The complex microbiota of raw milk

Current Trends of Enterococci in Dairy Products: A Comprehensive Review of Their Multiple Roles

As a genus that has evolved for resistance against adverse environmental factors and that readily exchanges genetic elements, enterococci are well adapted to the cheese environment and may reach high numbers in artisanal cheeses. Their metabolites impact cheese flavor, texture, and rheological properties, thus contributing to the development of its typical sensorial properties. Due to their antimicrobial activity, enterococci modulate the cheese microbiota, stimulate autolysis of other lactic acid bacteria (LAB), control pathogens and deterioration microorganisms, and may offer beneficial effects to the health of their hosts. They could in principle be employed as adjunct/protective/probiotic cultures; however, due to their propensity to acquire genetic determinants of virulence and antibiotic resistance, together with the opportunistic character of some of its members, this genus does not possess Qualified Presumption of Safety (QPS) status. It is, however, noteworthy that some putative virulence factors described in foodborne enterococci may simply reflect adaptation to the food environment and to the human host as commensal. Further research is needed to help distinguish friend from foe among enterococci, eventually enabling exploitation of the beneficial aspects of specific cheese-associated strains. This review aims at discussing both beneficial and deleterious roles played by enterococci in artisanal cheeses, while highlighting the need for further research on such a remarkably hardy genus.

Characterization of Chemical and Bacterial Compositions of Dairy Wastewaters

The dairy industry produces large amounts of wastewater, including white and cleaning wastewater originating principally from rinsing and cleaning-in-place procedures. Their valorization into process water and non-fat milk solids, in the case of white wastewater, or the renewal of cleaning solutions could be achieved using pressure-driven membrane processes. However, it is crucial to determine the intrinsic characteristics of wastewaters, such as proximate composition and bacterial composition, to optimize their potential for valorization. Consequently, white and cleaning wastewaters were sampled from industrial-scale pasteurizers located in two different Canadian dairy processing plants. Bacterial profiles of dairy wastewaters were compared to those of tap waters, pasteurized skim milk and unused cleaning solutions. The results showed that the physicochemical characteristics as well as non-fat milk solids contents differed drastically between the two dairy plants due to different processing conditions. A molecular approach combining quantitative real-time polymerase chain reaction (qPCR) and metabarcoding was used to characterize the bacteria present in these solutions. The cleaning solutions did not contain sufficient genomic DNA for sequencing. In white wastewater, the bacterial contamination differed depending on the dairy plant (6.91 and 7.21 log10 16S gene copies/mL). Psychrotrophic Psychrobacter genus (50%) dominated white wastewater from plant A, whereas thermophilic Anoxybacillus genus (56%) was predominant in plant B wastewater. The use of cold or warm temperatures during the pasteurizer rinsing step in each dairy plant might explain this difference. The detailed characterization of dairy wastewaters described in this study is important for the dairy sector to clearly identify the challenges in implementing strategies for wastewater valorization.

Pseudomonas crudilactis sp. nov., isolated from raw milk in France

Strains belonging to the Pseudomonas genus have been isolated worldwide from various biotic (humans, animals and plant tissues) and abiotic (food, soil, water and air) environments. Raw milk provides a favorable environment for the growth of a broad spectrum of microorganisms, including Pseudomonas. Here we present the description of Pseudomonas sp. UCMA 17988 isolated from raw milk, which was previously reported to produce new antimicrobial lipopeptides. MultiLocus Sequence Analysis of four housekeeping genes (16S rRNA, gyrB, rpoD and rpoB), whole genome sequence comparison (orthoANI value, original ANI value and dDDH value), microscopy, FAME analysis, and biochemical tests were performed. Digital DNA-DNA hybridization and average nucleotide identity values between strain UCMA 17988 and its closest relatives, P. helmanticensis CECT 8548^T (46.9%, 92.07%) and P. baetica CECT 7720^T (26.8%, 88.50%), rate well below the designed threshold for assigning prokaryotic strains to the same species. In conclusion, strain UCMA 17988 belongs to a novel species, for which the name Pseudomonas crudilactis sp. nov (type strain UCMA 17988^T = DSM 109949^T = LMG 31804^T) is proposed.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.

Sepsis and the evolution of human increased sensitivity to lipopolysaccharide

Among mammals, humans are exquisitely sensitive to lipopolysaccharide (LPS), an environmentally pervasive bacterial cell membrane component. Very small doses of LPS trigger powerful immune responses in humans and can even initiate symptoms of sepsis. Close evolutionary relatives such as African and Asian monkeys require doses that are an order of magnitude higher to do the same. Why humans have evolved such an energetically expensive antimicrobial strategy is a question that biological anthropologists are positioned to help address. Here we compare LPS sensitivity in primate/mammalian models and propose that human high sensitivity to LPS is adaptive, linked to multiple immune tactics against pathogens, and part of multi-faceted anti-microbial strategy that strongly overlaps with that of other mammals. We support a notion that LPS sensitivity in humans has been driven by microorganisms that constitutively live on us, and has been informed by human behavioral changes over our species' evolution (e.g., meat eating, agricultural practices, and smoking).

Growth interferences between bacterial strains from raw cow's milk and their impact on growth of Listeria monocytogenes and Staphylococcus aureus

AIMS

The purpose of this study was to detect growth enhancing or inhibiting activity between bacterial populations from raw milk under different conditions (temperature, medium).

METHODS AND RESULTS

The interference of 24 raw milk isolates on growth of each other and on Listeria monocytogenes, Staphylococcus aureus, Bacillus subtilis and Micrococcus luteus was screened by drop assay and for selected pairs in co-cultivation experiments. By drop assay, antibacterial activity was observed for 40% of the strains. About 30% of the strains showed growth-enhancing activity on other strains. Most of the isolates were well adapted to cold temperatures and showed consistent or even increased inhibiting or enhancing effects on growth of other strains at 10°C. The growth of L. monocytogenes DSM 20600^T and S. aureus DSM 1104^T was significantly (P < 0·05) reduced in co-cultivation with Pseudomonas protegens JZ R-192.

CONCLUSIONS

Growth interferences between bacterial populations have an impact on the structure of raw milk microbiota, especially when it develops under cold storage, and it may have an effect on the prevalence of certain foodborne pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates growth-inhibiting and also growth-enhancing interactions between raw milk bacteria, which must be considered when predicting bacterial growth and spoilage in food. A Ps. protegens strain isolated from raw milk showed an antagonistic effect on growth of L. monocytogenes in refrigerated raw milk.

