The complex microbiota of raw milk

Optimization of Preservation Methods Allows Deeper Insights into Changes of Raw Milk Microbiota

The temporal instability of raw milk microbiota drastically affects the reliability of microbiome studies. However, little is known about the microbial integrity in preserved samples. Raw cow milk samples were preserved with azidiol or bronopol and stored at 4 °C, or with dimethyl sulfoxide (DMSO) or a mixture of azidiol and DMSO and stored at −20 °C for up to 30 days. Aliquots of 5-, 10-, and 30-day post-storage were treated with propidium monoazide (PMA), then analyzed by sequencing the 16S rRNA gene V3-V4 and V6-V8 regions. The V6-V8 gave a higher richness and lower diversity than the V3-V4 region. After 5-day storage at 4 °C, the microbiota of unpreserved samples was characterized by a drastic decrease in diversity, and a significant shift in community structure. The treatment with azidiol and DMSO conferred the best community stabilization in preserved raw milk. Interestingly, the azidiol treatment performed as well for up to 10 days, thus appearing as a suitable alternative. However, neither azidiol nor bronopol could minimize fungal proliferation as revealed by PMA-qPCR assays. This study demonstrates the preservative ability of a mixture of azidiol and DMSO and provides deeper insights into the microbial changes occurring during the cold storage of preserved raw milk.

Milk Microbiota: What Are We Exactly Talking About?

The development of powerful sequencing techniques has allowed, albeit with some biases, the identification and inventory of complex microbial communities that inhabit different body sites or body fluids, some of which were previously considered sterile. Notably, milk is now considered to host a complex microbial community with great diversity. Milk microbiota is now well documented in various hosts. Based on the growing literature on this microbial community, we address here the question of what milk microbiota is. We summarize and compare the microbial composition of milk in humans and in ruminants and address the existence of a putative core milk microbiota. We discuss the factors that contribute to shape the milk microbiota or affect its composition, including host and environmental factors as well as methodological factors, such as the sampling and sequencing techniques, which likely introduce distortion in milk microbiota analysis. The roles that milk microbiota are likely to play in the mother and offspring physiology and health are presented together with recent data on the hypothesis of an enteromammary pathway. At last, this fascinating field raises a series of questions, which are listed and commented here and which open new research avenues.

Amplicon sequencing reveals the bacterial diversity in milk, dairy premises and Serra da Canastra artisanal cheeses produced by three different farms

In this work, the amplicon sequencing of the 16 S rRNA gene was employed to investigate the bacterial diversity in ingredients, processing environment, and ripened cheeses collected from three farms producing Serra da Canastra artisanal cheese. The data obtained indicated a remarkable variability in the bacteria consortia of the milk, whey, and environmental samples collected in farms 1, 2, and 3, despite their location in the same city. On the other hand, the starter culture and final product (ripened cheese) presented more constant and similar microbiota no matter the farm. The findings suggest that Streptococcus and Lactococcus have competitive advantages throughout Serra da Canastra cheese-making/ripening, which is crucial for their high relative abundance in the final products. An exploratory assessment based on sequencing data available in the literature showed that the Serra da Canastra cheeses sequences clustered with specific cheese varieties that are also made from raw milk but ripened for very different periods. The findings of this study highlight that despite the variability of milk and whey microbiota among the three farms, the starter culture ("pingo") has strong relevance in shaping the microbiota of the final product.

Campylobacteriosis associated with the consumption of unpasteurised milk: findings from a sentinel surveillance site

Campylobacteriosis is the most common notifiable disease in New Zealand. While the risk of campylobacteriosis has been found to be strongly associated with the consumption of undercooked poultry, other risk factors include rainwater-sourced drinking water, contact with animals and consumption of raw dairy products. Despite this, there has been little investigation of raw milk as a risk factor for campylobacteriosis. Recent increases in demand for untreated or ‘raw’ milk have also raised concerns that this exposure may become a more important source of disease in the future. This study describes the cases of notified campylobacteriosis from a sentinel surveillance site. Previously collected data from notified cases of raw milk-associated campylobacteriosis were examined and compared with campylobacteriosis cases who did not report raw milk consumption. Raw milk campylobacteriosis cases differed from non-raw milk cases on comparison of age and occupation demographics, with raw milk cases more likely to be younger and categorised as children or students for occupation. Raw milk cases were more likely to be associated with outbreaks than non-raw milk cases. Study-suggested motivations for raw milk consumption (health reasons, natural product, produced on farm, inexpensive or to support locals) were not strongly supported by cases. More information about the raw milk consumption habits of New Zealanders would be helpful to better understand the risks of this disease, especially with respect to increased disease risk observed in younger people. Further discussion with raw milk consumers around their motivations may also be useful to find common ground between public health concerns and consumer preferences as efforts continue to manage this ongoing public health issue.

