The complex microbiota of raw milk

Metabarcoding analysis of the microbiota in flocks naturally infected by Coxiella burnetii: First description of the global microbiota in domestic small ruminants

This study investigates Q fever in sheep and goats, key reservoirs for human infection, by metabarcoding and comparing it with q-PCR and serology. Samples from 26 small ruminants (aborted and normal-delivery) and six males across three Q fever-affected herds were analyzed. In sheep herds, seropositivity was 50 and 80 % respectively, with Coxiella (C.) burnetii shedding detected vaginally in the second herd. In goats, 100 % seropositivity and 90 % C. burnetii detection were observed, with nasal and vaginal samples showing the highest detection rates. Metabarcoding revealed significant differences in alpha diversity, with greater richness in blood and evenness in milk from normal-delivery sheep and higher evenness in faeces from aborted sheep. Beta diversity showed distinct vaginal microbiota in normal-delivery females compared to aborted ones. Firmicutes was the most abundant phylum observed. Dominant genera included: Moraxella (nasal), Mycoplasma (blood), Streptococcus (milk), Ureaplasma (vaginal and preputial), Rikenellaceae RC9 gut group (faeces). Significant differences in bacterial composition, including infertility-linked vaginal pathogens, were found across female groups in all herds in the anatomical locations studied, revealing new species and tropisms. Moreover, taxonomic analysis identified C. burnetii in vaginal, milk and environmental samples. This first report of C. burnetii in the caprine nasal cavity suggests an underestimated tropism that may improve Q fever diagnosis. These findings underscore the need for herd-wide Q fever control measures, including males and normal-delivery females. Our findings contribute to new insights into the pathogen's impact on small ruminant microbiota and a novel approach to studying infectious diseases in this sector.

The Effects of Sampling Sites, Collection Time, and Refrigerated Storage Duration on Microbiota of Raw Milk From a Chinese Dairy Farm: An Exploratory Study

Raw milk is the primary material for all dairy products, making it imperative to characterize and monitor its microbial composition to ensure product quality. To investigate microbial contamination from pasture to processing facilities and establish microbial traceability systems, eighty-seven raw milk samples were collected from a dairy farm in Shijiazhuang of China in August. The raw milk samples were categorized into three experimental groups based on: sampling sites along the production chain (manual milking, buffer tank, filter, refrigeration tank, milk truck, and plant factory), sampling time (before dawn, morning, noon, and afternoon), and refrigeration storage (0-72 h at 12 h intervals). The microbiota were evaluated by 16S rRNA sequencing. The results identified Pseudomonas, Lactobacillus, and Prevotella as the predominant bacterial genera across all sampling conditions. The α-diversity (Shannon and Chao1) and β-diversity analysis jointly revealed significant differences in microbial communities of raw milk samples. Specifically, raw milk collected from milk truck showed distinct bacterial communities compared with upstream collecting points, while morning-collected samples showed marked compositional differences from other time points. These findings were consistently supported by cluster heatmap analysis. In addition, the relative abundance of Pseudomonas in raw milk decreased but Lactococcus and Serratia increased with refrigerated time (P < 0.05). This inverse relationship was further evidenced in cooccurrence network showing a strong negative correlation between Lactococcus, Serratia, and Pseudomonas. These results indicated where and when (after being transported to milk truck and in the morning) we need to alert owing to potential contamination in raw milk. Our results also suggested that psychrotrophic bacteria in raw milk should be paid attention, especially Pseudomonas during early refrigerated storage and Serratia during late refrigerated storage.

Short-chain fatty acids in Huntington's disease: Mechanisms of action and their therapeutic implications

Huntington's disease (HD) is a progressive neurodegenerative disorder characterized by motor dysfunction, cognitive decline, and emotional instability, primarily resulting from the abnormal accumulation of mutant huntingtin protein. Growing research highlights the role of intestinal microbiota and their metabolites, particularly short-chain fatty acids (SCFAs), in modulating HD progression. SCFAs, including acetate, propionate, and butyrate, are produced by gut bacteria through dietary fiber fermentation and are recognized for their neuroprotective properties. Evidence suggests that SCFAs regulate neuroinflammation, neuronal communication, and metabolic functions within the central nervous system (CNS). In HD, these compounds may support neuronal health, reduce oxidative stress, and enhance blood-brain barrier (BBB) integrity. Their mechanisms of action involve binding to G-protein-coupled receptors (GPCRs) and modulating gene expression through epigenetic pathways, underscoring their therapeutic potential. This analysis examines the significance of SCFAs in HD, emphasizing the gut-brain axis and the benefits of dietary interventions aimed at modifying gut microbiota composition and promoting SCFA production. Further research into these pathways may pave the way for novel HD management strategies and improved therapeutic outcomes.

Differential effects of Lactococcus starter cultures on Cheddar cheese: Insights from texture, electronic sensory, and metabolomics analyses

Cheese-associated microbiota and their interactions are crucial in determining the properties of cheese. This study aimed to compare the effects of different starter cultures on Cheddar cheese production using texture analysis, electronic sensory evaluation, and both volatile and non-volatile metabolomics. Specifically, we examined Lactococcus lactis BL19 and Lactococcus cremoris LC99, both individually and in combination. The results revealed distinct electronic sensory profiles and varied volatile and non-volatile metabolomic characteristics among cheese samples produced with different starter combinations, although no significant differences in texture were observed. Notably, BL19 had a more pronounced effect on electronic sensory attributes and both volatile and non-volatile metabolites compared to LC99. Furthermore, the combination of starter cultures did not demonstrate an additive effect on these parameters. This study offers valuable insights into the interactions of cheese microorganisms and establishes a foundation for developing diverse flavor profiles in cheese through strategic starter culture selection.

Overview of endospore-forming bacteria in food: The road towards a harmonised method for the enumeration of their spores

Endospore-forming bacteria are an important challenge for the food industry due to their ubiquitous nature, widespread presence in the food chain and sophisticated survival mechanisms. An accurate method is needed that can provide insight into the quality of raw materials, predict spoilage potential and ensure food safety. A plethora of methods exist for the enumeration of spore-forming bacteria which vary among countries, industries and food producers. These methods describe a wide range of values in the key method parameters, such as heat treatment, growth medium, incubation time, and temperature. Consequently the results obtained can vary leading to misalignment and confusion. In addition, many of these methods are empirical and have not been validated. A harmonised international approach for the enumeration of spores is needed to provide consistent and reliable results on which to base food safety and quality decisions. A group of experts associated with the Internal Standardisation Organisation working group undertaking this task has identified the main endospore-forming bacterial species occurring in foods based on a wide selection of publications. Endospores are typically formed by bacteria belonging to twelve families originating from the Negativicutes, Bacilli and Clostridia classes, with the latter two being the most important for the food industry. This review will be used as a first step in method standardisation.

Comparative analysis of proteomics and transcriptomics reveals novel mechanism underlying the antibacterial activity and immune-enhancing properties of horse milk

Background

Horse milk is a highly valuable organic food that is a promising alternative to cow milk, exhibiting plenty of healthy and immune benefits to human. However, identification of proteins associated human wellness and underlying molecular mechanism in horse milk remain unclear.

Methodology

Label-free mass spectrometry-based protein quantification technology was employed to investigate protein composition of animal milk, including cow, goat, camel and horse milk. Prokaryotic expression and disk diffusion assay were applied to acquire and evaluate in vitro antimicrobial activity of candidate proteins. RAW264.7 macrophage model cell line was used to validate effect of proteins on cytotoxicity, apoptosis and immune induction. ROS probe detected cell ROS change and RT-qPCR verified expression of immune response genes induced by proteins. Microscopy was used to observe the effects of protein on the morphological characteristics of bacteria, further transcriptome analysis was performed to investigate transcriptional changes of bacteria induced by candidate proteins.

Results

A total of 1,335 proteins was identified in cow, goat, camel and horse milk. GO enrichment analysis showed that the proteins related to protein degradation were highly expressed in horse milk compared to other three types of milk, contributing to easier assimilation and palatability. KEGG analysis showed that horse milk contained abundant antimicrobial associated proteins relevant to pathogenic bacterial resistance, leading to the decreased risk of pathogenic diseases. A higher accumulation of proteins associated with caffeine metabolism, amino acid biosynthesis, and glycolysis/gluconeogenesis in horse milk contributes to its distinctive flavor. Notably, highly expressed proteins in horse milk were closely linked to immune signaling pathways, functioning as immune modulators. Importantly, we identified four highly expressed antimicrobial associated proteins in horse milk including LPO, B2M, CD14 and PGL, among them, PGL functioned dually by in vitro antibacterial activity and immune activation. Further transcriptome analysis demonstrated that PGL exerted significant transcriptional changes to bacteria. Enrichment analysis showed PGL could inhibit growth of P. aeruginosa and E. coli by repressing the biosynthesis of secondary metabolites.

