Where Do Milk Microbes Originate? Traceability of Microbial Community Structure in Raw Milk

Variations in ecological environments (including milk collection equipment and milk storage tanks in the pasture) and seasonal changes may contribute to raw milk contamination, thereby affecting food safety. The composition, structure, and relationships between raw milk and microbial communities in these environments are not well understood. In this study, 84 samples from spring and autumn in Luxian County, Yunnan Province, China, were collected for high-throughput sequencing technology. The results showed that the skin on the nipple surface and the environment (including the wiping samples of the automatic milking machine and the inner cover of the milk tank) had the greatest impact on microbial community composition in raw milk, followed by dung. In addition, microbial diversity in autumn samples was significantly higher, likely due to seasonal factors, including increased rainfall and reduced ultraviolet radiation. By analyzing the microbial community of raw milk and its environmental source, this study traced the origin of microorganisms in milk, providing insights for further exploration of the interaction between the pasture environment and raw milk microorganisms.

Relationship between microorganisms and milk metabolites during quality changes in refrigerated raw milk: A metagenomic and metabolomic exploration

Although cold storage at 4 °C can effectively prolong the shelf life of raw milk, it cannot prevent its eventual spoilage. In this study, we analyzed the main physicochemical and microbial indexes of raw milk stored at 4 °C for 6 days. The changes in microbial profiles and milk metabolites and their relationship during refrigeration were also explored. Metagenomic analysis performed using the Illumina Hiseq Xten sequencing platform revealed that the dominant genera in raw milk evolved from Acinetobacter, Streptococcus, Staphylococcus, and Anaplasma to Flavobacterium, Pseudomonas, and Lactococcus during cold storage. Using the UHPLC-Q-TOF MS method, 77 significantly different metabolites (p < 0.05) were identified, among which lipids were the most abundant (37). The most significant metabolic changes largely occurred at 3-4 days of refrigeration, coinciding with the rapid increase in dominant psychrotrophic bacteria. Subsequently, correlation analysis demonstrated that these lipid-related metabolites were significantly associated with Acinetobacter, Flavobacterium, and Pseudomonas. Both macro indicators and microanalysis indicated that the key stage of quality changes in raw milk was 3-4 days. Thus, this stage can be targeted for the quality control of raw milk.

Genetic Profile and Toxigenic Potential of Bacillus cereus Isolates from a Norwegian Ice Cream Production Plant

Members of the B. cereus group are spore-forming organisms commonly associated with spoilage of milk and dairy products. We have determined the genetic identity and growth characteristics of 57 B. cereus isolates collected from a Norwegian ice cream production plant. Our findings revealed persistence of B. cereus spp. strains for up to 19 months, suggesting the plant's susceptibility to long-term colonization. One of the mesophilic isolates, NVH-YM303, carried a complete cereulide synthetase operon. To assess the potential food poisoning risk associated with the presence of cereulide-producing strains in the production line, we examined the production of cereulide in ice cream and milk at different temperatures by NVH-YM303 and by the emetic psychrotrophic B. weihenstephanensis strain BtB2-4. Our findings revealed that NVH-YM303 produced higher levels of cereulide in ice cream as compared to milk. Furthermore, it was observed that NVH-YM303 produced more cereulide in ice cream at 25 °C compared to 15 °C. Conversely, BtB2-4 produced more cereulide in ice cream at 15 °C than at 25 °C. The results obtained in this study contribute to knowledge important for risk assessment of the potential hazards posed by the presence of B. cereus within ice cream production facilities.

Genomic diversity of Campylobacter jejuni and Campylobacter coli isolated from the Ethiopian dairy supply chain

Campylobacteriosis outbreaks have previously been linked to dairy foods. While the genetic diversity of Campylobacter is well understood in high-income countries, it is largely unknown in low-income countries, such as Ethiopia. This study therefore aimed to conduct the first genomic characterization of Campylobacter isolates from the Ethiopian dairy supply chain to aid in future epidemiological studies. Fourteen C. jejuni and four C. coli isolates were whole genome sequenced using an Illumina platform. Sequences were analyzed using the bioinformatics tools in the GalaxyTrakr platform to identify MLST types, and single nucleotide polymorphisms, and infer phylogenetic relationships among the studied isolates. Assembled genomes were further screened to detect antimicrobial resistance and virulence gene sequences. Among 14 C. jejuni, ST 2084 and ST 51, which belong to the clonal complexes ST-353 and ST-443, respectively, were identified. Among the 4 sequenced C. coli isolates, two isolates belonged to ST 1628 and two to ST 830 from the clonal complex ST-828. The isolates of C. jejuni ST 2084 and ST 51 carried β-lactam resistance gene blaOXA-605, a fluoroquinolone resistance-associated mutation T86I in the gryA gene, and a macrolide resistance-associated mutation A103V in 50S L22. Only ST 2084 isolates carried the tetracycline resistance gene tetO. Conversely, all four C. coli ST 830 and ST 1628 isolates carried tetO, but only ST 1628 isolates also carried blaOXA-605. Lastly, C. jejuni ST 2084 isolates carried a total of 89 virulence genes, and ST 51 isolates carried up to 88 virulence genes. Among C. coli, ST 830 isolates carried 71 genes involved in virulence, whereas two ST 1628 isolates carried up to 82 genes involved in virulence. Isolates from all identified STs have previously been isolated from human clinical cases, demonstrating a potential food safety concern. This finding warrants further monitoring of Campylobacter in dairy foods in Ethiopia to better understand and manage the risks associated with Campylobacter contamination and transmission.

Honey Added to Yogurt with Bifidobacterium animalis subsp. lactis DN-173 010/CNCM I-2494 Supports Probiotic Enrichment but Does Not Reduce Intestinal Transit Time in Healthy Adults: A Randomized, Controlled, Crossover Trial

BACKGROUND

Honey improves probiotic survival in vitro. However, if this effect translates to humans has not been investigated.