An indirect ELISA system for the detection of heat-stable Pseudomonas endopeptidases (AprX) in milk

Heat-stable endopeptidases in raw milk, especially the alkaline metallopeptidase AprX secreted by Pseudomonas spp., are a well-known challenge for the dairy industry. They can withstand UHT treatment and may cause quality defects over the shelf life of milk products. Therefore, we established an indirect ELISA for the detection of Pseudomonas AprX in milk. We developed a 2-step sample treatment for milk contaminated with AprX to avoid the interference of milk proteins with the detection system. First, casein micelles were destabilized by the detraction of Ca²⁺ using trisodium citrate; then, AprX was concentrated 10-fold using hydrophobic interaction chromatography. The recovery of AprX in spiked milk samples after the 2-step treatment was 43 ± 0.1%. Specific antibodies for purified AprX from Pseudomonas lactis were produced to establish the ELISA. Western blot experiments showed that the binding affinity of these antibodies depended on the sequence homology of the AprX from P. lactis and several other Pseudomonas spp. The indirect ELISA, which was completed in 6 to 7 h, had a limit of detection of 21.0 ng mL^-1 and a limit of quantification of 25.7 ng mL^-1. Milk proteins or milk endogenous peptidases were not detected by the antibodies. The ELISA had high precision, with a CV between 0.2 and 0.8% measured on the same day (intraday) and 5.6 and 6.8% measured on 5 separate days (interday). Milk samples were spiked with different AprX activity levels [7.5-150 nkat Na-caseinate/o-phthalaldehyde (OPA) mL^-1] and evaluated by ELISA. The recovery of the ELISA was 92.3 ± 1.6 to 105 ± 4.7%. The lowest AprX activity quantifiable in the spiked milk samples was 500 pkat Na-caseinate/OPA mL^-1. The proof of concept to detect heat-stable Pseudomonas AprX in milk by ELISA was established.

Study of the bacterial profile of raw milk butter, made during a challenge test with Listeria monocytogenes, depending on cream maturation temperature

Bacteria can play different roles and impart various flavors and characteristics to food. Few studies have described bacterial microbiota of butter. In this study, next-generation sequencing was used to determine bacterial content of raw milk butter, processed during a challenge test, depending on cream maturation temperature and on the presence or not of L. monocytogenes. Two batches were produced. pH and microbiological analyses were conducted during cream maturation and butter storage. DNA was also isolated from all samples for 16S rRNA amplicon sequencing analysis. For butter made from cream matured at 14 °C, a growth potential of L. monocytogenes of - 1.72 log cfu/g was obtained. This value corresponds to the difference between the median of counts at the end of storage and the median of counts at the beginning of storage. This butter (pH value of 4.75 ± 0.04) was characterized by a dominance of Lactococcus. The abundance of Lactococcus was significantly higher in inoculated samples than in control samples (p value < 0.05). Butter made from cream matured at 4 °C (pH value of 6.81 ± 0.01) presented a growth potential of 1.81 log cfu/g. It was characterized by the abundance of psychrotrophic bacteria mainly Pseudomonas. This study demonstrated that cream maturation temperature impacts butter microbiota, affecting thus product's characteristics and its ability to support or not the growth of pathogens like L. monocytogenes.

How multiple farming conditions correlate with the composition of the raw cow's milk lactic microbiome

Questionnaires on farming conditions were retrieved from 2129 dairy farms and clustered, resulting in 106 representative raw cow's milk samples analysed in winter and summer. Substantiating the efficiency of our survey, some farming conditions affected the milk physicochemical composition. Culturing identified several species of lactic acid bacteria (LAB) per milk, whose number increased through 16S ribosomal RNA (rRNA) gene sequencing and shotgun metagenome analyses. Season, indoor versus outdoor housing, cow numbers, milk substitutes, ratio cattle/rest area, house care system during lactation, and urea and medium-chain fatty acids correlated with the overall microbiome composition and the LAB diversity within it. Shotgun metagenome detected variations in gene numbers and uniqueness per milk. LAB functional pathways differed among milk samples. Focusing on amino acid metabolisms and matching the retrieved annotated genes versus non-starter lactic acid bacteria (NSLAB) references from KEGG and corresponding to those identified, all samples had the same gene spectrum for each pathway. Conversely, gene redundancy varied among samples and agreed with NSLAB diversity. Milk samples with higher numbers of NSLAB species harboured higher number of copies per pathway, which would enable steady-state towards perturbations. Some farming conditions, which affected the microbiome richness, also correlated with the NSLAB composition and functionality.

Distinct Changes Occur in the Human Breast Milk Microbiome Between Early and Established Lactation in Breastfeeding Guatemalan Mothers

Human breast milk contains a diverse community of bacteria, but as breast milk microbiome studies have largely focused on mothers from high income countries where few women breastfeed to 6 months, the temporal changes in the breast milk microbiome that occur during later lactation stages have not been explored. For this cross-sectional study, microbiota from breast milk samples of Mam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala were analyzed. All mothers delivered vaginally and breastfed their infants for 6 months. Breast milk from 76 unrelated mothers was used to compare two lactation stages, either “early” (6–46 days post-partum, n = 33) or “late” (109–184 days post-partum, n = 43). Breast milk microbial communities were assessed using 16S ribosomal RNA gene sequencing and lactation stages were compared using DESeq2 differential abundance analysis. A total of 1,505 OTUs were identified, including 287 which could be annotated as putative species. Among several maternal factors, lactation stage explained microbiome variance and inertia in ordination with the most significance (p < 0.001). Differential abundance analysis identified 137 OTUs as significantly higher in either early or late lactation. These included a general shift from Staphylococcus and Streptococcus species in early lactation to Sphingobium and Pseudomonas species in late lactation. Species enriched in early lactation included putative commensal bacteria known to colonize the infant oral and intestinal tracts whereas species enriched in late lactation had a uniform functional trait associated with aromatic compound degradation. Differentially abundant species also included several species which have not previously been reported within breast milk, such as Janthinobacterium agaricidamnosum, Novosphingobium clariflavum, Ottowia beijingensis, and Flavobacterium cucumis. These discoveries describe temporal changes to the breast milk microbiome of healthy Guatemalan mothers from early to late lactation. Collectively, these findings illustrate how studying under-represented human populations might advance our understanding of factors that modulate the human milk microbiome in low and middle income countries (LMIC).

Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar Cheese

Food production involves numerous control points for microorganisms to ensure quality and safety. These control points (e.g., pasteurization) are difficult to develop for fermented foods wherein some microbial contaminants are also expected to provide positive contributions to the final product and spoilage microbes may constitute only a small proportion of all microorganisms present.

