Microbial biodiversity, quality and shelf life of microfiltered and pasteurized extended shelf life (ESL) milk from Germany, Austria and Switzerland

Microbial food spoilage: impact, causative agents and control strategies

Microbial food spoilage is a major contributor to food waste and, hence, to the negative environmental sustainability impacts of food production and processing. Globally, it is estimated that 15-20% of food is wasted, with waste, by definition, occurring after primary production and harvesting (for example, in households and food service establishments). Although the causative agents of food spoilage are diverse, many microorganisms are major contributors across different types of foods. For example, the genus Pseudomonas causes spoilage in various raw and ready-to-eat foods. Aerobic sporeformers (for example, members of the genera Bacillus, Paenibacillus and Alicyclobacillus) cause spoilage across various foods and beverages, whereas anaerobic sporeformers (for example, Clostridiales) cause spoilage in a range of products that present low-oxygen environments. Fungi are also important spoilage microorganisms, including in products that are not susceptible to bacterial spoilage due to their low water activity or low pH. Strategies that can reduce spoilage include improved control of spoilage microorganisms in raw material and environmental sources as well as application of microbicidal or microbiostatic strategies (for example, to products and packaging). Emerging tools (for example, systems models and improved genomic tools) represent an opportunity for rational design of systems, processes and products that minimize microbial food spoilage.

Counts of mesophilic aerobic, mesophilic anaerobic, thermophilic aerobic sporeforming bacteria and persistence of Bacillus cereus spores throughout cocoa powder processing chain

Sporeforming bacteria are a concern in some food raw materials, such as cocoa powder. Samples (n = 618) were collected on two farms and at several stages during cocoa powder manufacture in three commercial processing lines to determine the impact of each stage on bacterial spore populations. Mesophilic aerobic, mesophilic anaerobic, thermophilic aerobic, and Bacillus cereus spore populations were enumerated in all the samples. Genetic diversity in B. cereus strains (n = 110) isolated from the samples was examined by M13 sequence-based PCR typing, partial sequencing of the panC gene, and the presence/absence of ces and cspA genes. The counts of different groups of sporeforming bacteria varied amongst farms and processing lines. For example, the counts of mesophilic aerobic spore-forming (MAS) populations of cocoa bean fermentation were lower than 1 log spore/g in Farm 1 but higher than 4 log spore/g in Farm 2. B. cereus isolated from cocoa powder was also recovered from cocoa beans, nibs, and samples after roasting, refining, and pressing, which indicated that B. cereus spores persist throughout cocoa processing. Phylogenetic group IV was the most frequent (73%), along with processing. Strains from phylogenetic group III (14 %) did not show the ces gene's presence.

Microbacterium represents an emerging microorganism of concern in microfiltered extended shelf-life milk products

Growing interest in the manufacture of extended shelf-life (ESL) milk, which is typically achieved by a high-temperature treatment called ultra-pasteurization (UP), is driven by distribution challenges, efforts to reduce food waste, and more. Even though high-temperature, short-time (HTST) pasteurized milk has a substantially shorter shelf life than UP milk, HTST milk is preferred in the United States because consumers tend to perceive UP milk as less desirable due to the "cooked" flavor associated with high-temperature processing. While ESL beyond 21 d may be possible for HTST, the survival and outgrowth of psychrotolerant aerobic spore-forming bacteria can still be a limitation to extending shelf life of HTST milk. Microfiltration (MF) is effective for reducing vegetative microorganisms and spores in raw milk, but it is unclear what the effects of membrane pore size, storage temperature, and milk type (i.e., skim vs. whole) are on the microbial shelf life of milk processed by both MF and HTST pasteurization. To investigate these factors, raw skim milk was MF using different pore sizes (0.8 or 1.2 μm), and then MF skim milk and standardized whole milk (MF skim with heat-treated [85°C for 20 s] cream) were HTST pasteurized at 75°C for 20 s. Subsequently, milk was stored at 3°C, 6.5°C, or 10°C and total bacteria counts were measured for up to 63 d. An ANOVA indicated that mean bacterial concentrations between storage temperatures were significantly different from each other, with mean maximum observed concentrations of 3.67, 5.33, and 8.08 log10 cfu/mL for storage temperatures 3°C, 6.5°C, and 10°C, respectively. Additionally, a smaller difference in mean maximum bacterial concentrations throughout shelf life was identified between pore sizes (<1 log cfu/mL), but no significant difference was attributed to milk type. An unexpected outcome of this study was the identification of Microbacterium as a major contributor to the bacterial population in MF ESL milk. Microbacterium is a psychrotolerant, thermoduric gram-positive, non-spore-forming rod with a small cell size (∼0.9 μm length and ∼0.3 μm width), which our data suggest was able to permeate the membranes used in this study, survive HTST pasteurization, and then grow at refrigeration temperatures. While spores continue to be a key concern for the manufacture of MF, ESL milk, our study demonstrates the importance of other psychrotolerant, thermoduric bacteria such as Microbacterium to these products.

