheese surfaces, which harbour numerous species of bacteria, yeasts and moulds. Diversity between cheeses is due particularly to wide variations in the dynamics of the same species in different cheeses. Flavour is more intense and rich in raw milk cheeses than in processed ones. This is mainly because an abundant native microbiota can express in raw milk cheeses, which is not the case in cheeses made from pasteurized or microfiltered milk. Compared to commercial strains, indigenous lactic acid bacteria isolated from milk/cheese, and surface bacteria and yeasts isolated from traditional brines, were associated with more complex volatile profiles and higher scores for some sensorial attributes. The ability of traditional cheeses to combat pathogens is related more to native antipathogenic strains or microbial consortia than to natural non-microbial inhibitor(s) from milk. Quite different native microbiota can protect against Listeria monocytogenes in cheeses (in both core and surface) and on the wooden surfaces of traditional equipment. The inhibition seems to be associated with their qualitative and quantitative composition rather than with their degree of diversity. The inhibitory mechanisms are not well elucidated. Both cross-sectional and cohort studies have evidenced a strong association of raw-milk consumption with protection against allergic/atopic diseases; further studies are needed to determine whether such association extends to traditional raw-milk cheese consumption. In the future, the use of meta-omics methods should help to decipher how traditional cheese ecosystems form and function, opening the way to new methods of risk-benefit management from farm to ripened cheese.

A selected core microbiome drives the early stages of three popular italian cheese manufactures

Mozzarella (M), Grana Padano (GP) and Parmigiano Reggiano (PR) are three of the most important traditional Italian cheeses. In the three cheese manufactures the initial fermentation is carried out by adding natural whey cultures (NWCs) according to a back-slopping procedure. In this study, NWCs and the corresponding curds from M, GP and PR manufactures were analyzed by culture-independent pyrosequencing of the amplified V1–V3 regions of the 16S rRNA gene, in order to provide insights into the microbiota involved in the curd acidification. Moreover, culture-independent high-throughput sequencing of lacS gene amplicons was carried out to evaluate the biodiversity occurring within the S. thermophilus species. Beta diversity analysis showed a species-based differentiation between GP-PR and M manufactures indicating differences between the preparations. Nevertheless, all the samples shared a naturally-selected core microbiome, that is involved in the curd acidification. Type-level variability within S. thermophilus species was also found and twenty-eight lacS gene sequence types were identified. Although lacS gene did not prove variable enough within S. thermophilus species to be used for quantitative biotype monitoring, the possibility of using non rRNA targets for quantitative biotype identification in food was highlighted.

New developments in the study of the microbiota of raw-milk, long-ripened cheeses by molecular methods: the case of Grana Padano and Parmigiano Reggiano

Microorganisms are an essential component of cheeses and play important roles during both cheese manufacture and ripening. Both starter and secondary flora modify the physical and chemical properties of cheese, contributing and reacting to changes that occur during the manufacture and ripening of cheese. As the composition of microbial population changes under the influence of continuous shifts in environmental conditions and microorganisms interactions during manufacturing and ripening, the characteristics of a given cheese depend also on microflora dynamics. The microbiota present in cheese is complex and its growth and activity represent the most important, but the least controllable steps. In the past, research in this area was dependent on classical microbiological techniques. However, culture-dependent methods are time-consuming and approaches that include a culturing step can lead to inaccuracies due to species present in low numbers or simply uncultivable. Therefore, they cannot be used as a unique tool to monitor community dynamics. For these reasons approaches to cheese microbiology had to change dramatically. To address this, in recent years the focus on the use of culture-independent methods based on the direct analysis of DNA (or RNA) has rapidly increased. Application of such techniques to the study of cheese microbiology represents a rapid, sound, reliable, and effective way for the detection and identification of the microorganisms present in dairy products, leading to major advances in understanding this complex microbial ecosystem and its impact on cheese ripening and quality. In this article, an overview on the recent advances in the use of molecular methods for thorough analysis of microbial communities in cheeses is given. Furthermore, applications of culture-independent approaches to study the microbiology of two important raw-milk, long-ripened cheeses such as Grana Padano and Parmigiano Reggiano, are presented.