Conclusion

Comparative proteomics revealed immune enhancement and nutrient composition of horse milk compared to cow, goat and camel milk. Identification of PGL showed antibacterial activity and potential medicinal value.

Microbial dynamics and Pseudomonas natural product production in milk and dairy products

Covering: 2000 up to the first half of 2024Milk and its derived dairy products have long been integral to the human diet, with evidence of consumption dating back over 9000 years. Milk's high nutritional value renders dairy products an important element of human diet while also offering a fertile environment for microbial growth. Beneficial microorganisms in dairy products are often associated with biogenic and probiotic effects, whereas spoilage or pathogenic microorganisms can pose health risks. Fermentation is a key method to preserve milk. Whereas dairying practices in most parts of the world have been highly altered by industrialization over the past century, nomadic pastoralists in Mongolia notably retain a rich tradition of household-level dairy fermentation that has been practiced since 3000 BC. Milk-associated microorganisms produce a vast number of low molecular weight natural products that can mediate beneficial and detrimental interactions. Bacteria of the genus Pseudomonas are found in traditional Mongolian dairy products and are common contaminants in commercial dairy products, and they can strongly impact the quality and shelf-life of dairy products. These bacteria are well known for their ability to produce a variety of secondary metabolites, including nonribosomal (lipo)peptides, which are both structurally and functionally diverse. Lipopeptides can have antimicrobial properties, act as quorum sensing molecules, and contribute to biofilm formation due to their amphiphilic nature. Although often associated with spoilage, some of these natural products can also exhibit positive effects with potential beneficial applications in the dairy industry. This review aims to provide a comprehensive overview of the interplay between culinary fermentation and the production and activities of microbial-derived natural products.

Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking

This review contributes to the knowledge on the complex and adaptive microbial ecosystems within cheese, emphasizing their critical role in determining cheese quality, flavor, and safety. This review synthesizes the current knowledge on the microbial interactions and the dynamics of lactic acid bacteria (LAB), encompassing both starter (SLAB) and non-starter (NSLAB) strains, which are pivotal to the curd fermentation and ripening processes. The adaptability of these microbial consortia to environmental and technological stressors is explored, highlighting their contributions to acidification, proteolysis, and the development of distinctive organoleptic characteristics. Historical and technological perspectives on cheesemaking are also discussed, detailing the impact of milk treatment, starter culture selection, and post-renneting procedures on microbial activity and biochemical transformations. This review underscores the importance of microbial diversity and cooperative interactions in fostering ecosystem resilience and metabolic functionality, and it addresses the challenges in mimicking the technological performance of natural starters using selected cultures. By understanding the ecological roles and interactions of cheese microbiota, this review aims to guide improvements in cheese production practices. Additionally, these insights could spark the development of innovative strategies for microbial community management.

Foodborne spore-forming bacteria: Challenges and opportunities for their control through the food production chain

Foodborne spore-forming bacteria represent a significant challenge within the food production chain due to their widespread occurrence and resistance to various processing methods. In addition to their role in food spoilage, these bacteria exhibit pathogenic properties, posing risks to public health. A comprehensive understanding of the impact of unit operations along the food production continuum, from farm or field to fork, is essential for ensuring both the safety and quality of food products. This chapter explores the factors influencing the growth, inactivation, and persistence of these bacteria, as well as the challenges and opportunities for their control. The discussion encompasses preventive measures, control strategies at the farm and field levels, and processing operations, including both thermal and non-thermal methods. Post-processing controls, such as storage and distribution practices, are also addressed. Furthermore, consumer behavior, education, and lessons learned from past outbreaks and product recalls contribute to a broader understanding of how to manage spore-forming bacteria within the food production chain. By assessing and quantifying the effects of each processing step, it becomes possible to implement effective control measures, thereby ensuring microbiological safety and enhancing the quality of food products.

Antimicrobial Resistance Characteristics of Fecal Escherichia coli and Enterococcus Species in U.S. Goats: 2019 National Animal Health Monitoring System Enteric Study

Escherichia coli and Enterococcus species are normal bacteria of the gastrointestinal tract and serve as indicator organisms for the epidemiology and emergence of antimicrobial resistance in their hosts and the environment. Some E. coli serovars, including E. coli O157:H7, are important human pathogens, although reservoir species such as goats remain asymptomatic. We describe the prevalence and antimicrobial resistance of generic E. coli, E. coli O157:H7, and Enterococcus species collected from a national surveillance study of goat feces as part of the National Animal Health Monitoring System (NAHMS) Goat 2019 study. Fecal samples were collected from 4918 goats on 332 operations across the United States. Expectedly, a high prevalence of E. coli (98.7%, 4850/4915) and Enterococcus species (94.8%, 4662/4918) was found. E. coli O157:H7 prevalence was low (0.2%; 10/4918). E. coli isolates, up to three per operation, were evaluated for antimicrobial susceptibility and 84.7% (571/674) were pansusceptible. Multidrug resistance (MDR; ≥3 classes) was uncommon among E. coli, occurring in 8.2% of isolates (55/674). Resistance toward seven antimicrobial classes was observed in a single isolate. Resistance to tetracycline alone (13.6%, 92/674) or to tetracycline, streptomycin, and sulfisoxazole (7.0% 47/674) was the most common pattern. All E. coli O157:H7 isolates were pansusceptible. Enterococcus isolates, up to four per operation, were prioritized by public health importance, including Enterococcus faecium and Enterococcus faecalis and evaluated. Resistance to lincomycin (93.8%, 1232/1313) was most common, with MDR detected in 29.5% (388/1313) of isolates. The combination of ciprofloxacin, lincomycin, and quinupristin resistance (27.1%, 105/388) was the most common pattern detected. Distribution and characteristics of antimicrobial resistance in E. coli and Enterococcus in the U.S. goat population from this study can inform stewardship considerations and public health efforts surrounding goats and their products.

Raw milk at refrigeration temperature displays an independent microbiota dynamic regardless Listeria monocytogenes contamination

Dairy products made of raw milk are associated with hypervirulent L. monocytogenes clonal complexes (CCs) CC1, CC4, and CC6, and cause half of the reported listeriosis outbreaks in Europe. However, it is currently unknown whether the overrepresentation of L. monocytogenes hypervirulent clones in dairy products made of raw milk is conditioned by an alteration in the native raw milk microbiota growth and/or composition. In this study, the lag phase, maximal growth rate, and the final maximal concentration of mesophilic aerobic bacteria from native raw milk bacteria were measured at refrigerated temperature (4 °C) in the presence and absence of L. monocytogenes contamination. The raw milk microbiota composition and dynamics were evaluated in the presence and absence of L. monocytogenes hypervirulent (CC1, CC4, CC6), and hypovirulent (CC9 and CC121) clones at 4 °C by using 16S rRNA high-throughput sequencing. Our results showed that the growth and composition of the microbial communities naturally present in raw milk are independent of the contamination with hyper- or hypovirulent L. monocytogenes CCs at refrigeration temperature. Pseudomonas was the most abundant genus in raw milk on days 11 and 21, while Carnobacterium was the second most abundant genus regardless of the contaminant L. monocytogenes CCs. Altogether these results suggest that the overrepresentation of hypervirulent L. monocytogenes CC1, CC4, and CC6 in dairy products is not the consequence of a differential alteration in the native composition of the raw milk microbiota.

Fungal and bacterial diversity present on the rind and core of Natural Bloomy Rind Artisanal Minas Cheese from the Canastra region, Brazil

Globally recognized for its unique sensory attributes, Natural Bloomy Rind Artisanal Minas Cheese (NBRAMC) from the Canastra microregion is made from raw cow's milk using a natural starter culture derived from the local environment. During ripening process, microorganisms, predominantly Geotrichum candidum, develop on the surface, with the microbial community playing a crucial role in shaping the cheese's distinctive characteristics. This study aimed to characterize the microbial community, including filamentous fungi, yeasts, and bacteria, present in the rind and core of NBRAMC. Amplicon sequencing of the ITS and 16S rRNA gene regions was performed on rind and core samples from cheeses produced at six distinct producers. Results indicated that G. candidum and Diutina catenulata were the most prevalent fungal species, and Candida intermedia being more abundant exclusively in the interior of the cheeses. The bacterial community displayed greater diversity in the rind, with genera such as Lactococcus, Brevibacterium, and Corynebacterium variabile, while Lactococcus and Streptococcus dominated the core. An inverse relationship between D. catenulata and G. candidum abundance was noted. Significant variations in microbial community profiles were found among producers, despite their geographical proximity. While low levels of undesirable fungi were detected, some samples showed a notable presence of undesirable bacteria, indicating potential hygiene issues during cheese handling. These findings provide valuable insights into the microbial dynamics of NBRAMC, supporting the implementation of strategies that can enhance the quality and safety of the product.