Short communication: Milk microbiota profiling on water buffalo with full-length 16S rRNA using nanopore sequencing

The identification of milk microbial communities in ruminants is relevant for understanding the association between milk microbiota and health status. The most common approach for studying the microbiota is amplifying and sequencing specific hypervariable regions of the 16S rRNA gene using massive sequencing techniques. However, the taxonomic resolution is limited to family and, in some cases, genus level. We aimed to improve taxonomic classification of the water buffalo milk microbiota by amplifying and sequencing the full-length 16S rRNA gene (1,500 bp) using Nanopore sequencing (single-molecule sequencing). When comparing with short-read results, we improved the taxonomic classification, reaching species level. We identified the main microbial agents of subclinical mastitis at the species level that were in accordance with the microbiological culture results. These results confirm the potential of single-molecule sequencing for in-depth analysis of microbial populations in dairy animals.

Microbiological analysis of the Robiola di Roccaverano cheese by means of traditional culturing methods

Robiola di Roccaverano is a Protected Designation of Origin soft cheese made with goat’s milk, produced in Piedmont region (Italy). The peculiarities of this cheese are: i) the use of the raw milk, ii) the addition of a Natural Milk Starter, iii) the application of traditional techniques of production and iv) the localization of the dairies in rural area. All these aspects influence the microbial flora of final product and make interesting its investigation. Samples were collected at different moment of the cheese making process and during the different seasons. In this preliminary study, the safety and the hygiene parameters of the production were evaluated. Lactic acid bacteria, moulds and yeasts involved in cheese-making process were also enumerated. Pathogens were not found in all samples and the counts of coagulase positive staphylococci were within the standard of law. The enumeration of microorganisms of technological interest demonstrated that, nevertheless the artisanal manufacturing process applied, the dairy was able to standardize the final products.

The Beneficial Effect of Farm Milk Consumption on Asthma, Allergies, and Infections: From Meta-Analysis of Evidence to Clinical Trial

The low prevalence of asthma and allergies in farm children has partially been ascribed to the consumption of raw cow's milk. A literature search identified 12 publications on 8 pertinent studies. A meta-analysis corroborated the protective effect of raw milk consumption early in life (<1 to 5 years, according to study) on asthma (odds ratio [OR], 0.58; 95% CI, 0.49-0.69), current wheeze (OR, 0.66; 95% CI, 0.55-0.78), hay fever or allergic rhinitis (OR, 0.68; 95% CI, 0.57-0.82), and atopic sensitization (OR, 0.76; 95% CI, 0.62-0.95). The effect particularly on asthma was observed not only in children raised on farms (OR, 0.62; 95% CI, 0.58-0.82) but also in children living in rural areas but not on a farm (OR, 0.60; 95% CI, 0.48-0.74). This demonstrates that the effect of farm milk consumption is independent of other farm exposures and that children not living on a farm can theoretically profit from this effect. Because of the minimal but real risk of life-threatening infections, however, consumption of raw milk and products thereof is strongly discouraged. Raw farm milk and industrially processed milk differ in many instances including removal of cellular components, manipulation of the fat fraction, and various degrees of heating. Preliminary evidence attributes the effect to heat-labile molecules and components residing in the fat fraction. The Milk Against Respiratory Tract Infections and Asthma (MARTHA) trial is currently testing the protective effect of microbiologically safe, minimally processed cow's milk against standard ultra-heat-treated milk in children from 6 months to 3 years with the primary outcome of an asthma diagnosis until age 5 years. If successful, this approach might provide a simple but effective prevention strategy.

High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses?

Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.

Maternal versus artificial rearing shapes the rumen microbiome having minor long-term physiological implications

Increasing productivity is a key target in ruminant science which requires better understanding of the rumen microbiota. This study investigated how maternal versus artificial rearing shapes the rumen microbiota using 24 sets of triplet lambs. Lambs within each sibling set were randomly assigned to natural rearing on the ewe (NN); ewe colostrum for 24 h followed by artificial milk feeding (NA); and colostrum alternative and artificial milk feeding (AA). Maternal colostrum feeding enhanced VFA production at weaning but not thereafter. At weaning, lambs reared on milk replacer had no rumen protozoa and lower microbial diversity, whereas natural rearing accelerated the rumen microbial development and facilitated the transition to solid diet. Differences in the rumen prokaryotic communities disappear later in life when all lambs were grouped on the same pasture up to 23 weeks of age. However, NN animals retained higher fungal diversity and abundances of Piromyces, Feramyces and Diplodiniinae protozoa as well as higher feed digestibility (+4%) and animal growth (+6.5%) during the grazing period. Nevertheless, no correlations were found between rumen microbiota and productive outcomes. These findings suggest that the early life nutritional intervention determine the initial rumen microbial community, but the persistence of these effects later in life is weak.

Human campylobacteriosis: A public health concern of global importance

Campylobacter species are among the leading cause of bacterial foodborne and waterborne infections. In addition, Campylobacter is one of the major causative agent of bacterial gastrointestinal infections and the rise in the incidence of Campylobacter infections have been reported worldwide. Also, the emergence of some Campylobacter species as one of the main causative agent of diarrhea and the propensity of these bacteria species to resist the actions of antimicrobial agents; position them as a serious threat to the public health. This paper reviews Campylobacter pathogenicity, infections, isolation and diagnosis, their reservoirs, transmission pathways, epidemiology of Campylobacter outbreaks, prevention and treatment option, antibiotics resistance and control of antibiotics use.

