The complex microbiota of raw milk

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables

Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (n = 241). Concurrent chemical analysis of the protein, fat, lactose, total solids, nonprotein nitrogen contents, and titratable acidity (TA) of the same raw milk were performed. Although the raw milk microbiota was highly diverse, a core microbiota was found, with Pseudomonas_E, Lactococcus, Acinetobacter, and Leuconostoc present in all samples. Microbiota diversity significantly differed by season and location, with differences in seasonality and geography corresponding to 11.8% and 10.5% of the variation in the microbiota. Functional and antibiotic resistance profiles also varied across season and location. The analysis of other metadata revealed additional interactions, such as an association between mean daily air and grass temperatures with the abundance of spoilage taxa like Pseudomonas species. Correlations were identified between pathogenic, mastitis-related species, fat content, and the number of sun hours, suggesting a seasonal effect. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables, and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota.

IMPORTANCE

The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.

The Transmission of Campylobacter Strains in Dairy Herds in Different Housing Systems

Cattle are frequent carriers of Campylobacter spp.; therefore, these bacteria may be transmitted to humans through meat or milk. Campylobacter spp. in raw milk derives most commonly from secondary fecal contamination during the milking process; however, the udder excretion of Campylobacter may be a cause of milk-borne infection. Studies were carried out on a Campylobacter-positive farm with two different housing systems (with free-stall and tie-stall systems). The sampling process comprised several stages, including samples being taken from animals, such as from raw milk and feces, and from the environment, such as the from floor in the milking parlor and from teat cups. None of the individual raw milk samples or swabs from the floor in the parlor before the milking process were positive for Campylobacter spp. Simultaneously, Campylobacter spp. was isolated from all swabs from the floor after the milking process and in the bulk tank milk samples from the two farms. The incidence of Campylobacter isolated from fecal and teat swab samples ranged from 15.4% to 26.7% and from 8.9% to 25%, respectively. Altogether, 59 recovered Campylobacter isolates were classified, based on sequencing of the flaA short variable region, showing 15 different allele types, and the majority of them were distributed among one farm. Analysis of the virulence and antimicrobial properties showed that genes related to adherence, invasion and cytotoxicity were widely distributed among the Campylobacter recovered strains. In relation to AMR, multidrug resistance was noted in 16.1% of strains.

Antibiograms, multidrug resistance, and milk-related parameters of bacteria isolated from milk of dairy cattle in Phatthalung, Thailand

Background and Aim

Milk, a nutritious food, is widely consumed in human diets; however, contamination by micro-organisms can negatively impact its quality and consumer health. Contamination by micro-organisms affects the quality of milk, which can affect the quality of the milk production chain. This study aimed to determine the changes in milk composition and antibiotic susceptibility related to bacteria isolated from dairy cow milk.

Materials and Methods

Raw milk samples were collected from 72 dairy cows. All milk samples were subjected to the California Mastitis Test (CMT) for CMT score determination. We also investigated milk composition, bacterial culture (BC), and antibiotic susceptibility.

Results

About 47.22% and 30.56% of dairy cattle were positive for CMT + BC and automatic somatic cell count (ASCC) + BC, respectively. Fecal appearance and animal age were found to be risk factors for ASCC + BC positivity in dairy cattle. Bacteria were found in approximately 76% of milk samples, with the most common isolated species being α-hemolytic Streptococcus spp., coagulase-negative Staphylococcus spp., and Escherichia coli. Of these, 70% are resistant to at least one antibiotic. Variation in the multidrug resistance pattern was high in Klebsiella spp.

Conclusions

Fecal appearance and animal age are risk factors for ASCC + BC positivity in dairy cattle. This study identified antibiotic and multidrug resistance patterns, which require comprehensive studies and effective surveillance systems. Remarkably, the use of antibiotic therapy in dairy cattle should be monitored.

Microbiological risk assessment and resistome analysis from shotgun metagenomics of bovine colostrum microbiome

Colostrum is known for its nutraceutical qualities, probiotic attributes, and health benefits. The aim of this study was to profile colostrum microbiome from bovine in rural sites of a developing country. The focus was on microbiological safety assessments and antimicrobial resistance, taking into account the risks linked with the consumption of raw colostrum. Shotgun sequencing was employed to analyze microbiome in raw buffalo and cow colostrum. Alpha and beta diversity analyses revealed increased inter and intra-variability within colostrum samples' microbiome from both livestock species. The colostrum microbiome was mainly comprised of bacteria, with over 90% abundance, whereas fungi and viruses were found in minor abundance. Known probiotic species, such as Leuconostoc mesenteroides, Lactococcus lactis, Streptococcus thermophilus, and Lactobacillus paracasei, were found in the colostrum samples. A relatively higher number of pathogenic and opportunistic pathogenic bacteria were identified in colostrum from both animals, including clinically significant bacteria like Clostridium botulinum, Pseudomonas aeruginosa, Escherichia coli, and Listeria monocytogenes. Binning retrieved 11 high-quality metagenome-assembled genomes (MAGs), with three MAGs potentially representing novel species from the genera Psychrobacter and Pantoea. Notably, 175 antimicrobial resistance genes (ARGs) and variants were detected, with 55 of them common to both buffalo and cow colostrum metagenomes. These ARGs confer resistance against aminoglycoside, fluoroquinolone, tetracycline, sulfonamide, and peptide antibiotics. In conclusion, this study describes a thorough overview of microbial communities in buffalo and cow colostrum samples. It emphasizes the importance of hygienic processing and pasteurization in minimizing the potential transmission of harmful microorganisms linked to the consumption of colostrum.

The usefulness of the MALDI-TOF MS technique in the determination of dairy samples' microbial composition: comparison of the new EXS 2600 system with MALDI Biotyper platform

This study compared the EXS 2600 system with the MALDI Biotyper for identifying microorganisms in dairy samples. Of the 196 bacterial isolates from milk, whey, buttermilk, cream, and dairy wastewater, the species and genus consistent identification between two systems showed 74% and 99%, respectively. However, the level of species identification rate exhibited a difference, which was higher in Zybio than in Bruker-76.0% and 66.8%, respectively. Notably, the EXS 2600 system performed better with certain yeast species and H. alvei, while the Biotyper excelled with Pseudomonas bacteria. Unique microbial compositions were found in 85% of dairy samples, with whey and buttermilk having the highest diversity. This research highlights the EXS 2600's potential as a reliable dairy microbial identification tool and underscores the need for a more diverse and comprehensive spectral database, despite the database's focus on clinical applications (as announced).

Microbial diversity in camel milk from Xinjiang, China as revealed by metataxonomic analysis

The quality of raw camel milk is affected by its bacterial composition and diversity. However, few studies have investigated the bacterial composition and diversity of raw camel milk. In this study, we obtained 20 samples of camel milk during spring and summer in Urumqi and Hami, Xinjiang, China. Single-molecule real-time sequencing technology was used to analyze the bacterial community composition. The results revealed that there were significant seasonal differences in the bacterial composition and diversity of camel milk. Overall, Epilithonimonas was the most abundant bacterial genus in our samples. Through the annotated genes inferred by PICRUSt2 were mapped against KEGG database. Non-parametric analysis of the bacterial community prediction function revealed a strong bacterial interdependence with metabolic pathways (81.83%). There were clear regional and seasonal differences in level 3 metabolic pathways such as fat, vitamins, and amino acids in camel milk. In addition, we identified lactic acid bacteria in camel milk with antibacterial and anti-tumor activities. Our findings revealed that camel milk from Xinjiang had serious risk of contamination by psychrophilic and pathogenic bacteria. Our research established a crucial theoretical foundation for ensuring the quality and safety of camel milk, thereby contributing significantly to the robust growth of China's camel milk industry.

