Understanding the Milk Microbiota

Nisin A-producing Lactococcus cremoris formulations for pre- and post-milking teat disinfection modulate the bovine milk microbiota

BACKGROUND

Bovine mastitis is a major challenge in dairy farms. Since the agents commonly used for pre- and post-dipping can affect the udder health by modifying milk microbiota, alternative products are needed. This study aimed to evaluate the effect of the use of pre- and post-dipping formulations containing the fermented broth of Nisin A-producing Lactococcus cremoris FT27 strain (treated group, TR) on the abundance and biodiversity of milk microbiota as compared to iodine-based commercial disinfectants (control group, CTR) during a three-month trial. The experiment was conducted on 20 dairy cows, divided into two groups (CTR and TR) of 10 lactating cows each. Milk samples were collected from two selected healthy quarters of each cow at 3 time-points. Microbial communities were investigated by cultural and sequence-based methods, and analyzed through bioinformatic and statistical approaches.

RESULTS

Clear differences in bacterial community composition were observed among groups, with higher species richness in TR, especially of Staphylococcus, Enterococcus, Lactococcus, and Streptococcus genera. The microbiota was dominated by Firmicutes, followed by Actinobacteriota, Proteobacteria, and Bacteroidota. Staphylococcaceae family was significantly higher in TR (p < 0.009), whereas Carnobacteriaceae, Mycobacteriaceae, and Pseudomonadaceae were significantly lower (p = 0.005, p = 0.001, and p = 0.040, respectively). CTR had considerably higher abundances of the genera Alkalibacterium (p = 0.011), Pseudomonas_E (p = 0.045), Corynebacterium (p = 0.004), and Alloiococcus (p = 0.004), and lower abundances of Staphylococcus (p < 0.009). Milk microbiota changed noticeably during the experimental period, regardless of treatment. A significant decrease was observed in both groups for Firmicutes_A phylum, with an increment in Actinobacteriota phylum, Propionibacteriaceae family, and Cutibacterium genus. Streptococcaceae significantly decreased in CTR (p = 0.013) and rose in TR (p = 0.001). Several differences were observed between the two groups during the experimental period. Streptococcus genus almost disappeared in CTR (p = 0.013), whereas it significantly increased in TR (p = 0.001). Three and twelve enriched groups were significantly identified respectively in CTR and TR using LEfSe.

CONCLUSIONS

The use of Nisin A-based teat dip formulations could be linked to greater microbial diversity compared to commercial products. Despite the influence of seasonality, the experimental formulations maintained higher milk biodiversity, suggesting that lactic acid bacteria metabolites prevent alterations in the milk microbiota.

Intractable Recurrent Abscess Around the Nipple Caused by Mastitis Remitted by Kampo Medicine Treatment: A Case Report

We present a case of a 46-year-old woman with recurrent breast abscess resistant to conventional treatments. Initial diagnosis of mastitis led to antibiotic therapy; however, abscess formation recurred. Subsequent interventions, including incision, drainage, and various antibiotics, were insufficient because of recurrent infections. Due to the side effects of long-term antibiotic use, the patient was referred to the Kampo medicine department to address the premenstrual symptoms and recurrent infections. Treatment with Kampo medicines resulted in significant symptom reduction within a month. After treatment, the patient experienced mild symptoms, and breast abscess recurrence was prevented for more than two years. This case highlights the potential role of Kampo medicine in the management of refractory breast abscesses associated with premenstrual symptoms. Further research is required to explore the efficacy and mechanisms of action of Kampo medicines in similar cases.

Microbial Diversity and Resistome in Milk of Cows with Subclinical Mastitis in a Coastal District of Odisha, India

Mastitis is a globally prevalent bacterial disease of lactating cows. Prevention and control of this multi-etiological complex disease relies upon administration of antibiotics. This has led to the emergence of newer multi-drug resistant strains. In the current study, milk samples from subclinical mastitis cows and their healthy counterparts were subjected to Illumina-based whole genome metagenome sequencing to explore bacterial communities and antibiotic resistance genes associated with mastitis-affected and healthy udder. Bovine milk microbiome in subclinical mastitis-affected cows were dominated by pathogenic bacteria such as Acinetobacter baylyi, Acinetobacter pittii, Streptococcus agalactiae, Streptococcus suis, Streptococcus uberis, Aeromonas hydrophila, Aeromonas enteropelogenes, Lactococcus lactis, Corynebacterium resistens and Kocuria rhizophila. We observed higher bacterial abundance and diversity in milk of cows suffering from subclinical mastitis as compared to apparently healthy cows. Resistant genes against fluoroquinolones, peptides, β-lactams, tetracyclines and macrolides were detected in the subclinical group. In contrast, genes resistant to aminoglycosides, penams and β-lactams were found in healthy cow milk. The findings of the study expand our knowledge of bacterial diversity and associated resistant genes found in the milk of mastitis-affected and healthy cow milk.