Development of a multiplex real time PCR to detect thermophilic lactic acid bacteria in natural whey starters

A multiplex real time PCR (mRealT-PCR) useful to rapidly screen microbial composition of thermophilic starter cultures for hard cooked cheeses and to compare samples with potentially different technological properties was developed. Novel primers directed toward pheS gene were designed and optimized for multiple detection of Lactobacillus helveticus, Lactobacillus delbrueckii, Streptococcus thermophilus and Lactobacillus fermentum. The assay was based on SYBR Green chemistry followed by melting curves analysis. The method was then evaluated for applications in the specific detection of the 4 lactic acid bacteria (LAB) in 29 different natural whey starters for Parmigiano Reggiano cheese production. The results obtained by mRealT-PCR were also compared with those obtained on the same samples by Fluorescence in Situ Hybridization (FISH) and Length-Heterogeneity PCR (LH-PCR). The mRealT-PCR developed in this study, was found to be effective for analyzing species present in the samples with an average sensitivity down to less than 600 copies of DNA and therefore sensitive enough to detect even minor LAB community members of thermophilic starter cultures. The assay was able to describe the microbial population of all the different natural whey starter samples analyzed, despite their natural variability. A higher number of whey starter samples with S. thermophilus and L. fermentum present in their microbial community were revealed, suggesting that these species could be more frequent in Parmigiano Reggiano natural whey starter samples than previously shown. The method was more effective than LH-PCR and FISH and, considering that these two techniques have to be used in combination to detect the less abundant species, the mRealT-PCR was also faster. Providing a single step sensitive detection of L. helveticus, L. delbrueckii, S. thermophilus and L. fermentum, the developed mRealT-PCR could be used for screening thermophilic starter cultures and to follow the presence of those species during ripening of derived dairy products. A major increase in understanding the starter culture contribution to cheese ecosystem could be harnessed to control cheese ripening and flavor formation.

Does milk treatment before cheesemaking affect microbial and chemical traits of ripened cheese? Grana Trentino as a case study

The aim of this study was to evaluate the influence of different storage temperatures and delivery system of the milk on the microbiological and physicochemical characteristics of Grana Trentino, a long-ripened hard-cooked Italian cheese. In particular, 3 kinds of milk storage and delivery were studied: milk delivered to the dairy in the traditional manner without temperature control, milk delivered at 18°C, and milk stored at the farm and delivered at 12°C. Milk, natural whey starter, and cheeses after 18 mo of ripening were sampled for microbiological profiles, physicochemical analysis, and proteolysis evaluation, and a study of cheese volatile compounds through a solid-phase microextraction gas chromatography-mass spectrometry technique was performed. Milk microbiota was not affected by any of the treatments. At the end of ripening, free fatty acid and ester contents were significantly higher in cheeses from milk without temperature control. This was probably due to the milk delivery to the dairy in churns causing the fat globule membrane break during transport and, consequently, a greater release of fat and deeper lipolysis. Milk refrigeration at 12°C for 12h before delivery affected the distribution of nitrogen fractions in cheeses. Lower temperatures of milk storage favored a larger soluble nitrogen fraction and greater cheese proteolysis, probably caused by an enhanced plasmin activity. From this work, it is concluded that both milk temperature storage and transport system could affect cheese ripening, leading to significant differences in chemical compounds: if milk was delivered by churns, higher free fatty acid and ester content in cheeses was observed; if milk was stored at 12°C for 12h before delivery, greater cheese proteolysis was induced with consequent faster ripening.

The spatial distribution of bacteria in Grana-cheese during ripening

The microbial composition and its spatial distribution of Grana Trentino, a hard Parmesan-like cheese, was determined, from vat milk to cheese. After cutting along the vertical axis of the cheese wheels, three layers were sampled diagonally across the cheese: under the cheese rind, an intermediate section and the cheese core. After two different ripening periods (9 and 18 months), the cheese samples were analysed using traditional culture dependent and culture independent methods. Milk samples were dominated by mesophilic and psychrophilic bacterial counts. Thermophilic bacteria (Lactobacillus helveticus) were found in high amounts in cooked whey and natural whey starter cultures. After 9 months of ripening, lactic acid bacteria (LAB) counts were higher than those after 18 months. Furthermore, the LAB numbers in the cheese core was lower than those under the rind or in the intermediate section. The main LAB species isolated from milk (Lactococcus lactis, Pediococcus pentosaceus, Streptococcus uberis and Lactococcus garvieae) were not found in the corresponding cheeses. Some differences were observed in the species composition among the three cheese sections. Microbiota under the rind and in the intermediate section was similar and dominated by Lactobacillus paracasei and Lactobacillus rhamnosus. The core, after 18 months of ripening, was characterized by a total absence of LAB. In each sample, all LAB were genotypically grouped and the different biotypes were subjected to several technological tests indicating that some non-starter LAB (NSLAB) displayed technological features that are favorable for the production of Grana Trentino cheese.