Development and deployment of a supply-chain digital tool to predict fluid-milk spoilage due to psychrotolerant sporeformers

Psychrotolerant sporeformers pose a challenge to maintaining fluid milk quality. Dynamic temperature changes along the supply chain can favor the germination and growth of these bacteria and lead to fluid milk spoilage. In this study, we aim to expand on our previous work on predicting milk spoilage due to psychrotolerant sporeformers. The key model innovations include (1) the ability to account for changing temperatures along the supply chain, and (2) a deployed user-friendly interface to allow easy access to the model. Using the frequencies and concentrations of 8 Bacillales subtypes specific to fluid milk collected in New York, the model simulated sporeformer growth in half-gallons of high-temperature, short-time (HTST) pasteurized fluid milk transported from processing facility to retail store and then to consumer. The Monte Carlo simulations predicted that 44.3% of half-gallons of milk were spoiled (defined as having a bacterial concentration >20,000 cfu/mL, a conservative estimate that represents the Pasteurized Milk Ordinance regulatory limit) after 21 d of refrigerated storage at consumer's home. Model validations showed that the model was the most accurate in predicting the mean sporeformer concentration at low temperatures (i.e., at 3°C and 4°C; compared with higher temperatures at 6°C and 10°C) within the first 21 d of consumer storage, with a root mean square error of 0.29 and 0.34 log10 cfu/mL, respectively. Global sensitivity analyses indicated that home storage temperature, facility-to-retail transportation temperature, and initial spore concentration were the 3 most influential factors for predicting milk spoilage on d 21 of shelf life. What-if scenarios indicated that microfiltration was predicted to be the most effective strategy to reduce spoilage. The implementation of this strategy (assumed to reduce initial spore concentration by 2.2 log10 cfu/mL) was predicted to reduce the percentage of spoiled milk by 17.0 percentage points on d 21 of storage and could delay the date by which 50% of half-gallons of milk were spoiled, from d 25 to 35. Overall, the model is readily deployed as a digital tool for assessing fluid milk spoilage along the supply chain and evaluating the effectiveness of intervention strategies, including those that target storage temperatures at different supply chain stages.

Preservation of high pressure pasteurised milk by hyperbaric storage at room temperature versus refrigeration on inoculated microorganisms, fatty acids, volatile compounds and lipid oxidation

High pressure pasteurised (HPP) milk was stored by hyperbaric storage at room temperature (HS/RT) (50-100 MPa at 20 °C) and compared with refrigeration (RF), to assess the effect on two pathogens surrogates and a pathogenic, up to 120 days, and on fatty acids, volatile organic compounds (VOCs) and secondary lipid oxidation over 60 days. HS/RT (75-100 MPa) was able to inactivate at least 6.68/6.31/6.03 log CFU/mL of Escherichia coli/Listeria innocua/Salmonella Senftenberg (to below the detection limit), while RF resulted only in minor changes. Overall, fatty acids profile remained stable under HS/RT, although secondary lipid oxidation showed slightly higher values. In addition, both HS/RT and RF showed stable and similar VOCs profiles and off-flavour indicative compounds were not detected, except for the lowest pressure (50 MPa) after 40 days. HS/RT preserved HPP milk with enhanced microbial safety, shelf-life and quality compared to RF, being in addition quasi-energetically costless and more sustainable than RF.

Deciphering the Microbiota and Volatile Profiles of Algerian Smen, a Traditional Fermented Butter

In Algeria, Smen is a fermented butter produced in households using empirical methods. Smen fermentation is driven by autochthonous microorganisms; it improves butter shelf-life and yields highly fragrant products used as ingredients in traditional dishes as well as in traditional medicine. The present study is aimed at investigating microbial diversity and dynamics during Algerian Smen fermentation using both culture-dependent and culture-independent approaches, as well as by monitoring volatile organic compound production. To reach this goal, fifteen Smen samples (final products) produced in households from different regions in Algeria were collected and analyzed. In addition, microbial and volatile compound dynamics at the different stages of Smen manufacturing were investigated for one Smen preparation. The results showed that Smen is a microbiologically safe product, as all hygiene and safety criteria were respected. The dominant microorganisms identified by both techniques were LAB and yeasts. Lactococcus spp. and Streptococcus thermophilus were the main bacterial species involved in spontaneous raw milk fermentation preceding butter-making, while lactobacilli and enterococci were the only bacteria found to be viable during Smen maturation. Regarding fungal diversity, yeast species were only recovered from two mature Smen samples by culturing, while different species (e.g., Geotrichum candidum, Moniliella sp.) were identified in all samples by the culture-independent approach. Using microbial analysis of a single batch, many of these were found viable during manufacturing. Concerning the volatile profiles, they were highly diverse and characterized by a high prevalence of short chain fatty acids, methylketones, and esters. Correlation analysis between microbial diversity and volatile profiles showed that several yeast (Moniliella sp., K. marxianus) and LAB (e.g., Lactococcus spp., S. thermophilus) species were strongly correlated with one or more volatile organic compound families, including several ethyl esters and methyl ketones that can be linked to pleasant, sweetly floral, fruity, buttery, and creamy odors. This study clearly identified key microorganisms involved in Smen fermentation and maturation that could be used in the future for better fermentation control and improvement of quality attributes.