Fecal microbiota colonization dynamics in dairy heifers associated with early-life rumen microbiota modulation and gut health

Early-life modulation of rumen microbiota holds promise for enhancing calf growth, health, and long-term production in ruminants. However, limited attention has been given to the impact of rumen microbiota modulation on the establishment of hindgut microbiota. In this study, fecal microbiota development was examined in identical twin calves for 12 months. The treatment group (T-group) received adult cow fresh rumen liquid inoculum during the pre-weaning period, while the control group did not (C-group). The effects of inoculum were assessed on calf gut health and as microbial seeding route into the hindgut. The early rumen modulation had no effect on age-related fecal microbiota development. The fecal bacterial community evolved gradually following dietary changes and categorized into pre-weaning and post-weaning communities. Bacterial richness increased with age and stabilized at month 9, while between-sample variation reduced in post-weaning samples. Archaeal load in fecal samples increased after month 4, while archaeal richness increased and stabilized in both groups by month 9. Between-sample similarity was higher during the pre-weaning period, with increased dissimilarity from month 4 onward. Anaerobic fungi were detected in feces at month 4, with richness peaking at month 7. Before month 6, fungal community composition distinctly differed from mature communities. When colostrum, calf rumen, and donor inoculum were evaluated as seeding sources for hindgut colonization, the calf's own rumen was identified as the primary seeding source for fecal bacteria and fungi. Colostrum was a source for several bacteria detected in feces, but these were of temporary importance until weaning. The donor inoculum had limited impact on gut health as diarrhea rates were similar between the T-group and C-group. In conclusion, early-life microbiota modulation shows potential in ruminant development. However, a more targeted approach with bacteria adapted to the hindgut environment may be necessary to modulate hindgut effectively. This research contributes to our understanding of the complex relationship between gut microbiota and calf health and growth.

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.

Fermented Mare Milk and Its Microorganisms for Human Consumption and Health

Mare milk is consumed by approximatively 30 million people in the world. In countries in Asia and East Europe, mare milk is mainly consumed as source of fermented products, called koumiss, airag or chigee, alcoholic beverages obtained by means of a culture of bacteria and lactose-fermenting yeasts. Recent research concerning mare milk and its derivatives deals mainly with their potential employment for human health. Studies about the isolation and characterization of Lactobacillus spp. and yeasts from koumiss have been aimed at assessing the potential functional properties of these micro-organisms and to find their employment for the industrial processing of mare milk. The aim of this literature review is to summarize recent research about microorganisms in fermented mare milk products and their potential functional properties.

Comparative analysis of microbial succession and proteolysis focusing on amino acid pathways in Asiago-PDO cheese from two dairies

In this study, a comprehensive and comparative analysis was conducted on Italian Asiago-PDO cheese obtained from two different dairies named Dairy I and Dairy II using industrial and natural fermented milk, respectively. The analysis encompassed the evaluation of chemical composition, the succession of the microbiota during manufacture and ripening, and proteolysis mainly focusing on free individual amino acid (FAA) profiles. A metagenomic approach was used to investigate the cheese microbiome functionality. Differences in gross chemical composition were more evident during ripening, with Dairy II showing higher variability within batches. The microbiota varied significantly between the two dairies and ripening stages. The choice of starter culture shaped the microbiota during production and affected the microbial diversity of non-starter lactic acid bacteria (NSLAB) originated from the raw milk during ripening. Peptide chromatographic profiles and FAA concentrations increased as ripening progressed, with Dairy I showing higher production of FAA. Functional analysis of the metagenomes linked species to specific amino acid metabolism/catabolism pathways. The amino acid metabolism pathways, particularly those related to aromatic amino acids, lysine, and branched-chain amino acids, were affected by the presence of specific NSLAB species, which differed between the two dairies. The results obtained in this study reveal the impact of starter culture on peculiar cheese microbiota assemblies, which selectively targets amino acid pathways, providing insights into the potential flavor and aroma characteristics of Asiago-PDO cheese.

The Investigation of Changes in Bacterial Community of Pasteurized Milk during Cold Storage

The quality of pasteurized milk is commonly assessed through microbiological analysis, with variations in storage conditions significantly impacting the suppression of bacterial growth throughout the milk's shelf life. This study investigated the dynamics of total bacterial counts (TBCs) and bacterial community shifts in milk that underwent pasteurization at 80 °C for 15 s. The milk was subsequently stored at 4 °C for varying intervals of 1, 4, 7, 10, 13, and 16 days. Culture-based testing revealed a significant TBC increase during the storage period spanning 1 to 16 days (up to -log10 4.2 CFU/mL at day 16). The TBC in pasteurized milk exhibited accelerated microbial growth from day 13 onwards, ultimately peaking on day 16. Bacillus was detected through 16S rRNA identification. Principal component analysis demonstrated a significant impact of storage time on bacterial communities in pasteurized milk. Analysis of bacterial diversity revealed a negative correlation between the Shannon index and the duration of pasteurized milk storage. Using high-throughput sequencing, Streptococcus and Acinetobacter were detected as prevalent bacterial genera, with Streptococcus dysgalactiae and Streptococcus uberis showing as dominant taxa. The presence of Streptococcus dysgalactiae and Streptococcus uberis in pasteurized milk might be attributed to the initial contamination from raw milk with mastitis. This study offers new evidence of the prevalence of bacterial community in pasteurized milk, thereby adding value to the enhancement of quality control and the development of strategies for reducing microbial risks.

The Role of Autochthonous Levilactobacillus brevis B1 Starter Culture in Improving the Technological and Nutritional Quality of Cow's Milk Acid-Rennet Cheeses-Industrial Model Study

In the study, an attempt was made to develop an innovative technology for cheese manufacturing. It was hypothesized that selected autochthonous lactic acid bacteria as a starter culture are more suitable for the production of acid-rennet cheeses of good technological and sensory quality. The study aimed to assess the possibility of using the strain Levilactobacillus brevis B1 (L. brevis B1) as a starter culture to produce acid-rennet cheeses using raw cow's milk. Two variants of cheese were manufactured. The control variant (R) was coagulated with microbial rennet and buttermilk, and the other variant (B1) was inoculated with rennet and L. brevis B1 starter culture. The effect of the addition of these autochthonous lactic acid bacteria on selected physicochemical characteristics, durability, the composition of fatty acids, cholesterol, Iipid Quality Indices, and microbiological and sensory quality of acid-rennet cheeses was determined during a 3-month period of storage. The dominant fatty acids observed in the tested cheeses were saturated fatty acids (SFA) (68.43-69.70%) and monounsaturated fatty acids (MUFA) (25.85-26.55%). Significantly higher polyunsaturated fatty acid (PUFA) content during storage was observed for B1 cheeses. The B1 cheeses were characterized by lower cholesterol content compared to cheese R and showed better indexes, including the Index of atherogenicity, Index of thrombogenicity, DFA, OFA, H/H, and HPI indexes, than the R cheese. No effect of the tested L. brevis B1 on sensory quality was observed in relation to the control cheeses during 3 months of storage. The results of the research indicate the possibility of using the L. brevis B1 strain for the production of high-quality, potentially probiotic acid-rennet cheeses.