Escherichia coli O157:H7, a Common Contaminant of Raw Milk from Ecuador: Isolation and Molecular Identification

Escherichia coli (E. coli), especially the Shiga toxin-producing O157:H7 strain, poses severe health risks. In rural Ecuador, raw milk consumption heightens contamination risks. This study analyzed 633 raw milk samples from Pichincha and Manabí to assess E. coli O157:H7 prevalence. The samples were enriched using BHI broth, and then specific culture media were used to isolate E. coli O157:H7. The pathogen in the enriched raw milk was identified, and the isolates were specifically confirmed through the application of a newly designed qPCR assay. The novel qPCR assay demonstrated remarkable sensitivity, capable of detecting up to one copy of genetic material, and specificity (no amplification of other bacteria). An extremely high E. coli O157:H7 prevalence of 0.63 (n = 401) was detected, where the province with the highest number of positive samples was Manabí with 72.8% (n = 225/309) and 54.3% (n = 179/324) for Pichincha. In both provinces, the presence of E. coli O157:H7 contamination exhibited a favorable correlation with small-scale farms and elevated temperatures. This research provides valuable data on the microbiological contamination of E. coli O157:H7 present in raw milk, in addition to an improved method that has been demonstrated to be faster, more sensitive, and more specific than conventional and previously published methods, highlighting the associated risk of food-borne infections and pointing out potential shortcomings in the regulation of agricultural practices and the need for periodic monitoring of bacterial contamination levels with updated methods.

Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheese

BACKGROUND

Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing.

RESULTS

The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia.

CONCLUSION

This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract.

Targeting Spore-Forming Bacteria: A Review on the Antimicrobial Potential of Selenium Nanoparticles

Spore-forming bacterial species pose a serious threat to food plants and healthcare facilities that use high-temperature processing and sterilizing techniques to sanitize medical equipment and food items. These severe processing conditions trigger sporulation, which is the process by which spore-forming bacteria, such as those of the Bacillus and Clostridium species, begin to produce spores, which are extremely resilient entities capable of withstanding adverse environmental circumstances. Additionally, these spores are resistant to a wide range of disinfectants and antibacterial therapies, such as hydrolytic enzymes, radiation, chemicals, and antibiotics. Because of their ability to combat bacteria through several biological pathways, selenium nanoparticles (SeNPs) have emerged as an effective method for either eliminating or preventing the formation of spore-forming bacteria. This review aims to investigate every potential pathway of entry and mechanism by which SeNPs impact bacterial species that produce spores. Additionally, SeNPs' antibacterial efficacy against several infections is reviewed. To precisely explain the antibacterial mechanism of SeNPs and the various factors that can affect their effectiveness, more research is necessary.

Metagenomics reveals differences in spore-forming bacterial diversity in raw milk in different regions and seasons in China

The spore-forming bacteria in the dairy industry are notable for their spores resilience and capacity to survive heating processes, allowing them to germinate and enter the vegetative stage, potentially leading to spoilage of the milk. Additionally, these spores can form biofilms, becoming a persistent source of contamination in processing environments. In this study, we collected a total of 165 raw milk from six different parts in China in spring, summer, autumn, and winter, respectively. Metagenomics sequencing method was used to explore and compare the differences in spore-forming bacterial composition and diversity in raw milk samples. Among these samples, four genera and 207 species of spore-forming bacteria were identified, with the genus Bacillus and the species Paenibacillus darwinianus dominant. Seasonal variations had a greater impact on the composition and abundance of spore-forming bacteria in raw milk than regional differences. Notable, raw milk samples collected during the spring and summer exhibited a higher number of unique spore-forming bacterial species compared to those collected in other seasons. Moreover, different regions and seasons have their own dominant bacteria. Metabolism of cofactors and vitamins, energy metabolism, carbohydrate metabolism, and amino acid metabolism were the main metabolic pathways. Hence, specific strategies need to be adopted to prevent and control spore-forming bacteria in raw milk in different regions and seasons.

Heat stress has divergent effects on the milk microbiota of Holstein and Brown Swiss cows

Heat stress (HS) is one of the pivotal causes of economic losses in dairy industries and affects welfare and performance, but its effect on milk microbiota remains elusive. It is also unclear if and how different breeds may cope with HS in sustaining productive performance. The objectives of this study were to compare (1) the performance of 2 dairy breeds, namely Holstein and Brown Swiss, subjected to HS and (2) the different effects of HS on the milk microbiota of the 2 breeds in thermal comfort conditions and HS. The study was carried out on 36 dairy cows, 18 per breed. The HS was induced by switching off the cooling system during a natural heat wave for 4 d. In addition to the temperature-humidity index, animal stress was confirmed by measuring respiratory frequency and rectal temperature twice daily at 0400 h and 1500 h. The HS affected the 2 breeds differently. The rectal temperature increased with HS in both breeds. Milk yield recording and sampling were performed during the morning milking of d 1 (at 0400 h) and afternoon milking of d 4 (at 1700 h). Productive parameters were also different: milk yield, FCM, ECM, protein and casein content, and renneting parameters were decreased in Holstein cows but remained unaffected in Brown Swiss cows. The HS also modified the milk microbiota of the 2 breeds differently. During HS, the Brown Swiss cows had milk microbiota that was richer (α diversity) than that of the Holstein cows. Comparing the time points before and during HS within breeds showed that Brown Swiss cow milk microbiota was less affected by HS than Holstein cow milk microbiota. Under the same thermal comfort condition, milk microbiota did not discriminate between Brown Swiss and Holstein. Consistently with α and β diversity, the number of operational taxonomic units (OTU) at the genus level that changed their abundance during HS was higher in Holstein (74 OTU) than in Brown Swiss (only 20 OTU). The most significant changes in abundance affected Acinetobacter, Chryseobacterium, Cutibacterium, Enterococcus, Lactococcus, Prevotella-9, Serratia, and Streptococcus. In conclusion, the present report confirms and extends previous studies by demonstrating that Brown Swiss cows regulate their body temperature better than the Holstein breed. The relative thermal tolerance to HS compared with Holstein cows is also confirmed by changes in milk uncultured microbiota, which were more evident in Holstein cows than in Brown Swiss cows.

Microbial diversity analysis and isolation of thermoresistant lactic acid bacteria in pasteurized milk

Pasteurization is a common method for dairy products, typically heating at 72 °C for 15 s or 63 °C for 30 min. The 17 samples of commercial pasteurized milk were divided into three groups according to the shelf life: group A (1-5 days), group B (6-10 days) and group C (11-15 days), and the diversity composition of microbial communities in the samples was analyzed. Among all groups, Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phyla. The lactic acid bacteria (LAB) were mostly Streptococcus, Weissella and Lactobacillus, and there were high proportions of Streptococcus thermophilus in group A, Weissella paramesenteroides in group B, and Lactobacillus plantarum in group C. Furthermore, a strain of Enterococcus faecium SFM2 was isolated from the A2 sample, which showed better temperature tolerance compared to the E. faecium SFM1 of oral origin. After treatment at 50 °C for 2 h, the survival rates of E. faecium SFM1 and SFM2 were 28.20 ± 0.04% and 82.58 ± 0.01%, respectively. This study investigated the diversity of microorganisms in pasteurized milk, providing effective information for analyzing the potential microbiota of commercial pasteurized milk. Meanwhile, it provided new ideas for expanding the resource pool of thermoresistant LAB.

Efficacy of Copper Ion Treatment on Bacteria and Antibiotic Residues Contained in Bovine Waste Milk

Background/Objectives: Waste milk harbors many bacteria and antibiotic residues. Calves fed with untreated waste milk have a higher incidence of scours and an increased risk of developing antimicrobial-resistant bacteria. This study aimed to evaluate the efficacy of treatment with copper ions on bacteria and antibiotics contained in bovine waste milk. Methods: Waste milk samples were collected from a dairy farm for seven weeks and were subjected to treatment with copper ions. Total bacterial counts, coliforms, Streptococcus, and Staphylococcus were assessed before and after treatment. Additionally, metagenomic analysis was performed to determine microbial diversity. Results: Before treatment, the total bacterial count average was 4.0 × 106 CFU/mL, 1.7 × 104 CFU/mL for coliforms, 2.6 × 106 CFU/mL for Streptococcus, and 5.4 × 102 CFU/mL for Staphylococcus Copper treatment significantly reduced bacterial counts within 15 min. Total bacteria decreased from 4.0 × 106 CFU/mL to 1.1 × 102 CFU/mL after 30 min; meanwhile, other groups were not detected. The most abundant groups were Lactococcus (29.94%), Pseudomonas (28.89%), and Enterobacteriaceae (21.19%). Beta-lactams were detected in five-sevenths samples, and in one sample they were detected before and at 15 min of treatment but not after 30 min. Conclusions: The effect of treatment with copper ions on the different bacterial groups was significantly effective but showed limited effect on the detection of antibiotics.