Pudding Proteomics: Cyclomaltodextrin Glucanotransferase and Microbial Proteases Can Liquefy Extended Shelf Life Dairy Products

In recent years, a lack of stability of dairy products with extended shelf life (e.g., yoghurt products, UHT desserts) has occurred, with the corresponding products liquefying significantly after days or weeks. This project aimed to identify the enzymes responsible for the liquefaction of the affected products based on differential proteomic analyses. No evidence was found for the presence of starch-degrading bacteria in the affected products. With zymography and proteome analysis, we detected the cause of liquefaction in a pudding by contamination of its aroma component with an engineered amylolytic enzyme, cyclomaltodextrin glucanotransferase (CGTase) from Thermoanaerobacterium thermosulfurigenes. In addition, we detected contamination with Pseudomonas-derived proteolytic ATP-dependent Clp protease in one pudding batch and proteases in technically used amylases, which degraded β-caseins in another batch. Identification of these agents with liquefying properties in dairy products are useful for adjustment of production protocols and/or composition of additives, and thus shelf life extension.

Cold Microfiltration as an Enabler of Sustainable Dairy Protein Ingredient Innovation

Classically, microfiltration (0.1–0.5 µm) of bovine skim milk is performed at warm temperatures (45–55 °C), to produce micellar casein and milk-derived whey protein ingredients. Microfiltration at these temperatures is associated with high initial permeate flux and allows for the retention of the casein fraction, resulting in a whey protein fraction of high purity. Increasingly, however, the microfiltration of skim milk and other dairy streams at low temperatures (≤20 °C) is being used in the dairy industry. The trend towards cold filtration has arisen due to associated benefits of improved microbial quality and reduced fouling, allowing for extended processing times, improved product quality and opportunities for more sustainable processing. Performing microfiltration of skim milk at low temperatures also alters the protein profile and mineral composition of the resulting processing streams, allowing for the generation of new ingredients. However, the use of low processing temperatures is associated with high mechanical energy consumption to compensate for the increased viscosity, and thermal energy consumption for inline cooling, impacting the sustainability of the process. This review will examine the differences between warm and cold microfiltration in terms of membrane performance, partitioning of bovine milk constituents, microbial growth, ingredient innovation and process sustainability.

Effects of microfiltration combined with ultrasonication on shelf life and bioactive protein of skim milk

To extend the shelf life and retain bioactive proteins in milk, this study utilized microfiltration (MF) combined with ultrasonication to treat skim milk and investigated its efficiency in removing bacteria and retaining bioactive proteins compared with HTST pasteurization and microfiltration alone. Results showed that microfiltration combined with ultrasonication at 1296 J/mL could completely remove the bacteria in skim milk. Ultrasonication further extended the shelf life (4 °C) of microfiltered skim milk, which could reach at least 40 days when MF was combined with ˃1296 J/mL ultrasonication. In addition, ELISA showed that HTST pasteurization significantly decreased the levels of IgG by ~30%, IgA by ~ 50%, IgM by ~60%, and lactoferrin by ~40%, whereas the activity of the enzymes lactoperoxidase and xanthine oxidase were also decreased by ~ 20%. Compared with HTST, MF alone or combined with ultrasonication retained these bioactive proteins to a larger degree. On the other hand, proteomics indicated both damage to casein micelle and fat globule structures in milk when ultrasonication at >1296 J/mL was applied, as shown by increases in caseins and milk fat globular proteins. Simultaneously, this ultrasound intensity also decreased levels of bioactive proteins, such as complement factors. Taken together, this study provided new insights that may help to implement this novel combination of non-thermal technologies for the dairy industry aimed at improving milk quality and functionality.

Toxigenic Potential of Bacillus cereus Strains Isolated from Retail Dairy Products in Egypt

Little is known about the virulence in Bacillus cereus strains isolated from retail dairy products in the Middle East and particularly from Egypt. In this study, the occurrence of B. cereus in 290 samples of dairy products (raw milk, Ras cheese, pasteurized extended shelf life [ESL] milk) collected from retail shops was investigated. The potential of 126 selected isolates of B. cereus to possess genes encoding nonhemolytic enterotoxin, hemolysin BL, and cytotoxin K (cytK), and to grow at 7°C was verified. The highest occurrence of B. cereus was found in raw milk (85%, 85/100) followed by Ras cheese (10%, 10/100) and ESL milk samples (8.8%, 8/90). A large proportion of the B. cereus isolates from raw milk (48.9%, 48/99) and Ras cheese (71.4%, 10/14) had at least one complete set of toxin genes (nhe or hbl). Enterotoxin genes, nheA, nheB, nheC, hblA, hblD, and hblC, were detected in 38.4% (5/13), 53.8% (7/13), 61.5% (8/13), 46.1% (6/13), 46.1% (6/13), and 23.1% (3/13) of ESL milk isolates, respectively. cytK was identified in 42.4% (42/99), 50% (7/14), and 46.2% (6/13) of raw milk, Ras cheese, and ESL milk isolates, respectively. The psychrotrophic ability was observed in 22.2% and 15.3% of isolates recovered from raw milk and ESL milk, respectively. The toxigenic potential of B. cereus strains described in this study may pose a health risk to the consumer and, therefore, the presence of these bacteria in retail dairy products should be monitored to ensure consumers' safety.