Utility of dairy microbiome as a tool for authentication and traceability

Milk microbiome contributes substantially to the formation of specific organoleptic and physicochemical characteristics of dairy products. The assessment of the composition and abundance of milk microbiota is a challenging task strongly influenced by many environmental factors. Specific dairy products may be designated by the Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) labeling, which however, occasionally fail to differentiate them according to specific quality characteristics, which are defined by different microbiota-driven reactions. Combining the above limitations, the scope of the present study, was to summarize the existing information toward three main issues. First, to assess the influence level of the diet type and grazing to rumen-GI tract, mammary gland, and udder microbiome formation in ruminants. Second, to discuss the factors affecting milk microbiota, as well as the effect of the endo-mammary route on milk microbial taxa. Lastly, to evaluate "milk microbiome" as a tool for product differentiation, according to origin, which will contribute to a more robust PDO and PGI labeling. Although the limitations are still a matter of fact (especially considering the sample collection, process, evaluation, and avoidance of its contamination), significant progress has been made, regarding the identification of the factors affecting dairy products' microbiota and its core composition. In conclusion, although so far not totally efficient in dairy products molecular identification, with the progress in soil, water, plant, and animal host's microbiota assembly's characterization, microbiomics could provide a powerful tool for authentication and traceability of dairy products.

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

BACKGROUND

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

AIM OF REVIEW

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

KEY SCIENTIFIC CONCEPTS OF REVIEW

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

Different Immune Control of Gram-Positive and Gram-Negative Mammary Infections in Dairy Cows

In the dairy industry, bovine mastitis represents a major concern due to substantial production losses and costs related to therapies and early culling. The mechanisms of susceptibility and effective response to intra-mammary infections are still poorly understood. Therefore, we investigated innate immunity in acellular bovine skim milk through cytofluorimetric analyses of bacterial killing activity against both Gram-positive and Gram-negative pathogens. Freshly cultured E. coli and S. aureus strains were incubated with colostrum and milk samples at different lactation time points from two groups of cows, purportedly representing mastitis-resistant and mastitis-susceptible breeds; bacterial cells were analyzed for vitality by flow cytometry following incorporation of vital dyes. N-acetyl-β-D-glucosaminidase (NAGase) activity was also investigated in milk and colostrum samples. Our findings revealed that colostrum and milk bacterial killing activity was greater against S. aureus compared to E. coli., with this activity correlated with milk NAGase levels. Furthermore, both killing of S. aureus and NAGase activity were negatively correlated to the elapsed time of lactation. Interestingly, samples from the allegedly mastitis-resistant breed displayed higher bacterial killing and NAGase activities. Our study suggests that diverse control mechanisms are exerted against Gram-positive and Gram-negative pathogens in the mammary glands of cows, probably beyond those already described in the literature.

Understanding mastitis: Microbiome, control strategies, and prevalence - A comprehensive review

Mastitis significantly affects the udder tissue in dairy cattle, leading to inflammation, discomfort, and a decline in both milk yield and quality. The condition can be attributed to an array of microbial agents that access the mammary gland through multiple pathways. The ramifications of this ailment are not merely confined to animal welfare but extend to the financial viability of the livestock industry. This review offers a historical lens on mastitis, tracing its documentation back to 1851, and examines its global distribution with a focus on regional differences in prevalence and antimicrobial resistance (AMR) patterns. Specific microbial genes and communities implicated in both mastitis and AMR are explored, including Staphylococcus aureus, Streptococcus agalactiae,Streptococcus dysagalactiae, Streptococcus uberis Escherichia coli, Klebsiella pneumoniae, Mycoplasma bovis, Corynebacterium bovis, among others. These microorganisms have evolved diverse strategies to elude host immune responses and neutralize commonly administered antibiotics, complicating management efforts. The review aims a comprehensive overview of the current knowledge and research gaps on mastitis and AMR, and to highlight the need for a One Health approach to address this global health issue. Such an approach entails multi-disciplinary cooperation to foster judicious antibiotic use, enhance preventive measures against mastitis, and bolster surveillance and monitoring of AMR in pathogens responsible for mastitis.