The Microbiological Quality of Raw Ovine Milk in the Banat Region of Romania with a Focus on Escherichia coli and Its Pathogenic Potential and Antimicrobial Resistance

This study investigated the bacteriological quality of raw ovine milk produced by farms located in the Banat region of Romania. Additionally, the pathogenic potential and antimicrobial resistance of the isolated Escherichia coli strains were evaluated. A total of 95.8% (69/72) of the screened bulk tank milk samples, collected at the farm level immediately after milking, demonstrated appropriate total aerobic mesophilic bacteria (TMB) counts, varying from 3.32 to 6.09 log10 CFU/mL. However, 4.2% (3/72) of the samples were above the regulatory limit of 6.18 log10 CFU/mL. E. coli was identified in 66.6% of the examined samples, and from the total number (n = 48) of isolates, 18.8% harbored the stx2 gene, highlighting pathogenic potential. Antimicrobial susceptibility testing with the Vitek2 system of the isolated E. coli strains revealed resistance against ampicillin (45.8%), gentamicin (20.8%), ticarcillin-clavulanic acid (18.8%), cephalexin (18.8%), amoxicillin-clavulanic acid (8.3%), and trimethoprim-sulfamethoxazole (2.1%). Additionally, 64.6% of the strains showed intermediate resistance against amoxicillin-clavulanic acid, while no resistance was recorded against imipenem. Five (18.5%) strains were multidrug-resistant. This study's results underline hygienic sanitary deficiencies during the milking phase and indicate that raw ovine milk can be contaminated with pathogenic and multidrug-resistant E. coli strains, highlighting a potential risk to public health. Further studies are encouraged to better understand the risk posed to the consumer via the consumption of ovine milk and derived products.

Insights into the microbiota of raw milk from seven breeds animals distributing in Xinjiang China

Owing to its high nutritional content, raw milk contains a rich microbiota. Thus, to study microorganisms present in raw milk available in Xinjiang China, 142 raw milk samples from seven animal breeds (cow, sheep, goat, donkey, horse, camel, and yak) and four regions (Hami, Tarbagatay, Kashgar, and Ili) were analyzed by high-throughput DNA sequencing. These microorganisms were characterized by 10 dominant phyla. Proteobacteria (68.33%) was the major phylum, followed by Firmicutes (18.80%) and Thermi (3.16%). Horse milk contained more Bacteroidetes, sheep milk contained more Gammaproteobacteria, and donkey milk contained more unclassified sequences. Camel and donkey milk contained the highest and lowest bacterial diversity compared with that contained by the remaining milk samples, respectively. Additionally, spoilage microorganisms, including Chryseobacterium, Propionibacterium, and Flavobacterium, and pathogenic bacteria, including Ochrobactrum anthropi and Sphingomonas, were more prevalent in horse and yak milk, whereas probiotic lactic acid bacteria (LAB), such as Leuconostoc, Lactococcus, or Lactobacillus, were more prevalent in goat, donkey, and camel milk. Furthermore, Moraxella was abundantly present in goat, camel, and yak milk, Acinetobacter was more abundant in camel milk, and Pseudomonas was relatively abundant in sheep and donkey milk. Overall, specific harmful microorganisms and probiotic lactic acid bacteria were found in the raw milk samples obtained from different animals, which provided a basis for preventing and controlling the growth of harmful bacteria, as well as investigating probiotic resources in raw milk.

Exploring resource competition by protective lactic acid bacteria cultures to control Salmonella in food: an Achilles' heel to target?

Salmonella is a pathogenic bacterium, being the second most commonly reported foodborne pathogen in Europe, due to the ability of its different serovars to contaminate a wide variety of foods, with differences among countries. Common chemical or physical control methods are not always effective, eco-sustainable and adapted to the diversity of Salmonella serovars. Thus, great attention is given to developing complementary or alternative control methods that can be tailor made for specific situations. One of these methods is biopreservation using lactic acid bacteria, with most studies on their antagonistic activity focused on the production of antimicrobials. Less attention has been given to competition by exploitation of nutrients. This review is thus set to investigate and highlight limiting resources that may be involved in the competitive exclusion of Salmonella in food matrices. To do this the needs for nutrients and microelements and the known homeostatic pathways of Salmonella and lactic acid bacteria are examined. Finally, milk, intended for the manufacture of fermented dairy foods, is pointed out as an example of food to investigate the bioavailable macronutrients, metals and vitamins that could be involved in competition between the different species and serovars, and could be exploited for targeted biopreservation.

Beyond Harmful: Exploring Biofilm Formation by Enterococci Isolated from Portuguese Traditional Cheeses

This study investigated the biofilm-forming capabilities of Enterococcus isolates from Portuguese traditional cheeses with protected designation of origin (PDO) status, specifically Azeitão and Nisa. Given the absence of added starter cultures in the cheesemaking process, the characteristics of these cheeses are intrinsically linked to the autochthonous microbiota present in the raw materials and the production environment. Our findings demonstrate that all isolates possess biofilm production abilities, which are crucial for their colonization and persistence within cheese factories, thereby maintaining factory-specific microbial heritage. Through an integrated analysis utilizing principal component analysis (PCA), a direct correlation between biofilm formation and cell viability was established. Notably, these results underscore the adaptive capacity of enterococci to survive environmental fluctuations and their role in the unique characteristics of Portuguese traditional cheeses. Overall, this research enhances our understanding of the microbial dynamics in cheese production and highlights the importance of enterococci in preserving cheese quality and heritage.

Recent Development in Detection and Control of Psychrotrophic Bacteria in Dairy Production: Ensuring Milk Quality

Milk is an ideal environment for the growth of microorganisms, especially psychrotrophic bacteria, which can survive under cold conditions and produce heat-resistant enzymes. Psychrotrophic bacteria create the great problem of spoiling milk quality and safety. Several ways that milk might get contaminated by psychrotrophic bacteria include animal health, cowshed hygiene, water quality, feeding strategy, as well as milk collection, processing, etc. Maintaining the quality of raw milk is critically essential in dairy processing, and the dairy sector is still affected by the premature milk deterioration of market-processed products. This review focused on the recent detection and control strategies of psychrotrophic bacteria and emphasizes the significance of advanced sensing methods for early detection. It highlights the ongoing challenges in the dairy industry caused by these microorganisms and discusses future perspectives in enhancing milk quality through innovative rapid detection methods and stringent processing controls. This review advocates for a shift towards more sophisticated on-farm detection technologies and improved control practices to prevent spoilage and economic losses in the dairy sector.

Onopordum platylepis (Murb.) Murb. as a novel source of thistle rennet: First application to the manufacture of traditional Italian raw ewe's milk cheese

In this study, for the very first time, aqueous extracts obtained from flowers of spontaneously grown or cultivated Onopordum platylepis (Murb.) Murb. thistles were used as coagulating agents for the pilot-scale manufacture of Caciofiore, a traditional Italian raw ewe's milk cheese. Cheese prototypes were compared to control cheeses curdled with a commercial thistle rennet obtained from flowers of Cynara cardunculus L. After 45 days of ripening under controlled conditions, both the experimental and control cheese prototypes were analyzed for: cheese yield, physico-chemical (pH, titratable acidity, aw, proximate composition), morpho-textural (color and texture), and microbiological parameters (viable cell counts and species composition assessed by Illumina sequencing), as well as volatile profile by SPME-GC-MS. Slight variations in titratable acidity, color, and texture were observed among samples. Based on the results overall collected, neither the yield nor the proximate composition was apparently affected by the type of thistle coagulant. However, the experimental cheese prototypes curdled with extracts from flowers of both spontaneous or cultivated thistles showed 10 % higher values of water-soluble nitrogen compared to the control prototypes. On the other hand, these latter showed slightly higher loads of presumptive lactococci, thermophilic cocci, coliforms, and eumycetes, but lower counts of Escherichia coli. No statistically significant differences were revealed by the metataxonomic analysis of the bacterial and fungal biota. Though most volatile organic compounds (VOCs) were consistent among the prototypes, significant variability was observed in the abundance of some key aroma compounds, such as butanoic, hexanoic, and octanoic acids, ethanol, propan-2-ol, isobutyl acetate, 2-methyl butanoic acid, and 3-methyl butanal. However, further investigations are required to attribute these differences to either the type of coagulant or the metabolic activity of the microorganisms occurring in the analyzed cheese samples. The results overall collected support the potential exploitation of O. platylepis as a novel source of thistle coagulant to produce ewe's milk cheeses.