Ultraviolet-C inactivation and hydrophobicity of Bacillus subtilis and Bacillus velezensis spores isolated from extended shelf-life milk

Bacterial spores are important in food processing due to their ubiquity, resistance to high temperature and chemical inactivation. This work aims to study the effect of ultraviolet C (UVC) on the spores of Bacillus subtilis and Bacillus velezensis at a molecular and individual level to guide in deciding on the right parameters that must be applied during the processing of liquid foods. The spores were treated with UVC using phosphate buffer saline (PBS) as a suspension medium and their lethality rate was determined for each sample. Purified spore samples of B. velezensis and B. subtilis were treated under one pass in a UVC reactor to inactivate the spores. The resistance pattern of the spores to UVC treatment was determined using dipicolinic acid (Ca-DPA) band of spectral analysis obtained from Raman spectroscopy. Flow cytometry analysis was also done to determine the effect of the UVC treatment on the spore samples at the molecular level. Samples were processed for SEM and the percentage spore surface hydrophobicity was also determined using the Microbial Adhesion to Hydrocarbon (MATH) assay to predict the adhesion strength to a stainless-steel surface. The result shows the maximum lethality rate to be 6.5 for B. subtilis strain SRCM103689 (B47) and highest percentage hydrophobicity was 54.9% from the sample B. velezensis strain LPL-K103 (B44). The difference in surface hydrophobicity for all isolates was statistically significant (P < 0.05). Flow cytometry analysis of UVC treated spore suspensions clarifies them further into sub-populations unaccounted for by plate counting on growth media. The Raman spectroscopy identified B4002 as the isolate possessing the highest concentration of Ca-DPA. The study justifies the critical role of Ca-DPA in spore resistance and the possible sub-populations after UVC treatment that may affect product shelf-life and safety. UVC shows a promising application in the inactivation of resistant spores though there is a need to understand the effects at the molecular level to design the best parameters during processing.

Enzymatic Time-Temperature Indicator Prototype Developed by Immobilizing Laccase on Electrospun Fibers to Predict Lactic Acid Bacterial Growth in Milk during Storage

Laccase was immobilized on a chitosan/polyvinyl alcohol/tetraethylorthosilicate electrospun film (ceCPTL) and colored with guaiacol to obtain a laccase time-temperature indicator (TTI) prototype. The activation energy (Ea) of coloration of the prototype was 50.89-33.62 kJ/mol when 8-25 μg/cm² laccase was immobilized on ceCPTL, and that of lactic acid bacteria (LAB) growth in milk was 73.32 kJ/mol. The Ea of coloration of the TTI prototype onto which 8-10 μg/cm² laccase was immobilized was in the required range for predicting LAB growth in milk. The coloration endpoint of the TTI prototype onto which 10 μg/cm² (0.01 U) laccase was immobilized could respond to the LAB count reaching 10⁶ colony-forming units (CFU)/mL in milk during a static temperature response test, and the prediction error was discovered to be low. In dynamic temperature response experiments with intermittent temperature changes between 4 and 25 °C, the coloration rate of the laccase TTI prototype was consistent with LAB growth. The results of this study indicate that the laccase TTI prototype can be applied as a visual monitoring indicator to assist in evaluating milk quality in cold chains.

Semi-industrial production of a minimally processed infant formula powder using membrane filtration

Infant formula (IF) is submitted to several heat treatments during production, which can lead to denaturation or aggregation of proteins and promote Maillard reaction. The objective of this study was to investigate innovative minimal processing routes for the production of first-age IF powder, thus ensuring microbial safety with minimal level of protein denaturation. Three nutritionally complete IF powders were produced at a semi-industrial scale based on ingredients obtained by fresh bovine milk microfiltration (0.8 and 0.1-µm pore size membranes). Low-temperature vacuum evaporation (50°C) and spray-drying (inlet and outlet temperatures of 160 and 70°C, respectively) were conducted to produce the T- formula with no additional heat treatment. The T+ formula was produced with a moderate heat treatment (75°C for 2 min) applied before spray-drying, whereas the T+++ formula received successive heat treatments (72°C for 30 s on the milk; 90°C for 2-3 s before evaporation; 85°C for 2 min before spray-drying), thus mimicking commercial powdered IF. Protein denaturation and Maillard reaction products were followed throughout the production steps and the physicochemical properties of the powders were characterized. The 3 IF powders presented satisfactory physical properties in terms of a_w, free fat content, glass transition temperature, and solubility index, as well as satisfactory bacteriological quality with a total flora <10³ cfu/g and an absence of pathogens when a high level of bacteriological quality of the ingredients was ensured. Protein denaturation occurred mostly during the heat treatments of T+ and T+++ and was limited during the spray-drying process. The IF powder produced without heat treatment (T-) presented a protein denaturation extent (6 ± 4%) significantly lower than that in T+++ (58 ± 0%), but not significantly different from that in T+ (10 ± 4%). Although T- tended to contain less Maillard reaction products than T+ and T+++, the Maillard reaction products did not significantly discriminate the infant formulas in the frame of this work. The present study demonstrated the feasibility of producing at a semi-industrial scale an infant formula being bacteriologically safe and containing a high content of native proteins. Application of a moderate heat treatment before spray-drying could further guarantee the microbiological quality of the IF powders while maintaining a low protein denaturation extent. This study opens up new avenues for the production of minimally processed IF powders.