OBJECTIVES

We aimed to determine effects of honey plus yogurt containing the probiotic Bifidobacterium animalis subsp. lactis DN-173 010/CNCM I-2494 (B. animalis) on intestinal transit time, probiotic enrichment, digestive health, mood, and cognition in adults.

METHODS

Sixty-six healthy adults (34 female; 33.6 ± 9.8 y; 24.6 ± 3.0 kg/m2) in a crossover trial were randomly assigned to 2-wk yogurt conditions in a counterbalanced order with ≥4-wk washout: 1) Honey (HON): yogurt plus honey and 2) Negative Control (NC): heat-treated yogurt plus sugar. Of the participants, n = 62 completed the trial, and n = 37 (17 female; 32.0 ± 8.3 y; 25.0 ± 2.9 kg/m2) elected to enroll in a third condition (a nonrandomized study extension) after ≥4-wk washout with a reference Positive Control (PC): yogurt plus sugar. At baseline and end of each of the 3 conditions, intestinal transit time was measured with dye capsules; probiotic abundance with fecal DNA 16S sequencing; digestive health with symptom/function records, Bristol stool consistency, Gastrointestinal Tolerability, and Gastrointestinal Quality of Life Index; mood with Positive and Negative Affect Schedule-Short Form, Depression Anxiety Stress Scales-42, Patient-Reported Outcomes Measurement Information System questionnaires, and an emotional image task; and cognition with a spatial reconstruction task. Data were analyzed using linear mixed-effects models (LMMs) with significance at P ≤ 0.05. Baseline and end data were included in the LMM, with fixed effects being treatment, time, treatment by time interaction, and baseline covariate, and the random effect being the participant.

RESULTS

B. animalis was enriched in HON (d = 3.54; P = 0.0002) compared to controls with linear discriminant analysis effect size. Intestinal transit time, gastrointestinal health, mood, and cognition did not differ between conditions (LMM: Ps > 0.05).

CONCLUSIONS

Yogurt + honey enriched B. animalis but did not reduce intestinal transit time or have other functional gastrointestinal, mood, or cognitive effects in adults. This trial was registered at www.

CLINICALTRIALS

gov as NCT04187950 and NCT04901390.

Microbial communities in feed, bedding material, and bulk milk - experiences from a feeding trial

There is an increasing interest in the microbiota of the dairy value chain, from field to fork. Studies to understand the effects of environmental, feed and management factors on the raw milk microbiota have been performed to elucidate the origin of the bacteria and find ways to control the presence or absence of specific bacteria. In this study, we explored the microbiota in feedstuff, bedding material and milk on a Swedish dairy farm to investigate the effects of feeding different silages on the bacterial compositions throughout the dairy value chain. Three ensiling treatments were evaluated: without additive, with acid treatment, and with inoculation of starter culture. The silage treatments were fed as partial mixed rations to 67 dairy cows for 3 weeks each, with one treatment fed twice to evaluate if a potential change in milk microbiota could be repeated. The highest average total bacteria counts were found in the used bedding material (9.6 log10 cfu/g), while milk showed the lowest (3.5 log10 cfu/g). Principal coordinate analysis of the weighted UniFrac distance matrix showed clear separation between 3 clusters of materials: 1) herbage, 2) silage and partial mixed ration, and 3) used bedding material and milk. Surprisingly, the expected effect of the ensiling treatments on silage microbiota was not clear. Transfer of major bacteria from the silages and resulting partial mixed rations to the used bedding material was observed, but rarely to milk. The milk microbiota showed most resemblance to that of the used bedding material. Lactobacillus was a major genus in both feed and milk, but investigations at amplicon sequence variant level showed that in most cases the sequences differed between materials. However, low total bacteria count in the milk in combination with a high diversity suggests that results may be biased due to environmental contamination of the milk samples. Considering that the study was performed on a research farm, strict hygienic measures during the feeding experiment may have contributed to the low transfer of bacteria from feed to milk.

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

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

The microbial and metabolite composition of Gouda cheese made from pasteurized milk is determined by the processing chain

Gouda cheeses of different production batches and ripening times often differ in metabolite composition, which may be due to the starter culture mixture applied or the growth of non-starter lactic acid bacteria (NSLAB) upon maturation. Therefore, a single Gouda cheese production batch was systematically investigated from the thermized milk to the mature cheeses, ripened for up to 100 weeks, to identify the main bacterial species and metabolites and their dynamics during the whole production and ripening. As this seemed to be starter culture strain- and NSLAB-dependent, it requested a detailed, longitudinal, and quantitative investigation. Hereto, microbial colony enumeration, high-throughput full-length 16S rRNA gene sequencing, and a metabolomic approach were combined. Culture-dependently, Lactococcus lactis was the most abundant species from its addition as part of the starter culture up to the first two months of cheese ripening. Afterward, the NSLAB Lacticaseibacillus paracasei became the main species during ripening. The milk was a possible inoculation source for the latter species, despite pasteurization. Culture-independently, the starter LAB Lactococcus cremoris and Lc. lactis were the most abundant species in the cheese core throughout the whole fermentation and ripening phases up to 100 weeks. The cheese rind from 40 until 100 weeks of ripening was characterized by a high relative abundance of the NSLAB Tetragenococcus halophilus and Loigolactobacillus rennini, which both came from the brine. These species were linked with the production of the biogenic amines cadaverine and putrescine. The most abundant volatile organic compound was acetoin, an indicator of citrate and lactose fermentation during the production day, whereas the concentrations of free amino acids were an indicator of the ripening time.

