Population dynamics of lactococci from industrial, artisanal and non-dairy origins in defined strain starters for Gouda-type cheese

Impact of Salting Techniques on the Physio-Chemical Characteristics, Sensory Properties, and Volatile Organic Compounds of Ras Cheese

Ras cheese is the main Egyptian hard cheese that is well-known worldwide. Herein, we investigated how different salting techniques affect the physio-chemical properties, sensory properties, and volatile compounds of Ras cheese over a six-month ripening period. Five Ras cheese treatments were made from pasteurized cow's milk using various salting techniques: traditional salting of Ras cheese, salting by applying all of the salt to the curd after the entire whey drainage, salting by applying all of the salt to the curd after half to two-thirds of the whey drainage, salting in a brine solution for 24 h without dry salting, and salting in a brine solution for 12 h and then dry salting. The obtained results by GC-MS recorded that thirty-eight volatile compounds were identified in Ras cheese treatments after six months of ripening, and the development of volatile compounds was affected by the salting technique as well as the ripening period of the cheeses, which played a major role in the type and concentration of volatile compounds. Results revealed that there are six esters, 15 fatty acids, five ketones, two aldehydes, four alcohols, and eight other compounds identified in most treatments. Some physio-chemical characteristics and sensory properties were found to have high correlations with the storage period, while some others have low correlations during the ripening period.

Gene-Trait Matching and Prevalence of Nisin Tolerance Systems in Lactococus lactis

Lactococcus lactis cheese starter cultures typically contain a mix of many strains and may include variants that produce and/or tolerate the antimicrobial bacteriocin nisin. Nisin is well-established as an effective agent against several undesirable Gram-positive bacteria in cheese and various other foods. In the current study, we have examined the effect of nisin on 710 individual L. lactis strains during milk fermentations. Changes in milk acidification profiles with and without nisin exposure, ranging from unaltered acidification to loss of acidification, could be largely explained by the type(s) and variants of nisin immunity and nisin degradation genes present, but surprisingly, also by genotypic lineage (L. lactis ssp. cremoris vs. ssp. lactis). Importantly, we identify that nisin degradation by NSR is frequent among L. lactis and therefore likely the main mechanism by which dairy-associated L. lactis strains tolerate nisin. Insights from this study on the strain-specific effect of nisin tolerance and degradation during milk acidification is expected to aid in the design of nisin-compatible cheese starter cultures.

The Effects of Adding Different Stabilizers in Brine on the Physicochemical, Sensory, Microbiological and Textural Properties of White Cheese

The aim of the present study was to determine the effect of four different thickening agents (guar gum, carrageenan, xanthan gum, and gelatin) on the textural and sensory properties of white cheese. For this purpose, various white cheeses were manufactured with brines (the salt ratio was 8% and 12%) that contained different types and concentrations of gums; white cheese textural and sensory properties were studied during storage (at 4 °C). Also, microbiological properties including lactic acid bacteria (LAB) and mesophilic aerobic bacteria were investigated. The physicochemical, textural, microbiological, and sensory properties of the cheeses were determined on the 1st, 15th, and 30th days of storage. During the storage period of cheese, the top-rated samples in terms of sensory properties were cheeses with gelatin and carrageenan gum. The microbiological data displayed that there was an inverse relationship between the number of bacteria and the amount of gum used, although it was not precisely linear. At the same time, the highest values were generally determined in the control samples, and although not to a very great extent, gelatinous examples were found to contain a lower number of lactic acid bacteria than others. Regarding the textural properties, the hardness value of all samples containing gelatin showed a continuous increasing trend, while the springiness values increased only in the samples with xanthan gum and guar gum. At the end of storage, it was observed that the inherent adhesiveness of the samples decreased by more than half and the use of gelatin resulted in an increase in the gumminess of the cheeses. As a result, it was determined that reducing the salt used in the brine by up to 8% did not cause any defect since stabilizers were preventing water passage into the cheese by holding water.