Comparative evaluation of automated ribotyping and RAPD-PCR for typing of Lactobacillus spp. occurring in dental caries

A group of 67 Lactobacillus spp. strains containing Lactobacillus casei/paracasei, Lactobacillus fermentum, Lactobacillus gasseri, Lactobacillus plantarum, Lactobacillus rhamnosus and Lactobacillus salivarius species isolated from early childhood caries and identified to the species level in a previous study (Svec et al., Folia Microbiol 54:53-58, 2009) was characterized by automated ribotyping performed by the RiboPrinter microbial characterization system and by randomly amplified polymorphic DNA fingerprinting (RAPD-PCR) with M13 primer to evaluate these techniques for characterization of lactobacilli associated with dental caries. Ribotyping revealed 55 riboprints among the analysed group. The automatic identification process performed by the RiboPrinter system identified 18 strains to the species level, however cluster analysis divided obtained ribotype patterns into individual clusters mostly corresponding to the species assignment of particular strains. RAPD-PCR fingerprints revealed by the individual Lactobacillus spp. showed higher variability than the ribotype patterns and the fingerprint profiles generated by the analysed species were distributed among one to four clusters. In conclusion, ribotyping is shown to be more convenient for the identification purposes while RAPD-PCR fingerprinting results indicate this method is a better tool for typing of Lactobacillus spp. strains occurring in dental caries.

Crucial role for insertion sequence elements in Lactobacillus helveticus evolution as revealed by interstrain genomic comparison

Lactobacillus helveticus is a versatile dairy bacterium found to possess heterogeneous genotypes depending on the ecosystem from which it was isolated. The recently published genome sequence showed the remarkable flexibility of its structure, demonstrated by a substantial level of insertion sequence (IS) element expansion in association with massive gene decay. To assess this diversity and examine the level of genome plasticity within the L. helveticus species, an array-based comparative genome hybridization (aCGH) experiment was designed in which 10 strains were analyzed. The aCGH experiment revealed 16 clusters of open reading frames (ORFs) flanked by IS elements. Four of these ORFs are associated with restriction/modification which may have played a role in accelerated evolution of strains in a commercially intensive ecosystem undoubtedly challenged through successive phage attack. Furthermore, analysis of the IS-flanked clusters demonstrated that the most frequently encountered ISs were also those most abundant in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65, and ISLhe63). These findings contribute to the overall viewpoint of the versatile character of IS elements and the role they may play in bacterial genome plasticity.

Analysis of microbial composition in acid whey for dairy fan making in Yunnan by conventional method and 16S rRNA sequencing

Dairy fan is a traditional milk product made by adding 'acid juice' and heating up. It has been consumed by people of minority ethnic region in Yunnan Province of China for over 1,000 years. In order to improve the quality of dairy fan for further industrial-scale production, we investigated the microbial composition, especially Lactic Acid Bacteria (LAB), by conventional method and 16S rRNA sequences analysis in acid whey, which was the starter culture for traditional dairy fan making. Twenty samples of acid whey were collected from Yunnan. Ninety-one phylotypes of LAB were isolated from these samples and identified by conventional method and 16S rRNA sequencing analysis. The results showed that all isolates belonged to three genera and nine different species. Moreover, Lactobacillus helveticus was the predominant population among these samples, mesophilic and thermophilic LAB could be considered as the major microbial composition of acid whey in the Yunnan Province of China. This paper systematically studied the LAB composition of acid whey, which may be valuable for designing starter culture for dairy fan production.

Recovery and differentiation of long ripened cheese microflora through a new cheese-based cultural medium

A partial picture of the typical microflora of PDO Parmigiano Reggiano cheese was achieved by studying the cultivability of lactic acid bacteria associated with its manufacturing and ripening. A comprehensive sampling design allowed for the analysis of the cheese microflora during its production over 20 months of ripening. An innovative cheese agar medium (CAM) was prepared after testing 18 formulations all based on grated Parmigiano Reggiano ripened cheese. During cheese manufacturing and ripening, different samples were sampled and their microflora was recovered using CAM in comparison with other traditional media. Colonies which formed units from the different agar media tested were picked and isolated; the phylogenetic positions of 154 isolated strains were studied at level of species by 16S-rRNA gene sequencing. CAM seems to be able to recover the minority population coming from milk and whey starter, hardly estimable, during the first hours of production, on traditional media.