Validated methods are needed to detect spoilage microbes present in low numbers in foods and ingredients prior to defect onset. We applied propidium monoazide combined with 16S rRNA gene sequencing, qPCR, isolate identification, and pilot-scale cheese making to identify the microorganisms that cause slit defects in industrially produced Cheddar cheese. To investigate milk as the source of spoilage microbes, bacterial composition in milk was measured immediately before and after high-temperature, short-time (HTST) pasteurization over 10-h periods on 10 days and in the resulting cheese blocks. Besides HTST pasteurization-induced changes to milk microbiota composition, a significant increase in numbers of viable bacteria was observed over the 10-h run times of the pasteurizer, including 68-fold-higher numbers of the genus Thermus. However, Thermus was not associated with slit development. Milk used to make cheese which developed slits instead contained a lower number of total bacteria, higher alpha diversity, and higher proportions of Lactobacillus, Bacillus, Brevibacillus, and Clostridium. Only Lactobacillus proportions were significantly increased during cheese aging, and Limosilactobacillus (Lactobacillus) fermentum, in particular, was enriched in slit-containing cheeses and the pre- and post-HTST-pasteurization milk used to make them. Pilot-scale cheeses developed slits when inoculated with strains of L. fermentum, other heterofermentative lactic acid bacteria, or uncultured bacterial consortia from slit-associated pasteurized milk, thereby confirming that low-abundance taxa in milk can negatively affect cheese quality. The likelihood that certain microorganisms in milk cause slit defects can be predicted based on comparisons of the bacteria present in the milk used for cheese manufacture.

IMPORTANCE Food production involves numerous control points for microorganisms to ensure quality and safety. These control points (e.g., pasteurization) are difficult to develop for fermented foods wherein some microbial contaminants are also expected to provide positive contributions to the final product and spoilage microbes may constitute only a small proportion of all microorganisms present. We showed that microbial composition assessments with 16S rRNA marker gene DNA sequencing are sufficiently robust to detect very-low-abundance bacterial taxa responsible for a major but sporadic Cheddar cheese spoilage defect. Bacterial composition in the (pasteurized) milk and cheese was associated with slit defect development. The application of Koch’s postulates showed that individual bacterial isolates as well as uncultured bacterial consortia were sufficient to cause slits, even when present in very low numbers. This approach may be useful for detection and control of low-abundance spoilage microorganisms present in other foods.

A review of microbes and chemical contaminants in dairy products in sub-Saharan Africa

Animal milk types in sub-Saharan Africa (SSA) are processed into varieties of products using different traditional methods and are widely consumed by households to support nutritional intake and diet. Dairy products contain several microorganisms, their metabolites, and other chemical compounds, some with health benefits and many others considered as potential health hazards. Consumption of contaminated milk products could have serious health implications for consumers. To access the safety of milk products across SSA, studies in the region investigating the occurrences of pathogens as well as chemical compounds such as heat stable toxins and veterinary drug residues in animal milk and its products were reviewed. This is done with a holistic view in light of the emerging exposome paradigm for improving food safety and consumer health in the region. Herein, we showed that several published studies in SSA applied conventional and/or less sensitive methods in detecting microbial species and chemical contaminants. This has serious implications in food safety because the correct identity of a microbial species and accurate screening for chemical contaminants is crucial for predicting the potential human health effects that undermine the benefits from consumption of these foods. Furthermore, we highlighted gaps in determining the extent of viral and parasitic contamination of milk products across SSA as well as investigating multiple classes of chemical contaminants. Consequently, robust studies should be conducted in this regard. Also, efforts such as development cooperation projects should be initiated by all stakeholders including scientists, regulatory agencies, and policy makers to improve the dairy product chain in SSA in view of safeguarding consumer health.

The bacterial diversity of raw Moroccon camel milk

Dromedary camel milk is generally considered a valuable and marketable commodity but its production suffers from poor hygienic conditions that result in low microbiological quality and the presence of various pathogens. The objective of the present study was to provide a detailed report of the bacterial species level composition of Moroccan raw camel milk samples that can serve as a starting point for the selection of starter cultures to facilitate a change in manufacturing practices to an improved and safer production system. The composition of the bacterial community in four freshly collected raw camel milk samples was analyzed by performing a large-scale isolation campaign combined with 16S rRNA gene amplicon sequencing. A total of 806 isolates were obtained from four raw camel milk samples using ten combinations of growth media and incubation conditions. Subsequent isolate dereplication using MALDI-TOF mass spectrometry and identification of representative isolates through sequence analysis of protein encoding and 16S rRNA genes revealed the presence of established and novel dairy lactic acid bacteria, as well as bacteria that are considered indicators of poor hygienic conditions and psychrotrophic spoilage organisms. The large numbers of Lactococcus and Enterococcus isolates obtained present an interesting resource for starter culture selection.

Characterization and association of bacterial communities and nonvolatile components in spontaneously fermented cow milk at different geographical distances

In the ecosystem of spontaneously fermented cow milk, the characteristics and relationship of bacterial communities and nonvolatile components at different scales of geographical distances (provincial, county, and village levels) are unclear. Here, 25 sampling sites from Xin Jiang and Tibet, 2 provinces of China, were selected based on the distribution of spontaneously fermented cow milk and used for metagenomic and metabolomic analysis. At the provincial geographical distance, the same predominant species, Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus, were detected in Xin Jiang and Tibet. Further, the richness of the bacterial composition of samples from Tibet was higher than those from Xin Jiang; specifically, at the species level, 28 species were identified in Tibet samples but only 7 species in Xin Jiang samples. At the provincial geographical level, we detected significant differences in bacterial structure, shown in principal coordinate analysis plots, and significant differences (Simpson index) in bacterial diversity were also detected. However, at the county and village levels, no significant differences were detected in bacterial communities and diversity, but a difference in bacterial compositions was detectable. This indicates that bacterial communities and diversity of spontaneously fermented milk dissimilarity significantly increased with geographic distance. For the nonvolatile component profiles, the partial least squares discriminant analysis plot (R²Y > 0.5 and Q² > 0.5 for the goodness-of-fit and predictive ability parameter, respectively) showed that samples from different geographical distances (provincial, county, and village) were all separated, which indicated that all the discriminations in nonvolatile components profiles were from different geographical distances. Investigating relationships between lactic acid bacteria and discriminatory nonvolatile components at the county level showed that 9 species were positively correlated with 16 discriminatory nonvolatile components, all species with low abundance rather than the predominant species L. delbrueckii ssp. bulgaricus and Strep. thermophilus, which indicates the importance of the selection of autochthonous nonpredominant bacteria.

Role prediction of Gram-negative species in the resistome of raw cow's milk

Extended use of antibiotics in dairy farming for therapeutic and prophylactic reasons, but also the higher prevalence of antibiotic resistant bacteria (ARB) in the farm environment raised the concern of consuming raw cow's milk and its derived products. The aim of this study was to predict by shotgun metagenomic analyses the presence of antibiotic resistance genes (ARGs) mainly correlated with Gram-negative bacteria in antibiotic residue free raw cow's milk derived exclusively from healthy animal from South Tyrol (Northern Italy), chosen as a model system. Assessment of shotgun metagenomic data of reconstructed scaffolds, revealed the existence of Pseudomonas spp. as the most abundant Gram-negative species in the raw cow's milk samples bearing ARGs. Besides, ARGs also linked to lactic acid bacteria such as Lactococcus sp. and Lactobacillus sp. ARGs correlated to microbiome found in milk samples conferred resistance towards aminoglycoside-streptothricin, beta-lactamase, macrolide, tetracycline, carbapenem, cephalosporin, penam, peptide, penem, fluoroquinolone, chloramphenicol and elfamycin antibiotics. Further bioinformatic processing included de-novo reassembly of all metagenomic sequences from all milk samples in one, to reconstruct metagenome assembled genomes (MAGs), which were further used to investigate mobile genetic elements (MGE). Analyses of the reconstructed MAGs showed that, MAG 9 (Pseudomonas sp1.) contained the oriT gene (origin of transfer gene) needed for transferring virulent factors. Although the presence of Pseudomonas is common in raw cow's milk, pasteurization treatment reduces their survivability. Nevertheless, attention should be paid on Pseudomonas spp. due to their intrinsic resistance to antibiotics and their capability of transferring virulent factors to other bacteria.