Effect of recycled manure solids as bedding on bulk tank milk and implications for cheese microbiological quality

The dairy farm environment influences the raw milk microbiota and consequently affects milk processing. Therefore, it is crucial to investigate farm management practices such as the bedding materials. The aim of this study was to evaluate the effect of recycled manure solids (RMS) as bedding material on bulk tank milk and microbiological implications for cheese quality. Bulk tank samples were collected from 84 dairy farms using RMS or straw bedding. The use of RMS did not influence thermophilic and mesophilic aerobic viable counts from spores. However, straw-milk samples gave higher values for mesophilic anaerobic spore-forming bacteria (0.44 log cfu/mL) than RMS-milk samples (0.17 log cfu/mL). The presence of thermoresistant lactic acid bacteria was not increased in milk from farms using RMS. Nevertheless, taxonomic profiles of thermoresistant bacteria isolated were different between the 2 types of milk. More Enterococcus faecalis and Streptococcus spp. were identified in RMS-milk samples. Thermoresistant enterococci and streptococci could easily end up in cheese. Therefore, milk proteolytic activities of these isolates were tested. Neither Streptococcus spp. nor Enterococcus faecium isolates exhibited proteolytic activities, whereas 53% of E. faecalis showed some. Also, only 1 vancomycin-resistant enterococcus was detected. Survival of selected RMS-milk samples isolates (3 E. faecalis and 1 Streptococcus thermophilus) was evaluated during a model Cheddar cheese manufacture. Although those strains survived well, they did not modify the acidification curve of milk. However, they might cause organoleptic defects during cheese maturing.

Validating DNA Extraction Protocols for Bentonite Clay

Bentonite clay is an integral component of the engineered barrier system of deep geological repositories (DGRs) that are planned for the long-term storage of high-level radioactive waste. Although nucleic acid extraction and analysis can provide powerful qualitative and quantitative data reflecting the presence, abundance, and functional potential of microorganisms within DGR materials, extraction of microbial DNA from bentonite clay is challenging due to the low biomass and adsorption of nucleic acids to the charged clay matrix. In this study, we used quantitative PCR, gel fingerprinting, and high-throughput sequencing of 16S rRNA gene amplicons to assess DNA extraction efficiency from natural MX-80 bentonite and the same material "spiked" with Escherichia coli genomic DNA. Extraction protocols were tested without additives and with casein and phosphate as blocking agents. Although we demonstrate improved DNA recovery by blocking agents at relatively high DNA spiking concentrations, at relatively low spiking concentrations, we detected a high proportion of contaminant nucleic acids from blocking agents that masked sample-specific microbial profile data. Because bacterial genomic DNA associated with casein preparations was insufficiently removed by UV treatment, casein is not recommended as an additive for DNA extractions from low-biomass samples. Instead, we recommend a kit-based extraction protocol for bentonite clay without additional blocking agents, as tested here and validated with multiple MX-80 bentonite samples, ensuring relatively high DNA recoveries with minimal contamination.IMPORTANCE Extraction of microbial DNA from MX-80 bentonite is challenging due to low biomass and adsorption of nucleic acid molecules to the charged clay matrix. Blocking agents improve DNA recovery, but their impact on microbial community profiles from low-biomass samples has not been characterized well. In this study, we evaluated the effect of casein and phosphate as blocking agents for quantitative recovery of nucleic acids from MX-80 bentonite. Our data justify a simplified framework for analyzing microbial community DNA associated with swelling MX-80 bentonite samples within the context of a deep geological repository for used nuclear fuel. This study is among the first to demonstrate successful extraction of DNA from Wyoming MX-80 bentonite.

Microbiota Associated with Dromedary Camel Milk from Algerian Sahara

Despite the fact that camel milk represents a valuable food source, the fungal diversity of raw camel milk has been poorly studied so far. Here, we investigated the fungal and bacterial communities found in dromedary camel milk from Ghardaia, a representative region of Algerian Sahara. The application of both culture-dependent and independent molecular techniques, based on dHPLC analysis and metabarcoding of ITS region, provided a complementary biodiversity assessment of camel milk fungi which was composed of 15 different taxa. Yeast species belonged to Filobasidium, Naganishia, Malassezia, Mrakia, Rhodotorula, and Yarrowia genera; and mold species belonged to Fusarium, Cladosporium, and Penicillium genera. All three techniques revealed that the fungal community was dominated by species belonging to the former genus Cryptococcus (Filobasidium and Naganishia) although none of them was able to encompass the entire fungal diversity alone. In addition, massive parallel 16S rRNA tag sequencing was applied to gain an insight into the diversity of bacterial communities which were dominated by Pseudomonas spp. Our results provide an initial insight about fungal and bacterial population found in dromedary camel milk from Algerian Sahara.