The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety

Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses.

Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia

Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.

The preterm human milk microbiota fluctuates by postpartum week and is characterized by gestational age and maternal BMI

IMPORTANCE

Despite a growing recognition that the type of nutrition received by preterm infants influences their intestinal microbiome and health outcomes, the microbiota of mother's own milk (MOM), pasteurized donor human milk (PDHM), and infant formula remain poorly characterized. In our study, we found that the structure of microbial communities, bacterial diversity, and relative abundances of specific genera were significantly different between MOM, PDHM, and formula. Additionally, our results suggest that the microbiota of MOM changes as a function of time and maternal factors. Lastly, we identified three lactotypes within MOM that have distinct microbial compositions and described the maternal factors associated with them. These findings set the stage for future research aimed at advancing our knowledge of the microbiota of preterm infant nutrition and the specific influence it may have on health outcomes.

Antilisterial activity of raw sheep milk from two native Epirus breeds: Culture-dependent identification, bacteriocin gene detection and primary safety evaluation of the antagonistic LAB biota

Raw milk from native small ruminant breeds in Epirus, Greece, is a valuable natural source of autochthonous lactic acid bacteria (LAB) strains with superior biotechnological properties. In this study, two bulk milks (RM1, RM2) from two local sheep yards, intended for traditional Kefalotyri cheese production, were preselected for bacteriocin-like antilisterial activity by in vitro tests. Their antagonistic LAB biota was quantified followed by polyphasic (16S rRNA gene sequencing; IGS for Enterococcus; a multiplex-PCR for Leuconostoc) identification of 42 LAB (RM1/18; RM2/24) isolates further evaluated for bacteriocin encoding genes and primary safety traits. Representative isolates of the numerically dominant mesophilic LAB were Leuconostoc mesenteroides (10) in both RMs, Streptococcus parauberis (7) in RM2, and Lactococcus lactis (1) in RM1; the subdominant thermophilic LAB isolates were Enterococcus durans (8), E. faecium (6), E. faecalis (3), E. hirae (1), E. hermanniensis (1), Streptococcus lutetiensis (2), S. equinus (1) and S. gallolyticus (1). Based on their rpoB, araA, dsr and sorA profiles, six Ln. mesenteroides strains (8 isolates) were atypical lying between the subspecies mesenteroides and dextranicum, whereas two strains profiled with Ln. mesenteroides subsp. jonggajibkimchi that is first-time reported in Greek dairy food. Two RM1 E. faecium strain biotypes (3 isolates) showed strong, enterocin-mediated antilisterial activity due to entA/entB/entP possession. One E. durans from RM1 possessed entA and entP, while additional nine RM2 isolates of the E. faecium/durans group processed entA or entP singly. All showed direct (cell-associated) antilisterial activity only, as also both S. lutetiensis strains from RM2 did strongly. Desirably, no LAB isolate was β-hemolyrtic, or cytolysin-positive, or possessed vanA, vanB for vancomycin resistance, or agg, espA, hyl, and IS16 virulence genes. However, all three E. faecalis from RM2 possessed gelE and/or ace virulence genes. In conclusion, all Ln. mesenteroides strains, the two safe, enterocin A-B-P-producing E. faecium strains, and the two antilisterial S. lutetiensis strains should be validated further as potential costarter or adjunct cultures in Kefalotyri cheese. The prevalence of α-hemolytic pyogenic streptococci in raw milk, mainly S. parauberis in RM2, requires consideration in respect to subclinical mastitis in sheep and the farm hygiene overall.

Phylogenetic variation in raw cow milk microbiota and the impact of forage combinations and use of silage inoculants

Introduction

The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.

Methods

We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.

Results and discussion

Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by Enterobacteriaceae, Microbacteriaceae, Beijerinckiaceae, and Sphingomonadaceae, the GL and GLICI communities showed high proportions of Leuconostocaceae and Acetobacteraceae, respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by Enterobacteriaceae and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.

High throughput qPCR analyses suggest that Enterobacterales of French sheep and cow cheese rarely carry genes conferring resistances to critically important antibiotics for human medicine

Bacteria present in raw milk can carry acquired or intrinsic antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, only a few studies have evaluated raw milk cheese as a potential reservoir of ARGs. This study thus aimed at providing new data regarding resistance markers present in raw milk cheese. Sheep (n = 360) and cow (n = 360) cheese samples produced in France were incubated in buffered peptone water supplemented with acriflavin or novobiocin; as corroborated by 16S metabarcoding, samples were enriched in Gram-negative bacteria since Escherichia coli and Hafnia alvei respectively accounted for 40 % and 20 % of the samples' microbiota. Screening of the samples for the presence of 30 ARGs and 16 MGEs by high throughput qPCR array showed that nine ARGs conferring resistances to 1st-generation beta-lactams, aminoglycosides, trimethoprim/sulfonamides and tetracyclines occurred in >75 % of both sheep and cow samples. This is neither surprising nor alarming since these resistance genes are widely spread across the One Health human, animal and environmental sectors. Conversely, genes conferring resistances to last-generations cephalosporins were rarely identified, while those conferring resistances to carbapenems or amikacin, which are restricted to human use, were never detected. Multiple MGEs were detected, the most frequent ones being IncF plasmids, confirming the potential transmission of ARGs. Our results are in line with the few studies of the resistome of milk or milk cheese showing that genes conferring resistances to 1st-generation beta-lactams, aminoglycosides and tetracyclines families are widespread, while those conferring resistances to critically important antibiotics are rare or absent.

Characterisation of Milk Microbiota from Subclinical Mastitis and Apparently Healthy Dairy Cattle in Free State Province, South Africa

Bovine mastitis is an inflammation of the udder tissue of the mammary gland brought on by microbial infections or physical damage. It is characterised by physical, chemical, and biological changes in the udder and milk. While several different bacterial species have been identified as causative agents of mastitis, many subclinical mastitis (SCM) cases remain culture-negative. The aim of this study was to characterise milk microbiota from SCM and apparently healthy dairy cows (non-SCM) by 16S rRNA sequencing. Alpha-diversity metrics showed significant differences between SCM cows and non-SCM counterparts. The beta-diversity metrics in the principal coordinate analysis significantly clustered samples by type (PERMANOVA test, p < 0.05), while non-metric dimensional scaling did not (PERMANOVA test, p = 0.07). The overall analysis indicated a total of 95 phyla, 33 classes, 82 orders, 124 families, 202 genera, and 119 bacterial species. Four phyla, namely Actinobacteriota, Bacteroidota, Firmicutes, and Proteobacteria collectively accounted for more than 97% of all sequencing reads from SCM and non-SCM cow samples. The most abundant bacterial classes were Actinobacteria, Bacilli, Bacteroidia, Clostridia, and Gammaproteobacteria in non-SCM cow samples, whilst SCM cow samples were mainly composed of Actinobacteria, Alphaproteobacteria, Bacilli, Clostridia, and Gammaproteobacteria. Dominant bacterial species in non-SCM cow samples were Anthropi spp., Pseudomonas azotoformans, P. fragi, Acinetobacter guillouiae, Enterococcus italicus, Lactococcus lactis, whilst P. azotoformans, Mycobacterium bovis, P. fragi, Acinetobacter guillouiae, and P. koreensis were dominant in the SCM cow samples. The current study found differences in bacterial species between SCM and non-SCM cow milk; hence, the need for detailed epidemiological studies.