Infantile Colic Treated With Bifidobacterium longum CECT7894 and Pediococcus pentosaceus CECT8330: A Randomized, Double-Blind, Placebo-Controlled Trial

Background: Colic is a common condition in infants <4 months of age. Attempts to treat infantile colic with probiotics have shown variable efficacy and overall low evidence of success. In this work, we tested the hypothesis that oral administration of Bifidobacterium longum CECT7894 (KABP042) and Pediococcus pentosaceus CECT8330 (KABP041) mix (1 × 10⁹ colony forming units) would improve the symptoms of infantile colic. Methods: A total of 112 exclusively breastfed or mixed fed infants aged <2 months and meeting the ROME IV criteria for infantile colic were recruited. The infants were randomized in a double-blind, placebo-controlled trial to receive orally administered probiotics (intervention group, IG, n = 48) or placebo (placebo group, PG, n = 42) daily for 21 days. Results: Infants in the IG had significantly shorter crying time (p < 0.001) on day 7 [IG vs. PG, median (25-75th percentile): 38 (3.5-40.5) vs. 62 (40-108) min/day], day 14 [IG vs. PG: 20 (0-40) vs. 50 (30-75) min/day], and day 21 [IG vs. PG: 14 (0-33) vs. 40 (28-62) min/day]. Higher responder ratio and fewer crying/fussing episodes on days 7, 14, and 21 and better stool consistency on day 21 were observed in the IG (p < 0.01) as compared to the PG. Conversely, no significant effects on stool frequency or quality of life were observed. Conclusions: In summary, daily oral administration of B. longum CECT7894 (KABP042) and P. pentosaceus CECT8330 (KABP041) was an effective treatment for shortening crying time due to infantile colic and for improving fecal consistency. This trial was registered retrospectively in December 2019 with a trial number of ISRCTN92431452.

Antimicrobial Blue Light versus Pathogenic Bacteria: Mechanism, Application in the Food Industry, Hurdle Technologies and Potential Resistance

Blue light primarily exhibits antimicrobial activity through the activation of endogenous photosensitizers, which leads to the formation of reactive oxygen species that attack components of bacterial cells. Current data show that blue light is innocuous on the skin, but may inflict photo-damage to the eyes. Laboratory measurements indicate that antimicrobial blue light has minimal effects on the sensorial and nutritional properties of foods, although future research using human panels is required to ascertain these findings. Food properties also affect the efficacy of antimicrobial blue light, with attenuation or enhancement of the bactericidal activity observed in the presence of absorptive materials (for example, proteins on meats) or photosensitizers (for example, riboflavin in milk), respectively. Blue light can also be coupled with other treatments, such as polyphenols, essential oils and organic acids. While complete resistance to blue light has not been reported, isolated evidence suggests that bacterial tolerance to blue light may occur over time, especially through gene mutations, although at a slower rate than antibiotic resistance. Future studies can aim at characterizing the amount and type of intracellular photosensitizers across bacterial species and at assessing the oxygen-independent mechanism of blue light-for example, the inactivation of spoilage bacteria in vacuum-packed meats.

Effectiveness of copper ions against Mycobacterium avium subsp. paratuberculosis and bacterial communities in naturally contaminated raw cow's milk

AIM

The focus of the present study was to evaluate the copper ions treatment on the viability of Mycobacterium avium subsp. paratuberculosis (MAP) and other bacterial communities in cow's milk.

METHODS AND RESULTS

A copper ions treatment was evaluated in naturally contaminated cow's milk to assay MAP load and/or viability, and relative abundance of other bacterial communities. In addition, physical-chemical analyses of the milk were also performed. All analyses were carried out before and after a copper ions treatment. After copper ions treatment, pH and copper concentration markedly increased in milk; the numbers of viable MAP significantly decreased. The relative abundance of the four target phyla decreased, with the phyla Bacteroidetes and Firmicutes surviving treatment in higher proportions (4 and 2·1% of original populations, respectively). A progressively higher percentage of dead bacterial cells after 5 and 20 min copper ions treatments was found (12 and 35%, respectively).

CONCLUSION

With the exception of some MAP-tolerant strains, we have once again demonstrated that copper ions have a significant inactivating effect on MAP as well as certain other bacterial communities found in naturally contaminated cow's milk.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study showed a significant inactivation of both MAP and other bacteria by copper ions in raw cow's milk, information that could be useful as a tool for MAP control.

Austrian Raw-Milk Hard-Cheese Ripening Involves Successional Dynamics of Non-Inoculated Bacteria and Fungi

Cheese ripening involves successional changes of the rind microbial composition that harbors a key role on the quality and safety of the final products. In this study, we analyzed the evolution of the rind microbiota (bacteria and fungi) throughout the ripening of Austrian Vorarlberger Bergkäse (VB), an artisanal surface-ripened cheese, by using quantitative and qualitative approaches. The real-time quantitative PCR results revealed that bacteria were more abundant than fungi in VB rinds throughout ripening, although both kingdoms were abundant along the process. The qualitative investigation was performed by high-throughput gene-targeted (amplicon) sequencing. The results showed dynamic changes of the rind microbiota throughout ripening. In the fresh products, VB rinds were dominated by Staphylococcus equorum and Candida. At early ripening times (14–30 days) Psychrobacter and Debaryomyces flourished, although their high abundance was limited to these time points. At the latest ripening times (90–160 days), VB rinds were dominated by S. equorum, Brevibacterium, Corynebacterium, and Scopulariopsis. Strong correlations were shown for specific bacteria and fungi linked to specific ripening periods. This study deepens our understanding of VB ripening and highlights different bacteria and fungi associated to specific ripening periods which may influence the organoleptic properties of the final products.

Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome

Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.