Dynamic microbial and metabolic changes during Apulian Caciocavallo cheesemaking and ripening produced according to a standardized protocol

The microbiota of a cheese play a critical role in influencing its sensory and physicochemical properties. In this study, traditional Apulian Caciocavallo cheeses coming from 4 different dairies in the same area and produced following standardized procedures were examined, as well as the different bulk milks and natural whey starter (NWS) cultures used. Moreover, considering the cheese wheels as the blocks of Caciocavallo cheeses as whole, these were characterized at different layers (i.e., core, under-rind, and rind) of the block using a multi-omics approach. In addition to physical-chemical characterization, culturomics, quantitative PCR, metagenomics, and metabolomics analysis were carried out after salting and throughout the ripening time (2 mo) to investigate major shifts in the succession of the microbiota and flavor development. Culture-dependent and 16S rRNA metataxonomics results clearly clustered samples based on microbiota biodiversity related to the production dairy plant as a result of the use of different NWS or the intrinsic conditions of each production site. At the beginning of the ripening, cheeses were dominated by Lactobacillus, and in 2 dairies (Art and SdC), Streptococcus genera were associated with the NWS. The analysis allowed us to show that although the diversity of identified genera did not change significantly between the rind, under-rind, and core fractions of the same samples, there was an evolution in the relative abundance and absolute quantification, modifying and differentiating profiles during ripening. The real-time PCR, also known as quantitative or qPCR, mainly differentiated the temporal adaptation of those species originating from bulk milks and those provided by NWS. The primary starters detected in NWS and cheeses contributed to the high relative concentration of 1-butanol, 2-butanol, 2-heptanol, 2-butanone, acetoin, delta-dodecalactone, hexanoic acid ethyl ester, octanoic acid ethyl ester, and volatile free fatty acids during ripening, whereas cheeses displaying low abundances of Streptococcus and Lactococcus (dairy Del) had a lower total concentration of acetoin compared with Art and SdC. However, the subdominant strains and nonstarter lactic acid bacteria present in cheeses are responsible for the production of secondary metabolites belonging to the chemical classes of ketones, alcohols, and organic acids, reaffirming the importance and relevance of autochthonous strains of each dairy plant although only considering a delimited production area.

Tracking the microbial communities from the farm to the processing facility of a washed-rind cheese operation

Milk residue and the accompanying biofilm accumulation in milking systems can compromise the microbial quality of milk and the downstream processes of cheese production. Over a six-month study, the microbial ecosystems of milk (n = 24), tap water (n = 24) and environmental swabs (n = 384) were cultured by plating decimal dilutions to obtain viable counts of total aerobic mesophilic lactose-utilizing bacteria (lactose-M17), lactic acid bacteria (MRS), yeasts and molds (Yeast, Glucose, Chloramphenicol (YGC) medium). Viable aerobic lactose-M17 plate counts of milk remained well below 4.7 log CFU/ml over five of the months, except for 1 week in November where milk at the facility exceeded 5 log CFU/ml. Swab samples of the farm milking equipment showed consistent viable counts after sanitation, while the bulk tank swabs contained the lowest counts. Viable counts from swabs of the facility were generally below the detection limit in the majority of samples with occasional residual contamination on some food contact surfaces. Extracted DNA was amplified using primers targeting the V3-V4 region of the 16S rRNA gene, and the amplicons were sequenced by MiSeq to determine the shared microbiota between the farm and the processing facility (8 genera). Culture independent analysis of bacterial taxa in milk, water and residual contamination after sanitation with swab samples revealed the shared and distinct microbiota between the sample types of both facilities. Amplicon sequence variants (ASVs) of the V3-V4 region of the 16S rRNA gene revealed that the microbiota of milk samples had lower diversity than water or environmental swabs (279 ASVs compared to 3,444 in water and 8,747 in environmental swabs). Brevibacterium and Yaniella (both Actinomycetota) were observed in all sampling types. Further studies will include whole genome sequencing of Brevibacterium spp. isolates to determine their functionality and diversity within the system.

Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods

Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. The farms were divided into two groups based on the milking method: mechanical milking (MM, n = 6) and hand milking (HM, n = 9). Somatic cell counts, bacterial cell counts and nutrients of the raw buffalo milk samples were analyzed. The comparison of raw buffalo milk samples was analyzed using metagenomic sequencing to detect any differences between the two groups. There was no significant difference in the basic nutritional compositions and somatic cell count of raw buffalo milk between the two milking methods. However, the HM samples had significantly higher bacterial counts and diversity compared to the MM samples. The results showed that Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Pseudomonas spp. were the major microbes present in canned raw buffalo milk. However, the differences between the two milking methods were the relative abundance of core microorganisms and their potential mastitis-causing genera, including the content of antibiotic-resistance genes and virulence genes. Our study revealed that Staphylococcus spp. and Streptococcus spp. were significantly more abundant in the MM group, while Klebsiella spp. was more abundant in the HM group. Regardless of the milking method used, Pseudomonas spp. was identified as the primary genus contributing to antibiotic resistance and virulence genes in canned raw buffalo milk. These findings affirm that there are differences in the microbial and genomic levels in canned raw milk. To prove the functional roles of the discovered genes and how these genes affect milk quality, further research and experimental validation are necessary.

Enterotoxigenic Staphylococcus aureus in Brazilian artisanal cheeses: Occurrence, counts, phenotypic and genotypic profiles

The present study aimed to assess the occurrence and counts of Staphylococcus aureus in Brazilian artisanal cheeses (BAC) produced in five regions of Brazil: Coalho and Manteiga (Northeast region); Colonial and Serrano (South); Caipira (Central-West); Marajó (North); and Minas Artisanal cheeses, from Araxá, Campos das Vertentes, Cerrado, Serro and Canastra microregions (Southeast). The resistance to chlorine-based sanitizers, ability to attach to stainless steel surfaces, and antibiogram profile of a large set of S. aureus strains (n = 585) were assessed. Further, a total of 42 isolates were evaluated for the presence of enterotoxigenic genes (sea, seb, sec, sed, see, seg, sei, sej, and ser) and submitted to typing using pulsed-field gel electrophoresis (PFGE). BAC presented high counts of S. aureus (3.4-6.4 log CFU/g), varying from 25 to 62.5%. From the S. aureus strains (n = 585) assessed, 16% could resist 200 ppm of sodium hypochlorite, whereas 87.6% produced strong ability to attach to stainless steel surfaces, corroborating with S. aureus ability to persist and spread in the environment. Furthermore, the relatively high frequency (80.5%) of multidrug-resistant S. aureus and the presence of enterotoxin genes in 92.6% of the strains is of utmost attention. It reveals the lurking threat of SFP that can survive when conditions are favorable. The presence of enterotoxigenic and antimicrobial-resistant strains of S. aureus in cheese constitutes a potential risk to public health. This result calls for better control of cheese contamination sources, and taking hygienic measures is necessary for food safety. More attention should be paid to animal welfare and hygiene practices in some dairy farms during manufacturing to enhance the microbiological quality of traditional cheese products.

Two-year investigation of spore-formers through the production chain at two cheese plants in Norway

Spore-forming bacteria are the most complex group of microbes to eliminate from the dairy production line due to their ability to withstand heat treatment usually used in dairy processing. These ubiquitous microorganisms have ample opportunity for multiple points of entry into the milk chain, creating issues for food quality and safety. Certain spore-formers, namely bacilli and clostridia, are more problematic to the dairy industry due to their possible pathogenicity, growth, and production of metabolites and spoilage enzymes. This research investigated the spore-forming population from raw milk reception at two Norwegian dairy plants through the cheesemaking stages until ripening. Samples were collected over two years and examined by amplicon sequencing in a culture independent manner and after an anaerobic spore-former enrichment step. In addition, a total of 608 isolates from the enriched samples were identified at the genus or species level using MALDI-TOF analysis. Most spore-forming isolates belong to the genera Bacillus or Clostridium, with the latter dominating the enriched MPN tubes of raw milk and bactofugate. Results showed a great variation among the clostridia and bacilli detected in the enriched MPN tubes. However, B. licheniformis and C. tyrobutyricum were identified in all sample types from both plants throughout the 2-year study. In conclusion, our results shed light on the fate of different spore-formers at different processing stages in the cheese production chain, which could facilitate targeted actions to reduce quality problems.