Lactobacillus reuteri inhibits Staphylococcus aureus-induced mastitis by regulating oxytocin releasing and gut microbiota in mice

Mastitis is the most frequent disease of cows and has well-recognized detrimental effects on animal wellbeing and dairy farm profitability. With the advent of the postantibiotic era, alternative antibiotic agents, especially probiotics, have received increasing attention in the treatment of mastitis. Based on research showing that Lactobacillus reuteri (L. reuteri) has anti-inflammatory effects, this study explored the protective effects and mechanisms of L. reuteri against mastitis induced by Staphylococcus aureus (S. aureus) in mice. First, mice with S. aureus-induced mastitis were orally administered L. reuteri, and the inflammatory response in the mammary gland was observed. The results showed that L. reuteri significantly inhibited S. aureus-induced mastitis. Moreover, the concentration of oxytocin (OT) and protein expression of oxytocin receptor (OTR) were measured, and inhibition of OTR or vagotomy reversed the protective effect of L. reuteri or its culture supernatant (LCS) on S. aureus-induced mastitis. In addition, in mouse mammary epithelial cells (MMECs), OT inhibited the inflammation induced by S. aureus by inhibiting the protein expression of OTR. It was suggested that L. reuteri protected against S. aureus-induced mastitis by releasing OT. Furthermore, microbiological analysis showed that the composition of the microbiota was altered, and the relative abundance of Lactobacillus was significantly increased in gut and mammary gland after treatment with L. reuteri or LCS. In conclusion, our study found the L. reuteri inhibited the mastitis-induced by S. aureus via promoting the release of OT, and treatment with L. reuteri increased the abundance of Lactobacillus in both gut and mammary gland.

Milk as diagnostic fluid for udder health management

BACKGROUND

Mastitis is the major disease affecting milk production of dairy cattle, and milk is an obvious substrate for the detection of both the inflammation and its causative infectious agents at quarter, cow, or herd levels. In this review, we examine the use of milk to detect inflammation based on somatic cell count (SCC) and other biomarkers, and for the detection of mastitis pathogens through culture-based and culture-free methods.

FINDINGS

The use of SCC at a cow or bulk milk level to guide udder health management in lactation is well-established, and SCC is increasingly used to guide selective dry cow treatment. Other markers of inflammation include electrical conductivity, which is used commercially, and markers of disease severity such as acute phase proteins but are not pathogen-specific. Some pathogen-specific markers based on humoral immune responses are available, but their value in udder health management is largely untested. Commercial pathogen detection is based on culture or polymerase chain reaction, with other tests, for example, loop-mediated isothermal amplification or 16S microbiome analysis still at the research or development stage. Matrix-assisted laser desorption ionisation time of flight (MALDI-ToF) is increasingly used for the identification of cultured organisms whilst application directly to milk needs further development. Details of test sensitivity, specificity, and use of the various technologies may differ between quarter, cow, and bulk milk applications.

CONCLUSIONS

There is a growing array of diagnostic assays that can be used to detect markers of inflammation or infection in milk. The value of some of these methods in on-farm udder health improvement programs is yet to be demonstrated whilst methods with proven value may be underutilised.

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.

Bovine Udder Health: From Standard Diagnostic Methods to New Approaches-A Practical Investigation of Various Udder Health Parameters in Combination with 16S rRNA Sequencing

Bovine udder health is an important factor for animal wellbeing and the dairy farm economy. Thus, researchers aim to understand factors causing mastitis. The gold standard for diagnosing mastitis in cows is the conventional culturing of milk samples. However, during the last few years, the use of molecular methods has increased. These methods, especially sequencing, provide a deeper insight into the diversity of the bacterial community. Yet, inconsistent results regarding the mammary microbiome have been published. This study aimed to evaluate the udder health of eight dairy cows at seven days postpartum with the standard methods in veterinary practice. Additionally, swabs from the teat canal and milk samples were analyzed using 16S rRNA gene amplicon sequencing. The sensitive low-biomass milk samples displayed only a few contaminations even though they were sampled in a field environment. In healthy udders, no bacterial communities were detected by the bacterial culture nor the 16S rRNA gene amplicons. The results from the standard examination of the cows, the cell count, and the bacteriological examination were comparable with the results from 16S rRNA gene amplicon sequencing when cows displayed subclinical or latent mastitis. Besides the pathogen detected in bacterial culturing, a second bacterial strain with low but significant abundance was detected by sequencing, which might aid in the understanding of mastitis incidence. In general, molecular biological approaches might lead to promising insights into pathological events in the udder and might help to understand the pathomechanism and infection source via epidemiological analyses.