Determination of changes in the microbial and chemical composition of Țaga cheese during maturation

Țaga cheese is a traditional Romanian smear-ripened cheese made from bovine milk and identified with the name of the village and caves where it is produced. As no previously reported microbiological and chemical studies have been undertaken on this product, this research aimed to investigate the microbiological and biochemical characteristics which ensure the uniqueness of Țaga cheese during the ripening process, to inform producers as to key quality determinants. Cheese samples, consisting of retail blocks, were collected on days 2, 5, 12, 18, and 25 of the ripening process. The evolution of lactic microbiota during the production and maturation of traditional cheeses involves isolating lactic acid microorganisms present in cheese. Cheese samples were analyzed for pH, fat, NaCl, fatty acids, and volatile compounds. The microbial ecosystem naturally changes during the maturation process, leading to variation in the microorganisms involved during ripening. Our results show that specific bacteria were identified in high levels during the entire ripening process and may be responsible for milk fat lipolysis contributing directly to cheese flavor by imparting detailed fatty acid flavor notes, or indirectly as precursors formation of other flavor compounds.

An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?

The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.

Investigation of donkey milk bacterial diversity by 16S rDNA high-throughput sequencing on a Cyprus donkey farm

The interest in milk originating from donkeys is growing worldwide due to its claimed functional and nutritional properties, especially for sensitive population groups, such as infants with cow milk protein allergy. The current study aimed to assess the microbiological quality of donkey milk produced in a donkey farm in Cyprus using culture-based and high-throughput sequencing techniques. The culture-based microbiological analysis showed very low microbial counts, whereas important food-borne pathogens were not detected in any sample. In addition, high-throughput sequencing was applied to characterize the bacterial communities of donkey milk samples. Donkey milk mostly composed of gram-negative Proteobacteria, including Sphingomonas, Pseudomonas, Mesorhizobium, and Acinetobacter; lactic acid bacteria, including Lactobacillus and Streptococcus; the endospores forming Clostridium; and the environmental genera Flavobacterium and Ralstonia, detected in lower relative abundances. The results of the study support existing findings that donkey milk contains mostly gram-negative bacteria. Moreover, it raises questions regarding the contribution of (1) antimicrobial agents (i.e., lysozyme, peptides) in shaping the microbial communities and (2) bacterial microbiota to the functional value of donkey milk.

Molecular detection, phylogenetic analysis, and antibacterial performance of lactic acid bacteria isolated from traditional cheeses, North-West Iran

Lactic acid bacteria (LAB) are candidate probiotic bacteria that can provide health benefits when delivered via functional foods. The purpose of this study was to isolate and characterize LAB from traditional cheeses consumed in north-west regions of Iran. A number of sixty traditional cheeses samples were collected and initially screened as LAB using biochemical and molecular methods. A fragment of 1,540 bp in size of 16s rRNA gene was amplified from 70 bacterial isolates. Restriction fragment length polymorphism (RFLP) was employed to differentiate LAB isolates. LAB isolates generated three different RFLP patterns using HinfI restriction enzyme. Phylogenetic analysis revealed that LAB isolates belonged to three genera including Enterococcus, Lactobacillus, and Lactococcus. Most of the isolated LAB strains belonged to Enterococcus spp. The antimicrobial performance of eight LAB isolates with different RFLP patterns ranged from 6.72 to 14.00 mm. It was concluded that molecular characterization of LAB strains in traditional cheeses will enhance our understanding of traditional food microbiota and will help to find bacterial strains with probiotic potential with great benefit both in health and industry.

Comparison of Bacterial Microbiota in Raw Mare's Milk and Koumiss Using PacBio Single Molecule Real-Time Sequencing Technology

Koumiss is a traditional fermented raw mare’s milk product. It contains high nutritional value and is well-known for its health-promoting effect as an alimentary supplement. This study aimed to investigate the bacterial diversity, especially lactic acid bacteria (LAB), in koumiss and raw mare’s milk. Forty-two samples, including koumiss and raw mare’s milk, were collected from the pastoral area in Yili, Kazakh Autonomous Prefecture, Xinjiang Uygur Autonomous Region in China. This work applied PacBio single-molecule real-time (SMRT) sequencing to profile full-length 16S rRNA genes, which was a powerful technology enabling bacterial taxonomic assignment to the species precision. The SMRT sequencing identified 12 phyla, 124 genera, and 227 species across 29 koumiss samples. Eighteen phyla, 286 genera, and 491 species were found across 13 raw mare’s milk samples. The bacterial microbiota diversity of the raw mare’s milk was more complex and diverse than the koumiss. Raw mare’s milk was rich in LAB, such as Lactobacillus (L.) helveticus, L. plantarum, Lactococcus (Lc.) lactis, and L. kefiranofaciens. In addition, raw mare’s milk also contained sequences representing pathogenic bacteria, such as Staphylococcus succinus, Acinetobacter lwoffii, Klebsiella (K.) oxytoca, and K. pneumoniae. The koumiss microbiota mainly comprised LAB, and sequences representing pathogenic bacteria were not detected. Meanwhile, the koumiss was enriched with secondary metabolic pathways that were potentially beneficial for health. Using a Random Forest model, the two kinds of samples could be distinguished with a high accuracy 95.2% [area under the curve (AUC) = 0.98] based on 42 species and functions. Comprehensive depiction of the microbiota in raw mare’s milk and koumiss might help elucidate evolutionary and functional relationships among the bacterial communities in these dairy products. The current work suffered from the limitation of a low sample size, so further work would be required to verify our findings.

Snapshot of Cyprus Raw Goat Milk Bacterial Diversity via 16S rDNA High-Throughput Sequencing; Impact of Cold Storage Conditions

In general, it is a common practice among dairy producers to store the milk in the refrigerator directly after milking, in order to preserve it and prevent the development of spoilage microbes. However, the impact of keeping the milk in the refrigerator overnight on milk microbial diversity has been poorly investigated. This study aimed to provide a snapshot of the bacterial composition of goat milk after direct storage at −80 °C and after being kept overnight at 4 °C and then in storage at −80 °, using high-throughput sequencing (HTS). Goat milk samples from four different farms were analyzed, to reveal that milk bacterial diversity differed between the two different storage conditions. Goat milk directly stored at −80 °C was characterized by the presence of the Gram-negative contaminants Pseudomonas and Acinetobacter, in addition to the genera Corynebacterium, Chryseobacterium, Bacteroides and Clostridium. Milk samples that were kept overnight at 4 °C were characterized by a reduction in their bacterial biodiversity and the predominance of the Gram-negative, aerobic Phyllobacterium. Overall, HTS methodologies provide an in-depth identification and characterization of the goat raw milk microbiome. Further, they offer a better understanding of the contribution of cold storage conditions to milk microbiota formation. This study may assist dairy producers in improving raw milk and raw milk cheeses quality and guaranteeing consumers’ safety.