HMO-primed bifidobacteria exhibit enhanced ability to adhere to intestinal epithelial cells

The ability of gut commensals to adhere to the intestinal epithelium can play a key role in influencing the composition of the gut microbiota. Bifidobacteria are associated with a multitude of health benefits and are one of the most widely used probiotics for humans. Enhanced bifidobacterial adhesion may increase host-microbe, microbe-nutrient, and/or microbe-microbe interactions, thereby enabling consolidated health benefits to the host. The objective of this study was to determine the ability of human milk oligosaccharides (HMOs) to enhance bifidobacterial intestinal adhesion in vitro. This study assessed the colonisation-promoting effects of HMOs on four commercial infant-associated Bifidobacterium strains (two B. longum subsp. infantis strains, B. breve and B. bifidum). HT29-MTX cells were used as an in vitro intestinal model for bacterial adhesion. Short-term exposure of four commercial infant-associated Bifidobacterium strains to HMOs derived from breastmilk substantially increased the adherence (up to 47%) of these probiotic strains. Interestingly, when strains were incubated with HMOs as a four-strain combination, the number of viable bacteria adhering to intestinal cells increased by >90%. Proteomic analysis of this multi-strain bifidobacterial mixture revealed that the increased adherence resulting from exposure to HMOs was associated with notable increases in the abundance of sortase-dependent pili and glycosyl hydrolases matched to Bifidobacterium bifidum. This study suggests that HMOs may prime infant gut-associated Bifidobacterium for colonisation to intestinal epithelial cells by influencing the expression of various colonization factors.

Maternal rumen and milk microbiota shape the establishment of early-life rumen microbiota in grazing yak calves

Early-life gut microbial colonization and development exert a profound impact on the health and metabolism of the host throughout the life span. The transmission of microbes from the mother to the offspring affects the succession and establishment of the early-life rumen microbiome in newborns, but the contributions of different maternal sites to the rumen microbial establishment remain unclear. In the present study, samples from different dam sites (namely, oral, rumen fluid, milk, and teat skin) and rumen fluid of yak calves were collected at 6 time points between d 7 and 180 postpartum to determine the contributions of the different maternal sites to the establishment of the bacterial and archaeal communities in the rumen during early life. Our analysis demonstrated that the dam's microbial communities clustered according to the sites, and the calves' rumen microbiota resembled that of the dam consistently regardless of fluctuations at d 7 and 14. The dam's rumen microbiota was the major source of the calves' rumen bacteria (7.9%) and archaea (49.7%) compared with the other sites, whereas the potential sources of the calf rumen microbiota from other sites varied according to the age. The contribution of dam's rumen bacteria increased with age from 0.36% at d 7 to 14.8% at d 180, whereas the contribution of the milk microbiota showed the opposite trend, with its contribution reduced from 2.7% at d 7 to 0.2% at d 180. Maternal oral archaea were the main sources of the calves' rumen archaea at d 14 (50.4%), but maternal rumen archaea became the main source gradually and reached 66.2% at d 180. These findings demonstrated the potential microbial transfer from the dam to the offspring that could influence the rumen microbiota colonization and establishment in yak calves raised under grazing regimens, providing the basis for future microbiota manipulation strategies during their early life.

Effectiveness of raw bacteriocin produced from lactic acid bacteria on biofilm of methicillin-resistant Staphylococcus aureus

Background and Aim

Probiotics are proven beneficial to health since they enhance immunity against dangerous pathogens and increase resistance to illness. Bacteriocin produced by lactic acid bacteria (LAB), demonstrates a broad inhibitory spectrum and therapeutic potential. This study aimed to isolate LAB-producing bacteriocin and investigate the effect of crude bacteriocin on biofilm from methicillin-resistant Staphylococcus aureus (MRSA).

Materials and Methods

This study used randomly collected 80 white soft local cheeses (40 each from cows and sheep) from different supermarkets in Basrah Province. The obtained samples were cultured and the bacterial suspension of S. aureus was prepared at 1.5 × 10⁸ cells/mL. The crude bacteriocin extracted from LAB was obtained, and the tube was dried and inverted to detect the biofilm loss at the bottom.

Results

There were 67 (83.75%) LAB isolates. Among 40 milk samples collected directly and indirectly, there were 36 (83.33%). Staphylococcus aureus isolates based on conventional bacteriological analysis and biochemical tests. Molecular testing was conducted to identify LAB and MRSA. Depending on genotypic results, the effect of white soft local cheese (cows and sheep) and the amplification results of the 16S rRNA gene were detected in 46 LAB isolates from white soft local cheese from cows and sheep. Based on the molecular identification of the mecA, results on Staphylococcus determined that only 2 of 36 isolates of S. aureus carried the mecA. Moreover, there were 26 (86.66%) isolates (MRSA) from samples of raw milk from local markets and subclinical mastitis in cows. The ability of LAB isolates was tested. The effects of bacteriocin production on preventing biofilm growth and formation were investigated. Results demonstrated that bacteriocin has high activity. Microtiter plates applied to investigate the ability of S. aureus to produce biofilms revealed that all isolates were either weak or moderate biofilm producers, with neither non-biofilm nor strong biofilm producers found among the tested isolates.

Conclusion

Lactic acid bacteria demonstrate a high ability to produce bacteriocin. Crude bacteriocin from LAB has a restrictive effect on biofilms produced by MRSA; thus, it can be used to reduce the pathogenicity of this bacterium.

Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing

Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, Republic of South Africa pertaining to their unsanitary practices associated with the use of cattle by-products.