An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management

Goat milk is produced on mainstream and artisanal farms. It was expected that the farm management may influence the microbial population of the milk. Therefore, we investigated the bacterial content and microbiota composition of raw milk in relation to Dutch goat farm management. After amplicon sequencing we analyzed the taxa at phylum and genus levels, and used the relative values enabling to provide information about the variation among the different samples. On ten farms our results indicated that the number of bacterial colony forming units and microbiota composition of the milk, directly after milking was variable among farms and not related to the farm management system. At the phylum level the phyla Firmicutes, Actinobacteria, Proteobacteria, and to a minor extend Bacteriodota were the dominant phyla in the raw goat milk, together usually comprising 90% of the total bacterial phyla. The most dominant genera were Staphylococcus, Pseudomonas, Lactococcus, Microbacteria, Acinetobacteria, and Corinebacteria. The number of bacterial phyla and genera does not differ between the mainstream and artisanal farms, although the Shannon index may be numerically higher in the mainstream farms as compared to artisanal farms. In addition, the variability is higher among artisanal farms, which may be due to less standardization of the management. The milk microbiota composition differed among farms. Repeated sampling of a farm showed that this changed over time. The lactic acid producing bacteria showed a similar pattern. Variable microbiota richness amount and diversity of microorganisms were present in different farming systems. We concluded that farm-specific management and sampling moment were the major determining factors for the milk microbiota composition.

Effects of Feeding Management System on Milk Production and Milk Quality from Sheep of the Turcana Breed

Milk and dairy products are among the foods preferred by consumers, as they are rich in nutrients, have high biological values, are easily accessible, and present a low risk to health. This study aimed to comparatively analyze the milk from sheep of the Turcana breed that were subjected to different feeding systems. The milk from the sheep was analyzed quantitatively and qualitatively; in this sense, the following were determined: daily milk production (DMY), physical parameters (pH, freezing point), chemical composition (lactose (L), fats (F), total proteins (TP), non-fat solids (Snf)), the content of heavy metals and trace elements (Zn, Cd, Cu, Fe, Mn, Pb), and microbiological parameters (the number of somatic cells (SCC), the total number of aerobic mesophilic germs that develop at 30 °C (NTG), the number of coliform bacteria (CT), the number of Staphylococcus aureus). Administration of the fodder complex produced, on the farm determined a slight quantitative increase in milk production, as well as in fat, protein and lactose content. The content of trace elements Zn, Fe, and Mn registered increases in milk samples from sheep that were administered the fodder complex. The content of heavy metals did not indicate any source of pollution in the grazing area. Furthermore, the microbiological parameters were within the allowed limits, indicating a good general state of health at the emergency level and the absence of microbiological contamination of the milk samples.

Outbreaks of Campylobacteriosis Caused by Drinking Raw Milk in Japan: Evidence of Relationship Between Milk and Patients by Using Whole Genome Sequencing

Raw milk may contain some infectious bacteria and usually requires pasteurization before drinking. In this study, we report rare outbreaks of campylobacteriosis associated with raw milk in Japan, and the application of whole genome sequencing (WGS) to studies on foodborne diseases. In August 2018, there were three outbreaks of campylobacteriosis, presumably caused by the consumption of unpasteurized raw milk, derived from the same farm; thus, these three outbreaks seemed to be associated with a single contaminant at the farm. Therefore, we analyzed Campylobacter jejuni isolates obtained at the three locations using several genetic methods. The sequence type of each isolate, revealed by multilocus sequence typing, was ST-61, and the profile determined using pulsed-field gel electrophoresis was the same; however, neither method could distinguish these from previously obtained strains. Subsequently, we performed WGS and single nucleotide variant (SNV) analysis that provided evidence of clonality, indicating that C. jejuni contamination was attributed to the farm. As in this study, evidence suggests that SNV analysis provides molecular biological support in cases with sufficient epidemiological information. Hence, similar analytical methods may be used in other sporadic cases to elucidate the relevance of the cases.

Dilution Reduces Sample Matrix Effects for Rapid, Direct, and Miniaturised Phenotypic Antibiotic Susceptibility Tests for Bovine Mastitis

The time-consuming nature of current methods for detecting antimicrobial resistance (AMR) to guide mastitis treatment and for surveillance, drives innovation towards faster, easier, and more portable technology. Rapid on-farm testing could guide antibiotic selection, reducing misuse that contributes to resistance. We identify challenges that arise when developing miniaturized antibiotic susceptibility tests (AST) for rapid on-farm use directly in milk. We experimentally studied three factors: sample matrix (specifically milk or spoiled milk); the commensal bacteria found in fresh bovine milk; and result time on the performance of miniaturised AST. Microfluidic "dip-and-test" devices made from microcapillary film (MCF) were able to monitor Gram-negative bacterial growth colourimetrically even in the presence of milk and yoghurt (used to simulate spoiled milk samples), as long as this sample matrix was diluted 1:5 or more in growth medium. Growth detection kinetics using resazurin was not changed by milk at final concentrations of 20% or lower, but a significant delay was seen with yoghurt above 10%. The minimum inhibitory concentration (MIC) for ciprofloxacin and gentamicin was increased in the presence of higher concentrations of milk and yoghurt. When diluted to 1% all observed MIC were within range, indicating dilution may be sufficient to avoid milk matrix interfering with microfluidic AST. We found a median commensal cell count of 6 × 105 CFU/mL across 40 healthy milk samples and tested if these bacteria could alter microfluidic AST. We found that false susceptibility may be observed at early endpoint times if testing some pathogen and commensal mixtures. However, such errors are only expected to occur when a susceptible commensal organism is present at higher cell density relative to the resistant pathogen, and this can be avoided by reading at later endpoints, leading to a trade-off between accuracy and time-to-result. We conclude that with further optimisation, and additional studies of Gram-positive organisms, it should be possible to obtain rapid results for microfluidic AST, but a trade-off is needed between time-to-result, sample dilution, and accuracy.