Raw Milk Microbiota Modifications as Affected by Chlorine Usage for Cleaning Procedures: The Trentingrana PDO Case

Milk microbiota represents a key point in raw milk cheese production and contributes to the development of typical flavor and texture for each type of cheese. The aim of the present study was to evaluate the influence of chlorine products usage for cleaning and sanitizing the milking equipment on (i) raw milk microbiota; (ii) the deriving whey-starter microbiota; and (iii) Trentingrana Protected Designation of Origin (PDO) cheese microbiota and volatilome. Milk samples from three farms affiliated to a Trentingrana PDO cheese factory were collected three times per week during a 6-weeks period in which a sodium hypochlorite detergent (period C) was used and during a subsequent 6-weeks period of non-chlorine detergent usage (period NC). Samples were subjected to microbiological [Standard Plate Count; coliforms; coagulase-positive staphylococci; and lactic acid bacteria (LAB)] and metagenomic analysis (amplification of V3-V4 regions of 16S rRNA gene performed on Illumina MiSeq platform). In addition, cheese volatilome was determined by SPME-GC-MS. In the transition from period C to period NC, higher SPC and LAB counts in milk were recorded. Milk metagenomic analysis showed a peculiar distinctive microbiota composition for the three farms during the whole experimental period. Moreover, differences were highlighted comparing C and NC periods in each farm. A difference in microbial population related to chlorine usage in bulk milk and vat samples was evidenced. Moreover, chlorine utilization at farm level was found to affect the whey-starter population: the usually predominant Lactobacillus helveticus was significantly reduced during NC period, whereas Lactobacillus delbrueckii had the exact opposite trend. Alpha- and beta-diversity revealed a separation between the two treatment periods with a higher presence of L. helveticus, L. delbrueckii, and Streptococcus thermophilus in cheese samples after NC detergent period. Cheese volatilome analysis showed a slight decrease in lipolysis during C period in the inner part of the cheese wheel. Although preliminary, these results suggest a profound influence on milk and cheese microbiota, as well as on raw milk cheese production and quality, due to the use of chlorine. However, further studies will be needed to better understand the complex relationship between chlorine and microbiota along all the cheese production steps.

Short communication: High-throughput sequencing approach to investigate Italian artisanal cheese production

In this study, high-throughput sequencing (HTS) was used to investigate the microbiota of Robiola di Roccaverano production, an artisanal Protected Designation of Origin soft cheese made with raw goat milk by addition of a natural milk starter (NMS), from the Piedmont region of Italy. Different steps of production of Robiola di Roccaverano cheese at one artisanal dairy were monitored. Matched samples of milk, NMS, curd, and 5-d and 15-d matured cheeses were collected at different periods of the year. The DNA sequences obtained by HTS belonged to 5 phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Tenericutes. In milk, Proteobacteria and Firmicutes were mainly found, and several operational taxonomic units (OTU) belonging to contaminant bacteria such as Pseudomonas, Serratia, and Staphylococcus were observed. However, in NMS, curd, and 5- and 15-d cheeses, Firmicutes were principally observed where OTU of Lactococcus lactis were predominant, followed by Leuconostoc mesenteroides OTU. The results of the analysis showed high bacterial diversity in milk samples compared with NMS, curd, and 5- and 15-d cheeses, suggesting strong action of NMS in driving the characteristics of the final products.

Compared analysis of microbial diversity in donkey milk from Xinjiang and Shandong of China through High-throughput sequencing

Donkey milk has received increasing attention from consumers and dairy industry because of its nutritional value, health benefits, and proximity to human milk. Microbial diversity in donkey milk has a great impact on its quality and safety, however, microbiota in donkey milk from the major donkey-breeding regions of China have not been well documented. In this study, bacterial communities in donkey milk from Yopurga County in Western China (XJ), and Dong'e County in Eastern China (SD) were determined using high-throughput sequencing. Major phyla identified in the two donkey milk groups consistently included Acinetobacter, Proteobacteria, Firmicutes, and Bacteroidetes but with very different abundance for each phylum. Prevelence of genera was found to be diverse between the two groups, with Macrococcus and Acinetobacter dominating in the XJ samples while Streptococcus, Pseudoclavibacter, and Pseudomonas being the most abundant ones in the XJ samples. Alpha diversity analysis showed that there was significant difference in richness between the two sample groups but no difference in bacterial community diversity or coverage. The presence of possible harmful bacteria and lactic acid bacteria in donkey milk in this study provides the microbial profiles of pathogens and spoilage bacteria that need to be controlled and proposes possible utilization of beneficial microbial resources for the future.

The Effect of Mixing Milk of Different Species on Chemical, Physicochemical, and Sensory Features of Cheeses: A Review

The yield and quality of cheese are associated with the composition, physicochemical, sensory, rheological, and microbiological properties of milk and with the technology applied to the milk before and/or during cheese processing. This review describes the most important research on cheeses obtained from processing mixtures of different milk species and discusses the effect of milk mixtures (i.e., species and mixture ratios) on composition, physicochemical, sensory, rheological, and microbiological properties of cheeses. More specifically, the present review paper will gather and focus only on studies that have provided a clear comparison between cheeses produced from a mixture of two milk species to cheeses produced from only one species.

Examination of milk microbiota, fecal microbiota, and blood metabolites of Jersey cows in cool and hot seasons

Microbiota of individual cow milk, bulk tank milk, and feces of Jersey cows were examined. Samples were collected from two farms (F1 and F2) in cool (November, Nov) and hot (July, Jul) seasons. Milk yield and milk composition were similar between the two farms and between the two seasons. Prevalent taxa of the fecal microbiota, i.e. Ruminococcaceae, Bacteroidaceae, Lachnospiraceae, Rikenellaceae, and Clostridiaceae, were unaffected by the farm and season. Relative abundance of milk microbiota for Pseudomonadaceae, Enterobacteriaceae, and Streptococcaceae (F1 > F2) and Lactobacillaceae, Bifidobacteriaceae, and Cellulomonadaceae (F1 < F2) were different between the two farms, and those for Staphylococcaceae, Bacillaceae, Ruminococcaceae, and Veillonellaceae (Nov < Jul) and Methylobacteriaceae and Moraxellaceae (Nov > Jul) were different between the two seasons. The microbiota of bulk tank milk was numerically different from that of individual cow milk. Principal coordinate analysis indicated that the milk microbiota was unrelated to the fecal microbiota. The finding that relative abundance of Pseudomonadaceae and Moraxellaceae appeared greater than those reported for Holstein milk suggested that higher protein and fat content may result in a greater abundance of proteolytic and lipolytic taxa in Jersey cow milk.