Milk microbiota: Characterization methods and role in cheese production

Milk is a complex body fluid aimed at addressing the nutritional and defensive needs of the mammal's newborns. Harbored microbiota plays a pivotal role throughout the cheesemaking process and contributes to the development of flavor and texture typical of different type of cheeses. Understanding the dairy microbiota dynamics is of paramount importance for controlling the qualitative, sensorial and biosafety features of the dairy products. Although many studies investigated the contribution of single or few microorganisms, still there is some information lacking about microbial communities. The widespread of the omics platforms and bioinformatic tools enable the investigation of the cheese-associated microbial community in both phylogenetical and functional terms, highlighting the effects of the diverse cheesemaking variables. In this review, the most relevant literature is revised to provide an introduction of the milk- and cheese-associated microbiota, along with their structural and functional dynamics in relation to the diverse cheesemaking technologies and influencing variables. Also, we focus our attention on the latest omics technologies adopted in dairy microbiota investigation. Discussion on the key-steps and major drawbacks of each omics discipline is provided along with a collection of results from the latest research studies performed to unravel the fascinating world of the dairy-associated microbiota. SIGNIFICANCE: Understanding the milk- and cheese- associated microbial community is nowadays considered a key factor in the dairy industry, since it allows a comprehensive knowledge on how all phases of the cheesemaking process impact the harbored microflora; thus, predict the consequences in the finished products in terms of texture, organoleptic characteristics, palatability and biosafety. This review, collect the pioneering and milestones works so far performed in the field of dairy microbiota, and provide the basic guidance to whom approaching the cheese microbiota investigation by means of the latest omics technologies. Also, the review emphasizes the benefits and drawbacks of the omics disciplines, and underline how the integration of diverse omics sciences enhance a comprehensive depiction of the cheese microbiota. In turn, a better consciousness of the dairy microbiota might results in the application of improved starter cultures, cheesemaking practices and technologies; supporting a bio-safe and standardized production of cheese, with a strong economic benefit for both large-scale industries and local traditional dairy farms.

Analyses of physicochemical properties, bacterial microbiota, and lactic acid bacteria of fresh camel milk collected in Inner Mongolia

Camel milk has significant economic value and is an important food in the region of Alxa Left Banner of Inner Mongolia. Fifteen fresh camel milk samples were collected from domesticated camels in a pasture of Alxa Left Banner. The physicochemical properties and bacterial diversity of camel milk samples were analyzed. The average values of fat, total protein, nonfat milk solids, acidity, and density were 4.40%, 3.87%, 9.50%, 16.95°T, and 1.02 g/cm³, respectively. The bacterial microbiota of the collected fresh camel milk was investigated using PacBio single-molecule real-time (Pacific Biosciences, Menlo Park, CA) sequencing. The camel milk microbiota was highly diverse and comprised 8,513 operational taxonomic units belonging to 32 phyla, 377 genera, and 652 species. The major phyla included Proteobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, and Actinobacteria. A small number of lactic acid bacteria sequences were detected, representing the species Streptococcus thermophilus, Lactobacillus helveticus, Lactococcus lactis, and Leuconostoc mesenteroides. A total of 72 strains of lactic acid bacteria were isolated and identified from 15 samples, including Lactobacillus paracasei, Enterococcus italicus, Enterococcus durans, Lactococcus lactis ssp. lactis, Weissella confusa, and Enterococcus faecium. These results confirm that fresh camel milk has a high bacterial diversity and is a valuable natural resource for isolation of novel lactic acid bacteria.

Bacterial community composition of biofilms in milking machines of two dairy farms assessed by a combination of culture-dependent and -independent methods

Dairy biofilms as a source of contamination of milk and its products are of great concern in the dairy industry. For a reliable risk assessment, knowledge about the microbial community composition of biofilms in the milking systems of dairy farms must be improved. In this work, swab samples of milking machine biofilms of two dairy farms were investigated by a combination of culture-dependent and -independent methods. Spots in the milking system with enhanced microbial colonization were identified by quantification on selective and non-selective media. In addition, stainless steel coupons were placed into the piping system of a milking machine, removed after several milking intervals, and investigated for colonization by cultivation and culture-independently. Isolates were differentiated and identified by a combination of chemotaxonomical methods and 16S rRNA sequencing. The culture-independent approach involved treatment of the samples with the viability dye propidium monoazide prior to direct DNA-extraction by enzymatic cell lysis and cloning to exclude bias from dead biomass. The milking equipment retainers and the outlet of the milk bulk tank were identified as highly colonized spots on both farms. A high bacterial diversity was detected covering the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Presence of biofilms was demonstrated on several materials including stainless steel and plastic, which are frequently used in milking machines, but also in dairy processing plants. Growth of mainly Gram-positive bacteria with high percentages of the phylum Actinobacteria was detected on the stainless steel coupons after exposition in the milking system for two to three days. Knowledge about the heterogenic microbial load on different parts of the milking machines and the stainless steel coupons will help to identify primary colonizers of the milking system, to assess the risk potential of biofilms for raw milk, to improve sanitation processes and to identify parts of the milking machine, which should be improved by hygienic design.