Microbial Dynamics during labneh Ambaris Production in Earthenware Jars

The responses of various microbial populations to modifications in the physicochemical properties of a food matrix, as well as interactions between these populations already present, are the main factors that shape microbial dynamics in that matrix. This work focused on the study of microbial dynamics during labneh Ambaris production, a traditional Lebanese concentrated fermented goat milk made in jars during 3 months. This was assessed in two earthenware jars at a production facility. DNA metabarcoding of the ITS2 region as well as the V3-V4 region of the 16S rRNA gene was used to characterize the fungal and bacterial communities, respectively. Viable bacterial isolates were also identified by Sanger sequencing of the V1-V4 region of the 16S rRNA gene. Our results showed that the dominant microorganisms identified within labneh Ambaris (Lactobacillus kefiranofaciens, Lentilactobacillus kefiri, Lactococcus lactis, Geotrichum candidum, Pichia kudriavzevii and Starmerella sp.) settle early in the product and remain until the end of maturation with varying abundances throughout fermentation. Microbial counts increased during early fermentation stage, and remained stable during mid-fermentation, then declined during maturation. While microbial compositions were globally comparable between the two jars during mid-fermentation and maturation stages, differences between the two jars were mainly detected during early fermentation stage (D0 until D10). No significant sensorial differences were observed between the final products made in the two jars. Neither coliforms nor Enterobacteriaceae were detected in their viable state, starting D7 in both jars, suggesting the antimicrobial properties of the product.

The microbiota of Mozzarella di Bufala Campana PDO cheese: a study across the manufacturing process

Introduction

Mozzarella di Bufala Campana PDO cheese (MBC) is a globally esteemed Italian cheese. The traditional cheesemaking process of MBC relies on natural whey starter culture, water buffalo's milk, and the local agroecosystem.

Methods

In this study, the microbial ecology of intermediate samples of MBC production, coming from two dairies with slightly different cheesemaking technology (dairy M large producer, and dairy C medium-small), was investigated using 16S rRNA amplicon sequencing. This research aimed to provide insights into the dynamics of microbial consortia involved in various cheesemaking steps.

Results and discussion

All samples, except for raw buffalo milk, exhibited a core microbiome predominantly composed of Streptococcus spp. and Lactobacillus spp., albeit with different ratios between the two genera across the two MBC producers. Notably, the microbiota of the brine from both dairies, analyzed using 16S amplicon sequencing for the first time, was dominated by the Lactobacillus and Streptococcus genera, while only dairy C showed the presence of minor genera such as Pediococcus and Lentilactobacillus. Intriguingly, the final mozzarella samples from both producers displayed an inversion in the dominance of Lactobacillus spp. over Streptococcus spp. in the microbiota compared to curd samples, possibly attributable to the alleviation of thermal stress following the curd stretching step. In conclusion, the different samples from the two production facilities did not exhibit significant differences in terms of the species involved in MBC cheesemaking. This finding confirms that the key role in the MBC cheesemaking process lies with a small-sized microbiome primarily composed of Streptococcus and Lactobacillus spp.

Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin

Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.

Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life

Milk production is an ancient adaptation that unites all mammals. Milk contains a microbiome that can contribute to offspring health and microbial-immunological development. We generated a comprehensive milk microbiome dataset (16S rRNA gene) for the class Mammalia, representing 47 species from all placental superorders, to determine processes structuring milk microbiomes. We show that across Mammalia, milk exposes offspring to maternal bacterial and archaeal symbionts throughout lactation. Deterministic processes of environmental selection accounted for 20% of milk microbiome assembly processes; milk microbiomes were similar from mammals with the same host superorder (Afrotheria, Laurasiathera, Euarchontoglires, and Xenarthra: 6%), environment (marine captive, marine wild, terrestrial captive, and terrestrial wild: 6%), diet (carnivore, omnivore, herbivore, and insectivore: 5%), and milk nutrient content (sugar, fat, and protein: 3%). We found that diet directly and indirectly impacted milk microbiomes, with indirect effects being mediated by milk sugar content. Stochastic processes, such as ecological drift, accounted for 80% of milk microbiome assembly processes, which was high compared to mammalian gut and mammalian skin microbiomes (69% and 45%, respectively). Even amid high stochasticity and indirect effects, our results of direct dietary effects on milk microbiomes provide support for enteromammary trafficking, representing a mechanism by which bacteria are transferred from the mother's gut to mammary gland and then to offspring postnatally. The microbial species present in milk reflect both selective pressures and stochastic processes at the host level, exemplifying various ecological and evolutionary factors acting on milk microbiomes, which, in turn, set the stage for offspring health and development.

Bacteria in Normal Canine Milk Analyzed by Blood Agar Medium

Studies of microbiota in normal canine milk from healthy dams are sparse. As is the case with blood and urine, it was considered that milk contains no microbiota. Any discovery of bacteria in canine milk is, therefore, often noted to be a result of contamination during sampling or interpreted as mastitis and treated with antibiotics. Milk was collected twice within 19 days after natural parturition from 11 lactating dams, with no general or local clinical signs of mastitis or other disease. The skin and teats were prepared with an antimicrobial protocol prior to each milk sampling. In total, 210 milk samples were collected and assessed for a number of bacterial colonies grown on each plate. Bacterial growth was detected in 180 samples (86%). Staphylococcus pseudintermedius, Enterococcus spp., Clostridium spp., Coagulase-Negative Staphylococci (CoNS), Streptococcus spp., Streptococcus canis, Bacillus spp., Pasteurella spp., and Escherichia coli were identified from pure and/or mixed bacterial growth, listed in descending order of occurrence. Despite the small sample size, the consistent occurrence of bacteria in early postpartum dams indicates a genuine occurrence of bacteria in canine milk, rather than random contamination. The finding of bacteria in the milk of dams should not, therefore, be the sole argument for the diagnosis of mastitis.

Bio surfactants from lactic acid bacteria: an in-depth analysis of therapeutic properties and food formulation

Healthy humans and animals commonly harbor lactic acid bacteria (LAB) on their mucosal surfaces, which are often associated with food fermentation. These microorganisms can produce amphiphilic compounds, known as microbial surface-active agents, that exhibit remarkable emulsifying activity. However, the exact functions of these microbial surfactants within the producer cells remain unclear. Consequently, there is a growing urgency to develop biosurfactant production from nonpathogenic microbes, particularly those derived from LAB. This approach aims to harness the benefits of biosurfactants while ensuring their safety and applicability. This review encompasses a comprehensive analysis of native and genetically modified LAB biosurfactants, shedding light on microbial interactions, cell signaling, pathogenicity, and biofilm development. It aims to provide valuable insights into the applications of these active substances in therapeutic use and food formulation as well as their potential biological and other benefits. By synthesizing the latest knowledge and advancements, this review contributes to the understanding and utilization of LAB biosurfactants in the food and nutritional areas.

Improvement of Fresh Ovine "Tuma" Cheese Quality Characteristics by Application of Oregano Essential Oils

In the present work, oregano essential oils (OEOs) were applied to process the fresh ovine cheese "Tuma" obtained by pressed cheese technology. Cheese making trials were performed under industrial conditions using ewe's pasteurized milk and two strains of Lactococcus lactis (NT1 and NT4) as fermenting agents. Two experimental cheese products (ECP) were obtained through the addition of 100 (ECP100) and 200 (ECP200) µL/L of OEO to milk, while the control cheese product (CCP) was OEO-free. Both Lc. lactis strains showed in vitro and in vivo ability to grow in the presence of OEOs and to dominate over indigenous milk lactic acid bacteria (LAB) resistant to pasteurization. In the presence of OEOs, the most abundant compound found in cheese was carvacrol, constituting more than 65% of the volatile fraction in both experimental products. The addition of OEOs did not influence ash, fat, or protein content, but it increased by 43% the antioxidant capacity of the experimental cheeses. ECP100 cheeses showed the best appreciation scores by the sensory panel. In order to investigate the ability OEOs to be used as a natural preservative, a test of artificial contamination was carried out, and the results showed a significant reduction of the main dairy pathogens in OEO-added cheeses.