Bioactive Compounds Produced by the Accompanying Microflora in Bulgarian Yoghurt

Bulgarian yoghurt is associated with health benefits and longevity of consumers. The specific microflora producing bioactive metabolites is responsible for this effect. The present study examines the biodiversity in four homemade yoghurts from regions containing endemic microflora. Metagenome sequencing indicated Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus were predominant in all samples. In addition, yoghurts contained accompanying lactic acid bacteria (LAB) including Lacticaseibacillus paracasei, Lb. helveticus, Limosilactobacillus fermentum, Lb. rhamnosus, Lactococcus lactis, Pediococcus acidilactici, Leuconostoc mesenteroides, and Leuc. pseudomesenteroides. A negligible amount of pollutant strains was found. Twenty-four LAB strains were isolated from the yoghurts and identified. Lb. delbrueckii subsp. bulgaricus strains were genotyped by randomly amplified polymorphic DNA–PCR (RAPD), multi-locus sequence typing (MLST), and pulse field gel electrophoresis (PFGE), which demonstrated their uniqueness and non-commercial origin. To estimate the bioactive metabolites produced by the accompanying microflora, yoghurts fermented by single LAB strains were analyzed using liquid chromatography and mass spectrometry (LC-MS). The fermented samples contained large amounts of free essential amino acids (arginine, citrulline, tryptophan, lysine, and histidine), the neuroprotector indole-3-propionic acid (IPA), and significant quantities of the cyclic antimicrobial peptides cyclo(phenylalanyl-prolyl) and cyclo(leucyloprolyl). The disclosure of these special qualities draws attention to the accompanying microflora as a source of potential probiotic strains that can fortify the yoghurts’ content with bioactive compounds.

Phenotypic and Genotypic Investigation of Two Representative Strains of Microbacterium Species Isolated From Micro-Filtered Milk: Growth Capacity and Spoilage-Potential Assessment

The microbiota that spoil long-life micro-filtered milk generally includes species of the genus Microbacterium. The metabolic properties of this of microorganisms that could potentially modify the quality of micro-filtered milk are still unexplored when compared to better-known microorganisms, such as the spore-forming Bacillus and Paenibacillus spp., and Gram-negative contaminants, such as species of the genera Pseudomonas and Acinetobacter. In this preliminary study, two strains of Microbacterium (M. lacticum 18H and Microbacterium sp. 2C) isolated from micro-filtered milk were characterized in depth, both phenotypically and genotypically, to better understand their role in long-term milk spoilage. The study highlights the ability of these strains to produce high cell numbers and low acidification in micro-filtered milk under storage and shelf-life conditions. Phenotypic analyses of the two Microbacterium sp. isolates revealed that both strains have low proteolytic and lipolytic activity. In addition, they have the ability to form biofilms. This study aims to be a preliminary investigation of milk-adapted strains of the Microbacterium genus, which are able to grow to high cellular levels and perform slight but not negligible acidification that could pose a potential risk to the final quality of micro-filtered milk. Furthermore, M. lacticum 18H and Microbacterium sp. 2C were genotypically characterized in relation to the characteristics of interest in the milk environment. Some protein-encoding genes involved in lactose metabolism were found in the genomes, such as β-galactosidase, lactose permease, and L-lactate dehydrogenase. The phenotypically verified proteolytic ability was supported in the genomes by several genes that encode for proteases, peptidases, and peptide transferases.

Effect of Temperature-Dependent Bacterial Growth during Milk Protein Fractionation by Means of 0.1 µM Microfiltration on the Length of Possible Production Cycle Times

This study determined the maximum possible filtration time per filtration cycle and the cumulated number of operational hours per year as a function of the processing temperature during milk protein fractionation by 0.1 µm microfiltration (MF) of pasteurized skim milk. The main stopping criteria were the microbial count (max. 105 cfu/mL) and the slope of the pH change as a function of filtration time. A membrane system in a feed and bleed configuration with partial recirculation of the retentate was installed, resembling an industrial plants' operational mode. Filtration temperatures of 10, 14, 16, 20, and 55 °C were investigated to determine the flux, pH, and bacterial count. While the processing time was limited to 420 min at a 55 °C filtration temperature, it could exceed 1440 min at 10 °C. These data can help to minimize the use of cleaning agents or mixing phase losses by reducing the frequency of cleaning cycles, thus maximizing the active production time and reducing the environmental impact.

