Evaluation of qPCR and plate counting for quantifying thermophilic starters in cheese.

The respective inputs of plate counting and qPCR for the quantification of starters in cheese were evaluated using hard-cooked cheeses made with various starter combinations. Five starter strains were quantified at their different growth phases, from 0.5 h to day 214 of manufacture: one strain of Streptococcus thermophilus (ST) and two strains each of Lactobacillus delbrueckii (LD) and Lactobacillus helveticus (LH). Numbers of colony-forming units (CFU) were obtained by plate counting (PC) and qPCR (GNCFU). The qPCR standard curves require a special attention since GNCFU depends on the degree of culturability of the standard culture. Discrepancies were evidenced from the vat milk to the end of ripening. During cheese making, GNCFU were lower than PC at the inoculation for all ST and LD samples and 83% of the LH samples, and during both the exponential and stationary phases for many of the ST and LD samples. During ripening which corresponds to the decline phase, GNCFU were higher than PC for 90% of the ST, 78% of the LD and 69% of the LH samples. Hypotheses are discussed to explain those discrepancies. The data provided by GNCFU and PC complement each other, providing a better description of starter growth in cheese.

Suitability of a new mixed-strain starter for manufacturing uncooked raw ewe's milk cheeses.

Most raw milk Ossau-Iraty cheeses are currently manufactured on-farm using the same commercial streptococcal-lactococcal starter (S1). One way to enhance the microbial diversity that gives raw milk its advantages for cheese-making is to formulate new starters combining diverse, characterized strains. A new starter (OI) combining 6 raw milk strains of lactococci, recently isolated and characterized, was tested in parallel with the current starter by making 12 Ossau-Iraty raw milk cheeses at 3 farmhouses under the conditions prevailing at each farm. Compliance of the sensory characteristics with those expected by the Ossau-Iraty professionals, physicochemical parameters and coliforms were quantified at key manufacturing steps. The new starter OI gave cheeses having proper compliance but having lower compliance than the S1 cheeses under most manufacturing conditions, while managing coliform levels equally well as starter S1. This lower compliance relied more on the absence of Streptococcus thermophilus in starter OI, than on the nature of the lactoccocal strains present in starter OI. The study also shows that variations in 5 technological parameters during the first day of manufacture, within the range of values applied in the 3 farmhouses, are powerful tools for diversifying the scores for the sensory characteristics investigated.

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.

Quantitative PCR for the specific quantification of Lactococcus lactis and Lactobacillus paracasei and its interest for Lactococcus lactis in cheese samples.

The first objective of this work was to develop real-time quantitative PCR (qPCR) assays to quantify two species of mesophilic lactic acid bacteria technologically active in food fermentation, including cheese making: Lactococcus lactis and Lactobacillus paracasei. The second objective was to compare qPCR and plate counts of these two species in cheese samples. Newly designed primers efficiently amplified a region of the tuf gene from the target species. Sixty-three DNA samples from twenty different bacterial species, phylogenetically related or commonly found in raw milk and dairy products, were selected as positive and negative controls. Target DNA was successfully amplified showing a single peak on the amplicon melting curve; non-target DNA was not amplified. Quantification was linear over 5 log units (R(2) > 0.990), down to 22 gene copies/µL per well for Lc. lactis and 73 gene copies/µL per well for Lb. paracasei. qPCR efficiency ranged from 82.9% to 93.7% for Lc. lactis and from 81.1% to 99.5% for Lb. paracasei. At two stages of growth, Lc. lactis was quantified in 12 soft cheeses and Lb. paracasei in 24 hard cooked cheeses. qPCR proved to be useful for quantifying Lc. lactis, but not Lb. paracasei.

Biodiversity and growth dynamics of lactic acid bacteria in artisanal PDO Ossau-Iraty cheeses made from raw ewe's milk with different starters.

The biodiversity and growth dynamics of Lactic Acid Bacteria (LAB) in farm-house Ossau-Iraty cheeses were investigated from vat milk to 180 days of ripening in six independent batches made from six raw ewe's milks using five typical cheese-making methods. Commercial starter S1 was used for three batches, starter S1 combined with S2 for one batch and no starter for two batches. Up to ten LAB species from five genera and up to two strains per species were identified per milk; up to eleven species from five genera and up to three strains per species were identified per cheese. Lactococcus lactis, Lactobacillus paracasei, Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, and Leuconostoc mesenteroides were detected in all cheeses. Lactococci reached the highest counts irrespective of the milk and starter used. Lactococci and enterococci increased during manufacture, and mesophilic lactobacilli increased during ripening. Strain and species numbers, the percentage of isolates originating from the raw milk, maximum counts of each genus/species and time for reaching them, all varied according to whether or not a starter was used and the composition of the starter. The genotypes of strains within species varied according to the raw milk used. This generated distinct LAB microbiotas throughout manufacture and ripening that will certainly impact on the characteristics of the ripened cheeses.