Development of quantitative PCR and metagenomics-based approaches for strain quantification of a defined mixed-strain starter culture

Although the strain composition of mixed cultures may hugely affect production of various fermented foods, such as e.g. cheese, tools for investigating it have so far been limited. In this study, two new approaches for quantification of seven Lactococcus lactis subsp. cremoris strains (S1-S7) in a defined mixed-strain starter culture were developed and verified. By mapping NGS reads from 47 sequenced L. lactis strains to de novo assembly contigs of the seven strains, two strain-specific sequence regions (SEQ1 and SEQ2) were identified for each strain for qPCR primer design (A1 and A2). The qPCR assays amplified their strain-specific sequence region target efficiently. Additionally, high reproducibility was obtained in a validation sample containing equal amounts of the seven strains, and assay-to-assay coefficients of variance (CVs) for six (i.e. S1, S2, S4-S7) of the seven strains correlated to the inter-plate CVs. Hence, at least for six strains, the qPCR assay design approach was successful. The metagenomics-based approach quantified the seven strains based on average coverage of SEQ1 and SEQ2 by mapping sequencing reads from the validation sample to the strain-specific sequence regions. Average coverages of the SEQ1 and SEQ2 in the metagenomics data showed CVs of ≤17.3% for six strains (i.e. S1-S4, S6, S7). Thus, the metagenomics-based quantification approach was considered successful for six strains, regardless of the strain-specific sequence region used. When comparing qPCR- and metagenomics-based quantifications of the validation sample, the identified strain-specific sequence regions were considered suitable and applicable for quantification at a strain level of defined mixed-strain starter cultures.

The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR

The purpose of this work was to study the bacterial communities in raw milk and in Danish raw milk cheeses using pyrosequencing of tagged amplicons of the V3 and V4 regions of the 16S rDNA and cDNA. Furthermore, the effects of acidification and ripening starter cultures, cooking temperatures and rate of acidification on survival of added Escherichia coli, Listeria innocua and Staphylococcus aureus in cheeses at different stages of ripening were studied by pyrosequencing and quantitative real time (qRT)-PCR. A high diversity of bacterial species was detected in raw milk. Lactococcus lactis, Streptococcus thermophilus, Lactobacillus casei and Lactobacillus rhamnosus were the main bacteria detected in raw milk and cheeses. Bacteria belonging to the genera Brevibacterium, Staphylococcus, Escherichia, Weissella, Leuconostoc, Pediococcus were also detected in both 16S rDNA and cDNA obtained from raw milk and cheeses. E. coli, which was added to milk used for production of some cheeses, was detected in both DNA and RNA extracted from cheeses at different stages of ripening showing the highest percentage of the total sequence reads at 7 days of ripening and decreased again in the later ripening stages. Growth of E. coli in cheeses appeared to be affected by the cooking temperature and the rate of acidification but not by the ripening starter cultures applied or the indigenous microbiota of raw milk. Growth of L. innocua and S. aureus added to milks was inhibited in all cheeses at different stages of ripening. The use of 16S rRNA gene pyrosequencing and qRT-PCR allows a deeper understanding of the behavior of indigenous microbiota, starter cultures and pathogenic bacteria in raw milk and cheeses.

Systems biology of lactic acid bacteria: a critical review

Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute.

There has been a tendency in the Systems Biology community to think that the collection and integration of data should continue ad infinitum, or that we will otherwise not be able to understand the systems that we study in their details. However, it may sometimes be useful to take a step back and consider whether the knowledge that we already have may not explain the system behaviour that we find so intriguing. Reasoning about systems can be difficult, and may require the application of mathematical techniques. The reward is sometimes the realization of unexpected conclusions, or in the worst case, that we still do not know enough details of the parts, or of the interactions between them.

We will discuss a number of cases, with a focus on LAB-related work, where a typical systems approach has brought new knowledge or perspective, often counterintuitive, and clashing with conclusions from simpler approaches. Also novel types of testable hypotheses may be generated by the systems approach, which we will illustrate. Finally we will give an outlook on the fields of research where the systems approach may point the way for the near future.