Analysis of Microbiota Persistence in Quebec's Terroir Cheese Using a Metabarcoding Approach

Environmental short amplicon sequencing, or metabarcoding, is commonly used to characterize the bacterial and fungal microbiota of cheese. Comparisons between different metabarcoding studies are complicated by the use of different gene markers. Here, we systematically compare different metabarcoding molecular targets using V3–V4 and V6–V8 regions of the bacterial 16S rDNA and fungal ITS1 and ITS2 regions. Taxonomic profiles varied depending on the molecular markers used. Based on data quality and detection capacity of the markers toward microorganisms usually associated with the dairy environment, the ribosomal regions V3–V4 and ITS2 were selected and further used to evaluate variability in the microbial ecosystem of terroir cheeses from the province of Quebec in Canada. Both fungal and bacterial ecosystem profiles were described for 32 different ready-to-eat bloomy-, washed- and natural-rind specialty cheese varieties. Among them, 15 were studied over two different production years. Using the Bray–Curtis dissimilarity index as an indicator of microbial shifts, we found that most variations could be explained by either a voluntary change in starter or ripening culture composition, or by changes in the cheesemaking technology. Overall, our results suggest the persistence of the microbiota between the two years studied—these data aid understanding of cheese microbiota composition and persistence during cheese ripening.

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

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

Human milk oligosaccharide-sharing by a consortium of infant derived Bifidobacterium species

Bifidobacteria are associated with a host of health benefits and are typically dominant in the gut microbiota of healthy, breast-fed infants. A key adaptation, facilitating the establishment of these species, is their ability to consume particular sugars, known as human milk oligosaccharides (HMO), which are abundantly found in breastmilk. In the current study, we aimed to characterise the co-operative metabolism of four commercial infant-derived bifidobacteria (Bifidobacterium bifidum R0071, Bifidobacterium breve M-16V, Bifidobacterium infantis R0033, and Bifidobacterium infantis M-63) when grown on HMO. Three different HMO substrates (2'-fucosyllactose alone and oligosaccharides isolated from human milk representing non-secretor and secretor status) were employed. The four-strain combination resulted in increased bifidobacterial numbers (> 21%) in comparison to single strain cultivation. The relative abundance of B. breve increased by > 30% during co-cultivation with the other strains despite demonstrating limited ability to assimilate HMO in mono-culture. HPLC analysis revealed strain-level variations in HMO consumption. Metabolomics confirmed the production of formate, acetate, 1,2-propanediol, and lactate with an overall increase in such metabolites during co-cultivation. These results support the concept of positive co-operation between multiple bifidobacterial strains during HMO utilisation which may result in higher cell numbers and a potentially healthier balance of metabolites.

The Influence of Holder Pasteurization on the Diversity of the Human Milk Bacterial Microbiota Using High-Throughput DNA Sequencing

BACKGROUND

Human milk is the best food for infants; however, when breastfeeding is not possible, pasteurized milk from human milk banks is the best alternative. Little has been reported about variations in the bacterial microbiota composition of human milk after pasteurization.

RESEARCH AIM

To characterize and compare the bacterial microbiota composition and diversity within human milk among Mexican mothers before and after the Holder pasteurization process.

METHODS

A cross-sectional, observational, and comparative design was used. The effect of the pasteurization process on the bacterial composition and diversity of human milk samples of donors (N = 42) from a public milk bank was assessed before and after pasteurization by high throughput deoxyribonucleic acid sequencing of V3-16S rRNA gene libraries. Sequencing data were examined using the Quantitative Insights into Microbial Ecology software and Phyloseq in R environment.

RESULTS

A varied community of bacteria was found in both raw and pasteurized human milk. The bacterial diversity of the milk samples was increased by the pasteurization, where some thermoduric bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were more abundant. The source tracker analysis indicated that at most 1.0% of bacteria may have come from another source, showing the safety of the process used to treat milk samples.

CONCLUSION

The pasteurization process increased the bacterial diversity. We selected taxa capable of surviving the process, which could proliferate after the treatment without being a risk for infants.

Characterization of Bacterial Microbiota of P.D.O. Feta Cheese by 16S Metagenomic Analysis

Background: The identification of bacterial species in fermented PDO (protected designation of origin) cheese is important since they contribute significantly to the final organoleptic properties, the ripening process, the shelf life, the safety and the overall quality of cheese. Methods: Ten commercial PDO feta cheeses from two geographic regions of Greece, Epirus and Thessaly, were analyzed by 16S metagenomic analysis. Results: The biodiversity of all the tested feta cheese samples consisted of five phyla, 17 families, 38 genera and 59 bacterial species. The dominant phylum identified was Firmicutes (49% of the species), followed by Proteobacteria (39% of the species), Bacteroidetes (7% of the species), Actinobacteria (4% of the species) and Tenericutes (1% of the species). Streptococcaceae and Lactobacillaceae were the most abundant families, in which starter cultures of lactic acid bacteria (LAB) belonged, but also 21 nonstarter lactic acid bacteria (NSLAB) were identified. Both geographical areas showed a distinctive microbiota fingerprint, which was ultimately overlapped by the application of starter cultures. In the rare biosphere of the feta cheese, Zobellella taiwanensis and Vibrio diazotrophicus, two Gram-negative bacteria which were not previously reported in dairy samples, were identified. Conclusions: The application of high-throughput DNA sequencing may provide a detailed microbial profile of commercial feta cheese produced with pasteurized milk.

Characterizing the microbiota of wooden boards used for cheese ripening

•

The phyla Actinobacteria, Firmicutes, and Proteobacteria dominated the microbiota of the boards.

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The boards displayed differences in both diversity and richness.

•

We identified 288 total operational taxonomic units (OTU), with 7 OTU forming a core microbiota across all boards.

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The boards appeared to select for salt- and cold-tolerant bacteria.

Wooden boards are commonly used for aging artisan cheeses. Although considered critical to the development of desired flavors and aromas, knowledge about the microbial communities associated with these boards is limited. To begin to address this need, we performed a 16S ribosomal RNA analysis of the bacterial communities present on the surface and within 5 wooden boards used for cheese ripening that were obtained from 3 cheese-processing facilities. The 5 boards were dominated by bacteria in the phyla Actinobacteria, Firmicutes, and Proteobacteria and displayed differences in both diversity and richness. Analysis of these boards also identified significant board-to-board variation. A total of 288 operational taxonomic units were identified across all samples, with 7 operational taxonomic units forming a core microbiota across all boards. Taken together, these data reflect the cheese-ripening environment, which appears to select for salt- and cold-tolerant bacteria.