Comparative metagenomics and characterization of antimicrobial resistance genes in pasteurized and homemade fermented Arabian laban

The aim of this study was to investigate bacterial diversity and function in a fermented milk drink called laban, which is traditionally served in the Middle East, Africa, and Indian subcontinent. Pasteurized laban (LBP) and unpasteurized, homemade, raw laban (LBR) underwent 16S rRNA gene amplicon and shotgun sequencing to analyze their bacterial community, presence of antimicrobial resistance genes (ARGs), and metabolic pathways. This study highlighted relatively greater diversity in LBR bacterial populations compared to LBP, despite containing similar major taxa that consisted primarily of Firmicutes followed by Proteobacteria, Bacteroidetes, and Actinobacteria. The dominant species, Streptococcus thermophilus, was relatively more abundant in LBP (80.7%) compared to LBR (47.9%). LBR had increased diversity and higher relative abundance of several known probiotic bacteria, such as Streptococcus salivarius and Lactococcus lactis, whereas Lactobacillus acidophilus was detected at a higher abundance in LBP. Pathogens like Acinetobacter baumannii, Streptococcus pneumoniae, Streptococcus pyogenes, and Escherichia coli had lower abundance in LBP compared to LBR. Thirty-three ARGs were detected in LBR compared to nine in LBP and are responsible for resistance to 11 classes of antibiotics. A significant proportion of the metagenomes from both types of laban were assigned to housekeeping functions, such as amino acid metabolism, translation, membrane transport, and carbohydrate metabolism. LBR demonstrated increased diversity in probiotics and metabolic functions compared to LBP. However, the relatively high diversity of pathogenic and opportunistic bacteria and ARGs in LBR raises safety concerns and highlights the need for a more hygienic environment for the processing of homemade fermented dairy foods.

Natural flavor biosynthesis by lipase in fermented milk using in situ produced ethanol

Abstract

Many flavoring agents on the market are extracted from natural sources or synthesized chemically. Due to the disadvantages of both methods, biotechnology is becoming a promising alternative. In this study, short chain ethyl esters with fruity notes were biosynthesized in UHT whole milk via coupling ethanolic fermentation with lipase (Palatase®) transesterification. Kluyveromyces marxianus, Lactobacillus fermentum and Lb. paracasei were used for fermentation. Milk fat was esterified with in situ produced ethanol by adding lipase at 0, 8 and 24 h of fermentation. Viable cell counts and pH were monitored during 48 h fermentation period. Flavor active ethyl esters, ethanol and free fatty acids were analyzed using headspace SPME-GC. Free fatty acid levels were lower in K. marxianus samples than lactobacilli. K. marxianus produced higher amounts of ethanol and esters than lactic acid bacteria. Viable cell counts decreased after lipase application at 0 and 8 h, possibly due to fatty acid production. Addition of lipase at 24 h resulted in improved cell counts as well as ethanol and ester production in the case of K. marxianus. This study demonstrated that fermenting milk with alcohol producing cultures in conjunction with lipase application can be an alternative to artificial flavorings in fermented milks.

Graphic abstract

Evaluation of Enzymatic Cleaning on Food Processing Installations and Food Products Bacterial Microflora

Biofilms are a permanent source of contamination in food industries and could harbor various types of microorganisms, such as spoiling bacteria. New strategies, such as enzymatic cleaning, have been proposed to eradicate them. The purpose of this study was to evaluate the impact of enzymatic cleaning on the microbial flora of installations in a processing food industry and of the final food product throughout its shelf life. A total of 189 samples were analyzed by classical microbiology and 16S rDNA metagenetics, including surface samples, cleaning-in-place (CIP) systems, and food products (at D₀, D_{end of the shelf life}, and D_{end of the shelf life +7 days}). Some surfaces were highly contaminated with spoiling bacteria during conventional cleaning while the concentration of the total flora decreased during enzymatic cleaning. Although the closed circuits were cleaned with conventional cleaning before enzymatic cleaning, there was a significant release of microorganisms from some parts of the installations during enzymatic treatment. A significant difference in the total flora in the food products at the beginning of the shelf life was observed during enzymatic cleaning compared to the conventional cleaning, with a reduction of up to 2 log CFU/g. Metagenetic analysis of the food samples at the end of their shelf life showed significant differences in bacterial flora between conventional and enzymatic cleaning, with a decrease of spoiling bacteria (Leuconostoc sp.). Enzymatic cleaning has improved the hygiene of the food processing instillations and the microbial quality of the food throughout the shelf life. Although enzymatic cleaning is not yet commonly used in the food industry, it should be considered in combination with conventional sanitizing methods to improve plant hygiene.

Evaluation of culture-based and molecular detection methods for Campylobacter in New Zealand raw cows' milk

AIMS

This study evaluated the performance of a commercial molecular detection method (mericon Campylobacter triple kit real-time/quantitative (q)PCR) and a selective plating medium (R&F Campylobacter jejuni/Campylobacter coli Chromogenic Plating Medium (CCPM)) against a culture-based reference method (ISO 10272-1:2017 detection procedure B) for the detection of Campylobacter from raw milk enrichment broths.

METHODS AND RESULTS

New Zealand raw cows' milk and Ultra-High Temperature-processed milk samples were inoculated with 50, 125 and 500 colony forming units of C. jejuni and C. coli cocktail per analytical unit. Samples were tested for Campylobacter after 0, 24- and 48 h refrigeration. ISO 10272-1:2017 proved to be a sensitive detection method (77/80 positive samples); detection only failed for some milk samples tested 48 h postinoculation. CCPM was as effective as Cefoperazone Charcoal Deoxycholate Agar for selective plating of Campylobacter raw milk enrichments (78/80 positive samples). However, the qPCR detected Campylobacter in only 42/80 samples and qPCR reaction inhibition was observed.

CONCLUSIONS

The ISO 10272-1:2017 method was a more sensitive method for Campylobacter detection from raw milk than the mericon Campylobacter triple kit qPCR, and CCPM was a useful complementary medium to mCCDA where one of these media is required by the standard.

SIGNIFICANCE AND IMPACT OF THE STUDY

In regions where testing is required or recommended, optimized methods for Campylobacter detection from raw milk will reduce risk to the raw milk consumer. Although molecular methods are generally touted as a rapid alternative to culture, issues with inhibition due to matrix components mean that culture-based methods might provide the most sensitive option for Campylobacter detection in raw milk. Findings also emphasize the importance of minimizing the time between milk collection and testing for Campylobacter.

Detection of Chlortetracycline Hydrochloride in Milk with a Solid SERS Substrate Based on Self-assembled Gold Nanobipyramids

This paper described how a high-yield, monodisperse Au nanobipyramids (Au NBs) sol was prepared by a seed-mediated method, and gold nanoparticles were assembled on the surface of a silicon wafer by self-assembly technology to obtain a solid SERS substrate. Scanning electron microscopy (SEM) showed that the average length of Au NBs was 34.31 nm, and the analysis enhancement factor (AEF) was approximately 7.3 × 10⁵ with rhodamine 6G (R6G) used as a probe. SERS detection of chlortetracycline hydrochloride (CCH) in milk was performed utilizing the prepared Au NBs substrate, and the limit of detection was 0.01 mg/mL. In the range of 0.01 - 1 mg/mL, the mass concentration of CCH and the SERS signal intensity satisfied the linear relationship y = 258.467x + 150.501; the value of the correlation coefficient was 0.9785. In addition, the recovery of spiked samples fluctuated between 96.80 to 111.38%. These results proved that the method is simple and fast, and it is promising to be applied to the field detection of antibiotics in milk.