Faecalibacterium diversity in dairy cow milk

The bacterial species, Faecalibacterium prausnitzii, beneficial to humans and animals and found in mammalian and avian gut, is also occasionally found in dairy cow milk. It is one of the butyrate-producing bacteria of the colon, has anti-inflammatory properties and its abundance in the gut is negatively correlated with obesity in humans. Several strains differing in their functional capability, have been identified. It is important therefore, milk being a potential source of F. prausnitzii as a novel probiotic, to investigate the diversity of this species in bovine milk. Using 16s rRNA gene amplicons we find 292 different dereplicated Faecalibacterium-related amplicons in a herd of 21 dairy cows. The distribution of the 20 most abundant amplicons with >97% identity to a Greengenes OTU varies from cow to cow. Clustering of the 292 pooled sequences from all cows at 99.6% identity finds 4 likely Faecalibacterium phylotypes with >98.5% identity to an F. prausnitzii reference sequence. Sequence alignment and phylogenetic analysis shows these phylotypes are distinct from 34 other species from the Ruminococcaceae family and displaying the sequence clusters as a network illustrates how each cluster is composed of sequences from multiple cows. We conclude there are several phylotypes of Faecalibacterium prausnitzii (the only species so far defined for the genus) in this dairy herd with cows being inoculated with a mixture of several strains from a common source. We conclude that not only can Faecalibacterium be detected in dairy cow milk (as noted by others) but that there exist multiple different strains in the milk of a dairy herd. Therefore milk, as an alternative to faeces, offers the opportunity of discovering new strains with potential probiotic application.

Insights into Psychrotrophic Bacteria in Raw Milk: A Review

HIGHLIGHTS

Levels of psychrotrophic bacteria in raw milk are affected by to habitats and farm hygiene. Biofilms formed by psychrotrophic bacteria are persistent sources of contamination. Heat-stable enzymes produced by psychrotrophic bacteria compromise product quality. Various strategies are available for controlling dairy spoilage caused by psychrotrophic bacteria.

Bacterial diversity and metabolite profiles of curd prepared by natural fermentation of raw milk and back sloping of boiled milk

Preparation of curd vary worldwide due to which its taste, texture and impact on human health also differ. In Assam, curd prepared from raw milk (RMC) is preferred over curd prepared from boiled milk (BMC), a tradition believed to have originated from the Mongoloid customs. Microbial diversity of raw milk (RM), boiled milk (BM), RMC and BMC collected from three farms were investigated by culture dependent and independent techniques. Additionally, metabolite profiles of RMC and BMC were studied by gas chromatography and mass spectroscopy. A total of 59 bacterial isolates were identified from the four different dairy products. In RM, lactic acid bacteria such as Lactococcus, Enterococcus, Lactobacillus and Leuconostoc were obtained along with the environmental bacteria like Bacillus, Staphylococcus, Acetobacter, Chryseobacterium, Streptococcus, Acinetobacter, Kocuria, Klebsiella and Macrococcus. Additionally, Prevotella, Oscillospira, Phascolarctobacterium and Akkermansia were also detected in BM by culture independent technique. In RMC and BMC, Lactococcus, Leuconostoc and Lactobacillus were prevalent. RM and RMC shared Enterococcus, Lactococcus, Streptococcus and Acinetobacter as common bacterial genera. However, no bacterial genus was common in BM and BMC. The correlation analysis revealed that Lactobacillus was negatively correlated to other bacterial genera. Oligotyping analysis revealed that Lactobacillus brevis and L.fermentum were abundant in RMC and BMC, respectively. In metabolomic study, ascorbic acid, dodecanoic acid and hexadecanoic acid were found to be significantly higher in RMC. Presence of different types of probiotics in these curds samples opens a new avenue to understand their effects on human health.

Hypervirulent Listeria monocytogenes clones' adaption to mammalian gut accounts for their association with dairy products

Listeria monocytogenes (Lm) is a major human and animal foodborne pathogen. Here we show that hypervirulent Lm clones, particularly CC1, are strongly associated with dairy products, whereas hypovirulent clones, CC9 and CC121, are associated with meat products. Clone adaptation to distinct ecological niches and/or different food products contamination routes may account for this uneven distribution. Indeed, hypervirulent clones colonize better the intestinal lumen and invade more intestinal tissues than hypovirulent ones, reflecting their adaption to host environment. Conversely, hypovirulent clones are adapted to food processing environments, with a higher prevalence of stress resistance and benzalkonium chloride tolerance genes and a higher survival and biofilm formation capacity in presence of sub-lethal benzalkonium chloride concentrations. Lm virulence heterogeneity therefore reflects the diversity of the ecological niches in which it evolves. These results also have important public health implications and may help in reducing food contamination and improving food consumption recommendations to at-risk populations.

