Shifts of microbiota during cheese production: impact on production and quality

Comparative analysis of microbial succession and proteolysis focusing on amino acid pathways in Asiago-PDO cheese from two dairies

In this study, a comprehensive and comparative analysis was conducted on Italian Asiago-PDO cheese obtained from two different dairies named Dairy I and Dairy II using industrial and natural fermented milk, respectively. The analysis encompassed the evaluation of chemical composition, the succession of the microbiota during manufacture and ripening, and proteolysis mainly focusing on free individual amino acid (FAA) profiles. A metagenomic approach was used to investigate the cheese microbiome functionality. Differences in gross chemical composition were more evident during ripening, with Dairy II showing higher variability within batches. The microbiota varied significantly between the two dairies and ripening stages. The choice of starter culture shaped the microbiota during production and affected the microbial diversity of non-starter lactic acid bacteria (NSLAB) originated from the raw milk during ripening. Peptide chromatographic profiles and FAA concentrations increased as ripening progressed, with Dairy I showing higher production of FAA. Functional analysis of the metagenomes linked species to specific amino acid metabolism/catabolism pathways. The amino acid metabolism pathways, particularly those related to aromatic amino acids, lysine, and branched-chain amino acids, were affected by the presence of specific NSLAB species, which differed between the two dairies. The results obtained in this study reveal the impact of starter culture on peculiar cheese microbiota assemblies, which selectively targets amino acid pathways, providing insights into the potential flavor and aroma characteristics of Asiago-PDO cheese.

The Use of Ozone Technology: An Eco-Friendly Method for the Sanitization of the Dairy Supply Chain

The dairy field has considerable economic relevance in the agri-food system, but also has the need to develop new 'green' supply chain actions to ensure that sustainable products are in line with consumer requirements. In recent years, the dairy farming industry has generally improved in terms of equipment and product performance, but innovation must be linked to traditional product specifications. During cheese ripening, the storage areas and the direct contact of the cheese with the wood must be carefully managed because the proliferation of contaminating microorganisms, parasites, and insects increases significantly and product quality quickly declines, notably from a sensory level. The use of ozone (as gas or as ozonated water) can be effective for sanitizing air, water, and surfaces in contact with food, and its use can also be extended to the treatment of waste and process water. Ozone is easily generated and is eco-sustainable as it tends to disappear in a short time, leaving no residues of ozone. However, its oxidation potential can lead to the peroxidation of cheese polyunsaturated fatty acids. In this review we intend to investigate the use of ozone in the dairy sector, selecting the studies that have been most relevant over the last years.

Lactose and Galactose Content in Spanish Cheeses: Usefulness in the Dietary Treatment of Patients with Galactosaemia

In galactosaemia, a strict galactose-free diet is necessary to prevent or resolve acute symptoms in infants. However, because the body produces up to 10 times more galactose than is found in a galactose-restricted diet, excessively restrictive diets should be avoided in children and adults to prevent nutritional deficiencies. Since cheese is a nutritional source of the calcium necessary for bone health, the latest international guidelines on the management of classical galactosaemia (2017) allow the consumption of cured cheeses with less than 25 mg of galactose/100 g and recommend that each country verifies the adequacy of the cheeses, since most mature cheeses do not always have a lower galactose content. In total, 32 cheese samples were purchased (19 Spanish and 13 international cheeses), and their lactose and galactose contents were analysed using ion chromatography with pulsed amperometric detection (IC-PAD). Five Spanish cheeses contained less than 25 mg of galactose/100 g: García Baquero semi-cured cheese; Hacendado, Gran Reserva and Mahón cured cheeses; and García Baquero Reserva 12-month cured cheese. In addition, eight international cheeses were confirmed as suitable: Comté, Gouda, Gruyere, Maasdam, Parmigiano, Edam, Emmental, and some samples of Cheddar. In addition to the well-known low-galactose Swiss and Dutch cheeses, according to the current results, five Spanish cheeses can be safely consumed. The greater availability of types of cheese favours better bone health in patients with galactosaemia.

Challenges and perspectives of quantitative microbiome profiling in food fermentations

Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.