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet

The factors that influence the diversity and composition of raw milk and fecal microbiota in healthy commercial dairy herds are not fully understood, partially because the majority of metataxonomic studies involve experimental farms and/or single factors. We analyzed the raw milk and fecal microbiota of 100 healthy cows from 10 commercial alpine farms from the Province of Trento, Italy, using metataxonomics and applied statistical modelling to investigate which extrinsic and intrinsic parameters (e.g. herd, diet and milk characteristics) correlated with microbiota richness and composition in these relatively small traditional farms. We confirmed that Firmicutes, Ruminococcaceae and Lachnospiraceae families dominated the fecal and milk samples of these dairy cows, but in addition, we found an association between the number of observed OTUs and Shannon entropy on each farm that indicates higher microbiota richness is associated with increased microbiota stability. Modelling showed that herd was the most significant factor affecting the variation in both milk and fecal microbiota composition. Furthermore, the most important predictors explaining the variation of microbiota richness were milk characteristics (i.e. percentage fat) and diet for milk and fecal samples, respectively. We discuss how high intra-herd variation could affect the development of treatments based on microbiota manipulation.

Potential of N2 Gas Flushing to Hinder Dairy-Associated Biofilm Formation and Extension

Worldwide, the dairy sector remains of vital importance for food production despite severe environmental constraints. The production and handling conditions of milk, a rich medium, promote inevitably the entrance of microbial contaminants, with notable impact on the quality and safety of raw milk and dairy products. Moreover, the persistence of high concentrations of microorganisms (especially bacteria and bacterial spores) in biofilms (BFs) present on dairy equipment or environments constitutes an additional major source of milk contamination from pre- to post-processing stages: in dairies, BFs represent a major concern regarding the risks of disease outbreaks and are often associated with significant economic losses. One consumption trend toward "raw or low-processed foods" combined with current trends in food production systems, which tend to have more automation and longer processing runs with simultaneously more stringent microbiological requirements, necessitate the implementation of new and obligatory sustainable strategies to respond to new challenges regarding food safety. Here, in light of studies, performed mainly with raw milk, that considered dominant "planktonic" conditions, we reexamine the changes triggered by cold storage alone or combined with nitrogen gas (N2) flushing on bacterial populations and discuss how the observed benefits of the treatment could also contribute to limiting BF formation in dairies.

Functional probiotics of lactic acid bacteria from Hu sheep milk

Background

Probiotics are being considered as valuable microorganisms related to human health. Hu sheep is referred as one of the important sheep breeds in China. Goat milk produced by Hu sheep is characterized with high nutritional value and hypoallergenic in nature. Particularly, this milk contains plenty of milk prebiotic and probiotic bacteria. This study was aimed to scrutinize more bacterial strains from Hu sheep milk with potential probiotic activity.

Results

Based on 16S rRNA sequence analysis, pool of forty bacterial strains were identified and evaluated their antimicrobial activities against Staphylococcus aureus, enterohemorrhagic Escherichia coli (EHEC), Salmonella typhimurium, Listeria monocytogenes enterotoxigenic E. coli (ETEC) and Aeromonas caviae. Four out of these isolated strains demonstrated their efficient bacteriostatic ability and potential healthy properties. We also examined the safety aspects of these bacterial candidates including three Lactococcus lactis strains (named as HSM-1, HSM-10, and HSM-18) and one Leuconostoc lactis strain (HSM-14), and were further evaluated via in vitro tests, including antimicrobial activity, cell surface characteristics (hydrophobicity, co-aggregation, and self-aggregation), heat treatment, antibiotic susceptibility, simulated transport tolerance in the gastrointestinal tract, and acid/bile tolerance. The obtained results revealed that HSM-1, HSM-10, HSM-14, and HSM-18 showed high survival rate at different conditions for example low pH, presence of bovine bile and demonstrated high hydrophobicity. Moreover, HSM-14 had an advantage over other strains in terms of gastrointestinal tract tolerance, antimicrobial activities against pathogens, and these results were significantly better than other bacterial candidates.

Conclusion

Hu sheep milk as a source of exploration of potential lactic acid bacteria (LAB) probiotics open the new horizon of probiotics usage from unconventional milk sources. The selected LAB strains are excellent probiotic candidates which can be used for animal husbandry in the future. Rationale of the study was to utilize Hu sheep milk as a source of potential probiotic LABs. The study has contributed to the establishment of a complete bacterial resource pool by exploring the Hu sheep milk microflora.

Occurrence, Virulence and Antimicrobial Resistance-Associated Markers in Campylobacter Species Isolated from Retail Fresh Milk and Water Samples in Two District Municipalities in the Eastern Cape Province, South Africa

Campylobacter species are among the major bacteria implicated in human gastrointestinal infections and are majorly found in faeces of domestic animals, sewage discharges and agricultural runoff. These pathogens have been implicated in diseases outbreaks through consumption of contaminated milk and water in some parts of the globe and reports on this is very scanty in the Eastern Cape Province. Hence, this study evaluated the occurrence as well as virulence and antimicrobial-associated makers of Campylobacter species recovered from milk and water samples. A total of 56 water samples and 72 raw milk samples were collected and the samples were processed for enrichment in Bolton broth and incubated for 48 h in 10% CO2 at 42 °C under microaerobic condition. Thereafter, the enriched cultures were further processed and purified. After which, presumptive Campylobacter colonies were isolated and later confirmed by PCR using specific primers for the detection of the genus Campylobacter, target species and virulence associated genes. Antimicrobial resistance profiles of the isolates were determined by disk diffusion method against a panel of 12 antibiotics and relevant genotypic resistance genes were assessed by PCR assay. A total of 438 presumptive Campylobacter isolates were obtained; from which, 162 were identified as belonging to the genus Campylobacter of which 36.92% were obtained from water samples and 37.11% from milk samples. The 162 confirmed isolates were further delineated into four species, of which, 7.41%, 27.16% and 8.64% were identified as C. fetus, C. jejuni and C. coli respectively. Among the virulence genes screened for, the iam (32.88%) was most prevalent, followed by flgR (26.87%) gene and cdtB and cadF (5.71% each) genes. Of the 12 antibiotics tested, the highest phenotypic resistance displayed by Campylobacter isolates was against clindamycin (95.68%), while the lowest was observed against imipenem (21.47%). Other high phenotypic resistance displayed by the isolates were against erythromycin (95.06%), followed by ceftriaxone (93.21%), doxycycline (87.65%), azithromycin and ampicillin (87.04% each), tetracycline (83.33%), chloramphenicol (78.27%), ciprofloxacin (77.78%), levofloxacin (59.88%) and gentamicin (56.17%). Relevant resistance genes were assessed in the isolates that showed high phenotypic resistance, and the highest resistance gene harbored by the isolates was catII (95%) gene while VIM, KPC, Ges, bla-OXA-48-like, tetC, tetD, tetK, IMI and catI genes were not detected. The occurrence of this pathogen and the detection of virulence and antimicrobial resistance-associated genes in Campylobacter isolates recovered from milk/water samples position them a risk to human health.