Microbiological Characterization of Protected Designation of Origin Serra da Estrela Cheese

Serra da Estrela is the oldest and most recognizable traditional protected designation of origin (PDO) cheese from Portugal. It has been extensively studied over the years, but the latest microbial characterization is 20 years old. Hence, this work aimed to perform an updated characterization of Serra da Estrela PDO cheeses and raw materials. Our analysis showed that lactic acid bacteria content on Serra da Estrela cheeses exceeded 8.8 log CFUsg^-1, in all analyzed samples, with lactococci, lactobacilli and Leuconostoc spp. predominating over enterococci strains. Moreover, lactococci and lactobacilli abundance increased across the production season, while enterococci dropped considerably in late manufactures. Lastly, Leuconostoc spp. content remained unchanged in all analyzed periods. A correspondence analysis showed that L. paracasei, L. lactis, E. durans, E. faecium and L. mesenteroides are transversal in Serra da Estrela cheese manufacturing and were closely associated with milk, curd and cheese matrices. Additionally, L. casei, L. plantarum and L. curvatus were specifically associated with cheese matrices, possibly active during ripening and contributing for the development of these cheeses' organoleptic characteristics.

Proteolytic activity and heat resistance of the protease AprX from Pseudomonas in relation to genotypic characteristics

AprX is an alkaline metalloprotease produced by Pseudomonas spp. and encoded by its initial gene of the aprX-lipA operon. The intrinsic diversity among Pseudomonas spp. regarding their proteolytic activity is the main challenge for the development of accurate methods for spoilage prediction of ultra-high temperature (UHT) treated milk in the dairy industry. In the present study, 56 Pseudomonas strains were characterized by assessing their proteolytic activity in milk before and after lab-scale UHT treatment. From these, 24 strains were selected based on their proteolytic activity for whole genome sequencing (WGS) to identify common genotypic characteristics that correlated with the observed variations in proteolytic activity. Four groups (A1, A2, B and N) were determined based on operon aprX-lipA sequence similarities. These alignment groups were observed to significantly influence the proteolytic activity of the strains, with an average proteolytic activity of A1 > A2 > B > N. The lab-scale UHT treatment did not significantly influence their proteolytic activity, indicating a high thermal stability of proteases among strains. Amino acid sequence variation of biologically-relevant motifs in the AprX sequence, namely the Zn²⁺-binding motif at the catalytic domain and the C-terminal type I secretion signaling mechanism, were found to be highly conserved within alignment groups. These motifs could serve as future potential genetic biomarkers for determination of alignment groups and thereby strain spoilage potential.

Milk-borne diseases through the lens of one health

Reviewing “zoonotic diseases” classically brings to mind human infections contracted in close association with animals, where outdoor occupations and afforested lands usually play a key role in the epidemiological triad. However, there is a very common, yet overlooked route of infection where humans may not come in direct contact with animals or implicated environments. Milk-borne diseases are a unique set of infections affecting all age groups and occupational categories of humans, causing 4% of all the foodborne diseases in the world. The infection reservoir may lie with milch animals and associated enzootic cycles, and the infectious agent is freely secreted into the animal’s milk. Commercial pooling and processing of milk create unique environmental challenges, where lapses in quality control could introduce infective agents during downstream processing and distribution. The infectious agent is finally brought to the doorstep of both rural and urban households through such animal products. The domestic hygiene of the household finally determines human infections. One health approach can target preventive measures like immunization in animals, pasteurization and stringent quality control during the commercial processing of milk, and finally, hygienic practices at the level of the consumer, to reduce the burden of milk-borne diseases. This review hopes to draw the attention of policymakers to this unique route of infection, because it can be easily regulated with cost-effective interventions, to ensure the safety of this precious food product, permeating the life and livelihood of humans from all walks of life.

Fungal communities on alpine cheese rinds in Southern Switzerland

BACKGROUND

The biodiversity of the mycobiota of soft cheese rinds such as Brie or Camembert has been extensively studied, but scant information is available on the fungi colonizing the rinds of cheese produced in the Southern Switzerland Alps. This study aimed at exploring the fungal communities present on rinds of cheese matured in five cellars in Southern Switzerland and to evaluate their composition with regards to temperature, relative humidity, type of cheese, as well as microenvironmental and geographic factors. We used macro- and microscopical morphology, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, and sequencing to characterize the fungal communities of the cheeses, and compared them with metabarcoding targeting the ITS region.

RESULTS

Isolation by serial dilution yielded 201 isolates (39 yeasts and 162 filamentous fungi) belonging to 9 fungal species. Mucor and Penicillium were dominant, with Mucor racemosus, M. lanceolatus, P. biforme, and P. chrysogenum/rubens being the most frequent species. All but two yeast isolates were identified as Debaryomyces hansenii. Metabarcoding detected 80 fungal species. Culture work and metabarcoding produced comparable results in terms of similarity of the fungal cheese rind communities in the five cellars.

CONCLUSIONS

Our study has shown that the mycobiota on the rinds of the cheeses studied is a comparatively species-poor community influenced by temperature, relative humidity, type of cheese, and manufacturing steps, as well as microenvironmental and possibly geographic factors.

Comparison of Activity of Commercial Protective Cultures and Thermophilic Lactic Acid Bacteria against Listeria monocytogenes: A New Perspective to Improve the Safety of Sardinian PDO Cheeses

Listeria monocytogenes contamination that occurs during and post-processing of dairy products is a serious concern for consumers, and bioprotective cultures can be applied to control the growth of the pathogen in sheep milk cheeses. However, to respect specifications provided for protected designation of origin (PDO) cheeses, only autochthonous microorganisms can be used as bioprotective cultures in these products. This in vitro study aimed to evaluate thermophilic lactic acid bacteria (LAB) isolated from sheep milk as bio-preservative agents to control L. monocytogenes growth in PDO cheese. Results were compared with those obtained with a commercial protective culture (cPC) composed of a Lactiplantibacillus plantarum bacteriocin producer designed to inhibit L. monocytogenes growth in cheese. The in vitro antilisterial activities of n.74 autochthonous LAB and a cPC were tested against 51 L. monocytogenes strains using an agar well diffusion assay. In addition, 16S rRNA sequencing of LAB isolates with antilisterial activity was conducted and strains of Lactobacillus helveticus, Lactobacillus delbrueckii subsp. indicus, Lactobacillus delbrueckii subsp. sunkii, Lactobacillus delbrueckii subsp. lactis and Enterococcus faecalis were identified. In this study, 33.6% (74/220) bacterial strains isolated from milk had characteristics compatible with thermophilic LAB, of which 17.6% (13/74) had in vitro antilisterial activity. These results demonstrate that raw sheep milk can be considered an important source of autochthonous thermophilic LAB that can be employed as protective cultures during the manufacturing of Sardinian PDO cheeses to improve their food safety. The use of bioprotective cultures should be seen as an additional procedure useful to improve cheese safety along with the correct application of good hygienic practices during manufacturing and the post-processing stages.