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.

Metataxonomic Profiling of Native and Starter Microbiota During Ripening of Gouda Cheese Made With Listeria monocytogenes-Contaminated Unpasteurized Milk

Unpasteurized milk is used to produce aged artisanal cheeses, which presents a safety concern due to possible contamination with foodborne pathogens, especially Listeria monocytogenes. The objective of this study was to examine the composition of the bacterial community in unpasteurized milk used to prepare Gouda cheese artificially contaminated with L. monocytogenes (~1 log CFU/ml) and assess the community dynamics and their potential interaction with L. monocytogenes during a 90-day ripening period using targeted 16S rRNA sequencing. The diversity of bacterial taxa in three batches of unpasteurized milk was not significantly different, and the microbiomes were dominated by species of Lactococcus, Streptomyces, Staphylococcus, and Pseudomonas. The highest relative abundances were observed for Pseudomonas fluorescens (31.84-78.80%) and unidentified operational taxonomic units (OTUs) of Pseudomonas (7.56-45.27%). After manufacture, both with and without L. monocytogenes-contaminated unpasteurized milk, Gouda cheese was dominated by starter culture bacteria (including Lactococcus lactis subsp. cremoris, lactis, lactis bv. diacetylactis, and Streptococcus thermophilus), in addition to unassigned members in the taxa L. lactis and Streptococcus. During ripening there was an overall decrease in L. lactis abundance and an increase in the number of taxa with relative abundances >0.1%. After 90-day ripening, a total of 82 and 81 taxa were identified in the Gouda cheese with and without L. monocytogenes, respectively. Of the identified taxa after ripening, 31 (Gouda cheese with L. monocytogenes) and 56 (Gouda cheese without L. monocytogenes) taxa had relative abundances >0.1%; 31 were shared between the two types of Gouda cheese, and 25 were unique to the Gouda cheese without added L. monocytogenes. No unique taxa were identified in the Gouda cheese with the added L. monocytogenes. This study provides information on the dynamics of the bacterial community in Gouda cheese during ripening, both with and without the addition of L. monocytogenes.

Effect of reduction of sodium content on the microbial ecology of Edam cheese samples

Sodium intake is a major risk factor for non-communicable diseases. Consequently, reformulation of cheeses such as Edam to contain less sodium may contribute to lowering disease risk. However, sodium is essential for cheese manufacture, influencing starter culture bacteria activity and abundance during fermentation. This study aimed to assess the microbial diversity of reformulated Edam cheese samples with a reduced sodium content using culture-independent technique. The microbial diversity of samples produced using simple sodium reduction, as well as by substituting salt with a mineral salt compound containing potassium, were analysed in comparison to regular control Edam samples during manufacture and the subsequent 6-week ripening period using 16S rDNA metagenomics. In addition, a challenge test using Listeria (List.) innocua as a surrogate species for List. monocytogenes was performed. Reducing sodium content did not influence the microbiological composition of reformulated samples in comparison to that of regular samples. The starter culture bacteria dominated the microbial diversity and no increase in spoilage or potentially pathogenic bacterial growth was detected, including that of List. innocua. From a microbiological perspective, it can be concluded that lowering sodium content in Edam samples without affecting the microbial composition is achievable through simple sodium reduction and through implementation of a mineral salt replacement approach.

Shaping the Future of Probiotics and Prebiotics

Recent and ongoing developments in microbiome science are enabling new frontiers of research for probiotics and prebiotics. Novel types, mechanisms, and applications currently under study have the potential to change scientific understanding as well as nutritional and healthcare applications of these interventions. The expansion of related fields of microbiome-targeted interventions, and an evolving landscape for implementation across regulatory, policy, prescriber, and consumer spheres, portends an era of significant change. In this review we examine recent, emerging, and anticipated trends in probiotic and prebiotic science, and create a vision for broad areas of developing influence in the field.

Multifaceted effects of milk-exosomes (Mi-Exo) as a modulator of scar-free wound healing

Scar-free treatment is complex involving many cells in the human body but a very elaborate reaction. This process demands regulation of various growth factors on behalf of TGFβ3 around the damaged tissue, and it is also important to protect cells from inflammatory reactions and oxidative stress to avoid abnormalities. Here, we focused on bovine derived milk exosomes (Mi-Exo) and their scar-free healing potential. The physiological properties (size and shape), biological markers (TSG101 and Bta-miR2478) and stability on storage of Mi-Exo were analyzed. Mi-Exo exhibited significant NP (number of Mi-Exo particles)-dependent scavenging activity in ABTS assay. In addition, Mi-Exo suppressed the expression of pro-inflammatory mediators, IL-6 and TNFα, and pro-inflammatory chemokines, COX-2 and iNOS. This study showed that cell migration was significantly inhibited in a Mi-Exo NP-dependent manner. We also evaluated the expression of TGFβ1 and TGFβ3 on the basis of mRNA and protein levels. Furthermore, the role of functional behavior of Mi-Exo in TGFβ1 maturation was explored. This is the first study to demonstrate that Mi-Exo may target the TGFβ signaling pathway, which plays important roles in scar-free wound healing.

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.