Bacillus cereus CwpFM induces colonic tissue damage and inflammatory responses through oxidative stress and the NLRP3/NF-κB pathway

Bacillus cereus (B. cereus) from cow milk poses a threat to public health, causing food poisoning and gastrointestinal disorders in humans. We identified CwpFM, an enterotoxin from B. cereus, caused oxidative stress and inflammatory responses in mouse colon and colonic epithelial cells. Colon proteomics revealed that CwpFM elevated proteins associated with inflammation and oxidative stress. Notably, CwpFM induced activation of the NLRP3/NF-κB signaling, but suppressed antioxidant NFE2L2/HO-1 expression in the intestine and epithelial cells. Consistently, CwpFM exposure led to cytotoxicity and ROS accumulation in Caco-2 cells in a dose-dependent manner. Further, NAC (ROS inhibitor) treatment abolished NLRP3/NF-κB activation due to CwpFM. Moreover, overexpression of Nfe2l2 or activation of NFE2L2 by NK-252 reduced ROS production and inhibited activation of the NLRP3/NF-κB pathway. Inhibition of NF-κB by ADPC and/or suppression of NLRP3 by MCC950 attenuated CwpFM-induced inflammatory responses in Caco-2 cells. Collectively, CwpFM induced oxidative stress and NLRP3/NF-κB activation by inhibiting the NFE2L2/HO-1 signaling and ROS accumulation, leading to the development of intestinal inflammation. Our data elucidate the role of oxidative stress and innate immunity in CwpFM enterotoxicity and contribute to developing diagnostic and therapeutic products for B. cereus-related food safety issues.

Phenotypic and genotypic characterization of antimicrobial resistances reveals the effect of the production chain in reducing resistant lactic acid bacteria in an artisanal raw ewe milk PDO cheese

Antimicrobial resistance (AMR) is a significant public health threat, with the food production chain, and, specifically, fermented products, as a potential vehicle for dissemination. However, information about dairy products, especially raw ewe milk cheeses, is limited. The present study analysed, for the first time, the occurrence of AMRs related to lactic acid bacteria (LAB) along a raw ewe milk cheese production chain for the most common antimicrobial agents used on farms (dihydrostreptomycin, benzylpenicillin, amoxicillin and polymyxin B). More than 200 LAB isolates were obtained and identified by Sanger sequencing (V1-V3 16S rRNA regions); these isolates included 8 LAB genera and 21 species. Significant differences in LAB composition were observed throughout the production chain (P ≤ 0.001), with Enterococcus (e.g., E. hirae and E. faecalis) and Bacillus (e.g., B. thuringiensis and B. cereus) predominating in ovine faeces and raw ewe milk, respectively, along with Lactococcus (L. lactis) in whey and fresh cheeses, while Lactobacillus and Lacticaseibacillus species (e.g., Lactobacillus sp. and L. paracasei) prevailed in ripened cheeses. Phenotypically, by broth microdilution, Lactococcus, Enterococcus and Bacillus species presented the greatest resistance rates (on average, 78.2 %, 56.8 % and 53.4 %, respectively), specifically against polymyxin B, and were more susceptible to dihydrostreptomycin. Conversely, Lacticaseibacillus and Lactobacillus were more susceptible to all antimicrobials tested (31.4 % and 39.1 %, respectively). Thus, resistance patterns and multidrug resistance were reduced along the production chain (P ≤ 0.05). Genotypically, through HT-qPCR, 31 antimicrobial resistance genes (ARGs) and 6 mobile genetic elements (MGEs) were detected, predominating Str, StrB and aadA-01, related to aminoglycoside resistance, and the transposons tnpA-02 and tnpA-01. In general, a significant reduction in ARGs and MGEs abundances was also observed throughout the production chain (P ≤ 0.001). The current findings indicate that LAB dynamics throughout the raw ewe milk cheese production chain facilitated a reduction in AMRs, which has not been reported to date.

Effect of Essential Oils and Dried Herbs on the Shelf Life of Fresh Goat Lump Cheese

In recent years, the use of natural preservatives in food products has gained significant attention due to their potential health benefits and effectiveness. A standardized microbiological analysis was conducted on Slovak farm-produced lump goat cheese samples to determine the antibacterial activity of dry herbs and essential oils added to vacuum-packed goat cheese. We employed five dried herbs and five essential oils derived from the same plants. The microbiological quality of 145 fresh and vacuum-packed goat cheese samples was assessed. The number of coliform bacteria, total viable count, lactic acid bacteria, and microscopic filamentous fungi were examined in raw cheese samples stored for 12 days at 4 °C. All cheese samples were vacuum-packed (control samples were packed without vacuum). This study evaluated the potential benefits of using essential oils and dried herbs from thyme (Thymus serpyllum L.), black pepper (Piper nigrum L.), clove (Eugenia caryophyllus Thunb.), mint (Mentha × piperita L.), and basil (Ocimum basilicum L.) as preservatives. The essential oils were obtained from Hanus Ltd., Nitra, Slovakia, and were applied at a concentration of 2%. The dried herbs were obtained from Popradský čaj (Poprad, Slovakia) and Mäspoma Ltd. (Zvolen, Slovakia). The results showed that all microorganism groups were significantly reduced in cheese samples following the application of essential oils throughout the entire storage period. During the preservation of cheese samples in polyethylene bags used for vacuum packing food, Lactococcus garvieae, L. lactis, Enterobacter cloacae, and Serratia liquefaciens were the most frequently isolated microbiota. Essential oils and dried herbs demonstrated antimicrobial potential during the storage of vacuum-packed goat cheese.

Identification and Characterization of Microorganisms Isolated from Non-compliant and/or Atypical Dairy Products in Canada

Despite good manufacturing practices and rigorous cleaning and sanitizing procedures established in dairy processing plants, microbiological contamination remains the main cause of products being non-compliant and/or atypical and hence not fit for human consumption. The objective of this study was to isolate, identify and characterize bacteria, yeasts and molds associated with substandard dairy products in Canada and to create a collection of reference isolates. In addition to conventional microbiological characterization, each isolate was tested for biofilm-forming ability and susceptibility to heat, antimicrobial agents, and common industrial disinfectants. Among the 105 microbial strains isolated from pasteurized milk, cream, and cheese samples, 24 bacterial isolates, belonging mainly to the genus Pseudomonas, were shown to be moderate or strong biofilm producers in 96-well plates and highly resistant to peracetic acid (100 ppm, 5 min contact time) and sodium hypochlorite (70 ppm, 5 min contact time). In addition, 56 bacterial isolates, including Acinetobacter baumannii, Enterobacter bugandensis, Klebsiella pneumoniae and Pseudomonas spp., were found resistant to ampicillin, fosfomycin and/or ceftriaxone, while 14 others, such as Bacillus spp. and Macrococcus spp., withstood a heat treatment equivalent to low-temperature long-time pasteurization (63°C for 30 min). This descriptive study provides new information on potential problematic microorganisms in dairies and will guide the development of novel control strategies intended to prevent and reduce microbiological contamination and the associated economic losses.

The impact of kit, environment, and sampling contamination on the observed microbiome of bovine milk

In low-microbial biomass samples such as bovine milk, contaminants can outnumber endogenous bacteria. Because of this, milk microbiome research suffers from a critical knowledge gap, namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelia and stripped and cisternal milk and used numerous negative controls, including air and sampling controls and extraction and library preparation blanks, to identify the potential sources of contamination. Two algorithms were used to mathematically remove contaminants and track the potential movement of microbes among samples. Results suggest that the majority (i.e., >75%) of sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. Contaminants in milk samples were primarily sourced from DNA extraction kits and the internal and external skin of the teat, while teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse, and compositionally distinct bacterial profile compared with epithelial samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in milk sample sequences, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during sample collection and processing workflows.IMPORTANCEObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.

One-Year Monitoring of Prevalence and Diversity of Dairy Propionic Acid Bacteria in Raw Milk by Means of Culture-Dependent and Culture-Independent Methods

Even low levels of dairy propionic acid bacteria (dPAB) can cause cheese defects, resulting in severe economic losses for the producers of selected raw milk cheeses. Therefore, routine quality control of raw cheese milk for dPAB contamination is essential if propionic acid fermentation is undesired. Although knowledge of dPAB contamination of raw milk is important to understand cheese spoilage, long-term dPAB screening data are outdated, and studies taking into account different farm management parameters and their potential influence on dPAB levels are scarce. This study aims to provide insight into the dPAB levels of raw milk over time, to identify farm management factors that potentially influence dPAB levels, and to compare a cultural yeast extract lactate agar (YELA) and lithium glycerol agar (LGA) and a culture-independent method (qPCR) for dPAB quantification with respect to their applicability in routine quality control for the dairy industry. For this purpose, bulk tank milk from 25 dairy farms was screened for dPAB contamination over a one-year period. We were able to identify significant differences in the dPAB contamination levels in raw milk depending on selected farm-specific factors and observed relationships between the different types of milking systems and dPAB contamination levels in raw milk. When dPAB were quantified by cultivation on YELA, strong overgrowth of commensal microbiota impeded counting. Therefore, we conclude that quantification on LGA or by qPCR is preferable. Both methods, colony counting on LGA as well as quantification of dPAB using qPCR, have advantages for the application in (routine) quality control of raw milk, one being low-tech and inexpensive, the other being fast and highly specific, but the detection of (low level) dPAB contamination in raw milk remains a challenge.