Complementary Use of Cultivation and High-Throughput Amplicon Sequencing Reveals High Biodiversity Within Raw Milk Microbiota

Raw milk microbiota are complex communities with a significant impact on the hygienic, sensory and technological quality of milk products. However, there is a lack of knowledge on factors determining their composition. In the present study, four bulk tank milk samples of two farms at two different time points were analyzed in detail for their microbiota using cultivation and 16S rRNA amplicon sequencing. Diversity in samples from the first time point was assessed via cultivation of 500 aerobic mesophilic bacterial isolates in each sample. A high biodiversity of 70 and 110 species per sample was determined, of which 25–28% corresponded to yet unknown taxa. The isolates were dominated by Gram-positive members of the genera Staphylococcus, Corynebacterium, Streptococcus, or Janibacter, whilst Chryseobacterium and Acinetobacter were most abundant among the Gram-negative taxa. At the second time point, samples of the same farms were analyzed via both cultivation (1,500 individual colonies each) and high-throughput 16S rRNA gene amplicon sequencing. The latter revealed a threefold higher biodiversity at the genus level, as anaerobic or fastidious species were also detected. However, cultivation identified genera not captured by sequencing, indicating that both approaches are complementary. Using amplicon sequencing, the relative abundance of a few genera was distorted, which seems to be an artifact of sample preparation. Therefore, attention needs to be paid to the library preparation procedure with special emphasis on cell lysis and PCR.

Microbial Populations of Fresh and Cold Stored Donkey Milk by High-Throughput Sequencing Provide Indication for A Correct Management of This High-Value Product

Donkey milk is receiving increasing interest due to its attractive nutrient and functional properties (but also cosmetic), which make it a suitable food for sensitive consumers, such as infants with allergies, the immunocompromised, and elderly people. Our study aims to provide further information on the microbial variability of donkey milk under cold storage conditions. Therefore, we analysed by high-throughput sequencing the bacterial communities in unpasteurized donkey milk just milked, and after three days of conservation at 4 °C, respectively. Results showed that fresh donkey milk was characterized by a high incidence of spoilage Gram-negative bacteria mainly belonging to Pseudomonas spp. A composition lower than 5% of lactic acid bacteria was found in fresh milk samples, with Lactococcus spp. being the most abundant. The occurrence of microbial species belonging to risk group 2 was found in fresh milk. After three days of cold storage, the bacterial biodiversity of donkey milk was strongly reduced, since about 93% of the bacterial communities were identified as different species of psychrotrophic Pseudomonas. In conclusion, we report a preliminary description of the microbial diversity of donkey milk by using a metagenomic approach and encouraging a correct exploitation of this high-value niche product.

Impact of yeast and lactic acid bacteria on mastitis and milk microbiota composition of dairy cows

This experiment was conducted to evaluate the impact of yeast and lactic acid bacteria (LAB) on mastitis and milk microbiota composition of dairy cows. Thirty lactating Holstein cows with similar parity, days in milk were randomly assigned to five treatments, including: (1) Health cows with milk SCC < 500,000 cells/mL, no clinical signs of mastitis were found, fed basal total mixed ration (TMR) without supplementation (H); (2) Mastitis cows with milk SCC > 500,000 cells/mL, fed basal TMR without supplementation (M); (3) Mastitis cows fed basal TMR supplemented with 8 g day^-1 yeast (M + Y); (4) Mastitis cows fed basal TMR supplemented with 8 g day^-1 LAB (M + L); (5) Mastitis cows (milk SCC > 500,000 cells/mL) fed basal TMR supplemented with 4 g day^-1 yeast and 4 g day^-1 LAB (M + Y + L). Blood and milk sample were collected at day 0, day 20 and day 40. The results showed efficacy of probiotic: On day 20 and day 40, milk SCC in H, M + Y, M + L, M + Y + L was significantly lower than that of M (P < 0.05). Milk concentration of TNF-α, IL-6 and IL-1β in M + Y + L were significantly reduced compared with that of M on day 40 (P < 0.05). Milk Myeloperoxidase (MPO) and N-Acetyl-β-D-Glucosaminidase (NAG) activity of M + Y, M + L, M + L + Y were lower than that of M on day 40 (P < 0.05). At genus level, Staphylococcus, Chryseobacterium and Lactococcus were dominant. Supplementation of LAB decreased abundance of Enterococcus and Streptococcus, identified as mastitis-causing pathogen. The results suggested the potential of LAB to prevent mastitis by relieving mammary gland inflammation and regulating milk microorganisms.

Paenibacillus odorifer, the Predominant Paenibacillus Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways

Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk.

Paenibacillus is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic diversity of Paenibacillus spp., we first used rpoB allelic typing data for a preexisting collection of 1,228 Paenibacillus species isolates collected from raw and processed milk, milk products, and dairy environmental sources. Whole-genome sequencing (WGS) and average nucleotide identity by BLAST (ANIb) analyses performed for a subset of 58 isolates representing unique and overrepresented rpoB allelic types in the collection revealed that these isolates represent 21 different Paenibacillus spp., with P. odorifer being the predominant species. Further genomic characterization of P. odorifer isolates identified two distinct phylogenetic clades, clades A and B, which showed significant overrepresentation of 172 and 164 ortholog clusters and 94 and 52 gene ontology (GO) terms, respectively. While nitrogen fixation genes were found in both clades, multiple genes associated with nitrate and nitrite reduction were overrepresented in clade A isolates; additional phenotypic testing demonstrated that nitrate reduction is specific to isolates in clade A. Hidden Markov models detected 9 to 10 different classes of cold shock-associated genetic elements in all P. odorifer isolates. Phenotypic testing revealed that all isolates tested here can grow in skim milk broth at 6°C, suggesting that psychrotolerance is conserved in P. odorifer. Overall, our data suggest that Paenibacillus spp. isolated from milk in the United States represent broad genetic diversity, which may provide challenges for targeted-control strategies aimed at reducing fluid milk spoilage.