Prevalence and antimicrobial resistance of Salmonella and the enumeration of ESBL E. coli in dairy farms in Hubei Province, China

Dairy cattle and their products have been linked to human outbreaks of Salmonella and Escherichia coli (E. coli). The objective of this study was to estimate the prevalence and antimicrobial resistance of Salmonella and to enumerate Extended-spectrum β-lactamase (ESBL)-producing E. coli in apparently healthy lactating dairy cows in Hubei Province, China. In a cross-sectional study, a total of 291 adult lactating dairy cows from 10 dairy farms were sampled for the detection of Salmonella and ESBL E. coli. Overall, Salmonella was cultured from 15 out of 291 sampled animals (5.2 %; 95 % confidence intervals (CI): 2.9, 8.4), all from two herds with a herd prevalence of 20.0 % (95 % CI: 2.5, 55.6) and the main serotype being S. Dublin. The within-herd prevalence ranged between 0.0 % and 33.3 %. ESBL E. coli was detected by culture in all farms with an animal level prevalence of 59.1 % (95 % CI: 53.2, 64.8) and 116 samples (39.9 %, 95 % CI: 34.2, 45.7) contained ESBL E. coli with a number exceeding 10⁴ CFU/g feces. Sixty percent (9/15) of Salmonella isolates were resistant to ampicillin, however all isolates were sensitive to the other 8 antimicrobials tested. Ninety percent (95 % CI: 84.6, 94.1) of ESBL E. coli contained the resistance gene bla_CTX-M, but no ESBL Salmonella was found. Our findings contribute to the understanding of the prevalence and antimicrobial resistance of Salmonella and the enumeration of ESBL E. coli and will assist in the decision-making for the control of Salmonella in Hubei Province.

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.

Core microbiome and bacterial diversity of the Italian Mediterranean river buffalo milk

Milk is one of the most nutritionally complete foods and plays an important role in the human diet. Buffalo milk represents 15% of worldwide milk production and is an important source of bioactive compounds. Buffalo milk has a great market in the Mediterranean area, and dairy products, such as Mozzarella and Ricotta di Bufala Campana, obtained with the Italian Mediterranean buffalo milk, are acknowledged with the Protected Designation of Origin (PDO). This study aimed to characterize, using high-throughput sequencing of the 16S rRNA gene, the milk core microbiome of water buffalo rises in the Amaseno Valley included in the Mozzarella PDO region. The principal features of the core and the auxiliary buffalo milk microbiome are the predominance of Firmicutes and Lactococcus, one of the most important lactic acid bacteria (LAB) taxa in the dairy industry. The comparative analysis of the core microbiomes indicated that the milk of the Italian Mediterranean Buffalo and other mammals share the presence of Streptococcus-affiliated OTUs (operational taxonomic units). Our data also demonstrated that the core microbiome of milk samples collected from PDO and non-PDO regions differ in the number and type of taxa. KEY POINTS: • Buffalo milk and their derivate products are becoming more popular worldwide. • Dairy locations and practice management affect the structure of the milk microbiota. • Next-generation sequencing (NGS) analysis allows to identify the features of the Italian Buffalo milk microbiome.

Distinct Bacterial Communities in São Jorge Cheese with Protected Designation of Origin (PDO)

São Jorge cheese is an iconic product of the Azores, produced from raw cow's milk and natural whey starter (NWS). Although it is produced according to Protected Designation of Origin (PDO) specifications, the granting of the PDO label depends crucially on sensory evaluation by trained tasters. The aim of this work was to characterize the bacterial diversity of this cheese using next-generation sequencing (NGS) and to identify the specific microbiota that contributes most to its uniqueness as a PDO by distinguishing the bacterial communities of PDO and non-PDO cheeses. The NWS and curd microbiota was dominated by Streptococcus and Lactococcus, whereas Lactobacillus and Leuconostoc were also present in the core microbiota of the cheese along with these genera. Significant differences (p < 0.05) in bacterial community composition were found between PDO cheese and non-certified cheese; Leuconostoc was found to play the chief role in this regard. Certified cheeses were richer in Leuconostoc, Lactobacillus and Enterococcus, but had fewer Streptococcus (p < 0.05). A negative correlation was found between contaminating bacteria, e.g., Staphylococcus and Acinetobacter, and the development of PDO-associated bacteria such as Leuconostoc, Lactobacillus and Enterococcus. A reduction in contaminating bacteria was found to be crucial for the development of a bacterial community rich in Leuconostoc and Lactobacillus, thus justifying the PDO seal of quality. This study has helped to clearly distinguish between cheeses with and without PDO based on the composition of the bacterial community. The characterization of the NWS and the cheese microbiota can contribute to a better understanding of the microbial dynamics of this traditional PDO cheese and can help producers interested in maintaining the identity and quality of São Jorge PDO cheese.

Calidad–inocuidad de la leche cruda de vaca que ingresa a centros de acopio de la provincia Cañar–Ecuador, en el contexto de las normativas Latinoamericanas

En esta investigación se analizaron parámetros físico–químicos y microbiológicos de la leche cruda de vaca, para evaluar su calidad–inocuidad con referencia a la normativa técnica ecuatoriana (INEN009–2012), y a las normativas de otros países: Perú, Colombia, Venezuela, México y Argentina. Se tomaron 203 muestras de leche cruda contenidas en medios de transporte provenientes de 6.214 productores, al ingreso a 28 centros de acopio de la provincia de Cañar, Ecuador. Se realizaron análisis in situ de temperatura, densidad y acidez titulable, mientras que grasa (G), sólidos totales (ST), sólidos no grasos (SNG), proteínas (P), punto de congelación (PC), Conteo de Células Somáticas (CCS), Conteo de Bacterias Totales (CBT), aerobios mesófilos y enterobacterias se realizaron en laboratorios de AGROCALIDAD y de la Universidad de Cuenca. Se observó que en las variables: densidad (15 °C), acidez titulable, G, ST, SNG, P, PC (°C); el 87,5 al 100 % de muestras cumplen, tanto con la normativa ecuatoriana como con las normativas de los países analizados. Las normativas de Colombia y Venezuela tienen valores referenciales más exigentes para densidad, proteína, acidez titulable y SNG, respectivamente. México y Argentina no hacen referencia para ST y Perú no considera proteínas. Sin embargo, los resultados en microbiología son desalentadores, del recuento de aerobios mesófilos solo 8 % de muestras analizadas cumplen la normativa de todos los países. La carga microbiológica es alta, a pesar que ninguna normativa analizada indica máximos para CBT, se encontró una media de 24.000 × 103 unidades formadoras de colonias por mililitro (UFC·mL–1). Como referencia, algunas normativas en EUA fijan un máximo de 300 × 103 UFC·mL–1 de CBT en leches mezcladas. Este trabajo aporta un conocimiento del estado actual de la calidad–inocuidad de la leche cruda de una importante zona lechera del Ecuador y analiza estos resultados en el contexto de normativas internacionales, sirviendo para focalizar esfuerzos en la mejora continua con miras a la exportación.