Effect of storage, temperature, and extraction kit on the phylogenetic composition detected in the human milk microbiota

Human milk is considered the optimum feeding regime for newborns and is a source of bacteria for the developing infant gastrointestinal tract. However, as with all low biomass samples, standardization across variabilities such as sample collection, storage, and extraction methods is needed to eliminate discrepancies in microbial composition across studies. The aim of this study was to investigate how different storage methods, temperatures, preservatives, and extraction kits influence the human milk microbiome, compared to fresh samples. Breast milk samples were processed via six different methods: fresh (Method 1), frozen at -80°C (Method 2), treated with RNAlater and stored at 4°C or -80°C (Methods 3 and 4), and treated with Milk Preservation Solution at room temperature (Methods 5 and 6). Methods 1-5 were extracted using PowerFoodTM Microbial DNA Isolation kit (Mobio), and Method 6 was extracted using Milk DNA Preservation and Isolation kit (Norgen BioTek). At genus level, the most abundant genera were shared across Methods 1-5. Samples frozen at -80°C had fewest significant changes while samples treated and extracted using Milk Preservation and Isolation kit had the most significant changes when compared to fresh samples. Diversity analysis indicated that variation in microbiota composition was related to the method and extraction kit used. This study highlighted that, when extraction from fresh milk samples is not an option, freezing at -80°C is the next best option to preserve the integrity of the milk microbiome. Furthermore, our results demonstrate that choice of extraction kit had a profound impact on the microbiota populations detected in milk.

PCR-Based Direct Detection of Streptococcus uberis from Subclinical and Clinical Dairy Cattle Milk Samples

Streptococcus uberis is one of the leading causes worldwide of mastitis in the dairy industry, with the most likely sources of infection attributed to environmental reservoirs such as contaminated bedding materials. Early detection of those cases most likely to progress to clinical disease would lead to improved animal welfare, a critical component of overall health and productivity. A multiplex PCR-based diagnostic test was developed for detection of S. uberis directly from milk and targeting two genes previously identified as important for intramammary colonisation and persistence in dairy cattle. Results indicated the threshold for detection directly from milk was 20,000 CFU/ml and this was achieved without the need for preenrichment. In addition, S. uberis could be identified from milk samples collected during intramammary challenge studies, prior to clinical signs of infection and at much lower detection limits. The PCR test developed for confirmation of the presence of S. uberis directly from infected milk has potential value as a diagnostic test to identify early infection and/or to confirm that antibiotic therapy has been successful.

High-throughput sequencing provides new insights into the roles and implications of core microbiota present in pasteurized milk

Residual microorganisms in dairy products are closely related to their quality deterioration and safety. Based on the minimum sterilization conditions required by Grade A Pasteurized Milk Ordinance, this study explored the microbiota present in milk products that were high temperature short time pasteurized at 72, 75, 80, 83, or 85 °C for 15 s, 20 s, and 30 s separately. Based on high-throughput sequencing results, 6 phyla and 18 genera were identified as dominant microbiota. Proteobacteria and Firmicutes were the maior bacteria in phyla, and each comprising more than 50%. Pseudomonas was account for more than 42% of all the genera detected in all samples. Moreover, the changes in flavor substances in pasteurized milk, including 16 free amino acids, 9 fatty acids, and 17 volatile compounds, were detected using principal component and multi factor analyses. The Pearson correlation coefficient analysis identified six bacteria genera as the core functional microbiota that significantly affected the flavor compounds and the safety and quality of pasteurized milk. Interestingly, Pseudomonas, Omithimimicrobium, Cyanobacteria and Corynebacterium had positive correlations with the flavor substances, whereas Streptococcus and Paeniclostridium had significant negative correlations with these substances. The results may help enhance the quality control of dairy products and can be used as indicators of microbial contamination of pasteurized dairy products.

Acinetobacter spp. in food and drinking water - A review

Acinetobacter spp. has emerged as a pathogen of major public health concern due to their increased resistance to antibiotics and their association with a wide range of nosocomial infections, community-acquired infections and war and natural disaster-related infections. It is recognized as a ubiquitous organism however, information about the prevalence of different pathogenic species of this genus in food sources and drinking water is scarce. Since the implementation of molecular techniques, the role of foods as a source of several species, including the Acinetobacter baumannii group, has been elucidated. Multidrug resistance was also detected among Acinetobacter spp. isolated from food products. This highlights the importance of foods as potential sources of dissemination of Acinetobacter spp. between the community and clinical environments and reinforces the need for further investigations on the potential health risks of Acinetobacter spp. as foodborne pathogens. The aim of this review was to summarize the published data on the occurrence of Acinetobacter spp. in different food sources and drinking water. This information should be taken into consideration by those responsible for infection control in hospitals and other healthcare facilities.

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.

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.

Short communication: Odd-chain and branched-chain fatty acid concentrations in bovine colostrum and transition milk and their stability under heating and freezing treatments

Although odd-chain fatty acids (OCFA) and branched-chain fatty acids (BCFA) are found in bovine milk and have some positive influences on human and animal health, their concentrations in bovine colostrum and transition milk have not been reported. In this study, we reported the OCFA and BCFA concentrations in colostrum and transition milk and their stability after heating or freezing treatments (or both), which are processes commonly applied in dairy calf management. Milk samples were collected from 12 Holstein dairy cows (6 primiparous and 6 multiparous) at the first milking (colostrum), fifth milking (transition milk), and ninth milking (mature milk) after calving, respectively, and were used for fatty acid analysis using gas chromatography. The sum concentration of OCFA and BCFA (termed OBCFA) was 134 mg/100 g of milk in the colostrum, which was 24% and 35% lower than that in the transition milk and mature milk, respectively. Among these fatty acids detected, C15:0 and C17:0 were the top 2 abundant fatty acids in all milk types, accounting for 20 to 25% and 21 to 24% of the total concentration of OBCFA, respectively. Additionally, anteiso-C17:0 was the most abundant BCFA, followed by iso-C17:0, anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C18:0, and iso-C14:0 in 3 types of milk. Significant interactions between milk type and cow parity were observed for all OCFA and BCFA concentrations. The milk samples were also treated with heating (at 65°C for 60 min), freezing (at -20°C for 30 d), and heating and freezing (at 65°C for 60 min and then at -20°C for 30 d), and milk OCFA and BCFA concentrations were similar between these treatments. In conclusion, the OBCFA concentration was lower in colostrum, compared with transition and mature milks, and it remained stable after heating and freezing treatments.