Microbiological quality of milk from farms to milk powder manufacture: an industrial case study

The experiments reported in this research paper aimed to track the microbiological load of milk throughout a low-heat skim milk powder (SMP) manufacturing process, from farm bulk tanks to final powder, during mid- and late-lactation (spring and winter, respectively). In the milk powder processing plant studied, low-heat SMP was produced using only the milk supplied by the farms involved in this study. Samples of milk were collected from farm bulk tanks (mid-lactation: 67 farms; late-lactation: 150 farms), collection tankers (CTs), whole milk silo (WMS), skim milk silo (SMS), cream silo (CS) and final SMP. During mid-lactation, the raw milk produced on-farm and transported by the CTs had better microbiological quality than the late-lactation raw milk (e.g., total bacterial count (TBC): 3.60 ± 0.55 and 4.37 ± 0.62 log 10 cfu/ml, respectively). After pasteurisation, reductions in TBC, psychrotrophic (PBC) and proteolytic (PROT) bacterial counts were of lower magnitude in late-lactation than in mid-lactation milk, while thermoduric (LPC-laboratory pasteurisation count) and thermophilic (THERM) bacterial counts were not reduced in both periods. The microbiological quality of the SMP produced was better when using mid-lactation than late-lactation milk (e.g., TBC: 2.36 ± 0.09 and 3.55 ± 0.13 cfu/g, respectively), as mid-lactation raw milk had better quality than late-lactation milk. The bacterial counts of some CTs and of the WMS samples were higher than the upper confidence limit predicted using the bacterial counts measured in the farm milk samples, indicating that the transport conditions or cleaning protocols could have influenced the microbiological load. Therefore, during the different production seasons, appropriate cow management and hygiene practices (on-farm and within the factory) are necessary to control the numbers of different bacterial groups in milk, as those can influence the effectiveness of thermal treatments and consequently affect final product quality.

Gut microbiome of pre-adolescent children of two ethnicities residing in three distant cities

Recent studies have realized the link between gut microbiota and human health and diseases. The question of diet, environment or gene is the determining factor for dominant microbiota and microbiota profile has not been fully resolved, for these comparative studies have been performed on populations of different ethnicities and in short-term intervention studies. Here, the Southern Chinese populations are compared, specifically the children of Guangzhou City (China), Penang City (west coast Malaysia) and Kelantan City (east coast Malaysia). These Chinese people have similar ancestry thus it would allow us to delineate the effect of diet and ethnicity on gut microbiota composition. For comparison, the Penang and Kelantan Malay children were also included. The results revealed that differences in microbiota genera within an ethnicity in different cities was due to differences in food type. Sharing the similar diet but different ethnicity in a city or different cities and living environment showed similar gut microbiota. The major gut microbiota (more than 1% total Operational Taxonomy Units, OTUs) of the children population are largely determined by diet but not ethnicity, environment, and lifestyle. Elucidating the link between diet and microbiota would facilitate the development of strategies to improve human health at a younger age.

The microbiome: toward preventing allergies and asthma by nutritional intervention

Allergies and asthma have increased in prevalence over recent decades while the development of therapies to treat or prevent them has stagnated. Genetic predisposition and lifestyle changes influence the constituents of the microbiome and these host-environment-microbe interactions represent a key underlying pressure influencing disease susceptibility. Consequently, there has been a surge of interest in shaping the microbiome to a health-promoting state particularly through nutritional intervention strategies. However, mechanistic insights into the nutrition-microbe-host interplay are still needed in order for such approaches to succeed. In addition, little is known about how trans-kingdom interactions might influence disease susceptibility and progression. Future steps toward revealing the underlying mechanisms of host-microbe interactions will be pivotal for the development of effective dietary intervention strategies for the prevention and treatment of allergic diseases.

Screening commercial teat disinfectants against bacteria isolated from bovine milk using disk diffusion

Background and Aim:

Teat disinfection is an important tool in reducing the incidence of bovine mastitis. Identifying the potential mastitis-causing bacterial species in milk can be the first step in choosing the correct teat disinfectant product. The objective of this study was to screen commercial teat disinfectants for inhibition against mastitis-associated bacteria isolated from various types of milk samples.

Materials and Methods:

Twelve commercially available teat disinfectant products were tested, against 12 mastitis-associated bacteria strains isolated from bulk tank milk samples and bacterial strains isolated from clinical (n=2) and subclinical (n=3) quarter foremilk samples using the disk diffusion method.

Results:

There was a significant variation (7-30 mm) in bacterial inhibition between teat disinfection products, with products containing a lactic acid combination (with chlorhexidine or salicylic acid) resulting in the greatest levels of bacterial inhibition against all tested bacteria (p<0.05).

Conclusion:

In this study, combined ingredients in teat disinfection products had greater levels of bacterial inhibition than when the ingredients were used individually. The disk diffusion assay is a suitable screening method to effectively differentiate the bacterial inhibition of different teat disinfectant products.