Deciphering microbial communities of three Savoyard raw milk cheeses along ripening and regarding the cheese process

Different Savoyard cheeses are granted with PDO (Protected Designation or Origin) and PGI (Protected Geographical Indication) which guarantees consumers compliance with strict specifications. The use of raw milk is known to be crucial for specific flavor development. To unravel the factors influencing microbial ecosystems across cheese making steps, according to the seasonality (winter and summer) and the mode of production (farmhouse and dairy factory ones), gene targeting on bacteria and fungus was used to have a full picture of 3 cheese making technologies, from the raw milk to the end of the ripening. Our results revealed that Savoyard raw milks are a plenteous source of biodiversity together with the brines used during the process, that may support the development of specific features for each cheese. It was shown that rinds and curds have very contrasted ecosystem diversity, composition, and evolution. Ripening stage was selective for some bacterial species, whereas fungus were mainly ubiquitous in dairy samples. All ripening stages are impacted by the type of cheese technologies, with a higher impact on bacterial communities, except for fungal rind communities, for which the technology is the more discriminant. The specific microorganism's abundance for each technology allow to see a real bar-code, with more or less differences regarding bacterial or fungal communities. Bacterial structuration is shaped mainly by matrices, differently regarding technologies while the influence of technology is higher for fungi. Production types showed 10 differential bacterial species, farmhouses showed more ripening taxa, while dairy factory products showing more lactic acid bacteria. Meanwhile, seasonality looks to be a minor element for the comprehension of both microbial ecosystems, but the uniqueness of each dairy plant is a key explicative feature, more for bacteria than for fungus communities.

The potential of pulsed electromagnetic field-generated shock waves for reducing microbial load and improving homogenization in raw milk

Milk is a highly nutritious food essential for human consumption. However, traditional thermal processing methods can reduce its nutritional value and cause unwanted changes. The use of shock waves produced by pulsed electromagnetic fields (PEMFs) has been explored as a means to reduce pathogenic microorganisms. The effect of shock wave treatment on microbial load and particle distribution in packaged fresh cow's milk was investigated. Additionally, the impact of shock wave treatment on Salmonella enterica counts in a bacterial suspension of phosphate-buffered saline (PBS) was evaluated, as this bacterium is a significant milkborne pathogen. Treatment with 1000 impulses from an electromagnetic shock wave generator resulted in a 0.7-log reduction in the total bacterial count of milk. In a separate experiment, a 300-impulse shock wave treatment applied to a Salmonella enterica suspension achieved a 3-log reduction in bacterial counts. Furthermore, shock wave treatment resulted in a decrease in milk particle size compared to untreated milk. Notably, the volume of milk used in this study aligns with commercially available packaged products, enhancing the experiment's industrial relevance. The use of PEMF to generate shock waves could provide a novel approach for future studies focused on reducing the microbial load of milk and improving its homogenization.

Alpine grazing management, breed and diet effects on coagulation properties, composition, and microbiota of dairy cow milk by commercial mountain based herds

Cow milk microbiota has received increased attention in recent years, not only because of its importance for human health but also because of its effect on the quality and technological properties of milk. Several studies, therefore, have investigated the effect of various production factors on the microbial composition of milk. However, most of the previous studies considered a limited number of animals from experimental or single farm, which could have biased the results. Therefore, this study aimed to understand the effect of different alpine production systems on the compositional and microbiological quality of milk, considering commercial herds with different feeding intensities and cattle breeds. The results obtained in this work indicated that the month/season of sampling (July for summer or February for winter) more than farm, breed and cow diet exerted significant effects on cow milk parameters and microbiota. In particular, significant differences were observed for urea content in milk between sampling seasons. Differences in milk fat were mainly related to breed specific effects. From a microbiological point of view, statistically significant differences were found in presumptive lactic acid bacteria counts. Based on a culture-independent method, milk obtained in February harbored the highest number of Firmicutes (e.g., Lactobacillus) and the lowest number of Actinobacteria (e.g., Corynebacterium). Moreover, bacterial richness and diversity were higher in July/summer during alpine pasture season indicating a significant effect of pasture feed on the growth of bacterial communities. The results of this study highlighted the effect of month/season mainly related to differences in feeding management (e.g., access to pasture during vegetation period, concentrates supplementation) on composition and microbiota in milk.

Dynamic Interplay between Microbiota Shifts and Differential Metabolites during Dairy Processing and Storage

Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy quality using traditional methods is challenging. In this study, raw milk, pasteurized milk, and ultra-heat-treated (UHT) milk samples were collectively analyzed using metagenomic next-generation sequencing (mNGS), high-throughput liquid chromatography-mass spectrometry (LC-MS), and gas chromatography-mass spectrometry (GC-MS). The results revealed that raw milk and its corresponding heated dairy products exhibited different trends in terms of microbiota shifts and metabolite changes during storage. Via the analysis of differences in microbiota and correlation analysis of the microorganisms present in differential metabolites in refrigerated pasteurized milk, the top three differential microorganisms with increased abundance, Microbacterium (p < 0.01), unclassified Actinomycetia class (p < 0.05), and Micrococcus (p < 0.01), were detected; these were highly correlated with certain metabolites in pasteurized milk (r > 0.8). This indicated that these genera were the main proliferating microorganisms and were the primary genera involved in the metabolism of pasteurized milk during refrigeration-based storage. Microorganisms with decreased abundance were classified into two categories based on correlation analysis with certain metabolites. It was speculated that the heat-resistant enzyme system of a group of microorganisms with high correlation (r > 0.8), such as Pseudomonas and Acinetobacter, was the main factor causing milk spoilage and that the group with lower correlation (r < 0.3) had a lower impact on the storage process of pasteurized dairy products. By comparing the metabolic pathway results based on metagenomic and metabolite annotation, it was proposed that protein degradation may be associated with microbial growth, whereas lipid degradation may be linked to raw milk's initial heat-resistant enzymes. By leveraging the synergy of metagenomics and metabolomics, the interacting factors determining the quality evolution of dairy products were systematically investigated, providing a novel perspective for controlling dairy processing and storage effectively.

Biodiversity and antibiotic resistance profile provide new evidence for a different origin of enterococci in bovine raw milk and feces

Enterococci are widely distributed in dairy sector. They are commensals of the gastrointestinal tract of animals, thus, via fecal contamination, could reach raw milk and dairy products. The aims of this study were: 1) to investigate the enterococcal diversity in cow feces and milk samples and 2) to evaluate the antibiotic resistance (AR) of dairy-related enterococci and their ability to transfer resistance genes. E. faecalis (59.9%), E. faecium (18.6%) and E. lactis (12.4%) were prevalent in milk, while E. faecium (84.2%) and E. hirae (15.0%) were dominant in bovine feces. RAPD-PCR highlighted a high number of Enterococcus biotypes (45 from milk and 37 from feces) and none of the milk strains exhibited genetic profiles similar to those of feces biotypes. A high percentage of enterococci isolated from milk (71%) were identified as multidrug resistant and resistance against streptomycin and tetracycline were widespread among milk strains while enterococci from feces were commonly resistant to linezolid and quinupristin/dalfopristin. Only E. faecalis strains were able to transfer horizontally the tetM gene to Lb. delbrueckii subsp. lactis. Our results indicated that Enterococcus biotypes from milk and bovine feces belong to different community and the ability of these microorganisms to transfer AR genes is strain-dependent.

Comparative study of the bacterial community of organic and conventional cow's milk

Agricultural practises such as conventional and organic farming can potentially affect the microbial communities in milk. In the present study, the bacterial diversity of milk was investigated using high-throughput sequencing on ten organic and ten conventional farms in the Azores, a region where milk production is largely based on year-round grazing systems. The microbiota of milk from both production systems was dominated by Bacillota, Pseudomonadota, Actinomycetota and Bacteroidota. The organic milk showed greater heterogeneity between farms, as reflected in the dispersion of diversity indices and the large variation in the relative abundances of the dominant genera. In contrast, conventionally produced milk showed a high degree of similarity within each season. In the conventional production system, the season also had a strong influence on the bacterial community, but this effect was not observed in the organic milk. The LEfSe analysis identified the genus Iamia as significantly (p < 0.05) more abundant in organic milk, but depending on the season, several other genera were identified that distinguished organic milk from conventionally produced milk. Of these, Bacillus, Iamia and Nocardioides were associated with the soil microbiota in organic farming.