Multiple interactions between Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii strongly affect their growth kinetics during the making of hard cooked cheeses.

In hard cooked cheeses, any interactions between the thermophilic starters as they grow during the cheese-making are critical, since they modify bacterial growth kinetics and acidification kinetics, so affecting the ripening process and the final characteristics of the cheese. Twenty-four experimental hard cooked cheeses were made under controlled conditions, the milk being inoculated with various combinations of thermophilic strains of Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. Over the first day of manufacturing we recorded a wide range of different growth kinetics for each starter species used, and a wide range of pH kinetics, depending on the starter combination. Most of the bacterial variability could be statistically explained by the nature, quantity, and/or presence or absence of the different strains inoculated. Four main interactions between the three species were evidenced during cheese-making. There was antagonism between L. helveticus and L. delbrueckii. The lactobacilli had a positive effect on S. thermophilus, which was reciprocal for L. helveticus. L. helveticus had a negative effect on S. thermophilus cultivability. And the combination of S. thermophilus inoculated in large quantities and L. helveticus strain H2 had a negative effect on the growth of the L. delbrueckii strain D2. While the positive effect of L. delbrueckii on S. thermophilus probably corresponds to interactions in milk that have already been described and published, the other interactions were hitherto unknown. These interactions are of major importance for the growth kinetics of streptococci and thermophilic lactobacilli during cheese-making.

Rapid identification of the three major species of dairy obligate heterofermenters Lactobacillus brevis, Lactobacillus fermentum and Lactobacillus parabuchneri by species-specific duplex PCR.

In this study, the biodiversity of 154 strains of lactic acid bacteria, including 112 dairy product isolates presumptively identified as obligately heterofermentative lactobacilli (OHL) by classical microbiological tests, as well as 23 OHL-type strains, was investigated by PCR-based methods and gene sequencing. Using these techniques, 51% of the cheese isolates were actually identified as OHL. The non-OHL isolates were identified to the Leuconostoc, Lactobacillus, Weisella, Pediococcus or Streptococcus genera. Among the OHL cheese isolates, five species were directly identified including three of the most frequently isolated species -Lactobacillus fermentum, Lactobacillus parabuchneri and Lactobacillus brevis- and two rarely isolated species - Lactobacillus diolivorans and Lactobacillus reuteri. A sixth group made up of two dairy isolates was also identified and according to 16S rRNA gene and intergenic spacer region (ISR) sequencing data corresponded to Lactobacillus sp. and may constitute a new species. Species-specific primers were designed for the rapid and reliable detection of the three most frequently isolated species by species-specific duplex PCR.

Safety assessment of dairy microorganisms: bacterial taxonomy.

Safety assessment requires uniform and reproducible nomenclature schemes for all the micro-organisms deliberately added in fermented food products. The QPS approach described by EFSA is based on the identity of an isolate at the highest taxonomic unit that is appropriate for the purpose for which the evaluation is intended. This depends upon the body of knowledge available for the micro-organism to be assessed and upon the nature of the micro-organism being assessed. Species identification is the fundamental unit of biological classification and is critical for describing, understanding and comparing biological diversities at different levels among ecological niches. Accurate taxonomic identification of a micro-organism is essential for assessing safety assessment, and this section describes current and advanced knowledge on bacterial taxonomy.

Efficient transformation of Lactobacillus sake by electroporation.

A procedure to transform intact Lactobacillus sake cells by electroporation was developed through a systematic examination of the effect of changes in various parameters on the transformation efficiency of Lact. sake strain 64F. The most critical factors were found to be the electrical parameters, the composition of washing and electroporation/storage solutions, and the presence of MgCI2 in the expression medium. Under optimal conditions transformation efficiencies up to 107 transformants (µg supercoiled DNA)-1 were obtained. The optimized procedure was successfully applied to other Lact. sake strains and consistently yielded from 104 to 107 transformants (µg supercoiled DNA)-1.