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.

Characterization of Bacillus cereus sensu lato isolates from milk for consumption; phylogenetic identity, potential for spoilage and disease

This study addresses the biodiversity of Bacillus cereus group population present along the value chain of milk for consumption. The B. cereus population did not grow and remained mainly unaltered during storage of milk at 4 °C while storage at a suboptimal temperature at 8 °C (representative of a broken cold chain) caused a major shift in its composition. Mesophilic strains dominated the B. cereus population in raw milk and after storage at 4 °C, while psycrotrophic strains dominated after storage at 8 °C. All psycrotrophic and mesophilic isolates (n = 368) demonstrated high spoilage potentials of the milk components. Fifteen out of 20 mesophilic isolates but only two out of 40 psychrotrophic isolates, exhibited vero cell toxicity. No genes encoding the emetic toxin cereulide were detected in the genomes of 100 milk isolates while 14 of them harbored the enterotoxin genes cytK1/cytK2. Both psycrotrophic and mesophilic isolates carried the enterotoxin genes nheA and hblA. Together, the results provide insight into the composition and properties, of the B. cereus population present in milk along the value chain and during storage at optimal refrigerated temperature and at suboptimal temperature. This knowledge is useful in the dairy industry's work to assure high quality products and for risk assessment.

Microbial composition of sweetness-enhanced yoghurt during fermentation and storage

The reformulation of dairy products to contain less added sugar can contribute to reducing sugar consumption, thereby reducing the risk of non-communicable diseases. The objective of this study was to investigate the microbial ecology of reformulated yoghurt, which was produced using bi-enzymatic modification of lactose to increase its sweetness by a factor of 2–3. Ultimately, this reformulation strategy could reduce the amount of added sugar needed for equal sweetness of the end product. The bi-enzymatic modification relied on utilisation of a β-galactosidase enzyme to convert the milk sugar lactose to galactose and glucose, followed by the enzymatic conversion of the glucose moiety to fructose using a glucose isomerase. The microbial ecology of reformulated yoghurt produced with two mixed starter culture preparations containing either Streptococcus (S.) thermophilus and Lactobacillus (Lb.) delbrueckii or S. thermophilus, Lb. acidophilus and Bifidobacterium sp. strains, was analysed during fermentation and cool storage using 16S rRNA based metagenomics. None of the yoghurt samples showed a significant difference in microbial composition between sweetness-enhanced and regular milk at all sampling time points during manufacture and storage of yoghurt. However, a significant difference between the microbiota of inoculated milk before and after fermentation was observed. In both types of yoghurt, the starter culture genera dominated the microbial ecology at the end of fermentation as expected, reducing the possibility of growth of potentially pathogenic or spoilage bacteria possibly resulting from a changed carbohydrate spectrum.

Criteria to Qualify Microorganisms as "Probiotic" in Foods and Dietary Supplements

Still relevant after 19 years, the FAO/WHO definition of probiotics can be translated into four simple and pragmatic criteria allowing one to conclude if specific strains of microorganisms qualify as a probiotic for use in foods and dietary supplements. Probiotic strains must be (i) sufficiently characterized; (ii) safe for the intended use; (iii) supported by at least one positive human clinical trial conducted according to generally accepted scientific standards or as per recommendations and provisions of local/national authorities when applicable; and (iv) alive in the product at an efficacious dose throughout shelf life. We provide clarity and detail how each of these four criteria can be assessed. The wide adoption of these criteria is necessary to ensure the proper use of the word probiotic in scientific publications, on product labels, and in communications with regulators and the general public.

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

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

Recipe for a Healthy Gut: Intake of Unpasteurised Milk Is Associated with Increased Lactobacillus Abundance in the Human Gut Microbiome

INTRODUCTION

The gut microbiota plays a role in gut-brain communication and can influence psychological functioning. Diet is one of the major determinants of gut microbiota composition. The impact of unpasteurised dairy products on the microbiota is unknown. In this observational study, we investigated the effect of a dietary change involving intake of unpasteurised dairy on gut microbiome composition and psychological status in participants undertaking a residential 12-week cookery course on an organic farm.

METHODS

Twenty-four participants completed the study. The majority of food consumed during their stay originated from the organic farm itself and included unpasteurised milk and dairy products. At the beginning and end of the course, participants provided faecal samples and completed self-report questionnaires on a variety of parameters including mood, anxiety and sleep. Nutrient intake was monitored with a food frequency questionnaire. Gut microbiota analysis was performed with 16S rRNA gene sequencing. Additionally, faecal short chain fatty acids (SCFAs) were measured.

RESULTS

Relative abundance of the genus Lactobacillus increased significantly between pre- and post-course time points. This increase was associated with participants intake of unpasteurised milk and dairy products. An increase in the faecal SCFA, valerate, was observed along with an increase in the functional richness of the microbiome profile, as determined by measuring the predictive neuroactive potential using a gut-brain module approach.

CONCLUSIONS

While concerns in relation to safety need to be considered, intake of unpasteurised milk and dairy products appear to be associated with the growth of the probiotic bacterial genus, Lactobacillus, in the human gut. More research is needed on the effect of dietary changes on gut microbiome composition, in particular in relation to the promotion of bacterial genera, such as Lactobacillus, which are recognised as being beneficial for a range of physical and mental health outcomes.