A high-throughput cheese manufacturing model for effective cheese starter culture screening

Cheese making is a process in which enzymatic coagulation of milk is followed by protein separation, carbohydrate removal, and an extended bacterial fermentation. The number of variables in this complex process that influence cheese quality is so large that the developments of new manufacturing protocols are cumbersome. To reduce screening costs, several models have been developed to miniaturize the cheese manufacturing process. However, these models are not able to accommodate the throughputs required for systematic screening programs. Here, we describe a protocol that allows the parallel manufacturing of approximately 600 cheeses in individual cheese vats each with individual process specifications. Protocols for the production of miniaturized Gouda- and Cheddar-type cheeses have been developed. Starting with as little as 1.7 mL of milk, miniature cheeses of about 170 mg can be produced and they closely resemble conventionally produced cheese in terms of acidification profiles, moisture and salt contents, proteolysis, flavor profiles, and microstructure. Flavor profiling of miniature cheeses manufactured with and without mixed-strain adjunct starter cultures allowed the distinguishing of the different cheeses. Moreover, single-strain adjunct starter cultures engineered to overexpress important flavor-related enzymes revealed effects similar to those described in industrial cheese. Benchmarking against industrial cheese produced from the same raw materials established a good correlation between their proteolytic degradation products and their flavor profiles. These miniature cheeses, referred to as microcheeses, open new possibilities to study many aspects of cheese production, which will not only accelerate product development but also allow a more systematic approach to investigate the complex biochemistry and microbiology of cheese making.

Starter culture development for improving safety and quality of Domiati cheese

Eleven lactococci strains (sp. lactis and cremoris) were collected according to specific or selected characteristics for development of defined strain starter (DSS) to improve safety and nutritional quality of traditional and low salt Domiati cheese. Thirteen DSS; nisin-producing system or/and folate-producing strains were prepared. The behaviour of the strains in DSS was studied in milk and in two series of Domiati cheese; the first one made with 5% NaCl and salt tolerant strains, the second made with 3% NaCl and the control cheeses were made without starters. The population dynamics of strains and sensory evaluation of cheese corroborated the results in milk. All strains can grow well together and appeared to produce pleasant flavours, normal (typical) body and texture Domiati cheese. There was no apparent difference in cheese composition between cheeses in each series; the levels were within margins for composition of Domiati cheese. The levels of nisin (IU g(-1)) ranged from 204 to 324 IU g(-1) in 3-months' cheeses. Folate concentration increased in cheeses made with DSS cultures than control and the level ranged from 5.5 to 11.1 microg 100 g(-1) in cheeses after 3 months. All results revealed that selected DSS can be used for improving Domiati cheese.

Growth stimulation of a proteinase positive Lactococcus lactis strain by a proteinase negative Lactococcus lactis strain

Lactococcus lactis AMP15/pAMP31(D471R) is a proteinase negative, lactose negative strain with a modified oligopeptide transport system, and potential as a debittering agent due to its efficient utilization of hydrophobic peptides. Five wild L. lactis strains of dairy origin, which produced cheeses of high flavour quality, were cocultured with L. lactis AMP15/pAMP31(D471R) in an attempt to select adequate combinations of strains for use as defined cheese starters with potential debittering ability. Four of these strains, L. lactis B6, K16, M21 and P21, inhibited growth of L. lactis AMP15/pAMP31(D471R) at a level of 10(6) to 10(7) cfu mL(-1) after 24 h of incubation, even though production of bacteriocin-like compounds could only be proven for L. lactis M21. When L. lactis AMP15/pAMP31(D471R) was cocultured with the fifth strain, L. lactis N22, its growth was significantly (P<0.001) inhibited whereas growth of L. lactis N22 was significantly stimulated. The nature of the interaction was studied and it was established that L. lactis N22 is auxotrophic for folate, a compound produced and excreted by L. lactis AMP15/pAMP31(D471R).