Characterization of rumen, fecal, and milk microbiota in lactating dairy cows

Targeting the gastrointestinal microbiome for improvement of feed efficiency and reduction of production costs is a potential promising strategy. However little progress has been made in manipulation of the gut microbiomes in dairy cattle to improve milk yield and milk quality. Even less understood is the milk microbiome. Understanding the milk microbiome may provide insight into how the microbiota correlate with milk yield and milk quality. The objective of this study was to characterize similarities between rumen, fecal, and milk microbiota simultaneously, and to investigate associations between microbiota, milk somatic cell count (SCC), and milk yield. A total of 51 mid-lactation, multiparous Holstein dairy cattle were chosen for sampling of ruminal, fecal, and milk contents that were processed for microbial DNA extraction and sequencing. Cows were categorized based on low, medium, and high SCC; as well as low, medium, and high milk yield. Beta diversity indicated that ruminal, fecal, and milk populations were distinct (p &lt; 0.001). Additionally, the Shannon index demonstrated that ruminal microbial populations were more diverse (p &lt; 0.05) than were fecal and milk populations, and milk microbiota was the least diverse of all sample types (p &lt; 0.001). While diversity indices were not linked (p &gt; 0.1) with milk yield, milk microbial populations from cows with low SCC demonstrated a more evenly distributed microbiome in comparison to cows with high SCC values (p = 0.053). These data demonstrate the complexity of host microbiomes both in the gut and mammary gland. Further, we conclude that there is a significant relationship between mammary health (i.e., SCC) and the milk microbiome. Whether this microbiome could be utilized in efforts to protect the mammary gland remains unclear, but should be explored in future studies.

Changes in bovine milk bacterial microbiome from healthy and subclinical mastitis affected animals of the Girolando, Gyr, Guzera, and Holstein breeds

Raw milk samples were collected from 200 dairy cows belonging to Girolando 1/2, Gyr, Guzera, and Holstein breeds, and the bacterial diversity was explored using 16S rRNA amplicon sequencing. SCC analysis showed that 69 animals were classified as affected with subclinical mastitis. The milk bacterial microbiome was dominated by Firmicutes, Proteobacteria, and Actinobacteria, with an increase of Firmicutes in animals with subclinical mastitis and Proteobacteria in healthy animals. At the family and genus level, the milk bacterial microbiome was dominated by Staphylococcus, Acinetobacter, Pseudomonas, members of the family Enterobacteriaceae, Lactococcus, Aerococcus, members of the family Rhizobiaceae, Anaerobacillus, Streptococcus, members of the family Intrasporangiaceae, members of the family Planococcaceae, Corynebacterium, Nocardioides, and Chryseobacterium. Significant differences in alpha and beta diversity analysis suggest an effect of udder health status and breed on the composition of raw bovine milk microbiota. LEfSe analysis showed 45 and 51 discriminative taxonomic biomarkers associated with udder health status and with one of the four breeds respectively, suggesting an effect of subclinical mastitis and breed on the microbiota of milk in cattle.

The bovine milk microbiome - an evolving science

Improved access to genome based, culture independent methods has generated great interest in defining the bovine milk microbiome. Several comprehensive reviews of this subject have recently been published and the purpose of this short review is to consolidate current understanding of the relevance and biological significance of this emerging topic. In contrast to mucosal organs that contain rich and well-characterized culturable and nonculturable microbial communities, milk obtained from the healthy bovine mammary gland usually contains few or no viable bacteria. The low bacterial biomass of milk has created methodological challenges that have resulted in considerable variability in results of studies that have used genomic methods to define the microbiota of milk obtained from healthy or diseased mammary glands. While genomes from several bacterial genera are routinely identified from samples of milk, teat skin and the teat canal, the viability, origin, and function of these organisms is uncertain as environmental factors have been shown to strongly influence the composition of these bacterial populations. Possible sources of microbial DNA include bacteria introduced from skin or the environment, bacteria trapped in teat canal keratin or bacteria engulfed by phagocytes. Researchers have not achieved consensus about key concepts such as the presence of a core commensal milk microbiome or dysbiosis as part of a causal pathway disrupting udder health. Understanding of the bovine milk microbiome has been greatly impeded by a lack of standardized methods used to collect, process, and assess bovine milk samples. Sample collection is a critical first step that will determine the validity of results. To minimize contamination with external sources of bacterial DNA, teat sanitation methods used for collection of milk samples that will be subjected to extraction and amplification of bacteria DNA should far exceed aseptic techniques used for collection of milk samples that will be submitted for microbiological culture. A number of laboratory issues have yet to be resolved. Contamination of low biomass samples with bacterial DNA from laboratory reagents is a well-known issue that has affected results of studies using bovine milk samples and results of sequencing of negative controls should always be reported. Replication of experiments has rarely been performed and consistency in results are lacking. While progress has been made, standardization of methods and replication using samples originating from differing farm conditions are critically needed to solidify knowledge of this emerging topic.