A Fibrin-Thrombin Based In Vitro Perfusion System to Study Flow-Related Prosthetic Heart Valves Thrombosis

Prosthetic heart valve (PHV) replacement has increased the survival rate and quality of life for heart valve-diseased patients. However, PHV thrombosis remains a critical problem associated with these procedures. To better understand the PHV flow-related thrombosis problem, appropriate experimental models need to be developed. In this study, we present an in vitro fibrin clot model that mimics clot accumulation in PHVs under relevant hydrodynamic conditions while allowing real-time imaging. We created 3D-printed mechanical aortic valve models that were inserted into a transparent glass aorta model and connected to a system that simulates human aortic flow pulse and pressures. Thrombin was gradually injected into a circulating fibrinogen solution to induce fibrin clot formation, and clot accumulation was quantified via image analysis. The results of valves positioned in a normal versus a tilted configuration showed that clot accumulation correlated with the local flow features and was mainly present in areas of low shear and high residence time, where recirculating flows are dominant, as supported by computational fluid dynamic simulations. Overall, our work suggests that the developed method may provide data on flow-related clot accumulation in PHVs and may contribute to exploring new approaches and valve designs to reduce valve thrombosis.

Prevalence, toxin-genotype distribution, and transmission of Clostridium perfringens from the breeding and milking process of dairy farms

This study aimed to elucidate the distribution, transmission, and cross-contamination of Clostridium perfringens during the breeding and milking process from dairy farms. The prevalence of 22.3% (301/1351) yielded 494 C. perfringens isolates; all isolates were type A, except for one type D, and 69.8% (345/494) of the isolates carried atyp. cpb2 and only 0.6% (3/494) of the isolates carried cons. cpb2. C. perfringens detected throughout the whole process but without type F. 150 isolates were classified into 94 pulsed-field gel electrophoresis (PFGE) genotypes; among them, six clusters contained 34 PFGE genotypes with 58.0% isolates which revealed epidemic correlation and genetic diversity; four PFGE genotypes (PT57, PT9, PT61, and PT8) were the predominant genotypes. The isolates from different farms demonstrated high homology. Our study confirmed that C. perfringens demonstrated broad cross-contamination from nipples and hides of dairy cattle, followed by personnel and tools and air-introduced raw milk during the milking process. In conclusion, raw milk could serve as a medium for the transmission of C. perfringens, which could result in human food poisoning. Monitoring and controlling several points of cross-contamination during the milking process are essential as is implementing stringent hygiene measures to prevent further spread and reduce the risk of C. perfringens infection.

Evaluating the efficacy of a phage cocktail against Pseudomonas fluorescens group strains in raw milk: microbiological, physical, and chemical analyses

The objective of this study was to investigate the effectiveness of a phage cocktail against Pseudomonas fluorescens group and its effect on the microbial, physical and chemical properties of raw milk during different storage conditions. A phage cocktail consisting of Pseudomonas fluorescens, Pseudomonas tolaasii, and Pseudomonas libanensis phages was prepared. As a result, reductions in fluorescent Pseudomonas counts of up to 3.44 log units for the storage at 4 °C and 2.38 log units for the storage at 25 °C were achieved. Following the phage application, it is found that there was no significant difference in the total mesophilic aerobic bacteria and Enterobacteriaceae counts. However, it was observed that the number of lactic acid bacteria was higher in phage-treated groups. The results also showed that pH values in the phage added groups were lower than the others and the highest titratable acidity was obtained only in the bacteria-inoculated group. As a future perspective, this study suggests that, while keeping the number of target microorganisms under control in the milk with the use of phages during storage, the microbiota and accordingly the quality parameters of the milk can be affected. This work contributes to the development of effective strategies for maintaining the quality and extending the shelf life of milk and dairy products.

Rapid detection of major enterotoxin genes and antibiotic resistance of Staphylococcus aureus isolated from raw milk in the Yazd province, Iran

INTRODUCTION

Raw milk is a nutrient-rich food, but it may harbour harmful bacteria, such as enterotoxigenic Staphylococcus aureus (S. aureus), which can cause staphylococcal food poisoning. Antibiotic resistance of S. aureus in raw milk can increase the risk of such infections, particularly among susceptible individuals.

OBJECTIVE

This study aimed to investigate the prevalence of enterotoxin genes a, d, g, i and j and the antibiotic resistance of S. aureus isolated from raw milk samples.

METHODS

During a 6-month sampling period, 60 raw milk specimens were obtained from diverse locations in Yazd province, Iran. Antibiogram profiling was conducted via the disc diffusion method. In addition, staphylococcal enterotoxin (SE) genes a, d, g, i, and j were detected through real-time PCR analysis.

RESULTS

Bacteriological assays confirmed the presence of S. aureus in 11 samples (18.3%). All isolates demonstrated 100% resistance to penicillin G but exhibited sensitivity to vancomycin, while resistance to other antibiotics ranged from 36.4% to 45.5%. The prevalence of enterotoxin genes in these strains showed variable distribution, with sea being the predominant SE (45.5%), followed by sed (36.4%), seg (18.2), sej and sei (9.1% each).

CONCLUSIONS

This study discovered the presence of multiple enterotoxins in S. aureus strains obtained from raw milk samples. These strains also demonstrated resistance to a variety of antibiotics. Since enterotoxigenic S. aureus is known to cause human food poisoning, monitoring food hygiene practices, especially during raw milk production, is critical.

Bovine milk microbiota: Key players, origins, and potential contributions to early-life gut development

BACKGROUND

Bovine milk is a significant substitute for human breast milk and holds great importance in infant nutrition and health. Apart from essential nutrients, bovine milk also contains bioactive compounds, including a microbiota derived from milk itself rather than external sources of contamination.

AIM OF REVIEW

Recognizing the profound impact of bovine milk microorganisms on future generations, our review focuses on exploring their composition, origins, functions, and applications.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Some of the primary microorganisms found in bovine milk are also present in human milk. These microorganisms are likely transferred to the mammary gland through two pathways: the entero-mammary pathway and the rumen-mammary pathway. We also elucidated potential mechanisms by which milk microbiota contribute to infant intestinal development. The mechanisms include the enhancing of the intestinal microecological niche, promoting the maturation of immune system, strengthening the intestinal epithelial barrier function, and interacting with milk components (e.g., oligosaccharides) via cross-feeding effect. However, given the limited understanding of bovine milk microbiota, further studies are necessary to validate hypotheses regarding their origins and to explore their functions and potential applications in early intestinal development.

Microbiological and Physicochemical Evaluation of Hydroxypropyl Methylcellulose (HPMC) and Propolis Film Coatings for Cheese Preservation

Dairy products are highly susceptible to contamination from microorganisms. This study aimed to evaluate the efficacy of hydroxypropyl methylcellulose (HPMC) and propolis film as protective coatings for cheese. For this, microbiological analyses were carried out over the cheese' ripening period, focusing on total mesophilic bacteria, yeasts and moulds, lactic acid bacteria, total coliforms, Escherichia coli, and Enterobacteriaceae. Physicochemical parameters (pH, water activity, colour, phenolic compounds content) were also evaluated. The statistical analysis (conducted using ANOVA and PERMANOVA) showed a significant interaction term between the HPMC film and propolis (factor 1) and storage days (factor 2) with regard to the dependent variables: microbiological and physicochemical parameters. A high level of microbial contamination was identified at the baseline. However, the propolis films were able to reduce the microbial count. Physicochemical parameters also varied with storage time, with no significant differences found for propolis-containing films. Overall, the addition of propolis to the film influenced the cheeses' colour and the quantification of phenolic compounds. Regarding phenolic compounds, their loss was verified during storage, and was more pronounced in films with a higher percentage of propolis. The study also showed that, of the three groups of phenolic compounds (hydroxybenzoic acids, hydroxycinnamic acids, and flavonoids), hydroxycinnamic acids showed the most significant losses. Overall, this study reveals the potential of using HPMC/propolis films as a coating for cheese in terms of microbiological control and the preservation of physicochemical properties.

Comparison of canine colostrum and milk using a multi-omics approach

BACKGROUND

A mother's milk is considered the gold standard of nutrition in neonates and is a source of cytokines, immunoglobulins, growth factors, and other important components, yet little is known about the components of canine milk, specifically colostrum, and the knowledge related to its microbial and metabolic profiles is particularly underwhelming. In this study, we characterized canine colostrum and milk microbiota and metabolome for several breeds of dogs and examined profile shifts as milk matures in the first 8 days post-whelping.

RESULTS

Through untargeted metabolomics, we identified 63 named metabolites that were significantly differentially abundant between days 1 and 8 of lactation. Surprisingly, the microbial compositions of the colostrum and milk, characterized using 16S rRNA gene sequencing, were largely similar, with only two differentiating genera. The shifts observed, mainly increases in several sugars and amino sugars over time and shifts in amino acid metabolites, align with shifts observed in human milk samples and track with puppy development.

CONCLUSION

Like human milk, canine milk composition is dynamic, and shifts are well correlated with developing puppies' needs. Such a study of the metabolic profile of canine milk, and its relation to the microbial community, provides insights into the changing needs of the neonate, as well as the ideal nutrition profile for optimal functionality. This information will add to the existing knowledge base of canine milk composition with the prospect of creating a quality, tailored milk substitute or supplement for puppies.