Determination of the microbial community of traditional Mongolian cheese by using culture-dependent and independent methods

Mongolian cheese is not only a requisite source of food for the nomadic Mongolian but also follows a unique Mongolian dairy artisanal method of production, possessing high nutritional value and long shelf-life. In this study, the ancient technique for the production of Mongolian cheese was investigated. The nutritional value of Mongolian cheese was characterized by its high-protein content (30.13 ± 2.99%) and low-fat content (9.66 ± 3.36%). Lactobacillus, Lactococcus, and Dipodascus were the predominant bacterial and fungal genera, and Lactobacillus helveticus, Lactococcus piscium, and Dipodascus geotrichum were the predominant species in the Mongolian cheese. The microbiota of products from different cheese factories varies significantly. The high-temperature (85°C-90°C) kneading of coagulated curds could eliminate most of the thermosensitive microorganisms for extending the shelf-life of cheese. The indigenous spore-forming microbes, which included yeasts, belonging to Pichia and Candida genera, and molds, belonging to Mucor and Penicillium genera, which originated from the surroundings during the process of cooling, drying, demolding, and vacuum packaging could survive and cause the package to swell and the cheese to grow mold. The investigation of production technology, nutrition, microbiota, and viable microbes related to shelf-life contributes to the protection of traditional technologies, extraction of highlights (nutritional profiles and curd scalding) for merchandise marketing, and standardization of Mongolian cheese production, including culture starters and aseptic technique.

Lactic Acid Bacteria in Raw-Milk Cheeses: From Starter Cultures to Probiotic Functions

Traditional cheeses produced from raw milk exhibit a complex microbiota, characterized by a sequence of different microorganisms from milk coagulation and throughout maturation. Lactic acid bacteria (LAB) play an essential role in traditional cheese making, either as starter cultures that cause the rapid acidification of milk or as secondary microbiota that play an important role during cheese ripening. The enzymes produced by such dynamic LAB communities in raw milk are crucial, since they support proteolysis and lipolysis as chief drivers of flavor and texture of cheese. Recently, several LAB species have been characterized and used as probiotics that successfully promote human health. This review highlights the latest trends encompassing LAB acting in traditional raw milk cheeses (from cow, sheep, and goat milk), and their potential as probiotics and producers of bioactive compounds with health-promoting effects.

Bacterial Composition and Interactions in Raw Milk and Teat Skin of Dairy Cows

The microbiota in raw milk plays an important role in the health of dairy cows and the safety of dairy products, which might be influenced by that in teat skin. However, the microbiota composition in raw milk and teat skin, as well as the bacterial interaction between the two adjacent spatial locations, remains elusive. Here, we investigated the composition, diversity, and co-occurrence network of the bacterial communities in raw milk and on teat skin, as well as the shift of bacterial communities during the teat bath using 469 samples from 156 individual cows. We observed that raw milk and teat skin harbored significantly different bacterial communities according to an assessment of the genera numbers (p < 0.05) and PCoA analysis (ANOSIM p < 0.05). The microbiota in raw milk was dominated by Proteobacteria (58.5% in relative abundance) at the phylum level and by Pseudomonas (51.2%) at the genus level, while that in teat skin was dominated by Firmicutes (46.9%) at the phylum level and by Pseudomonas (11.0%) at the genus level. We observed a massive difference between the bacterial subnetworks in raw milk and teat, and the bacterial abundance in these two adjacent spatial locations was positively correlated (p < 0.05). Using Bayesian algorithms, we identified that 92.1% of bacteria in raw milk were transferred from teat skin, while 63.6% of bacteria on teat skin were transferred from raw milk. Moreover, microbiota composition in teat skin could be affected by the teat bath with iodine disinfectant, which tended to be more similar to that in raw milk after the teat bath (p < 0.05), while the abundance of the dominant genus Pseudomonas significantly increased (p < 0.05). These findings expand our knowledge on the microbiota composition in teat skin and raw milk, as well as the interaction between these two adjacent spatial locations.

Microbial and chemical composition of Cheddar cheese supplemented with prebiotics from pasteurized milk to aging