Distribution and antimicrobial activity of lactic acid bacteria from raw camel milk

Consumer demand for natural pathogen-control agents for substitution of synthetic food preservatives and traditional antibiotics is increasing. This study aimed to reveal the distribution of lactic acid bacteria (LAB) in raw camel milk and to characterize their antimicrobial traits. The genetic identification by 16S rRNA sequencing of 58 LAB isolates showed the predominance of Enterococcus (24.2%), Lactococcus (22.4%) and Pediococcus (20.7%) genera in raw camel milk. These genera exhibited inhibitory activity against a broad spectrum of Gram-positive and Gram-negative bacteria including multidrug-resistant Salmonella. Among these LAB, two isolates-identified as Pediococcus pentosaceus CM16 and Lactobacillus brevis CM22-were selected for their strong bacteriocinogenic anti-listerial activity estimated at 1600 and 800 AU/mL, respectively. The bacteriocins produced were partially purified by ammonium sulphate precipitation and gel filtration and then biochemically characterized. The proteinaceous nature of bacteriocins was confirmed by the susceptibility to enzymes. These bacteriocins showed significant technological characteristics such as heat-resistance, and stability over a wide range of pH (2.0-10.0). In conclusion, these results indicated that Pediococcus pentosaceus CM16 and Lactobacillus brevis CM22 could be useful as potential probiotics. Moreover, their partially purified bacteriocins may play an important role as food preservatives and feed additives. To our knowledge, this is the first report describing the distribution of LAB population in raw camel milk and the characterization of their bacteriocins from the Arabian Peninsula of western Asia.

Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment

The genus Brevibacterium harbors many members important for cheese ripening. We performed real-time quantitative PCR (qPCR) to determine the abundance of Brevibacterium on rinds of Vorarlberger Bergkäse, an Austrian artisanal washed-rind hard cheese, over 160 days of ripening. Our results show that Brevibacterium are abundant on Vorarlberger Bergkäse rinds throughout the ripening time. To elucidate the impact of Brevibacterium on cheese production, we analysed the genomes of three cheese rind isolates, L261, S111, and S22. L261 belongs to Brevibacterium aurantiacum, whereas S111 and S22 represent novel species within the genus Brevibacterium based on 16S rRNA gene similarity and average nucleotide identity. Our comparative genomic analysis showed that important cheese ripening enzymes are conserved among the genus Brevibacterium. Strain S22 harbors a 22 kb circular plasmid which encodes putative iron and hydroxymethylpyrimidine/thiamine transporters. Histamine formation in fermented foods can cause histamine intoxication. We revealed the presence of a putative metabolic pathway for histamine degradation. Growth experiments showed that the three Brevibacterium strains can utilize histamine as the sole carbon source. The capability to utilize histamine, possibly encoded by the putative histamine degradation pathway, highlights the importance of Brevibacterium as key cheese ripening cultures beyond their contribution to cheese flavor production.

Unveiling hákarl: A study of the microbiota of the traditional Icelandic fermented fish

Hákarl is produced by curing of the Greenland shark (Somniosus microcephalus) flesh, which before fermentation is toxic due to the high content of trimethylamine (TMA) or trimethylamine N-oxide (TMAO). Despite its long history of consumption, little knowledge is available on the microbial consortia involved in the fermentation of this fish. In the present study, a polyphasic approach based on both culturing and DNA-based techniques was adopted to gain insight into the microbial species present in ready-to-eat hákarl. To this aim, samples of ready-to-eat hákarl were subjected to viable counting on different selective growth media. The DNA directly extracted from the samples was further subjected to Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and 16S amplicon-based sequencing. Moreover, the presence of Shiga toxin-producing Escherichia coli (STEC) and Pseudomonas aeruginosa was assessed via qualitative real-time PCR assays. pH values measured in the analyzed samples ranged from between 8.07 ± 0.06 and 8.76 ± 0.00. Viable counts revealed the presence of total mesophilic aerobes, lactic acid bacteria and Pseudomonadaceae. Regarding bacteria, PCR-DGGE analysis highlighted the dominance of close relatives of Tissierella creatinophila. For amplicon sequencing, the main operational taxonomic units (OTUs) shared among the data set were Tissierella, Pseudomonas, Oceanobacillus, Abyssivirga and Lactococcus. The presence of Pseudomonas in the analyzed samples supports the hypothesis of a possible role of this microorganism on the detoxification of shark meat from TMAO or TMA during fermentation. Several minor OTUs (<1%) were also detected, including Alkalibacterium, Staphylococcus, Proteiniclasticum, Acinetobacter, Erysipelothrix, Anaerobacillus, Ochrobactrum, Listeria and Photobacterium. Analysis of the yeast and filamentous fungi community composition by PCR-DGGE revealed the presence of close relatives of Candida tropicalis, Candida glabrata, Candida parapsilosis, Candida zeylanoides, Saccharomyces cerevisiae, Debaryomyces, Torulaspora, Yamadazyma, Sporobolomyces, Alternaria, Cladosporium tenuissimum, Moristroma quercinum and Phoma/Epicoccum, and some of these species probably play key roles in the development of the sensory qualities of the end product. Finally, qualitative real-time PCR assays revealed the absence of STEC and Pseudomonas aeruginosa in all of the analyzed samples.