IMPORTANCE Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk.

High-throughput quantitation of bovine milk proteins and discrimination of commercial milk types by external cavity-quantum cascade laser spectroscopy and chemometrics

Mid-infrared (IR) external cavity-quantum cascade laser (EC-QCL) spectroscopy combined with partial least square modeling (PLS) enables quantitation of bovine milk proteins and discrimination of commercial milk types.

Radio Frequency Heating of Milk–Effects on Quality, Safety, and Shelf Life Assessed Using Artificial Senses and Chemometric Tools

Thermal treatments are widely-used strategies in the food industry to inactivate microorganisms and enzymes in order to guarantee safe products without the need for preservatives, while still prolonging their shelf life. Commercial sterilization usually relies on pressurized hot water or steam, often leading to long process times and to surface dehydration phenomena and overheating. However, from the recent studies in the field of radio frequency heating, it has emerged that food products can be processed with time-temperature regimes that are much milder than those required with conventional techniques, resulting in minimal modification of the sensory and nutritive attributes of the food product itself. In the present work, raw bovine milk was sterilized through a combination of steam and radio frequencies, at various temperatures. Alongside the chemical composition, the pH, acidity, and total mesophilic count have been evaluated before and after the process and at the different exit temperatures, in order to study the impact of this technique on milk quality and safety aspects, during a storage period of 55 days at +4°C. Moreover, the organoleptic properties of milk have been studied using artificial senses coupled with chemometrics. Different temperatures lead to homogenous physicochemical and microbiological results, which conform to those expected for a good quality bovine milk. The assessment of flavor and appearance revealed retained or the minimally modified milk sensorial properties. Therefore, RF heating appears to be a suitable technique for the production of safe milk with a prolonged shelf life up to 40–45 days and without significant alterations of the organoleptic and nutritional attributes.

The role of the surface smear microbiome in the development of defective smear on surface-ripened red-smear cheese

The complex smear microbiota colonizing the surface of red-smear cheese fundamentally impacts the ripening process, appearance and shelf life of cheese. To decipher the prokaryotic composition of the cheese smear microbiome, the surface of a semi-hard surface ripened cheese was studied post-ripening by culture-based and culture-independent molecular approaches. The aim was to detect potential bacterial alterations in the composition of the cheese smear microbiota resulting from cheese storage in vacuum film-prepackaging, which is often accompanied by the development of a surface smear defect. Next-generation sequencing of amplified 16S rRNA gene fragments revealed an unexpected high diversity of a total of 132 different genera from the domains Bacteria and Archaea on the cheese surface. Beside typical smear organisms, our study revealed the presence of several microorganisms so far not associated with cheese, but related to milk, farm and cheese dairy environments. A 16S ribosomal RNA based analysis from total RNA identified the major metabolically active populations in the cheese surface smear as Actinobacteria of the genera Corynebacterium, Brevibacterium, Brachybacterium and Agrococcus. Comparison of data on a higher phylogenetic level revealed distinct differences in the composition of the cheese smear microbiome from the different samples. While the proportions of Proteobacteria and Bacteroidetes were increased in the smear of prepacked samples and in particular in defective smear, staphylococci showed an opposite trend and turned out to be strongly decreased in defective smear. In conclusion, next-generation sequencing of amplified 16S rRNA genes and 16S rRNA from total RNA extracts provided a much deeper insight into the bacterial composition of the cheese smear microbiota. The observed shifts in the microbial composition of samples from defect surface smear suggest that certain members of the Proteobacteria contribute to the observed negative organoleptic properties of the surface smear of cheese after prepacking in plastic foil.

Cheese brines from Danish dairies reveal a complex microbiota comprising several halotolerant bacteria and yeasts

The Danish Danbo cheese is a surface ripened semi-hard cheese, which before ripening is submerged in brine for up to 24 h. The brining is required in order to obtain the structural and organoleptic properties of the cheeses. Likewise, the content of NaCl in the cheese will influence especially the surface microbiota being of significant importance for flavour development and prevention of microbial spoilage. Even though the microbiota on cheese surfaces have been studied extensively, limited knowledge is available on the occurrence of microorganisms in cheese brine. The aim of the present study was to investigate by both culture-dependent and -independent techniques the brine microbiota in four Danish dairies producing Danbo cheese. The pH of the brines varied from 5.1 to 5.6 with a dry matter content from 20 to 27% (w/w). The content of lactate varied from 4.1 to 10.8 g/L and free amino acids from 65 to 224 mg/L. Bacteria were isolated on five different media with NaCl contents of 0.85-23.0% (w/v) NaCl. The highest count of 6.3 log CFU/mL was obtained on TSA added 4% (w/v) NaCl. For yeasts, the highest count was 3.7 log CFU/mL on MYGP added 8% (w/v) NaCl. A total of 31 bacterial and eight eukaryotic species were isolated including several halotolerant and/or halophilic species. Among bacteria, counts of ≥6.0 log CFU/mL were obtained for Tetragenococcus muriaticus and Psychrobacter celer, while counts between ≥4.5 and < 6.0 log CFU/mL were obtained for Lactococcus lactis, Staphylococcus equorum, Staphylococcus hominis, Chromohalobacter beijerinckii, Chromohalobacter japonicus and Microbacterium maritypicum. Among yeasts, counts of ≥3.5 log CFU/mL were only obtained for Debaryomyces hansenii. By amplicon-based high-throughput sequencing of 16S rRNA gene and ITS2 regions for bacteria and eukaryotes respectively, brines from the same dairy clustered together indicating the uniqueness of the dairy brine microbiota. To a great extent the results obtained by amplicon sequencing fitted with the culture-dependent technique though each of the two methodologies identified unique genera/species. Dairy brine handling procedures as e.g. microfiltration were found to influence the brine microbiota. The current study proves the occurrence of a specific dairy brine microbiota including several halotolerant and/or halophilic species most likely of sea salt origin. The importance of these species during especially the initial stages of cheese ripening and their influence on cheese quality and safety need to be investigated. Likewise, optimised brine handling procedures and microbial cultures are required to ensure an optimal brine microbiota.