Metagenomic and volatile profiles of ripened cheese obtained from dairy ewes fed a dietary hemp seed supplementation

Chemical and organoleptic properties of dairy products largely depend on the action of microorganisms that tend to be selected in cheese during ripening in response to the availability of specific substrates. The aim of this work was to evaluate the effects of a diet enriched with hemp seeds on the microbiota composition of fresh and ripened cheese produced from milk of lactating ewes. Thirty-two half-bred ewes were involved in the study, in which half (control group) received a standard diet, and the other half (experimental group) took a diet enriched with 5% hemp seeds (on a DM basis) for 35 d. The dietary supplementation significantly increased the lactose in milk, but no variations in total fat, proteins, caseins, and urea were observed. Likewise, no changes in total fat, proteins, or ash were detected in the derived cheeses. The metagenomic approach was used to characterize the microbiota of raw milk and cheese. The phyla Proteobacteria and Firmicutes were in equally high abundance in both control and experimental raw milk samples, whereas Bacteroidetes was less abundant. The scenario changed when considering the dairy products. In all cheese samples, Firmicutes was clearly predominant, with Streptococcaceae being the most abundant family in the experimental group. The reduction of taxa observed during ripening was in accordance with the increment (relative abundance) of the starter culture Lactococcus lactis and Streptococcus thermophilus, which together dominate the microbial community. The analysis of the volatile profile in ripened cheeses led to the identification of 3 major classes of compounds: free fatty acids, ketones, and aldehydes, which indicate a prevalence of lipolysis compared with the other biochemical mechanisms that characterize the cheese ripening.

Antimicrobial resistance genes in raw milk for human consumption

The increasing prevalence of antimicrobial resistance (AMR) is a significant threat to global health. More and more multi-drug-resistant bacterial strains cause life-threatening infections and the death of thousands of people each year. Beyond disease control animals are often given antibiotics for growth promotion or increased feed efficiency, which further increase the chance of the development of multi-resistant strains. After the consumption of unprocessed animal products, these strains may meet the human bacteriota. Among the foodborne and the human populations, antimicrobial resistance genes (ARGs) may be shared by horizontal gene transfer. This study aims to test the presence of antimicrobial resistance genes in milk metagenome, investigate their genetic position and their linkage to mobile genetic elements. We have analyzed raw milk samples from public markets sold for human consumption. The milk samples contained genetic material from various bacterial species and the in-depth analysis uncovered the presence of several antimicrobial resistance genes. The samples contained complete ARGs influencing the effectiveness of acridine dye, cephalosporin, cephamycin, fluoroquinolone, penam, peptide antibiotics and tetracycline. One of the ARGs, PC1 beta-lactamase may also be a mobile element that facilitates the transfer of resistance genes to other bacteria, e.g. to the ones living in the human gut.

Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder

Microorganisms from the environment can enter the dairy supply chain at multiple stages, including production, milk collection, and processing, with potential implications for quality and safety. The ability to track these microorganisms can be greatly enhanced by the use of high-throughput DNA sequencing (HTS). Here HTS, both 16S rRNA gene amplicon and shotgun metagenomic sequencing were applied to investigate the microbiomes of fresh mid- and late-lactation milk collected from farm bulk tanks, collection tankers, milk silos, skimmed milk silos, a cream silo, and powder samples to investigate the microbial changes throughout a skim milk powder manufacturing process. 16S rRNA gene analysis established that the microbiota of raw milks from farm bulk tanks and in collection tankers were very diverse but that psychrotrophic genera associated with spoilage, Pseudomonas and Acinetobacter, were present in all samples. Upon storage within the whole-milk silo at the processing facility, the species Pseudomonas fluorescens and Acinetobacter baumannii became dominant. The skimmed milk powder generated during the mid-lactation period had a microbial composition that was very different from that of raw milk; specifically, two thermophilic genera, Thermus and Geobacillus, were enriched. In contrast, the microbiota of skimmed milk powder generated from late-lactation milk more closely resembled that of the raw milk and was dominated by spoilage-associated psychrotrophic bacteria. This study demonstrates that the dairy microbiota can differ significantly across different sampling days. More specifically, HTS can be used to trace microbial species from raw milks through processing to final powdered products.IMPORTANCE Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from raw milk to the end product. Routine implementation of high-throughput sequencing would elucidate the factors that influence population dynamics. This will enable a manufacturer to adopt control measures specific to each stage of processing and respond in an effective manner, which would ultimately lead to increased food safety and quality.

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

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

Analysis of the Bacterial Diversity of Paipa Cheese (a Traditional Raw Cow's Milk Cheese from Colombia) by High-Throughput Sequencing

Background: Paipa cheese is a traditional, semi-ripened cheese made from raw cow’s milk in Colombia. The aim of this work was to gain insights on the microbiota of Paipa cheese by using a culture-independent approach. Method: two batches of Paipa cheese from three formal producers were sampled during ripening for 28 days. Total DNA from the cheese samples was used to obtain 16S rRNA gene sequences by using Illumina technology. Results: Firmicutes was the main phylum found in the cheeses (relative abundances: 59.2–82.0%), followed by Proteobacteria, Actinobacteria and Bacteroidetes. Lactococcus was the main genus, but other lactic acid bacteria (Enterococcus, Leuconostoc and Streptococcus) were also detected. Stapylococcus was also relevant in some cheese samples. The most important Proteobacteria were Enterobacteriaceae, Aeromonadaceae and Moraxellaceae. Enterobacter and Enterobacteriaceae (others) were detected in all cheese samples. Serratia and Citrobacter were detected in some samples. Aeromonas and Acinetobacter were also relevant. Other minor genera detected were Marinomonas, Corynebacterium 1 and Chryseobacterium. The principal coordinates analysis suggested that there were producer-dependent differences in the microbiota of Paipa cheeses. Conclusions: lactic acid bacteria are the main bacterial group in Paipa cheeses. However, other bacterial groups, including spoilage bacteria, potentially toxin producers, and bacteria potentially pathogenic to humans and/or prone to carry antimicrobial resistance genes are also relevant in the cheeses.

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.