Microbial and chemical properties of cheese is crucial in the dairy industry to understand their effects on cheese quality. Microorganisms within this fat, protein, and water matrix are largely responsible for physiochemical characteristics and associated quality. Prebiotics can be used as an energy source for lactic acid bacteria in cheese by altering the microbial community and provide the potential for value-added foods, with a more stable probiotic population. This research focuses on the addition of fructooligosaccharides (FOS) or inulin to the Cheddar cheese-making process to evaluate the effects on microbial and physicochemical composition changes. Laboratory-scale Cheddar cheese produced in 2 replicates was supplemented with 0 (control), 0.5, 1.0, and 2.0% (wt/wt) of FOS or inulin using 18 L of commercially pasteurized milk. A total of 210 samples (15 samples per replicate of each treatment) were collected from cheese-making procedure and aging period. Analysis for each sample were performed for quantitative analysis of chemical and microbial composition. The prevalence of lactic acid bacteria (log cfu/g) in Cheddar cheese supplemented with FOS (6.34 ± 0.11 and 8.99 ± 0.46; ± standard deviation) or inulin (6.02 ± 0.79 and 9.08 ± 1.00) was significantly higher than the control (5.84 ± 0.27 and 8.48 ± 0.06) in whey and curd, respectively. Fructooligosaccharides supplemented cheeses showed similar chemical properties to the control cheese, whereas inulin-supplemented cheeses exhibited a significantly higher moisture content than FOS and the control groups. Streptococcus and Lactococcus were predominant in all cheeses and 2% inulin and 2% FOS-supplemented cheeses possessed significant amounts of nonstarter lactic acid bacteria found to be an unidentified group of Lactobacillaceae, which emerged after 90 d of aging. In conclusion, this study demonstrates that prebiotic supplementation of Cheddar cheese results in differing microbial and chemical characteristics.

High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota

Background

Next-generation sequencing (NGS) methods and especially 16S rRNA gene amplicon sequencing have become indispensable tools in microbial ecology. While they have opened up new possibilities for studying microbial communities, they also have one drawback, namely providing only relative abundances and thus compositional data. Quantitative PCR (qPCR) has been used for years for the quantification of bacteria. However, this method requires the development of specific primers and has a low throughput. The constraint of low throughput has recently been overcome by the development of high-throughput qPCR (HT-qPCR), which allows for the simultaneous detection of the most prevalent bacteria in moderately complex systems, such as cheese and other fermented dairy foods. In the present study, the performance of the two approaches, NGS and HT-qPCR, was compared by analyzing the same DNA samples from 21 Raclette du Valais protected designation of origin (PDO) cheeses. Based on the results obtained, the differences, accuracy, and usefulness of the two approaches were studied in detail.

Results

The results obtained using NGS (non-targeted) and HT-qPCR (targeted) show considerable agreement in determining the microbial composition of the cheese DNA samples studied, albeit the fundamentally different nature of these two approaches. A few inconsistencies in species detection were observed, particularly for less abundant ones. The detailed comparison of the results for 15 bacterial species/groups measured by both methods revealed a considerable bias for certain bacterial species in the measurements of the amplicon sequencing approach. We identified as probable origin to this PCR bias due to primer mismatches, variations in the number of copies for the 16S rRNA gene, and bias introduced in the bioinformatics analysis.

Conclusion

As the normalized microbial composition results of NGS and HT-qPCR agreed for most of the 21 cheese samples analyzed, both methods can be considered as complementary and reliable for studying the microbial composition of cheese. Their combined application proved to be very helpful in identifying potential biases and overcoming methodological limitations in the quantitative analysis of the cheese microbiota.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02451-y.

The Raw Milk Microbiota from Semi-Subsistence Farms Characteristics by NGS Analysis Method

The aim of this study was to analyze the microbiome of raw milk obtained from three semi-subsistence farms (A, B, and C) located in the Kuyavian-Pomeranian Voivodeship in Poland. The composition of drinking milk was assessed on the basis of 16S rRNA gene sequencing using the Ion Torrent platform. Based on the conducted research, significant changes in the composition of the milk microbiome were found depending on its place of origin. Bacteria belonging to the Bacillus (17.0%), Corynebacterium (12.0%) and Escherichia-Shigella (11.0%) genera were dominant in the milk collected from farm A. In the case of the milk from farm B, the dominant bacteria belonged to the Acinetobacter genus (21.0%), whereas in the sample from farm C, Escherichia-Shigella (24.8%) and Bacillus (10.3%) dominated the microbiome. An analysis was performed using the PICRUSt tool (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) in order to generate a profile of genes responsible for bacterial metabolism. The conducted analysis confirmed the diversity of the profile of genes responsible for bacterial metabolism in all the tested samples. On the other hand, simultaneous analysis of six KEGG Orthologs (KO), which participated in beta-lactam resistance responsible for antibiotic resistance of bacteria, demonstrated that there is no significant relationship between the predicted occurrence of these orthologs and the place of existence of microorganisms. Therefore, it can be supposed that bacterial resistance to beta-lactam antibiotics occurs regardless of the environmental niche, and that the antibiotic resistance maintained in the population is a factor that shapes the functional structure of the microbial consortia.