Longitudinal Study of Shiga Toxin-Producing Escherichia coli and Campylobacter jejuni on Finnish Dairy Farms and in Raw Milk

Shiga toxin-producing Escherichia coli (STEC) and Campylobacter jejuni are notable health hazards associated with the consumption of raw milk. These bacteria may colonize the intestines of asymptomatic cattle and enter bulk tank milk via fecal contamination during milking. We studied the frequency of STEC O157:H7 and C. jejuni contamination in tank milk (n = 785) and the in-line milk filters of milking machines (n = 631) versus the frequency of isolation from cattle feces (n = 257) on three Finnish dairy farms for 1 year. Despite simultaneous isolation of STEC O157:H7 (17%) or C. jejuni (53%) from cattle, these bacteria were rarely isolated from milk filters (2% or <1%, respectively) and milk (0%). As revealed by phylogenomics, one STEC O157:H7 strain at a time was detected on each farm and persisted for ≤12 months despite rigorous hygienic measures. C. jejuni strains of a generalist sequence type (ST-883 and ST-1080) persisted in the herds for ≥11 months, and several other C. jejuni types were detected sporadically. The stx gene carried by STEC was detected more frequently from milk filters (37%) than from milk (7%), suggesting that milk filters are more suitable sampling targets for monitoring than milk. A questionnaire of on-farm practices suggested lower stx contamination of milk when major cleansing in the barn, culling, or pasturing of dairy cows was applied, while a higher average outdoor temperature was associated with higher stx contamination. Because pathogen contamination occurred despite good hygiene and because pathogen detection from milk and milk filters proved challenging, we recommend heat treatment for raw milk before consumption.IMPORTANCE The increased popularity of raw milk consumption has created demand for relaxing legislation, despite the risk of contamination by pathogenic bacteria, notably STEC and C. jejuni However, the epidemiology of these milk-borne pathogens on the herd level is still poorly understood, and data are lacking on the frequency of milk contamination on farms with cattle shedding these bacteria in their feces. This study suggests (i) that STEC contamination in milk can be reduced, but not prevented, by on-farm hygienic measures while fecal shedding is observable, (ii) that milk filters are more suitable sampling targets for monitoring than milk although pathogen detection from both sample matrices may be challenging, and (iii) that STEC and C. jejuni genotypes may persist in cattle herds for several months. The results can be utilized in developing and targeting pathogen monitoring and risk management on the farm level and contributed to the revision of Finnish legislation in 2017.

Colonization of the human gut by bovine bacteria present in Parmesan cheese

The abilities of certain microorganisms to be transferred across the food production chain, persist in the final product and, potentially, colonize the human gut are poorly understood. Here, we provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese. We characterize the microbial communities in samples taken from five different locations across the Parmesan cheese production chain, confirming that the final product contains microorganisms derived from cattle gut, milk, and the nearby environment. In addition, we carry out a human pilot study showing that Bifidobacterium mongoliense strains from cheese can transiently colonize the human gut, a process that can be enhanced by cow milk consumption.

Some microorganisms may be transferred across the food production chain and, potentially, colonize the human gut. Here, Milani et al. provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese.

Production of Naturally γ-Aminobutyric Acid-Enriched Cheese Using the Dairy Strains Streptococcus thermophilus 84C and Lactobacillus brevis DSM 32386

The cheese-derived strains Streptococcus thermophilus 84C isolated from Nostrano cheese, and Lactobacillus brevis DSM 32386 isolated from Traditional Mountain Malga cheese have been previously reported as γ-aminobutyric acid (GABA)-producers in vitro. In the present study, the ability of these strains to produce GABA was studied in experimental raw milk cheeses, with the aim to investigate the effect of the culture and the ripening time on the GABA concentration. The cultures used consisted on S. thermophilus 84C alone (84C) or in combination with L. brevis DSM 32386 (84C-DSM). The control culture was a commercial S. thermophilus strain, which was tested alone (CTRL) or in combination with the L. brevis DSM 32386 (CTRL-DSM). The pH evolution, microbiological counts, MiSeq Illumina and UHPLC-HQOMS analysis on milk and cheese samples were performed after 2, 9, and 20 days ripening. During the whole ripening, the pH was always under 5.5 in all batches. The concentration of GABA increased during ripening, with the highest content in 84C after 9 days ripening (84 ± 37 mg/kg), in 84C-DSM and CTRL-DSM after 20 days ripening (91 ± 28 and 88 ± 24 mg/kg, respectively). The data obtained support the hypothesis that S. thermophilus 84C and L. brevis DSM 32386 could be exploited as functional cultures, improving the in situ bio-synthesis of GABA during cheese ripening.

Two Heat Resistant Endopeptidases from Pseudomonas Species with Destabilizing Potential during Milk Storage

In the current study, the extracellular endopeptidases from Pseudomonas lundensis and Pseudomonas proteolytica were investigated. The amino acid sequence identity between both endopeptidases is 68%. Both endopeptidases were purified to homogeneity and partially characterized. They were classified as metallopeptidases with a maximum activity at pH 10.0 ( P. lundensis) or 8.5 ( P. proteolytica) at 35 °C. Both remained active in skim milk with 39.7 ± 2.4% and 24.5 ± 3.3%, respectively, of the initial enzyme activity after UHT processing (138 °C for 20 s), indicating the relevance for milk destabilization. The transition points in buffer were determined at 50 °C ( P. lundensis) and 43 °C ( P. proteolytica) using circular dichroism spectroscopy. The loss of the secondary structure at different temperatures was correlated with residual peptidase activities after heat treatment. The ability to destabilize UHT milk was proven by supplementation of skim milk with endopeptidase and storage for 4 weeks.