Bovine milk microbiota: Evaluation of different DNA extraction protocols for challenging samples

The use of an adequate protocol that accurately extracts microbial DNA from bovine milk samples is of importance for downstream analysis such as 16S ribosomal RNA gene sequencing. Although sequencing platforms such as Illumina are very common, there are reservations concerning reproducibility in challenging samples that combine low bacterial loads with high amounts of host DNA. The objective of this study was to evaluate six different DNA extraction protocols applied to four different prototype milk samples (low/high level of colony‐forming units [cfu] and somatic cells). DNA extracts were sequenced on Illumina MiSeq with primers for the hypervariable regions V1V2 and V3V4. Different protocols were evaluated by analyzing the yield and purity of DNA extracts and the number of clean reads after sequencing. Three protocols with the highest median number of clean reads were selected. To assess reproducibility, these extraction replicates were resequenced in triplicates (n = 120). The most reproducible results for α‐ and β‐diversity were obtained with the modified DNeasy Blood & Tissue kit after a chemical pretreatment plus resuspension of the cream fraction. The unmodified QIAamp DNA Mini kit performed particularly weak in the sample representing unspecific mastitis. These results suggest that pretreatment in combination with the modified DNeasy Blood & Tissue kit is useful in extracting microbial DNA from challenging milk samples. To increase reproducibility, we recommend that duplicates, if not triplicates, should be sequenced. We showed that high counts of somatic cells challenged DNA extraction, which shapes the need to apply modified extraction protocols.

Effect of Peanut Shell and Rice Husk Bedding for Dairy Cows: An Analysis of Material Properties and Colostrum Microbiota

Simple Summary

The provision of appropriate bedding is important for the welfare of dairy cows. Before bedding can be selected, it is critical to understand the properties of the bedding, including its impact on milk microbiota. The objective of this article was to evaluate the influence of three materials for use as bedding on physicochemical properties, bacterial counts and colostrum microbiota of cows. Our results demonstrate that peanut shells appear to be a suitable bedding material for cows. These experiments provide empirical support for the use of peanut shells and rice husks as bedding material for dairy cows and illustrates the effects of bedding types on the colostrum microbiota of dairy cows.

Abstract

The aim of this study was to evaluate peanut shells and rice husks as bedding for dairy cows. We analyzed material properties including dry matter, water holding capacity, pH level and bacterial counts. Bedding treatments were compared with a one-way ANOVA using twelve cows split into three groups. Colostrum microbiota was analyzed by sequencing of the V3–V4 region of the 16S rRNA gene. Dry matter content was higher in rice husks compared with peanut shells. No treatment effects were found for water holding capacity and pH level. Streptococcus agalactia counts in peanut shell bedding were lower than in rice husk bedding, and Pseudomonas aeruginosa counts were not different between beddings. A significant enrichment for Enhydrobacter and Pantoea were detected in the colostrum of cows that used peanut shells compared with other beddings. Colostrum of cows housed on a peanut–rice combination had a greater relative abundance of Pseudomonas and Corynebacterium than those housed on peanut shells or rice husks. Higher numbers of Bacteroides, Akkermansia, Alistipes, Ruminococcaceae_UCG-014, Coriobacteriaceae_UCG-002 and Intestinimona were found in the colostrum of cows housed on rice husk bedding over other bedding types. These results suggest that bedding types were associated with the growth and diversity of colostrum bacterial loads. In addition, dry matter in peanut shells was lower than found in rice husks, but there was also a lower risk of mastitis for peanut shell bedding than other beddings.

Colonization and local host response following intramammary Staphylococcus chromogenes challenge in dry cows

Although extensive research has been performed on bovine non-aureus staphylococci (NAS), several aspects such as bacteria-host interaction remain largely unstudied. Moreover, only a few mastitis pathogen challenge studies in cows have been conducted in the dry period, an important period that allows intramammary infection (IMI) to cure and new IMI to occur. We challenged 16 quarters of 4 Holstein Friesian cows at dry off with 100; 100 000 or 10 000 000 CFU of the udder-adapted S. chromogenes IM strain. Four quarters from one cow served as negative controls. Internally sealed quarters remained untouched, whereas non-sealed quarters were sampled 3 times during the dry period. After parturition, colostrum and daily milk samples were taken during the first week of lactation of all quarters. In total, 8 quarters appeared to be colonized, since S. chromogenes IM was recovered at least once during the experiment, as substantiated using Multilocus Sequence Typing. S. chromogenes IM shedding was highest in dry quarters inoculated with 10 000 000 CFU. Colonized quarters had the highest quarter somatic cell count (qSCC) in early lactation. Inoculated quarters (both colonized and non-colonized) had lower IL-6 and IL-10 concentrations in the dry period, whilst IFN-γ levels tended to be higher in colonized quarters compared to non-inoculated quarters. Also, IgG2 levels were higher in inoculated compared to non-inoculated quarters and the IgG2/IgG1 ratio was on average above 1. To conclude, we showed that dry quarters can be colonized with S. chromogenes IM, resulting in a shift towards a Th1 response in late gestation and early lactation characterised by an increased IgG2 concentration. However, further research is needed to confirm our findings.

