Search Results (247)

While bulk RNA sequencing provides a comprehensive view of transcriptomes, it lacks cell type specificity. Single-cell RNA sequencing (scRNA-seq) overcomes this limitation by providing detailed insights at the individual cell level, though it involves higher costs. Deconvolution methods can estimate cell type proportions in bulk RNA-seq data, but their results may vary based on the scRNA-seq reference data and software used. This study investigates the estimation of muscle fiber type proportions through deconvolution analysis of Longissimus dorsi muscle bulk RNA-seq data from late-gestation Holstein Friesian multiparous cows. Four software tools (i.e., CIBERSORTx, Cellanneal, DeconvR-NNLS, and DeconvR-RLM) were compared using scRNA-seq reference data from Brahman and Wagyu cattle breeds, which included proportions of types I, IIa, and IIx myofibers. Kruskal–Wallis and Dunn’s tests revealed that the breed of reference data significantly influenced the proportions of type IIa and IIx muscle fibers across different deconvolution methods. To the best of our knowledge, this is the first study to show that the cattle breed used in reference scRNA-seq data can substantially impact deconvolution outcomes, highlighting a critical consideration for accurate cell type proportion estimation in livestock genomics. These findings suggest that future deconvolution studies should carefully consider breed compatibility between reference and target datasets. Full article

Previous studies of direct-fed microbial (DFM) supplements showed variable effects on the microbiota and physiology of dairy cows. The main aims of this study were to investigate the milk microbiota of cows supplemented with a lactobacilli-based DFM compared to untreated cows; describe the changes; and quantify the association between the taxa and cow productivity. The study followed seventy-five Holstein–Friesian dairy cows supplemented with a DFM over 16 months compared to seventy-five non-supplemented cows. Twenty-five cows from each group were sampled for microbiota analysis. The top taxa significantly associated with the variables were as follows: Age (Mammaliicoccus_319276, Turicibacter), milk production (Turicibacter, Bifidobacterium_388775), DIM (Stenotrophomonas_A_615274, Pedobacter_887417), milk fat percentage (Pseudomonas_E_647464, Lactobacillus), calendar month (Jeotgalicoccus_A_310962, Planococcus), milk protein percentage (Tistrella, Pseudomonas_E_650325), experimental group (Enterococcus_B, Aeromonas), SCC (Paenochrobactrum, Pseudochrobactrum), and trimester of pregnancy (Dyadobacter_906144, VFJN01 (Acidimicrobiales)). These were identified using multivariable analysis. Twenty-six genera were associated with the differences between experimental groups, including Pseudomonas, Lactococcus and Staphylococcus. Microbial taxa that changed in relative abundance over time included Atopostipes, Brevibacterium and Succinivibrio. Many of these genera were also part of the core microbiota. Supplementation with the DFM significantly altered the milk microbiota composition in the dairy cows, highlighting the impact of long-term DFM supplementation on microbial communities. Full article

Vitamin D is essential for calcium homeostasis, bone mineralization, immunity, and disease prevention. In a field study with Holstein-Friesian dairy cows, the impact of prepartum vitamin D₃ treatment on early postpartum placental gene expression, focusing on calcium metabolism, feto-placental growth, and immune response, had been investigated. Eight multiparous cows were treated with 10 mL vitamin D₃ (1 million IU cholecalciferol/mL) intramuscularly on day 273 of pregnancy, while eight others remained untreated and served as controls. Placental tissues were collected post-calving, and gene expression was analyzed using quantitative real-time PCR. Among 23 genes, 5 showed significant downregulation in the treated group: CaBP-9k (reduced by 88.1% from 32.80 ± 91.50 to 3.90 ± 8.54), ESR1 (reduced by 95.7% from 7.89 ± 17.87 to 0.34 ± 0.34), LHR (reduced by 96.5% from 3.75 ± 5.45 to 0.13 ± 0.17), NOD1 (reduced by 94.1% from 4.21 ± 7.00 to 0.25 ± 0.30), and TLR1 (reduced by 99.7% from 24.80 ± 61.45 to 0.07 ± 0.08). These results suggest that vitamin D₃ supplementation affects key pathways related to calcium transport, reproductive function, and immune response in the bovine placenta. These molecular changes may help to explain improved calcium homeostasis and reduced postpartum complications, offering insights into how targeted nutritional interventions can enhance reproductive efficiency in high-producing dairy cows. Full article

Ketosis and fatty liver syndrome are metabolic disorders apparent in dairy cows during the transition period. The study focused on examining how varying levels of milk production in dairy cows might reflect or influence specific blood biochemical markers and liver health as assessed through ultrasonography. A total of 65 Holstein-Friesian cows from six farms were evaluated at three time points as follows: 7 days before expected calving and at 7 and 21 ± 3 days postpartum. Each evaluation included the body condition score (BCS), blood sampling for biochemical analysis, and liver ultrasonography. Based on average farm milk yield, cows were divided into three production groups as follows: GR1 (38.4 ± 6.45 L/day, n = 23), GR2 (42.9 ± 2.77 L/day, n = 24), and GR3 (45.69 ± 7.49 L/day, n = 18). Parameters assessed included liver lipid content and ultrasonographic measurements such as portal vein diameter and depth, liver depth, and liver angle. Significant time-dependent changes were observed in liver size, fat metabolism, and electrolyte balance, especially postpartum. However, no significant differences emerged among the production groups, indicating that these changes likely represent physiological adaptations to lactation. These findings support the use of blood analysis and ultrasonography as practical, minimally invasive tools for routine metabolic health monitoring in dairy cows during the transition period. Full article

This study examined the impact of heat stress during specific periods before and after insemination to identify the most critical time affecting insemination success in dairy cows. A total of 47,199 insemination records from 6751 Holstein-Friesian cows (2002–2024) were analysed using generalised linear mixed models (GLMMs) with a binomial distribution. The periods assessed were the day of insemination, 21–6 days before (P1), 5–2 days before (P2), 1 day before to 1 day after (P3), 2–7 days after (P4), and 8–30 days after insemination (P5). Mild heat stress significantly reduced insemination success on the day of insemination, with a critical THI threshold of 60. Among all periods, P1 was the most sensitive to heat stress, with even mild stress negatively affecting outcomes. Severe heat stress (THI ≥ 72) also impacted P3 and P5, whereas P2 and P4 showed no significant effect. Heritability estimates increased with heat stress intensity, suggesting genetic variability in resilience. These findings highlight the importance of managing heat stress from three weeks before to one month after insemination and support the potential for genetic selection to improve reproductive performance under heat stress conditions. Full article

In dairy cattle, abomasal ulcers are a serious but sometimes disregarded ailment that can have detrimental effects on health and cause financial losses. Due to inconclusive clinical symptoms, abomasal ulcers are typically misdiagnosed and treated improperly. Specialized diagnostic methods should be considered to ensure a correct diagnosis and the well-being of cattle. This report focuses on a 4-year-old Holstein-Friesian cow which began her third lactation two weeks before she started showing general clinical signs of an elevated fat–protein ratio in the milk and was diagnosed with an abomasum displacement. The clinical signs can also be mistaken for other conditions such as traumatic reticuloperitonitis and left dislocated abomasum. The patient was brought to the LUHS Large Animal Clinic, and after a short while, sudden death occurred. The autopsy concluded that death had occurred due to hypovolemic shock caused by abomasal ulcer perforation, which caused bleeding into the abomasum and intestines. Also, the type 3 ulcer caused severe peritonitis and anemia, and feed and fibrin could be seen on the outside of organs in the abdomen. Blood clots mixed with feed had formed in the inside of the abomasum and intestinal tract. Based on the work of previous scientific studies, it has been established that the occurrence of ulcers is more frequent in dairy cows during the first four to six weeks of lactation. And the most probable cause could be intensive feeding and dietary changes. Ulcers in the abomasum are very difficult to diagnose, because they require special diagnostic equipment such as an ultrasound or surgical interventions. Due to the similarity with other diseases, this pathological condition of the abomasum is most frequently only identified in post-mortem examinations. Full article

This study examined the prevalence, distribution, and detection methods linked to Treponema species associated with active bovine digital dermatitis (BDD) in dairy cattle. Tissue, surface swabs, interdigital space swabs, and faecal samples were collected from 20 Holstein-Friesian cows from a farm in Eastern Slovakia. Molecular analysis revealed that all cows tested positive for at least one Treponema species. The most prevalent species were Treponema medium (100%), Treponema pedis (95%), and Treponema brennaborense (75%). Distribution analysis demonstrated significant differences in the occurrence of these species across sampling methods, with T. pedis being more prevalent in tissue biopsies and surface swabs (p < 0.001), and T. brennaborense in surface swabs (p < 0.001). A comparison of qualitative real-time PCR and standard PCR revealed that real-time PCR detected T. pedis and T. brennaborense in 70% and 75% of tissue samples, respectively, while standard PCR failed to detect T. brennaborense. Furthermore, real-time PCR showed a significantly higher prevalence of T. brennaborense (p < 0.001). These findings underscore the enhanced sensitivity of real-time PCR in detecting T. brennaborense and highlight the complex distribution of Treponema species in BDD lesions, which may inform the development of more effective control strategies for BDD. Full article

An in vitro and an in vivo study were conducted to investigate the effects of a blend of cinnamaldehyde, eugenol, and capsicum oleoresin (CEC) on rumen fermentation parameters, animal performance, and methane (CH₄) emissions in dairy cows. Continuous culture fermenters (CCF) were utilized to test one of two treatments: (1) CON; no supplementation and (2) CEC supplemented at 0.0125 g/d. The basal diet consisted of grass hay and concentrate (50:50). Supplementation with CEC increased (p < 0.01) total volatile fatty acids (VFA; mM) and decreased (p = 0.02) CH₄ concentration compared with CON in vitro. Additionally, protozoa abundance tended (p = 0.07) to decrease in CEC compared with CON. The in vivo experiment utilized forty Holstein-Friesian dairy cows (32% primiparous and 68% multiparous) averaging 163 ± 48 days in milk (DIM) and 38 ± 6.2 kg/d of milk yield (MY). Cows were blocked by parity and randomly assigned to one of two treatments: (1) CON; no supplementation and (2) CEC supplemented at 1.2 g/cow/d. The basal diet consisted of grass hay and concentrate (40:60). Individual CH₄ emissions were recorded using the sniffer technique. Dry matter intake (DMI) and eating rate were increased (p < 0.01; 3.6% and 5.2%, respectively), while feed efficiency decreased (p < 0.05) in CEC compared with CON. Additionally, CEC decreased (p = 0.02) CH₄ yield by 16.4% and tended to reduce daily CH₄ production (p = 0.09) and CH₄ intensity (p = 0.08) by 13.4% and 14.0%, respectively. Supplementing CEC decreased CH₄ concentration in vitro and CH₄ yield in vivo without negatively impacting performance parameters. Full article

This study presents the development of a database for detecting active mounts, utilizing IoT collars equipped with Inertial Measurement Units (IMUs) installed on eight Holstein Friesian cows, along with video recordings from a long-range PTZ camera mounted in a central pole for event labeling in the natural environment when free grazing. The resulting database comprises 415 labeled events associated with various behaviors, containing acceleration signals in both the Body and World Frame of reference and gyroscope signals. A Support Vector Machine (SVM) algorithm is implemented to evaluate the effectiveness of the dataset in detecting active mounts and to compare training performance using both frames. The algorithm achieves an average F1 Score of 88.6% for the World Frame of reference, showing a significant improvement compared to the algorithm trained with Body Frame (78.6%) when both are trained with the same 112 features. After applying feature selection using Sequential Backward Selection (SBS), the SVM exhibits a minor performance difference between the F1 Score obtained with the two reference frames (89.7% World Frame vs. 91.5% Body Frame). This study provides a public dataset and a replicable methodology, facilitating future research on movement-based behavior classification in cattle. Full article

In lactating dairy cows, negative energy balance (NEB) induces metabolic shifts, including enhanced lipolysis, leading to elevated concentrations of free fatty acids (FFAs) in circulation. Metabolic changes affect milk fat synthesis and the characteristics of milk fat globules (MFGs), particularly their size and distribution. Systemic FFA release inversely correlates with the restoration of the body condition score (BCS), suggesting that recovering the BCS may mitigate the negative effects of NEB on milk fat composition. This study aimed to investigate the relationship between BCS restoration, metabolic burden, and their effects on MFG characteristics in lactating cows. The study was conducted on two dairy farms (F1 and F2) with 80 Holstein-Friesian cows. Cows were grouped according to farm and diet, with average lactation yields of 9653 ± 259 kg (F1) and 9548 ± 341 kg (F2). Milk composition was analyzed, and blood and milk samples were collected at four lactation stages. The results showed a significant correlation between elevated circulating FFA concentrations, resulting from adipose tissue lipolysis during NEB, and alterations in MFG size and distribution. The restoration of BCS was inversely correlated with FFA release, suggesting that improvements in the BCS may mitigate the adverse effects of NEB on milk fat synthesis by regulating lipolysis. Additionally, higher β-hydroxybutyrate (BHBA) levels were associated with a reduction in MFG diameter, indicating disruptions in lipogenesis during metabolic stress. These findings highlight the complex relationship between metabolic stress, BCS restoration, and MFG characteristics, with implications for milk fat synthesis in lactating cows. Full article

This study aimed to evaluate the heritability (h²) estimates of some important udder conformation traits, their relationship to each other and with production, and their phenotypic and genetic trends over a 10-year period in relatively high-yielding Holstein-Friesian cows. A total of 15,032 cows from six herds in Hungary were tested for milk (MY), butterfat (FY), and protein (PY) production yields over 305 days in first lactation. In addition, their udder conformation was scored for udder attachment (FU), rear udder height (RUH), central ligament (CL), udder depth (UD), front teat placement (FTP), and udder texture (UT) on a 1–9 linear udder score scale. REML and BLUP single-step animal model and linear regression model were used for data analysis and estimation. The production traits of the cows were quite reasonable, with 10,179.4 kg milk, 380.3 kg fat, and 333.1 kg protein in a standard lactation of 305 days. The scores of the udder conformation traits (5.4 to 6.1) were slightly above the mean of 5 on a linear scale of 1–9. The h² for MY, FY, and PY were obtained from 0.30 to 0.35, while those for udder traits were from 0.22 to 0.41. Phenotypic (r_p) and genetic (r_g) correlations for the relationship between production and udder conformation were weak or negligible (ranged from −0.33 to +0.15). Most of the associations between different udder traits were generally weak, but moderate positive correlations were observed between FU and UD (r_p = 0.42, r_g = 0.50 or 0.57), and between FU and UT (r_p= 0.36, r_g = 0.33 or 0.35). There were increasing genetic trends in the milk production (b = 2.2 to 16.5), but the studied udder conformation traits did not change over time (b = 0.00 to 0.03). In our study, despite an increase in milk yield over the studied ten-year period, udder conformation traits did not change. Therefore, considering that udder conformation scores were slightly above average and that udder traits were included in the selection index, we believe that it may be necessary to reconsider the udder conformation scoring system and its inclusion in the selection index. Full article

Pastoral systems in New Zealand are under societal pressure due to their increasing negative environmental impact in terms of greenhouse gas emissions. This study was conducted to investigate the effects of supplementing a mixture containing hydrolysable and condensed tannins on the in vitro fermentation characteristics and gas production of three different forages, Lolium perenne, Medicago sativa, and Plantago lanceolata. Three fermentation runs of 48 h were conducted using the ANKOM gas production technique, with each pertaining to a particular forage with or without (control) tannin. Tannins were added to the fermentable substrate (i.e., forage) at a level of 0.3%. For each run, rumen fluid was collected from two fistulated Holstein Friesian × Jersey cows. The ANKOM RF gas production modules were used to monitor gas pressure and temperature every 5 min. At the end of each run, the pH of the fluid was measured, gas vials were taken for methane (CH₄) measurements and liquor samples were taken to measure volatile fatty acids (VFA) and NH₃ concentrations. The addition of tannins reduced the fractional rate of gas production for alfalfa (p ≤ 0.04) but increased it for ryegrass and plantain. There was a tendency for reduced gas production for ryegrass when tannins were added (p = 0.10). There was also a tendency for CH₄ production to reduce (p < 0.10) and N₂O to increase (p = 0.10) when tannins were added. Iso-butyrate tended to be lower for ryegrass control than to ryegrass with tannins (p = 0.08). Valerate concentration was lower for plantain control than to plantain with tannins. No effects were detected for gas composition (p > 0.05) or VFA concentrations (p > 0.05) when fermenting alfalfa. Under the condition of this study, these results may suggest that low-level tannin addition to the diet may affect rumen-fermentation pattern with a potential reduction of CH₄ production in Lolium perenne-based diets. Further research is required on the effect of low levels of tannin supplementation under ex vitro and in vivo conditions as tannin supplementation effects might be substrate-dependent. Full article

Background: The presence and concentration of lipids in serum of dairy cows have significant implications for both animal health and productivity and are potential biomarkers for several common diseases. However, information on serum lipid composition is rather fragmented, and lipid remodelling during the transition period is only partially understood. Methods: Using a combination of reversed-phase liquid chromatography-mass spectrometry (RP-LC-MS), hydrophilic interaction-mass spectrometry (HILIC-MS), and lipid annotation software, we performed a comprehensive identification and quantification of serum of dairy cows in pasture-based Holstein-Friesian cows. The lipid remodelling induced by negative energy balance was investigated by comparing the levels of all identified lipids between the fresh lactation (5–14 days in milk, DIM) and full lactation (65–80 DIM) stages. Results: We identified 535 lipid molecular species belonging to 19 classes. The most abundant lipid class was cholesteryl ester (CE), followed by phosphatidylcholine (PC), sphingomyelin (SM), and free fatty acid (FFA), whereas the least abundant lipids included phosphatidylserine (PS), phosphatidic acid (PA), phosphatidylglycerol (PG), acylcarnitine (AcylCar), ceramide (Cer), glucosylceramide (GluCer), and lactosylceramide (LacCer). Conclusions: A remarkable increase in most lipids and a dramatic decrease in FFAs, AcylCar, and DHA-containing species were observed at the full lactation compared to fresh lactation stage. Several serum lipid biomarkers for detecting negative energy balance in cows were also identified. Full article

Summary-data-based Mendelian randomization (SMR) analysis identified a novel cis-expression quantitative loci (cis-eQTL) associated with the upregulation of the expression of the early growth response factor 4 (EGR4) gene in animals with paratuberculosis (PTB)-associated multifocal lesions, which has been suggested to be modulating the NF-kβ-induced proinflammatory immune response to Mycobacterium avium subsp. paratuberculosis (Map) infection. To confirm these findings and to study the role of EGR4 expression in PTB resilience, the number of EGR4-expressing cells were analysed in paraffin-fixed gut tissues and regional lymph nodes of naturally Map-infected Holstein Friesian cows with focal, multifocal (subclinical and clinical), and diffuse lesions (intermediate and multibacillary), and in controls without lesions by quantitative anti-EGR4 immunohistochemistry. Subclinical animals with multifocal lesions showed a significantly higher number of EGR4-positive cells and were sacrificed at a significantly older average age than the remaining groups (p < 0.001 in all cases). We hypothesize that EGR4 could be mitigating the negative impact of Map infection on host clinical status through its involvement in three molecular mechanisms that promote resilience: (i) limiting NF-kβ-mediated proinflammatory responses, (ii) controlling tissue damage, acting as a brake on T-cell proliferation and cytokine production, and (iii) favouring tissue repair through interaction with epidermal growth factor receptor (EGFR). Full article

This study, conducted on a commercial dairy farm using a robotic milking system in Victoria, Australia, examined the effects of Polygain™ (The Product Makers Australia), a polyphenol-rich sugarcane feed material (PRSFM), on CH₄ emissions in grazing dairy cattle using an inverse-dispersion model (IDM) combined with open-path laser techniques. Thirty lactating Holstein Friesian cows (aged 2–5 years with an average body weight of 663 kg and average daily milk production of 28.9 kg) were divided into two dietary treatment groups of fifteen cows each. Before the measurement, the PRSFM (0.25%) was supplemented for 3 weeks as an adaptation period and mixed with pellet feed for the treatment group. Over the 2-week measurement period, CH₄ production (MP) was 495 ± 12 and 377 ± 12 (mean ± standard error) g CH₄/animal/day for the control and treatment groups, respectively. Methane intensity (MI) was 17.04 and 13.01 g CH₄/animal/kg milk/day in the control and treatment groups, respectively. On average, Polygain supplementation reduced MP and MI by 24%. This potential CH₄ reduction extrapolated across Australia contributes to a 2.63% reduction in national agricultural emissions. This study underscores the potential of Polygain for CH₄ mitigation in dairy cattle. Full article