Application of a novel amplicon-based sequencing approach reveals the diversity of the Bacillus cereus group in stored raw and pasteurized milk

Members of the Bacillus cereus sensu lato (B. cereus group) are spore-forming organisms commonly associated with spoilage of milk and dairy products. Previous studies have shown, by using 16S marker gene sequencing, that the genus Bacillus is part of the core microbiota of raw bovine milk and that some members of this genus are able to grow during sub-optimal storage (8 °C) of pasteurized consumption milk. Here, the composition of this genus in pasteurized consumption milk samples, collected from two dairies, over a one-year period and stored at 4 or 8 °C up to the end of shelf life is uncovered. Our results show that the B. cereus group is the dominant Bacillus group in stored consumption milk. By applying a new marker gene sequencing approach, several dominating phylogenetic clusters were identified within the B. cereus group populations from the milk samples. There was a higher phylogenetic diversity among bacteria from milk stored at 8 °C compared to milk stored at 4 °C. Sampling period and the dairy the samples were collected from, also significantly influenced the diversity, which shows that the B. cereus group population in consumption milk is heterogeneous and subjected to temporal and spatial changes. The new approach applied in this study will facilitate the identification of isolates within the B. cereus group, of which some are potential spoilage bacteria and pathogenic contaminants of milk and dairy products.

Monitoring Shelf Life of Pasteurized Whole Milk Under Refrigerated Storage Conditions: Predictive Models for Quality Loss

The shelf life of pasteurized milk is generally determined through microbiological analysis. The objective of this study was to correlate microbial quality parameters then to design predictive models for shelf life of pasteurized milk. We analyzed pasteurized milk (3.9% fat) for aerobic plate counts (APCs), psychrotrophic bacteria counts (PBCs), and Bacillus spp. counts at 5, 7, 10, 13, 15, and 19 (±1 °C) to the end of storage time. We also monitored titratable acidity, pH, and, lipase, and protease activity and correlated this with APC, which is the principal index defining shelf life. Results indicate that the shelf life of pasteurized milk was 24, 36, and 72 h at 19, 15, and 13 °C respectively, as determined by APC and acidity indicators. However, milk stored at lower temperatures of 5, 7, and 10 °C had longer shelf life of 30, 24, and 12 d, respectively. A sharp increase in titratable acidity, while decrease pH were observed when APCs reached 5.0 log₁₀ CFU/mL at all storage temperatures. Lipase and protease activities increased with storage temperature. At 5 and 7 °C, however, protease activity was very low. Therefore, we eliminated this parameter from our quality parameters as a potential spoilage indicator.

PRACTICAL APPLICATION

Findings of this research are useful for monitoring the quality of commercial pasteurized milk, particularly in locations where environmental conditions make longer storage difficult. The study also provides valuable information for development of colorimetric shelf life indicators.

Optimum Thermal Processing for Extended Shelf-Life (ESL) Milk

Extended shelf-life (ESL) or ultra-pasteurized milk is produced by thermal processing using conditions between those used for traditional high-temperature, short-time (HTST) pasteurization and those used for ultra-high-temperature (UHT) sterilization. It should have a refrigerated shelf-life of more than 30 days. To achieve this, the thermal processing has to be quite intense. The challenge is to produce a product that has high bacteriological quality and safety but also very good organoleptic characteristics. Hence the two major aims in producing ESL milk are to inactivate all vegetative bacteria and spores of psychrotrophic bacteria, and to cause minimal chemical change that can result in cooked flavor development. The first aim is focused on inactivation of spores of psychrotrophic bacteria, especially Bacillus cereus because some strains of this organism are pathogenic, some can grow at ≤7 °C and cause spoilage of milk, and the spores of some strains are very heat-resistant. The second aim is minimizing denaturation of β-lactoglobulin (β-Lg) as the extent of denaturation is strongly correlated with the production of volatile sulfur compounds that cause cooked flavor. It is proposed that the heating should have a bactericidal effect, B* (inactivation of thermophilic spores), of >0.3 and cause ≤50% denaturation of β-Lg. This can be best achieved by heating at high temperature for a short holding time using direct heating, and aseptically packaging the product.