Minimum inhibitory concentrations of chlorhexidine- and lactic acid-based teat disinfectants: An intervention trial assessing bacterial selection and susceptibility

Teat disinfection is a recommended preventive tool to improve udder health and to prevent new intramammary infections. However, side effects are discussed, such as bacterial selection of less-susceptible bacteria with the application of certain teat disinfectants. The objective of this study was to assess the species composition and bacterial in vitro susceptibility by means of an interventive trial. For this purpose, 3 different postmilking teat treatments (disinfection with 0.215% chlorhexidine or 3.5% lactic acid, or control group with no dipping) were applied to 28 cows in a 6-d intervention approach using a split-udder design. Milk samples were taken before and after intervention. Bacteria were cultured and differentiated to species or genus level by MALDI-TOF mass spectrometry. Minimum inhibitory concentrations (MIC) were determined, and MIC changes over time were recorded. Susceptibilities to chlorhexidine and lactic acid were compared between species of the genera Staphylococcus, Streptococcus, Corynebacterium, and others. Species composition changed during the intervention. Under the treatment of chlorhexidine and lactic acid, the proportion of coagulase-negative staphylococci (CNS) decreased. An increased proportion of species belonging to the genus Corynebacterium was observed especially under the application of lactic acid. Although both teat disinfectants were basically effective, isolates differed in their susceptibility to both teat disinfectants. Populations of CNS, Staphylococcus aureus, and Corynebacterium spp. showed significantly lower absolute MIC values for chlorhexidine. Compared with other species, Corynebacterium spp. showed the lowest susceptibility for chlorhexidine as well as for lactic acid. A significant increase in MIC values after 6 d of intervention was observed with the lactic acid treatment in all isolates, as well as in CNS. This increase can be interpreted as either adaptation of isolates or displacement of more-susceptible species by less-susceptible species. Further studies using long-term intervention might reveal more pronounced effects on MIC values and species composition.

Microbiota of Cow's Milk with Udder Pathologies

Mastitis is the most common disease for cattle, causing great economic losses for the global dairy industry. Recent studies indicate the multi-agent and microbiome diversity of this disease. To understand the nature of mastitis and investigate the role of the microbiome in the development of pathologies in the udder of bovines, we performed NGS sequencing of the 16S rRNA gene of cow’s milk with pathologies of the udder. The obtained data show a significant increase in the Cutibacterium, Blautia, Clostridium sensu stricto 2, Staphylococcus, Streptococcus and Microbacterium genera for groups of cows with udder pathologies. Increasing relative abundance of the Staphylococcus and Streptococcus genera was associated with subclinical mastitis. Our data show that a relative increase in abundance of the Staphylococcus and Microbacterium genera may be an early sign of infection. We have shown, for the first time, an increase in the Colidextribacter, Paeniclostridium and Turicibacter genera in groups of cows with mastitis. These results expand our understanding of the role of the microbiome in the development of bovine mastitis.

Both sampling seasonality and geographic origin contribute significantly to variations in raw milk microbiota, but sampling seasonality is the more determining factor

Accurately profiling and characterizing factors shaping raw milk microbiota would provide practical information for detecting microbial contamination and unusual changes in milk. The current work was an observational study aiming to profile the microbiota of raw milk collected across wide geographic regions in China in different seasons and to investigate the contribution of geographical, seasonal, and environmental factors in shaping the raw milk microbiota. A total of 355 raw cow milk samples from healthy Holsteins and 41 environmental samples (farm soil and surface of milking room floor) were collected from 5 dairy farms in 5 Chinese provinces (namely, Daqing in Heilongjiang province, Jiaozuo in Henan province, Qingyuan in Guangdong province, Suqian in Jiangsu province, and Yinchuan in Ningxia Hui Autonomous Region) in January, May, and September 2018. The microbial communities in raw milk and farm environmental samples were determined using the PacBio small-molecule real-time circular consensus sequencing, which generated high-fidelity microbiota profiles based on full-length 16S rRNA genes; such technology was advantageous in producing accurate species-level information. Our results showed that both seasonality and sampling region were significant factors influencing the milk microbiota; however, the raw milk microbiota was highly diverse according to seasonality, and sampling region was the less determining factor. The wide variation in raw milk microbial communities between samples made it difficult to define a representative species-level core milk microbiota. Nevertheless, 3 most universal milk-associated species were identified: Lactococcus lactis, Enhydrobacter aerosaccus, and Acinetobacter lwoffii, which were consistently detected in 99%, 95%, and 94% of all analyzed milk samples, respectively (n = 355). The top taxa accounting for the overall seasonal microbiota variation were Bacillus (Bacillus cereus, Bacillus flexus, Bacillus safensis), Lactococcus (Lactococcus lactis, Lactococcus piscium, Lactococcus raffinolactis), Lactobacillus (Lactobacillus helveticus, Lactobacillus delbrueckii), Lactiplantibacillus plantarum, Streptococcus agalactiae, Enhydrobacter aerosaccus, Pseudomonas fragi, and Psychrobacter cibarius. Unlike the milk microbiota, the environmental microbiota did not exhibit obvious pattern of seasonal or geographic variation. However, this study was limited by the relatively low number and types of environmental samples, making it statistically not meaningful to perform further correlation analysis between the milk and environmental microbiota. Nevertheless, this study generated novel information on raw milk microbiota across wide geographic regions of China and found that seasonality was more significant in shaping the raw milk microbiota compared with geographic origin.