Raw milk kefir: microbiota, bioactive peptides, and immune modulation

This study aims to characterize the microbiota and peptidomic composition of raw milk kefir, and to address the potential anti-allergic effects of raw milk kefir using validated research models for food allergy. Raw milk kefir was produced after incubation with a defined freeze-dried starter culture. Kefir was sampled during fermentation at seven time intervals. For comparison, kefir was also prepared from heat-treated milk. Peptide compositions were determined for the raw and heated milk, and kefir end products made from these milks. In a murine food allergy model, the two kefir end products were investigated for their allergy modulating effects. In both kefirs, we identified amplicon sequence variants identical to those in the starter culture, matching the bacteria Lactococcus lactis, Streptococcus thermophilus, Leuconostoc and the yeast Debaryomyces. In raw milk kefir, additional sequence variants of Lactococcus lactis and the yeasts Pichia and Galactomyces could be identified, which were absent in heated milk kefir. Analysis of peptide compositions in both kefirs indicated that the number and intensity of peptides drastically increased after fermentation. Heating of the milk negatively affected the diversity of the peptide composition in kefir. Only raw milk kefir suppressed the acute allergic skin response to the food allergen ovalbumin in sensitised mice. These effects coincided with differences in the T-cell compartment, with lower percentages of activated Th1 cells and IFNg production after treatment with kefir made from heated milk. The results of this study indicate specific properties of raw milk kefir that may contribute to its additional health benefits.

Interrogating the role of the milk microbiome in mastitis in the multi-omics era

There is growing interest in a functional understanding of milk-associated microbiota as there is ample evidence that host-associated microbial communities play an active role in host health and phenotype. Mastitis, characterized by painful inflammation of the mammary gland, is prevalent among lactating humans and agricultural animals and is associated with significant clinical and economic consequences. The etiology of mastitis is complex and polymicrobial and correlative studies have indicated alterations in milk microbial community composition. Recent evidence is beginning to suggest that a causal relationship may exist between the milk microbiota and host phenotype in mastitis. Multi-omic approaches can be leveraged to gain a mechanistic, molecular level understanding of how the milk microbiome might modulate host physiology, thereby informing strategies to prevent and ameliorate mastitis. In this paper, we review existing studies that have utilized omics approaches to investigate the role of the milk microbiome in mastitis. We also summarize the strengths and challenges associated with the different omics techniques including metagenomics, metatranscriptomics, metaproteomics, metabolomics and lipidomics and provide perspective on the integration of multiple omics technologies for a better functional understanding of the milk microbiome.

Effect of biofilm formation by antimicrobial-resistant gram-negative bacteria in cold storage on survival in dairy processing lines

Antimicrobial-resistant gram-negative bacteria in dairy products can transfer antimicrobial resistance to gut microbiota in humans and can adversely impact the product quality. In this study, we aimed to investigate their distribution in dairy processing lines and evaluate biofilm formation and heat tolerance under dairy processing line-like conditions. Additionally, we compared the relative expression of general and heat stress-related genes as well as spoilage-related gene between biofilm and planktonic cells under consecutive stresses, similar to those in dairy processing lines. Most species of gram-negative bacteria isolated from five different dairy processing plants were resistant to one or more antimicrobials. Biofilm formation by the bacteria at 5 °C increased with the increase in exposure time. Moreover, cells in biofilms remained viable under heat treatment, whereas all planktonic cells of the selected strains died. The expression of heat-shock-related genes significantly increased with heat treatment in the biofilms but mostly decreased in the planktonic cells. Thus, biofilm formation under raw milk storage conditions may improve the tolerance of antimicrobial-resistant gram-negative bacteria to pasteurization, thereby increasing their persistence in dairy processing lines and products. Furthermore, the difference in response to heat stress between biofilm and planktonic cells may be attributed to the differential expression of heat stress-related genes. Therefore, this study contributes to the understanding of how gram-negative bacteria persist under consecutive stresses in dairy processing procedures and the potential mechanism underlying heat tolerance in biofilms.

Extending the Shelf Life of Raw Milk and Pasteurized Milk with Plantaricin FB-2

Raw milk and pasteurized milk are characterized by a short shelf life, and drinking expired raw milk and pasteurized milk causes illness. In the study, Plantaricin FB-2 (extracted from Lactiplantibacillus plantarum FB-2) was added to liquid milk. By evaluating the microbial growth, acidity changes, protein content, and sensory changes in raw milk and pasteurized milk during storage, it was found that when Plantaricin FB-2 was added at 0.4 g/kg, the shelf life of raw milk was extended by 3 days (7 days if not added). The shelf life of pasteurized milk with Plantaricin FB-2 was extended to 31 days (25 days in the control group), and the optimal amount was 0.3 g/kg. This confirmed that Plantaricin FB-2 can effectively prolong the shelf life of raw and pasteurized milk. This study provides valuable information for the application of bacteriocins produced by Lactiplantibacillus plantarum in raw milk and pasteurized milk to improve their shelf life.

Microbiological, Physicochemical and Nutritional Properties of Fresh Cow Milk Treated with Industrial High-Pressure Processing (HPP) during Storage

The safety, shelf life, and quality of fresh cow milk treated using industrial High-Pressure Processing (HPP) treatment at 600 MPa for 10 min was studied to identify the novelty of this non-thermal technology in milk processing. Changes in microbiological and physicochemical properties, including nutritional values of vitamins and amino acid profiles, were measured for a 60-day storage period at 6 °C +/- 1 °C. The HPP treatment produced milk that met all microbial safety requirements and exhibited a shelf life beyond 60 days in a hot and humid region. High physicochemical stability was achieved, with consistent pH and undetectable titratable acidity. The HPP treatment successfully retained all vitamins and minerals, including calcium (99.3%), phosphorus (99.4%), and magnesium (99.1%). However, the 60-day storage caused some degradation of Vitamin A (25%), B3 (91%), B5 (35%), B6 (80%), and C (85%), and minerals, including potassium (5%) and zinc (18%) when compared with fresh milk. This research has shown that the adoption of advanced treatment with HPP is very beneficial to the dairy industry in preserving milk quality in terms of its physicochemical and nutritional properties and extending its storage shelf life beyond 60 days.

Development and Evaluation of a Next-Generation Sequencing Panel for the Multiple Detection and Identification of Pathogens in Fermented Foods

These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic Escherichia coli, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium, respectively. Evaluation of the primer sets using singleplex PCR, crosscheck PCR and multiplex PCR revealed high specificity and selectivity without interference of primers or genomic DNAs. Subsequent NGS panel analysis with six artificially contaminated food samples using those primer sets showed that all target genes were multi-detected in one reaction at 10⁸-10⁵ CFU of target strains. However, a few false-positive results were shown at 10⁶-10⁵ CFU. To validate this NGS panel analysis, three sets of qPCR analyses were independently performed with the same contaminated food samples, showing the similar specificity and selectivity for detection and identification. While this NGS panel still has some issues for detection and identification of specific foodborne pathogens, it has much more advantages, especially multiple detection and identification in one reaction, and it could be improved by further optimized NGS panel primer sets and even by application of a new real-time NGS sequencing technology. Therefore, this study suggests the efficiency and usability of NGS panel for rapid determination of origin strain in various foodborne outbreaks in one reaction.

Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing

Background

The Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated.

Methods

In this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function.

Results

After filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan.