Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 2. Label-free relative quantitative proteomics

Overview of Bovine Mastitis: Application of Metabolomics in Screening Its Predictive and Diagnostic Biomarkers

Bovine mastitis is an inflammatory disease of the mammary glands, and its pathogenesis and diagnosis are complicated. Through qualitative and quantitative analysis of small-molecule metabolites, the metabolomics technique plays an important role in finding biomarkers and studying the metabolic mechanism of bovine mastitis. Therefore, this paper reviews the predictive and diagnostic biomarkers of bovine mastitis that have been identified using metabolomics techniques and that are present in samples such as milk, blood, urine, rumen fluid, feces, and mammary tissue. In addition, the metabolic pathways of mastitis-related biomarkers in milk and blood were analyzed; it was found that the tricarboxylic acid (TCA) cycle was the most significant (FDR = 0.0015767) pathway in milk fluid, and glyoxylate and dicarboxylate metabolism was the most significant (FDR = 0.0081994) pathway in blood. The purpose of this review is to provide useful information for the prediction and early diagnosis of bovine mastitis.

Biomarkers for subclinical bovine mastitis: a high throughput TMT-based proteomic investigation

Mastitis represents the biggest threat to the health and productivity of dairy cows, leading to substantial economic losses in milk production. It manifests in two forms: clinical mastitis, easily diagnosed by visible symptoms, and subclinical mastitis (SCM), which lacks overt clinical signs. SCM's elusive nature often results in it going undetected, thus facilitating the spread of the disease-causing agent due to lack of treatment. Finding a reliable biomarker for early SCM would reduce the possibility of mastitis spreading in the herd, reduce the need for antibiotic use and ultimately reduce milk losses for producers. Utilizing state-of-the-art proteomics techniques, 138 milk samples from dairy cows in continental Croatia underwent analysis. These samples were categorized into four groups based on the Zagreb Mastitis Test (ZMT) and microbiological analysis: lowSCC- (n = 20), lowSCC + (n = 20), medSCC + (n = 79), and highSCC + (n = 19). A total of 386 proteins were identified and quantified, with 76 proteins showing significant differential abundances among the groups. Many of these proteins are linked to the innate immune system, as well as neutrophil and platelet degranulation processes. Through fold changes observed between groups, 15 proteins exhibiting biomarker characteristics for subclinical mastitis (SCM) were identified. Among these, five proteins-cathelicidins (-1, -4, and -7), lactoferrin, and haptoglobin-showed particular promise.

Microbiome and metabolome analyses of milk and feces from dairy cows with healthy, subclinical, and clinical mastitis

Mastitis is commonly recognized as a localized inflammatory udder disease induced by the infiltration of exogenous pathogens. In the present study, our objective was to discern fecal and milk variations in both microbiota composition and metabolite profiles among three distinct groups of cows: healthy cows, cows with subclinical mastitis and cows with clinical mastitis. The fecal microbial community of cows with clinical mastitis was significantly less rich and diverse than the one harbored by healthy cows. In parallel, mastitis caused a strong disturbance in milk microbiota. Metabolomic profiles showed that eleven and twenty-eight molecules exhibited significant differences among the three groups in feces and milk, respectively. Similarly, to microbiota profile, milk metabolome was affected by mastitis more extensively than fecal metabolome, with particular reference to amino acids and sugars. Pathway analysis revealed that amino acids metabolism and energy metabolism could be considered as the main pathways altered by mastitis. These findings underscore the notable distinctions of fecal and milk samples among groups, from microbiome and metabolomic points of view. This observation stands to enhance our comprehension of mastitis in dairy cows.

Biomarker and proteome analysis of milk from dairy cows with clinical mastitis: Determining the effect of different bacterial pathogens on the response to infection

Antimicrobial usage (AMU) could be reduced by differentiating the causative bacteria in cases of clinical mastitis (CM) as either Gram-positive or Gram-negative bacteria or identifying whether the case is culture-negative (no growth, NG) mastitis. Immunoassays for biomarker analysis and a Tandem Mass Tag (TMT) proteomic investigation were employed to identify differences between samples of milk from cows with CM caused by different bacteria. A total of 94 milk samples were collected from cows diagnosed with CM across seven farms in Scotland, categorized by severity as mild (score 1), moderate (score 2), or severe (score 3). Bovine haptoglobin (Hp), milk amyloid A (MAA), C-reactive protein (CRP), lactoferrin (LF), α-lactalbumin (LA) and cathelicidin (CATHL) were significantly higher in milk from cows with CM, regardless of culture results, than in milk from healthy cows (all P-values <0.001). Milk cathelicidin (CATHL) was evaluated using a novel ELISA technique that utilises an antibody to a peptide sequence of SSEANLYRLLELD (aa49-61) common to CATHL 1-7 isoforms. A classification tree was fitted on the six biomarkers to predict Gram-positive bacteria within mastitis severity scores 1 or 2, revealing that compared to the rest of the samples, Gram-positive samples were associated with CRP < 9.5 μg/ml and LF ≥ 325 μg/ml and MAA < 16 μg/ml. Sensitivity of the tree model was 64%, the specificity was 91%, and the overall misclassification rate was 18%. The area under the ROC curve for this tree model was 0.836 (95% bootstrap confidence interval: 0.742; 0.917). TMT proteomic analysis revealed little difference between the groups in protein abundance when the three groups (Gram-positive, Gram-negative and no growth) were compared, however when each group was compared against the entirety of the remaining samples, 28 differentially abundant protein were identified including β-lactoglobulin and ribonuclease. Whilst further research is required to draw together and refine a suitable biomarker panel and diagnostic algorithm for differentiating Gram- positive/negative and NG CM, these results have highlighted a potential panel and diagnostic decision tree. Host-derived milk biomarkers offer significant potential to refine and reduce AMU and circumvent the many challenges associated with microbiological culture, both within the lab and on the farm, while providing the added benefit of reducing turnaround time from 14 to 16 h of microbiological culture to just 15 min with a lateral flow device (LFD).

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.

Genomic clues of association between clinical mastitis and SNPs identified by ddRAD sequencing in Murrah buffaloes

The total milk production of India is 209.96 MT out of which 45% is contributed by the indigenous buffalo and due to their high producing virtue, the prevalence of mastitis is 5-20%. Despite the increasing level of technological advancement, mastitis is still an issue of concern for dairy industry in India as well as across the world. Therefore, the present study aimed to identify the SNPs and associate them with the incidence of clinical mastitis in Murrah buffalo using the ddRAD sequencing approach taking mastitis incidence data of 96 Murrah buffaloes. A total of 246 million quality controlled reads were obtained with an average alignment rate of 99.01% and at a read depth of 10, quality controlled SNPs obtained were 18,056. The logistic regression model was used and a total of seven SNPs were found significantly associated (p < 0.001) with mastitis incidence and seven genes were identified viz., NCBP1, FOXN3, TPK1, XYLT2, CPXM2, HERC1, and OPCML. The majority of them were having tumor suppressing action, related to immunogenetics or glycolytic and energy production. Conclusively, the SNPs identified in this study may be useful for future studies on mastitis incidence in Murrah buffalo and the SNP associations can be further validated.

Transcriptome-wide mapping of milk somatic cells upon subclinical mastitis infection in dairy cattle

BACKGROUND

Subclinical intramammary infection (IMI) represents a significant problem in maintaining dairy cows' health. Disease severity and extent depend on the interaction between the causative agent, environment, and host. To investigate the molecular mechanisms behind the host immune response, we used RNA-Seq for the milk somatic cells (SC) transcriptome profiling in healthy cows (n = 9), and cows naturally affected by subclinical IMI from Prototheca spp. (n = 11) and Streptococcus agalactiae (S. agalactiae; n = 11). Data Integration Analysis for Biomarker discovery using Latent Components (DIABLO) was used to integrate transcriptomic data and host phenotypic traits related to milk composition, SC composition, and udder health to identify hub variables for subclinical IMI detection.

RESULTS

A total of 1,682 and 2,427 differentially expressed genes (DEGs) were identified when comparing Prototheca spp. and S. agalactiae to healthy animals, respectively. Pathogen-specific pathway analyses evidenced that Prototheca's infection upregulated antigen processing and lymphocyte proliferation pathways while S. agalactiae induced a reduction of energy-related pathways like the tricarboxylic acid cycle, and carbohydrate and lipid metabolism. The integrative analysis of commonly shared DEGs between the two pathogens (n = 681) referred to the core-mastitis response genes, and phenotypic data evidenced a strong covariation between those genes and the flow cytometry immune cells (r² = 0.72), followed by the udder health (r² = 0.64) and milk quality parameters (r² = 0.64). Variables with r ≥ 0.90 were used to build a network in which the top 20 hub variables were identified with the Cytoscape cytohubba plug-in. The genes in common between DIABLO and cytohubba (n = 10) were submitted to a ROC analysis which showed they had excellent predictive performances in terms of discriminating healthy and mastitis-affected animals (sensitivity > 0.89, specificity > 0.81, accuracy > 0.87, and precision > 0.69). Among these genes, CIITA could play a key role in regulating the animals' response to subclinical IMI.

CONCLUSIONS

Despite some differences in the enriched pathways, the two mastitis-causing pathogens seemed to induce a shared host immune-transcriptomic response. The hub variables identified with the integrative approach might be included in screening and diagnostic tools for subclinical IMI detection.

Immunological and Oxidative Biomarkers in Bovine Serum from Healthy, Clinical, and Sub-Clinical Mastitis Caused by Escherichia coli and Staphylococcus aureus Infection

The study aimed to investigate the mastitis' emerging causative agents and their antimicrobial sensitivity, in addition to the hematological, biochemical indicators, oxidative biomarkers, acute phase protein (APP), and inflammatory cytokine changes in dairy farms in Gamasa, Dakahlia Governorate, Egypt. One hundred Holstein Friesian dairy cattle with clinical and subclinical mastitis were investigated and were allocated into three groups based on a thorough clinical examination. Escherichia coli and Staphylococcus aureus were found responsible for the clinical and subclinical mastitis in dairy farms, respectively. Multiple drug resistance (MDR) was detected in 100%, and 94.74% of E. coli and S. aureus isolates, respectively. Significantly low RBCs count, Hb, and PCV values were detected in mastitic cows compared with both subclinical mastitic and control groups; moreover, WBCs, lymphocytes, and neutrophil counts were significantly diminished in mastitic cows compared to the controls. Significantly higher levels of AST, LDH, total protein, and globulin were noticed in both mastitic and subclinical mastitic cows. The haptoglobin, fibrinogen, amyloid A, ceruloplasmin, TNF-α, IL-1β, and IL-6 levels were statistically increased in mastitic cows compared to the controls. Higher MDA levels and reduction of TAC and catalase were identified in all the mastitic cases compared to the controls. Overall, the findings suggested potential public health hazards due to antimicrobial resistance emergence. Meanwhile, the APP and cytokines, along with antioxidant markers can be used as early indicators of mastitis.

Diagnostic Screening of Bovine Mastitis Using MALDI-TOF MS Direct-Spotting of Milk and Machine Learning

Novel strategies for diagnostic screening of animal and herd health are crucial to contain disease outbreaks, maintain animal health, and maximize production efficiency. Mastitis is an inflammation of the mammary gland in dairy cows, often resulting from infection from a microorganism. Mastitis outbreaks result in loss of production, degradation of milk quality, and the need to isolate and treat affected animals. In this work, we evaluate MALDI-TOF mass spectrometry as a diagnostic for the culture-less screening of mastitis state from raw milk samples collected from regional dairies. Since sample preparation requires only minutes per sample using microvolumes of reagents and no cell culture, the technique is promising for rapid sample turnaround and low-cost diagnosis. Machine learning algorithms have been used to detect patterns embedded within MALDI-TOF spectra using a training set of 226 raw milk samples. A separate scoring set of 100 raw milk samples has been used to assess the specificity (spc) and sensitivity (sens) of the approach. Of machine learning models tested, the gradient-boosted tree model gave global optimal results, with the Youden index of J = 0.7, sens = 0.89, and spc = 0.81 achieved for the given set of conditions. Random forest models also performed well, achieving J > 0.63, with sens = 0.83 and spc = 0.81. Naïve Bayes, generalized linear, fast large-margin, and deep learning models failed to produce diagnostic results that were as favorable. We conclude that MALDI-TOF MS combined with machine learning is an alternative diagnostic tool for detection of high somatic cell count (SCC) and subclinical mastitis in dairy herds.

The Future of Biomarkers in Veterinary Medicine: Emerging Approaches and Associated Challenges

Simple Summary

In this review we seek to outline the role of new technologies in biomarker discovery, particularly within the veterinary field and with an emphasis on ‘omics’, as well as to examine why many biomarkers-despite much excitement-have not yet made it to clinical practice. Further we emphasise the critical need for close collaboration between clinicians, researchers and funding bodies and the need to set clear goals for biomarker requirements and realistic application in the clinical setting, ensuring that biomarker type, method of detection and clinical utility are compatible, and adequate funding, time and sample size are available for all phases of development.

Abstract

New biomarkers promise to transform veterinary practice through rapid diagnosis of diseases, effective monitoring of animal health and improved welfare and production efficiency. However, the road from biomarker discovery to translation is not always straightforward. This review focuses on molecular biomarkers under development in the veterinary field, introduces the emerging technological approaches transforming this space and the role of ‘omics platforms in novel biomarker discovery. The vast majority of veterinary biomarkers are at preliminary stages of development and not yet ready to be deployed into clinical translation. Hence, we examine the major challenges encountered in the process of biomarker development from discovery, through validation and translation to clinical practice, including the hurdles specific to veterinary practice and to each of the ‘omics platforms–transcriptomics, proteomics, lipidomics and metabolomics. Finally, recommendations are made for the planning and execution of biomarker studies with a view to assisting the success of novel biomarkers in reaching their full potential.

The Analysis of the Ubiquitylomic Responses to Streptococcus agalactiae Infection in Bovine Mammary Gland Epithelial Cells

Purpose

Streptococcus agalactiae is one of the primary pathogens responsible for subclinical mastitis, a significant economic burden for dairy farms. An essential component of the immune response to infection is ubiquitination, which plays important roles in the complex interactions between the pathogen and host.

Materials and Methods

In the present study, quantitative ubiquitylomics was performed to profile changes in the global ubiquitinome of bovine mammary gland epithelial cells (BMECs) infected with S. agalactiae.

Results

The most notable changes in the BMEC ubiquitinome were related to the adherens junction, ribosome, and tight junction pathways. Ubiquitination of CTNNB1, EGFR, ITGB1, CTNNA1, CTNNA2, CDH1, YES1, and SLC9A3R1 appears to be fundamental for regulating multiple cellular processes in BMECs in response to S. agalactiae infection. In addition, broad ubiquitination of various effectors and outer membrane proteins was observed. Ubiquitinated proteins in S. agalactiae-infected BMECs were associated with regulating cell junctions in the host, with potential implications for susceptibility to infection.

Conclusion

The preliminary findings suggest that extensive ubiquitination of CTNNB1, CDH1 and SLC9A3R1 and proteins closely related to cell junctions might play an important role in mastitis progression in dairy cows. The results provide evidence that ubiquitin modification of certain proteins in S. agalactiae-infected BMECs could be a promising therapeutic strategy for reducing mammary gland injury and mastitis.

Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research

Due to their unique multi-gastric digestion system highly adapted for rumination, dairy livestock has complicated physiology different from monogastric animals. However, the microbiome-based mechanism of the digestion system is congenial for biology approaches. Different omics and their integration have been widely applied in the dairy sciences since the previous decade for investigating their physiology, pathology, and the development of feed and management protocols. The rumen microbiome can digest dietary components into utilizable sugars, proteins, and volatile fatty acids, contributing to the energy intake and feed efficiency of dairy animals, which has become one target of the basis for omics applications in dairy science. Rumen, liver, and mammary gland are also frequently targeted in omics because of their crucial impact on dairy animals’ energy metabolism, production performance, and health status. The application of omics has made outstanding contributions to a more profound understanding of the physiology, etiology, and optimizing the management strategy of dairy animals, while the multi-omics method could draw information of different levels and organs together, providing an unprecedented broad scope on traits of dairy animals. This article reviewed recent omics and multi-omics researches on physiology, feeding, and pathology on dairy animals and also performed the potential of multi-omics on systematic dairy research.

Development of a bioinformatics platform for analysis of quantitative transcriptomics and proteomics data: the OMnalysis

BACKGROUND

In the past decade, RNA sequencing and mass spectrometry based quantitative approaches are being used commonly to identify the differentially expressed biomarkers in different biological conditions. Data generated from these approaches come in different sizes (e.g., count matrix, normalized list of differentially expressed biomarkers, etc.) and shapes (e.g., sequences, spectral data, etc.). The list of differentially expressed biomarkers is used for functional interpretation and retrieve biological meaning, however, it requires moderate computational skills. Thus, researchers with no programming expertise find difficulty in data interpretation. Several bioinformatics tools are available to analyze such data; however, they are less flexible for performing the multiple steps of visualization and functional interpretation.

IMPLEMENTATION

We developed an easy-to-use Shiny based web application (named as OMnalysis) that provides users with a single platform to analyze and visualize the differentially expressed data. The OMnalysis accepts the data in tabular form from edgeR, DESeq2, MaxQuant Perseus, R packages, and other similar software, which typically contains the list of differentially expressed genes or proteins, log of the fold change, log of the count per million, the P value, q-value, etc. The key features of the OMnalysis are multiple image type visualization and their dimension customization options, seven multiple hypothesis testing correction methods to get more significant gene ontology, network topology-based pathway analysis, and multiple databases support (KEGG, Reactome, PANTHER, biocarta, NCI-Nature Pathway Interaction Database PharmGKB and STRINGdb) for extensive pathway enrichment analysis. OMnalysis also fetches the literature information from PubMed to provide supportive evidence to the biomarkers identified in the analysis. In a nutshell, we present the OMnalysis as a well-organized user interface, supported by peer-reviewed R packages with updated databases for quick interpretation of the differential transcriptomics and proteomics data to biological meaning.

AVAILABILITY

The OMnalysis codes are entirely written in R language and freely available at https://github.com/Punit201016/OMnalysis. OMnalysis can also be accessed from - http://lbmi.uvlf.sk/omnalysis.html. OMnalysis is hosted on a Shiny server at https://omnalysis.shinyapps.io/OMnalysis/. The minimum system requirements are: 4 gigabytes of RAM, i3 processor (or equivalent). It is compatible with any operating system (windows, Linux or Mac). The OMnalysis is heavily tested on Chrome web browsers; thus, Chrome is the preferred browser. OMnalysis works on Firefox and Safari.

Comparative Structural and Compositional Analyses of Cow, Buffalo, Goat and Sheep Cream

Factors affecting milk and milk fraction composition, such as cream, are poorly understood, with most research and human health application associated with cow cream. In this study, proteomic and lipidomic analyses were performed on cow, goat, sheep and Bubalus bubalis (from now on referred to as buffalo), bulk milk cream samples. Confocal laser scanning microscopy was used to determine the composition, including protein, lipid and their glycoconjugates, and the structure of the milk fat globules. BLAST2GO was used to annotate functional indicators of cream protein. Functional annotation of protein highlighted a broad level of similarity between species. However, investigation of specific biological process terms revealed distinct differences in antigen processing and presentation, activation, and production of molecular mediators of the immune response. Lipid analyses revealed that saturated fatty acids were lowest in sheep cream and similar in the cream of the other species. Palmitic acid was highest in cow and lowest in sheep cream. Cow and sheep milk fat globules were associated with thick patches of protein on the surface, while buffalo and goat milk fat globules were associated with larger areas of aggregated protein and significant surface adsorbed protein, respectively. This study highlights the differences between cow, goat, sheep, and buffalo milk cream, which can be used to support their potential application in functional foods such as infant milk formula.

The untargeted lipidomic profile of quarter milk from dairy cows with subclinical intramammary infection by non-aureus staphylococci

This observational study determined the lipidome of cow milk during subclinical intramammary infection (IMI) by non-aureus staphylococci (NAS), also defined as coagulase-negative staphylococci, using an untargeted approach. Among the pathogens causing bovine IMI, NAS have become the most frequently isolated bacteria from milk samples. Although the application of system biology approaches to mastitis has provided pivotal information by investigating the transcriptome, proteome, peptidome, and metabolome, the milk lipidome during mammary gland inflammation remains undisclosed. To cover this gap, we determined the milk lipidome of 17 dairy cows with IMI caused by NAS (NAS-IMI), and we compared the results with those of healthy quarter milk from 11 cows. The lipidome was determined following a liquid chromatography-quadrupole time-of-flight mass spectrometry approach. Sixteen subclasses of lipids were identified in both groups of animals. From 2,556 measured lipids, the abundance of 597 changed more than 10-fold in quarter milk with NAS-IMI compared with healthy quarters. The results demonstrate the influence of NAS-IMI on the milk lipidome, implying significant changes in lipid species belonging to the family of triacylglycerols and sphingomyelins, and contribute to the understanding of inflammatory processes in the bovine udder, highlighting potential novel biomarkers for improving mastitis diagnostics.

Milk and serum proteomes in subclinical and clinical mastitis in Simmental cows

Bovine mastitis causes changes in the milk and serum proteomes. Here changes in both proteomes caused by naturally occurring subclinical and clinical mastitis have been characterised and quantified. Milk and serum samples from healthy dairy cows (n = 10) were compared to those of cows with subclinical (n = 12) and clinical mastitis (n = 10) using tandem mass tag (TMT) proteomics. Proteins that significantly increased or decreased in milk (n = 237) or serum (n = 117) were quantified and classified by the type of change in subclinical and clinical mastitis. A group of the proteins (n = 38) showed changes in both milk and serum a number of which decreased in the serum but increased in milk, suggesting a particular role in host defence for maintaining and restoring homeostasis during the disease. Proteins affected by bovine mastitis included proteins in host defence and coagulation pathways. Investigation of the modified proteomes in milk and serum was assessed by assays for haptoglobin, serum amyloid A and α₁ acid glycoprotein validating the results obtained by quantitative proteomics. Alteration of abundance patterns of milk and serum proteins, together with pathway analysis reveal multiple interactions related to proteins affected by mastitis. Data are available via ProteomeXchange with identifier PXD022595. SIGNIFICANCE: Mastitis is the most serious condition to affect dairy cows and leads to reduced animal welfare as well as having a negative economic effect for the dairy industry. Proteomics has previously identified changes in abundance of milk proteins during mastitis, but there have been few investigations addressing changes that may affect proteins in the blood during the infection. In this study, changes in the abundance of proteins of milk and serum, caused by naturally occurring mastitis have been characterised by proteomics using a quantitative approach and both subclinical and clinical cases of mastitis have been investigated. In both milk and serum, change in individual proteins was determined and classified into varying types of altering abundance, such as increasing in subclinical mastitis, but showing no further increase in clinical mastitis. Of special interest were the proteins that altered in abundance in both milk and serum which either showed similar trends - increasing or decreasing in both biological fluids or showed reciprocal change decreasing in serum but increasing in milk. As well as characterising proteins as potential markers of mastitis and the severity of the disease, these results provide insight into the pathophysiology of the host response to bovine mastitis.

A Paradox in Bacterial Pathogenesis: Activation of the Local Macrophage Inflammasome Is Required for Virulence of Streptococcus uberis

Streptococcus uberis is a common cause of intramammary infection and mastitis in dairy cattle. Unlike other mammary pathogens, S. uberis evades detection by mammary epithelial cells, and the host–pathogen interactions during early colonisation are poorly understood. Intramammary challenge of dairy cows with S. uberis (strain 0140J) or isogenic mutants lacking the surface-anchored serine protease, SUB1154, demonstrated that virulence was dependent on the presence and correct location of this protein. Unlike the wild-type strain, the mutant lacking SUB1154 failed to elicit IL-1β from ex vivo CD14+ cells obtained from milk (bovine mammary macrophages, BMM), but this response was reinstated by complementation with recombinant SUB1154; the protein in isolation elicited no response. Production of IL-1β was ablated in the presence of various inhibitors, indicating dependency on internalisation and activation of NLRP3 and caspase-1, consistent with inflammasome activation. Similar transcriptomic changes were detected in ex vivo BMM in response to the wild-type or the SUB1154 deletion mutant, consistent with S. uberis priming BMM, enabling the SUB1154 protein to activate inflammasome maturation in a transcriptionally independent manner. These data can be reconciled in a novel model of pathogenesis in which, paradoxically, early colonisation is dependent on the innate response to the initial infection.

Novel Biomarkers of Mastitis in Goat Milk Revealed by MALDI-TOF-MS-Based Peptide Profiling

Mastitis is the most common infection of dairy goats impairing milk production and quality, which is usually recognized by mammary gland visual inspection and palpation. Subclinical forms of the disease are also widely represented, which lack the typical signs of the clinical ones but are still associated with reduced production and safety for human consumption of milk, generally presenting a high bacterial count. In order to obtain novel analytical tools for rapid and non-invasive diagnosis of mastitis in goats, we analyzed milk samples from healthy, subclinical and clinical mastitic animals with a MALDI-TOF-MS-based peptidomic platform, generating disease group-specific spectral profiles whose signal intensity and mass values were analyzed by statistics. Peculiar spectral signatures of mastitis with respect to the control were identified, while no significant spectral differences were observed between clinical and subclinical milk samples. Discriminant signals were assigned to specific peptides through nanoLC-ESI-Q-Orbitrap-MS/MS experiments. Some of these molecules were predicted to have an antimicrobial activity based on their strong similarity with homolog bioactive compounds from other mammals. Through the definition of a panel of peptide biomarkers, this study provides a very rapid and low-cost method to routinely detect mastitic milk samples even though no evident clinical signs in the mammary gland are observed.

Tandem Mass Tag (TMT)-based quantitative proteomics reveals potential targets associated with onset of Sub-clinical Mastitis in cows

Bovine milk is vital for infant nutrition and is a major component of the human diet. Bovine mastitis is a common inflammatory disease of mammary gland in cattle. It alters the immune profile of the animal and lowers the quality and yield of milk causing huge economic losses to dairy industry. The incidence of sub-clinical mastitis (SCM) is higher (25-65% worldwide) than clinical mastitis (CM) (>5%), and frequently progresses to clinical stage due to lack of sensitive and specific detection method. We used quantitative proteomics to identify changes in milk during sub-clinical mastitis, which may be potential biomarkers for developing rapid, non-invasive, sensitive detection methods. We performed comparative proteome analysis of the bovine milk, collected from the Indian hybrid cow Karan Fries. The differential proteome in the milk of Indian crossbred cows during sub-acute and clinical intramammary gland infection has not been investigated to date. Using high-resolution mass spectrometry-based quantitative proteomics of the bovine whey proteins, we identified a total of 1459 and 1358 proteins in biological replicates, out of which 220 and 157 proteins were differentially expressed between normal and infected samples. A total of 82 proteins were up-regulated and 27 proteins were down-regulated, having fold changes of ≥2 and ≤0.8 respectively. Among these proteins, overexpression of CHI3L1, LBP, GSN, GCLC, C4 and PIGR proteins was positively correlated with the events that elicit host defence system, triggering production of cytokines and inflammatory molecules. The appearance of these potential biomarkers in milk may be used to segregate affected cattle from the normal herd and may support mitigation measures for prevention of SCM and CM.

Quantitative alterations in bovine milk proteome from healthy, subclinical and clinical mastitis during S. aureus infection

Bovine mastitis, caused by Staphylococcus aureus, is a major impediment to milk production and lacks markers to indicate disease progression in cows and buffaloes. Thus, the focus of this study was to identify proteins marking the transition from subclinical to clinical mastitis. Whey proteins were isolated from 6 group's i.e. healthy, subclinical and clinical mastitis of Holstein Friesian cow and Murrah buffalo. Mass spectrometry and statistical analysis (ANOVA and t-tests) were performed on 12 biological samples each from cow and buffalo (4 per healthy, subclinical and clinical mastitis) resulting in a total of 24 proteome datasets. Collectively, 1479 proteins were identified of which significant proteins were shortlisted by a combination of fold change (≤ 0.5 or ≥ 2) and q < 0.05. Of these proteins, 128 and 163 indicated disease progression in cow and buffalo, respectively. Change in expression of haptoglobin and fibronectin from Holstein Friesian while spermadhesin and osteopontin from Murrah correlated with disease progression. Similarly, angiogenin and cofilin-1 were upregulated while ubiquitin family members were downregulated during disease transition. Subsequently, selected proteins (e.g. osteopontin and fibrinogen-α) were validated by Western blots. The results of this study provide deeper insights into whey proteome dynamics and signature patterns indicative of disease progression. BIOLOGICAL SIGNIFICANCE: Bovine mastitis is the most lethal infectious disease causing a huge economic loss in the dairy industry. In an attempt, to understand the dynamics of whey proteome in response to S. aureus infection, whey protein collected from healthy, subclinical and clinical mastitic HF and Mu were investigated. A total of 1479 proteins were identified, of which 128 and 163 had signature pattern in each stage indicative of the progression of the disease. The results of the present study provide a foundation to better understand the complexity of mastitis that will ultimately help facilitate early therapeutic and husbandry-based intervention to improve animal health and milk quality.

Staphylococcus aureus-induced proteomic changes in the mammary tissue of rats: A TMT-based study

Staphylococcus aureus is one of the most important pathogens causing mastitis in dairy cows. The objective of this study was to establish a rat model of mastitis induced by S. aureus infection and to explore changes in the proteomes of mammary tissue in different udder states, providing a better understanding of the host immune response to S. aureus mastitis. On day 3 post-partum, 6 rats were randomly divided into two groups (n = 3), with either 100 μL of PBS (blank group) or a S. aureus suspension containing 2×10⁷ CFU·mL⁻¹ (challenge group) infused into the mammary gland duct. After 24 h of infection, the rats were sacrificed, and mammary gland tissue was collected. Tandem mass tag (TMT)-based technology was applied to compare the proteomes of healthy and mastitic mammary tissues. Compared with the control group, the challenge group had 555 proteins with significant differences in expression, of which 428 were significantly upregulated (FC>1.2 and p<0.05) and 127 were downregulated (FC>0.83 and p<0.05 or p<0.01). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that upregulated differentially significant expressed proteins (DSEPs) were associated with mainly immune responses, including integrin alpha M, inter-α-trypsin inhibitor heavy chain 4, and alpha-2-macroglobulin. This study is the first in which a rat model of S. aureus-induced mastitis was used to explore the proteins related to mastitis in dairy cows by TMT technology, providing a model for replication of dairy cow S. aureus-induced mastitis experiments.

Impact of Staphylococcus aureus infection on the late lactation goat milk proteome: New perspectives for monitoring and understanding mastitis in dairy goats

The milk somatic cell count (SCC) is a standard parameter for monitoring intramammary infections (IMI) in dairy ruminants. In goats, however, the physiological increase in SCC occurring in late lactation heavily compromises its reliability. To identify and understand milk protein changes specifically related to IMI, we carried out a shotgun proteomics study comparing high SCC late lactation milk from goats with subclinical Staphylococcus aureus IMI and from healthy goats to low SCC mid-lactation milk from healthy goats. As a result, we detected 52 and 19 differential proteins (DPs) in S. aureus-infected and uninfected late lactation milk, respectively. Unexpectedly, one of the proteins higher in uninfected milk was serum amyloid A. On the other hand, 38 DPs were increased only in S. aureus-infected milk and included haptoglobin and numerous cytoskeletal proteins. Based on STRING analysis, the DPs unique to S. aureus infected milk were mainly involved in defense response, cytoskeleton organization, cell-to-cell, and cell-to-matrix interactions. Being tightly and specifically related to infectious/inflammatory processes, these proteins may hold promise as more reliable markers of IMI than SCC in late lactation goats. SIGNIFICANCE: The biological relevance of our results lies in the increased understanding of the changes specifically related to bacterial infection of the goat udder in late lactation. The DPs present only in S. aureus infected milk may find application as markers for improving the specificity of subclinical mastitis monitoring and detection in dairy goats in late lactation, when other widespread tools such as the SCC lose diagnostic value.

Biomarkers of fitness and welfare in dairy cattle: healthy productivity

Milk production intensification has led to several unwanted aspects, such as sustainability issues and environmental pollution. Among these, increased milk outputs that have been achieved over the last 70 years have led to several health and pathophysiological conditions in high yielding dairy animals, including metabolic diseases that were uncommon in the past. Increased occurrence of diverse metabolic diseases in cattle and other domestic animals is a key feature of domestication that not only affects the animals' health and productivity, but also may have important and adverse health impacts on human consumers through the elevated use of drugs and antibiotics. These aspects will influence economical and ethical aspects in the near future. Therefore, finding and establishing proper biomarkers for early detection of metabolic diseases is of great interest. In the present review, recent work on the discovery of fitness, stress and welfare biomarkers in dairy cows is presented, focusing in particular on possible biomarkers of energy balance and oxidative stress in plasma and milk, and biomarkers of production-related diseases and decreased fertility.

BoMiProt: A database of bovine milk proteins

Bovine milk has become an important biological fluid for proteomic research due to its nutritional and immunological benefits. To date, over 300 publications have reported changes in bovine milk protein composition based on seasons, lactation stages, breeds, health status and milk fractions while there are no reports on consolidation or overlap of data between studies. Thus, we have developed a literature-based, manually curated open online database of bovine milk proteome, BoMiProt (http://bomiprot.org), with over 3100 proteins from whey, fat globule membranes and exosomes. Each entry in the database is thoroughly cross-referenced including 397 proteins with well-defined information on protein function, biochemical properties, post-translational modifications and significance in milk from different publications. Of 397 proteins, over 199 have been reported with a structural gallery of homology models and crystal structures in the database. The proteome data can be retrieved using several search parameters such as protein name, accession IDs, FASTA sequence. Furthermore, the proteome data can be filtered based on milk fractions, post-translational modifications and/or structures. Taken together, BoMiProt represents an extensive compilation of bovine milk proteins from literature, providing a foundation for future studies to identify specific milk proteins which may be linked to mammary gland pathophysiology. BIOLOGICAL SIGNIFICANCE: Protein data identified from different previously published proteomic studies on bovine milk samples (21 publications) were gathered in the BoMiProt database. Unification of the identified proteins will give researchers an initial reference database on bovine milk proteome to understand the complexities of milk as a biological fluid. BoMiProt has a user-friendly interface with several useful features, including different search criteria for primary and secondary information of proteins along with cross-references to external databases. The database will provide insights into the existing literature and possible future directions to investigate further and improve the beneficial effects of bovine milk components and dairy products on human health.

Detection of Cathelicidin-1 in the Milk as an Early Indicator of Mastitis in Ewes

The objective of the study was the investigation of the behaviour of cathelicidin-1 in the milk after experimental infection with two prominent bacterial pathogens (experiment 1: Mannheimia haemolytica, experiment 2: M. haemolytica and Staphylococcus chromogenes) as a potential early indicator for diagnosis of mastitis in sheep. In two experiments, after bacterial inoculation into the udder of ewes, bacteriological and cytological examinations of milk samples as well as proteomics examinations [two-dimensional gel electrophoresis analysis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS) analysis] were performed sequentially. Cathelicidin-1 was detected and spot densities obtained from PDQuest v.8.0 were recorded. Associations were calculated between cell content and spot densities as well as between presence of mastitis in a mammary gland at a given time-point and detection of cathelicidin-1 in the respective milk sample. All inoculated mammary glands developed mastitis, confirmed by the consistent bacterial isolation from mammary secretion and increased leucocyte content therein. Spot density of cathelicidin-1 in samples from inoculated glands increased 3 h post-inoculation; spot density of cathelicidin-1 in samples from inoculated glands was higher than in samples from uninoculated controls. There was clear evidence of correlation between cell content and cathelicidin-1 spot densities in milk samples. There was significant association between presence of mastitis in the mammary gland and detection of cathelicidin-1 in the respective milk sample; overall accuracy was 0.818-this was significantly greater during the first 24 h post-challenge (0.903) than after the first day (0.704). In conclusion, detection of cathelicidin-1 in milk was significantly associated with presence of mastitis in ewes. The associations were stronger during the first 24 h post-infection than after the first day. Cathelicidin-1 has the advantage that it can be a non-specific biomarker, as simply a "positive" / "negative" assessment would be sufficient.

Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci

Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 differential proteins and higher abundance changes (P < 0.0005). The 119 increased proteins had mostly structural (n = 43, 28.29%) or innate immune defence functions (n = 39, 25.66%) and included vimentin, cathelicidins, histones, S100 and neutrophil granule proteins, haptoglobin, and lysozyme. The 33 decreased proteins were mainly involved in lipid metabolism (n = 13, 59.10%) and included butyrophilin, xanthine dehydrogenase/oxidase, and lipid biosynthetic enzymes. The same biological processes were significantly affected also upon STRING analysis. Cathelicidins were the most increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis. S100A8 and haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buffalo milk protein dataset and defined the changes occurring in SAU and NAS mastitis, with potential for improving detection (ProteomeXchange identifier PXD012355).

Review: the cellular mechanisms underlying mammary tissue plasticity during lactation in ruminants

The mammary tissue is characterized by its capacity to adapt in response to a wide variety of changing conditions. This adaptation capacity is referred to as the plasticity of mammary tissue. In dairy ruminants, lactation is challenged by modifications that can either be induced on purpose, such as by modifying management practices, or occur involuntarily, when adverse environmental constraints arise. These modifications can elicit both immediate changes in milk yield and composition and carryover effects that persist after the end of the challenge. This review focuses on the current knowledge concerning the cellular mechanisms underlying mammary tissue plasticity. The main mechanisms contributing to this phenomenon are changes in the activity and number of mammary epithelial cells (MECs). Changes in the number of these cells result from variations in the rates of cell proliferation and death as well as changes in the rate MEC exfoliation. The number of MECs also depends on the number of resident adult mammary stem cells and their progenitors, which can regenerate the pools of the various mammary cells. Several challenges, including changes in milking frequency, changes in level of feed supply and hormonal manipulations, have been shown to modulate milk yield together with changes in mammary cell activity, turnover and exfoliation. Epigenetic changes may be an additional mechanism of adaptation. Indeed, changes in DNA methylation and reductions in milk yield have been observed during once-daily milking and during mastitis in dairy cows and may affect cell activity persistently. In contrast to what has been assumed for a long time, no carryover effect on milk yield were observed after feed supply challenges in dairy cows and modification of milking frequency in dairy goats, even though the number of mammary cells was affected. In addition, mammary tissue plasticity has been shown to be influenced by the stage of lactation, health status and genetic factors. In conclusion, the cellular mechanisms underlying mammary tissue plasticity are diverse, and the mammary tissue either does or does not show elastic properties (with no permanent deformation), in response to environmental changes.

Review: Proteomic approaches to control lactational parameters in dairy cows

The use of a proteomic approach to investigate changes in the milk proteome is growing and has parralleled the increasing technological developments in proteomics moving from early investigation using a gel-based two-dimensional separation approach to more quantitative method of current focus applying chromatography and mass spectrometry. Proteomic approaches to investigate lactational performance have made substantial findings especially in the alterations in lactation during mastitis. An experimental model of Streptococcus uberis infection of the mammary gland has been used as a means to determine change not only in the milk proteome, but also in the peptidome and in the metabolome caused by the infection. Examination of the peptidome, that is the peptides of less than 25 kDa in molecular weight, demonstrated an increase in small peptides most of which were casein degradation products but also included small bioactive peptides such as mammary-associated serum amyloid A3 (MSAA3). The peptidome has also been shown to differ depending on the causative bacteria of naturally occuring mastitis. The use of a non-gel-based relative quantitative proteomic methodology has revealed major changes in the protein component of milk in mastitis. The S. uberis infection lead to increases in the concentrations of proteins such as cathelicidins, haptoglobin, MSAA3 and decreases milk content of proteins such as xanthine oxidase, butyrophilin and β-1,4-galactosyltransferase. Analysis of all protein change data identified the acute phase, coagulation and complement pathways as well as proteins related to bile acid metabolism as being most modified. Examination of the small molecular weight organic molecules of milk using a metabolomic approach identified an increase in the content in milk during mastitis of bile acids such as taurochenodeoxycholic acid. Notable changes were also found in metabolites responding to infection of the mammary gland. Carbohydrate and nucleic acid metabolites were reduced, whereas lipid and nitrogen containing metabolites were increased. The latter included increases in amino acids along with di and tri peptides, likely to be the result of casein degradation. The use of proteomics and other omic technology is in its infancy in investigation of lactational parameters, but can already provide additional insight into the changes involved in disease and will have further value in physiological and nutritional investigation of lactation.

Milk proteome from in silico data aggregation allows the identification of putative biomarkers of negative energy balance in dairy cows

A better knowledge of the bovine milk proteome and its main drivers is a prerequisite for the modulation of bioactive proteins in milk for human nutrition, as well as for the discovery of biomarkers that are useful in husbandry and veterinary medicine. Milk composition is affected by lactation stage and reflects, in part, the energy balance of dairy cows. We aggregated the cow milk proteins reported in 20 recent proteomics publications to produce an atlas of 4654 unique proteins. A multistep assessment was applied to the milk proteome datasets according to lactation stages and milk fractions, including annotations, pathway analysis and literature mining. Fifty-nine proteins were exclusively detected in milk from early lactation. Among them, we propose six milk proteins as putative biomarkers of negative energy balance based on their implication in metabolic adaptative pathways. These proteins are PCK2, which is a gluconeogenic enzyme; ACAT1 and IVD, which are involved in ketone metabolism; SDHA and UQCRC1, which are related to mitochondrial oxidative metabolism; and LRRC59, which is linked to mammary gland cell proliferation. The cellular origin of these proteins warrants more in-depth research but may constitute part of a molecular signature for metabolic adaptations typical of early lactation.

Calibration of Novel Protein Biomarkers for Veterinary Clinical Pathology: A Call for International Action

Research into the identification and use of protein biomarkers for use in veterinary clinical pathology has produced numerous potential analytes that could become common tests in the future. One problem that has to be overcome in the general acceptance of a novel biomarker is that differing standards for calibration may be developed by individual laboratories or the diagnostic companies that will provide kits for widespread use. This has been apparent in the development of acute phase protein biomarkers such as canine C-reactive protein. In order to overcome this problem an international initiative is required to ensure that assays developed in separate laboratories would have a consistent calibration protocol so that results produced are equivalent. International reference preparations for serum protein analysis for each relevant species should be established for use as primary standard in the calibration of biomarkers for veterinary diagnosis.

Proteomic Analyses of Mammary Glands Provide Insight into the Immunity and Metabolism Pathways Associated with Clinical Mastitis in Meat Sheep

Simple Summary

Clinical mastitis is one of the most common diseases in sheep and is of major economic concern due to treatment costs, inadequate lamb growth and premature eliminate of ewes. To preliminarily explore possible regulatory roles of proteins involved in the host-pathogen interactions during intramammary infection triggered by this disease in meat sheep, mammary tissues were harvested from sheep with healthy and clinical mastitis caused by natural infection, and the differentially expressed proteins were identified in an infected group when compared to a healthy group, using comparative proteomics based on two-dimensional electrophoresis. Further enrichment analyses indicated that most of the differentially expressed proteins mainly engaged in regulating immune responses and metabolisms. These findings offer candidate proteins for further studies on molecular mechanisms of host defense response and metabolism in sheep cases.

Abstract

Clinical mastitis is still an intractable problem for sheep breeding. The natural immunologic mechanisms of the mammary gland against infections are not yet understood. For a better understanding of the disease-associated proteins during clinical mastitis in meat sheep, we performed two-dimensional electrophoresis (2-DE)-based comparative proteomic analyses of mammary tissues, including from healthy mammary tissues (HMTs) and from mammary tissues with clinical mastitis (CMMTs). The 2-DE results showed that a total of 10 up-regulated and 16 down-regulated proteins were identified in CMMTs when compared to HMTs. Of these, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses revealed that most proteins were associated with immune responses or metabolisms. The results of qRT-PCR and Western blot for randomly selected four differentially expressed proteins (DEPs) including superoxide dismutase [Mn] (SOD2), annexin A2 (ANAX2), keratin 10 (KRT10) and endoplasmic reticulum resident protein 29 (ERP29) showed that their expression trends were consistent with 2-DE results except ANXA2 mRNA levels. This is an initial report describing the 2-DE-based proteomics study of the meat sheep mammary gland with clinical mastitis caused by natural infection, which provides additional insight into the immune and metabolic mechanisms during sheep mastitis.

In vitro and in vivo properties of the bovine antimicrobial peptide, Bactenecin 5

Antimicrobial peptides (AMP), part of the innate immune system, are well studied for their ability to kill pathogenic microorganisms. However, many also possess important immunomodulatory effects, and this area has potential for the development of novel therapies to supplement traditional methods such as the use of antibiotics. Here, we characterise the microbicidal and immunomodulatory potential of the proline-rich bovine AMP, Bactenecin 5 (Bac5). We demonstrate broad antimicrobial activity, including against some mycobacterial species, which are important pathogens of fish, cattle and humans. Bac5 is able to activate macrophage-like THP-1 cells and can synergistically trigger the upregulation of tnf-α when co-stimulated with M. marinum. Furthermore, Bac5 sensitises A549 epithelial cells to stimulation with TNF-α. For the first time, we characterise the activity of Bac5 in vivo, and show it to be a potent chemokine for macrophages in the zebrafish (Danio rerio) embryo model of infection. Bac5 also supports the early recruitment of neutrophils in the presence of M. marinum. In the absence of host adaptive immunity, exogenous injected Bac5 is able to slow, although not prevent, infection of zebrafish with M. marinum.

Reference 1D and 2D electrophoresis maps for potential disease related proteins in milk whey from lactating buffaloes and blood serum from buffalo calves (Water buffalo, Bubalus bubalis)

The aim of this study was to identify potential disease related proteins in milk whey of lactating buffaloes and blood serum of buffalo calves, in order to define a reference electrophoresis map for 1-DE and 2-DE. Additionally, changes in some protein patterns from buffalo calves during salmonellosis and lactating buffaloes during mastitis are presented. Milk samples were collected and distributed into groups: Milk samples from healthy buffaloes (SCC < 100.000 cells/ml, negative microbiology and CMT) (G1, n = 5) and buffaloes with subclinical mastitis (SCC > 500.000 cells/ml, positive microbiology and CMT) (G2, n = 5). Blood samples from buffalo calves (n = 6) were collected, and three calves were experimentally infected with Salmonella Dublin and samples analyzed before (M0) and 72 h after inoculation (M1). 1-DE was accomplished by loading 10 μg of TP into SDS-PAGE, stained with Coomassie blue. 2-DE was accomplished by loading 200 μg of TP into 11 cm, pH 3-10 non-linear IPG strips, followed by SDS-PAGE, stained with Coomassie blue. Protein bands/spots were excised, subjected to tryptic in-gel digestion and analyzed by LC/ESI-MS/MS. Protein identity was assigned using NCBI databases. After bands/spots from 1-DE and 2-DE were analyzed, a protein map with 35 and 40 different identified proteins in blood serum and milk whey, respectively, was generated. Significant changes in patterns of haptoglobin were observed in buffalo calves with salmonellosis and in patterns of IgLC, β-lactoglobulin and α-lactalbumin of lactating buffaloes during mastitis. The establishment of a protein map for 1-DE and 2-DE, identifying potential disease related proteins, can help to address alterations during diseases in buffaloes.

Identification of Host Defense-Related Proteins Using Label-Free Quantitative Proteomic Analysis of Milk Whey from Cows with Staphylococcus aureus Subclinical Mastitis

Staphylococcus aureus is the most common contagious pathogen associated with bovine subclinical mastitis. Current diagnosis of S. aureus mastitis is based on bacteriological culture of milk samples and somatic cell counts, which lack either sensitivity or specificity. Identification of milk proteins that contribute to host defense and their variable responses to pathogenic stimuli would enable the characterization of putative biomarkers of subclinical mastitis. To accomplish this, milk whey samples from healthy and mastitic dairy cows were analyzed using a label-free quantitative proteomics approach. In total, 90 proteins were identified, of which 25 showed significant differential abundance between healthy and mastitic samples. In silico functional analyses indicated the involvement of the differentially abundant proteins in biological mechanisms and signaling pathways related to host defense including pathogen-recognition, direct antimicrobial function, and the acute-phase response. This proteomics and bioinformatics analysis not only facilitates the identification of putative biomarkers of S. aureus subclinical mastitis but also recapitulates previous findings demonstrating the abundance of host defense proteins in intramammary infection. All mass spectrometry data are available via ProteomeXchange with identifier PXD007516.

Proteomics and metabolomics characterizing the pathophysiology of adaptive reactions to the metabolic challenges during the transition from late pregnancy to early lactation in dairy cows

The transition from late pregnancy to early lactation is a critical period in a dairy cow's life due to the rapidly increasing drain of nutrients from the maternal organism towards the foetus and into colostrum and milk. In order to cope with the challenges of parturition and lactation, comprehensive adaptive reactions comprising the endocrine and the immune system need to be accomplished. There is high variation in this coping ability and both metabolic and infectious diseases, summarized as "production diseases", such as hypocalcaemia (milk fever), fatty liver syndrome, laminitis and ketosis, may occur and impact welfare, productive lifespan and economic outcomes. Proteomics and metabolomics have emerged as valuable techniques to characterize proteins and metabolite assets from tissue and biological fluids, such as milk, blood and urine. In this review we provide an overview on metabolic status and physiological changes during the transition period and the related production diseases in dairy cows, and summarize the state of art on proteomics and metabolomics of biological fluids and tissues involved in metabolic stress during the peripartum period. We also provide a current and prospective view of the application of the recent achievements generated by omics for biomarker discovery and their potential in diagnosis.

BIOLOGICAL SIGNIFICANCE

For high-yielding dairy cows there are several "occupational diseases" that occur mainly during the metabolic challenges related to the transition from pregnancy to lactation. Such diseases and their sequelae form a major concern for dairy production, and often lead to early culling of animals. Beside the economical perspective, metabolic stress may severely influence animal welfare. There is a multitude of studies about the metabolic backgrounds of such so called production diseases like ketosis, fatty liver, or hypocalcaemia, although the investigations aiming to assess the complexity of the pathophysiological reactions are largely focused on gene expression, i.e. transcriptomics. For extending the knowledge towards the proteome and the metabolome, the respective technologies are of increasing importance and can provide an overall view of how dairy cows react to metabolic stress, which is needed for an in-depth understanding of the molecular mechanisms of the related diseases. We herein review the current findings from studies applying proteomics and metabolomics to transition-related diseases, including fatty liver, ketosis, endometritis, hypocalcaemia and laminitis. For each disease, a brief overview of the up to date knowledge about its pathogenesis is provided, followed by an insight into the most recent achievements on the proteome and metabolome of tissues and biological fluids, such as blood serum and urine, highlighting potential biomarkers. We believe that this review would help readers to be become more familiar with the recent progresses of molecular background of transition-related diseases thus encouraging research in this field.

Cathelicidin production and release by mammary epithelial cells during infectious mastitis

Cathelicidins are well-characterized antimicrobial peptides (AMPs) that are present in significant amounts in mastitic milk. Neutrophils are believed to be the main producers of these AMPs, while the role of mammary epithelial cells (MECs) in their production and release is still unclear. In this work, cathelicidin production patterns were investigated in mammary tissues of ewes infected by Staphylococcus aureus, Streptococcus uberis, or Mycoplasma agalactiae, with a combined approach including immunohistochemistry, immune-colocalization, and fluorescent in situ hybridization. Our results confirm that MECs produce and release cathelicidins in response to different mastitis pathogens. As opposed to neutrophils, however, MECs do not seem to store the preformed protein precursor in their cytoplasm, but appear to synthesize and release it only upon exposure to the microorganisms. Cathelicidin production by MECs appears to occur before leukocyte influx in the milk, suggesting a role for these cells in the initial response of the mammary epithelium to microbial infection. Once in the milk, infiltrating neutrophils release massive amounts of cathelicidin by degranulation and production of neutrophil extracellular traps, acting as the main contributor for cathelicidin abundance in mastitic milk. Taken together, our results support the active contribution of MECs to cathelicidin production and release, and reinforce the value of cathelicidins as sensitive and pathogen-independent mastitis markers.

Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 1. High abundance proteins, acute phase proteins and peptidomics

A peptidomic investigation of milk from an experimental model of Streptococcus uberis mastitis in dairy cows has incorporated a study of milk high abundance and acute phase (APP) proteins as well as analysis of low molecular weight peptide biomarkers. Intramammary infection (IMI) with S. uberis caused a shift in abundance from caseins, β-lactoglobulin and α-lactalbumin to albumin, lactoferrin and IgG with the increase in lactoferrin occurring last. The APP response of haptoglobin, mammary associated serum amyloid A3 and C-reactive protein occurred between 30-48 hours post challenge with peak concentrations of APPs at 72-96 hours post challenge and declined thereafter at a rate resembling the fall in bacterial count rather than the somatic cell count. A peptide biomarker panel for IMI based on capillary electrophoresis and mass spectrometry was developed. It comprised 77 identified peptides (IMI77) composed mainly of casein derived peptides but also including peptides of glycosylation dependent cell adhesion molecule and serum amyloid A. The panel had a biomarker classification score that increased from 36 hour to 81 hour post challenge, significantly differentiating infected from non-infected milk, thus suggesting potential as a peptide biomarker panel of bovine mastitis and specifically that of S. uberis origin. The use of omic technology has shown a multifactorial cross system reaction in high and low abundance proteins and their peptide derivatives with changes of over a thousand fold in analyte levels in response to S. uberis infection.

Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 3. Untargeted metabolomics

Metabolomic investigation of milk from cows with bovine mastitis has revealed major changes in carbohydrates, lipids, amino acids, nucleotides and bile acids.