Comparative Analysis of Milk Microbiomes and Their Association with Bovine Mastitis in Two Farms in Central Russia

Bovine mastitis is a widespread infectious disease. In addition to the economic damages associated with reduced milk yield due to mastitis, the problem of food contamination by microorganism metabolites, in particular toxins, is also a concern. Horizontal transfer of microorganisms from animal populations to humans can also be complicated by antibiotic resistance. Therefore, bovine mastitis is relevant to the study of microbiology and veterinary medicine. In this study, we investigated the microbiome of milk samples from healthy cows and cows with different forms of mastitis from individual quarters of the udder of cows during first and second lactation. Total DNA was extracted from milk samples. The V3-V4 regions of the bacterial 16S rRNA genes from each sample were amplified to generate a library via high-throughput sequencing. We revealed significant dominance of several operational taxonomic units (OTUs) corresponding mostly to groups of Staphylococcus aureus, Aerococcus spp., and Streptococcus spp. In addition, we unexpectedly identified Streptococcus thermophilus in samples with high SCC quantities. We found some infectious agents that characterized summer mastitis. We demonstrated that in Central Russia, mastitis is associated with a wide variety of causal organisms. We observed some differences in the diversity of the two investigated farms. However, we did not find any significant difference among healthy, mastitis and subclinical samples according to their SCC status from either farms by principal component analysis. Linear discriminant analysis effect size (LEfSe) confirmed the presence of several indicator genera in farms from Moscow and the Tula Region. These results confirm the complex bacterial etiology of bovine mastitis.

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

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

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

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

Microbiota of bovine milk, teat skin, and teat canal: Similarity and variation due to sampling technique and milk fraction

The aim of this study was to evaluate the effect of sampling technique and milk fraction on bovine milk microbiota data and to compare the microbiota in milk to microbiota on the teat end and in the teat canal. Representative milk samples are highly important for assessment of bacteriological findings and microbiota in milk. Samples were obtained from 5 healthy lactating dairy cows at udder quarter level during 1 milking. Swab samples from the teat end and teat canal, and milk samples collected using different techniques and in different milk fractions were included. Milk was collected by hand stripping and through a teat canal cannula before and after machine milking, through a trans-teat wall needle aspirate after milking, and from udder quarter composite milk. The microbiota of the samples was analyzed with sequencing of the V1-V3 region of the 16S rRNA gene. In addition, somatic cell counts and bacterial cultivability were analyzed in the milk samples. Microbiota data were analyzed using multivariate methods, and differences between samples were tested using analysis of similarity (ANOSIM). Differences between samples were further explored via individual studies of the 10 most abundant genera. The microbiota on the teat end, in the teat canal, and in udder quarter composite milk, collected using a milking machine, differed in composition from the microbiota in milk collected directly from the udder quarter. No differences in milk microbiota composition were detected between hand-stripped milk samples, milk samples taken through a teat canal cannula, or milk samples taken as a trans-teat wall needle aspirate before or after milking. We conclude that for aseptic milk samples collected directly from the lactating udder quarter, sampling technique or milk fraction has minor effect on the microbiota composition.

Composition and co-occurrence patterns of the microbiota of different niches of the bovine mammary gland: potential associations with mastitis susceptibility, udder inflammation, and teat-end hyperkeratosis

Background

Within complex microbial ecosystems, microbe-microbe interrelationships play crucial roles in determining functional properties such as metabolic potential, stability and colonization resistance. In dairy cows, microbes inhabiting different ecological niches of the udder may have the potential to interact with mastitis pathogens and therefore modulate susceptibility to intramammary infection. In the present study, we investigated the co-occurrence patterns of bacterial communities within and between different niches of the bovine mammary gland (teat canal vs. milk) in order to identify key bacterial taxa and evaluate their associations with udder health parameters and mastitis susceptibility.

Results

Overall, teat canal microbiota was more diverse, phylogenetically less dispersed, and compositionally distinct from milk microbiota. This, coupled with identification of a large number of bacterial taxa that were exclusive to the teat canal microbiota suggested that the intramammary ecosystem, represented by the milk microbiota, acts as a selective medium that disfavors the growth of certain environmental bacterial lineages. We further observed that the diversity of milk microbiota was negatively correlated with udder inflammation. By performing correlation network analysis, we identified two groups of phylogenetically distinct hub species that were either positively (unclassified Bacteroidaceae and Phascolarctobacterium) or negatively (Sphingobacterium) correlated with biodiversity metrics of the mammary gland (MG). The latter group of bacteria also showed positive associations with the future incidence of clinical mastitis.

Conclusions

Our results provide novel insights into the composition and structure of bacterial communities inhabiting different niches of the bovine MG. In particular, we identified hub species and candidate foundation taxa that were associated with the inflammatory status of the MG and/or future incidences of clinical mastitis. Further in vitro and in vivo interrogations of MG microbiota can shed light on different mechanisms by which commensal microbiota interact with mastitis pathogens and modulate udder homeostasis.

Milk Microbiota: What Are We Exactly Talking About?

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

Metataxonomic and immunological analysis of milk from ewes with or without a history of mastitis

Mastitis is a highly prevalent condition that has a great impact on milk production and animal welfare, and often requires substantial management efforts. For this reason, it is generally considered an important threat to the dairy industry. Many microbial, host, and environmental factors can protect against, predispose to, or influence the development of mastitis. The objective of this work was to characterize the milk microbiota of Manchega ewes, and to compare samples from animals with and without a history of mastitis. We analyzed milk samples from 36 ewes belonging to 2 different farms (18 ewes from each farm) using culture-dependent and culture-independent techniques. We also analyzed several immune compounds to investigate associations of mastitis with 3 main variables: farm; history of mastitis or no mastitis; and parity number. Both culture-dependent and culture-independent techniques showed that ewe milk harbored a site-specific complex microbiota and microbiome. Staphylococcus epidermidis was the main species driving the difference between farm A (where it was the dominant species) and B (where it was not). In contrast, samples from farm B were characterized by the presence of a wide spectrum of other coagulase-negative staphylococci. Some of these species have already been associated with subclinical intramammary infections in ruminants. Of the 10 immune compounds assayed in this study, 3 were related to a history of mastitis [IL-8, IFN-γ, and IFN-gamma-induced protein 10 (IP-10)]. Increases in IL-8 concentrations in milk seemed to be a feature of subclinical mastitis in sheep, and in this study, this immune factor was detected only in samples from ewes with some episodes of mastitis and from the group with the highest somatic cell count. We also observed a positive correlation between the samples with the highest somatic cell count and IFN-γ and IP-10 levels. Our results suggest that these 3 compounds could be used as biomarkers for the negative selection of mastitis-prone animals, particularly when somatic cell count is very high.

Bovine milk microbiome: a more complex issue than expected

The aim of this study was to analyze bacterial profiles of bovine mastitic milk samples and samples from healthy quarters using Next Generation Sequencing of amplicons from 16S rRNA genes and to compare results with microbiological results by PCR assays of the same samples. A total of 49 samples were collected from one single dairy herd during the same day. The samples were divided in two sample sets, which were used in this study. The DNA extraction as well as the library preparation and sequencing of these two sets were performed separately, and results of the two datasets were then compared. The vast majority of genera detected appeared with low read numbers and/or in only a few samples. Results of PCR and microbiome analyses of samples infected with major pathogens Staphylococcus aureus or Streptococcus uberis were consistent as these genera also covered the majority of reads detected in the microbiome analysis. Analysis of alpha diversity revealed a much higher species richness in set 1 than in set 2. The dominating bacterial genera with the highest read numbers clearly differed between datasets, especially in PCR negative samples and samples positive for minor pathogens. In addition to this, linear discriminant analysis (LDA) was conducted between the two sets to identify significantly different genera/family level microbes. The genus Methylobacterium was much more common in set 2 compared to set 1, and genus Streptococcus more common in set 1. Our results indicate amplification of contaminating bacteria in excess in samples with no or minor amounts of pathogen DNA in dataset 2. There is a need for critical assessment of results of milk microbiome analyses.