[This corrects the article DOI: 10.3168/jdsc.2024-0668.].
Cheese ripening is a complex microbial process marked by significant shifts in microbial composition. Considering that propidium monoazide (PMA) depletes DNA from nonviable cells, we hypothesized that PMA treatment of cheese samples could affect the microbiota characterization of 60-d-ripened raw goat curd cheese by 16S rRNA metabarcoding sequencing. After ripening, PMA-treated and nontreated (control) samples from the same cheese units were processed for DNA extraction, library preparation, and 16S rRNA metabarcoding sequencing on an Illumina MiSeq platform. Downstream bioinformatic analyses for microbial diversity assessment were performed using QIIME 2 and the phyloseq package in R. Statistical analyses included permutational multivariate analysis of variance (PERMANOVA), Wilcoxon tests, and linear discriminant analysis effect size (LEfSe). No significant differences were observed in either α or β diversity metrics between PMA-treated and nontreated samples. However, PMA treatment significantly reduced the abundance of farm environment-associated Dickeya and Pectobacteriaceae taxa in cheese samples, thus improving the accuracy of determining the cheese microbial structure using next-generation sequencing technologies. Further longitudinal studies focusing on different sampling periods during ripening, as well as other cheese types, may shed light on the potential benefits of using PMA for improving the accuracy of cheese microbial community characterization by next-generation sequencing.
Among κ-CN variants in milk, κ-CN B is the most reactive to chymosin activity, enhancing the quality, profitability, and sustainability of the final cheese product. The aim of this study was to assess the agreement between reverse phase HPLC (RP-HPLC) reference method and a rapid ELISA technique for the quantification of κ-CN B in individual bovine milk samples. Chromatographic and immunoenzymatic analyses were performed on individual milk samples from 933 Brown Swiss cows, with κ-CN B expressed as (1) milligrams per milliliter of milk, (2) percentage of κ-CN B over total milk protein content, and (3) grams of κ-CN B yielded on a milking event. The agreement between κ-CN B phenotypes measured through RP-HPLC and ELISA was evaluated through r and z-scores. Results suggested a general agreement between the 2 techniques, with r ranging from 0.88 for κ-CN B expressed in milligrams per milliliter and as a percentage to 0.90 for κ-CN B expressed in grams. This is further supported by relatively low z-scores (<0.5), which suggested the absence of significant differences between the values obtained from RP-HPLC and ELISA. Observed discrepancies were likely because ELISA does not provide quantitative results for concentrations of κ-CN B >10 mg/mL, and to the limited sensitivity of the ELISA at low concentrations of κ-CN B. Overall, findings of the present study demonstrated a strong agreement between the 2 techniques.
At calving, 2,213 Holstein cows from 5 farms were enrolled in a study to establish potential associations between postcalving health disorders and reproductive performance and to determine the effectiveness in achieving pregnancy at first artificial insemination (AI) and the consequences on the proportion of cows pregnant by 150 DIM when using 2 different reproductive management programs for first service. Within farm, cows were randomly allocated to 2 reproductive schemes: (1) inseminating based on estrus detection with a backup synchronization program (SP) on open cows with DIM ≥ 80 (HD; 1,141 cows, 34% primiparous [PPC]) or (2) after an SP (1,072 cows, 35% PPC). Cows on HD were inseminated when detected in estrus using an accelerometer if DIM >50, and those not inseminated based on estrus by 80 ± 3 DIM (28.8%) were submitted to an Ovsynch protocol, if a corpus luteum (CL) was present, or to the same Ovsynch protocol but with the addition of a progesterone-releasing intravaginal device if CL was absent. Cows on SP were submitted to a simplified double-Ovsynch protocol (the first GnRH injection was omitted) and serviced between 74 and 80 DIM. On average, cows on HD were first inseminated at 72.4 ± 1.63 DIM, whereas those on SP were first inseminated at 78.3 ± 1.63 DIM. At first AI, PPC had a greater (P < 0.01) pregnancy at first AI (P/AI; 55.3%) than multiparous cows (MPC; 38.6%). But PPC submitted to SP had the greatest P/AI during the cold season (63.8%), followed by PPC on SP (57.5%) and on HD (54.6%) during the hot season. During the cold season, P/AI in PPC on HD was lower (45.6%) than that of PPC on SP (63.8%); whereas P/AI in MPC was similar among treatments and seasons, except for MPC in HD during the hot season (32.2%) compared with those on SP (41.9%). By 150 DIM, there were no differences in the proportion of pregnant cows between SP and HD. Cows with retained placenta tended to be inseminated later than those that expelled the placenta within 24 h. Cows that experienced metritis tended to have lower P/AI than cows that stayed healthy after calving, but cows on SP that incurred metritis tended to have better P/AI than cows on HD with metritis. Relying on estrus detection may allow for a first AI at lower DIM, but at 150 DIM, the proportions of pregnant cows was similar between the 2 strategies.
When trying to achieve optimum production, lactating, and dry dairy cows must be provided with relief from heat stress. The most practical and common methods to alleviate the negative effects of heat and humidity on lactating and dry dairy cows consist of 3 main approaches: shade, natural ventilation, and active cooling, with active cooling being the most advantageous. Our objective was to determine if an automated smart system (Agpro, Paris, TX) for controlling soaker output is as effective as the conventional approach to controlling soakers, which relies on a set frequency after a threshold temperature is reached. Nulliparous (n = 12) and multiparous (n = 30) pregnant Holsteins cows were dried off 40 ± 9 d (multiparous only) before expected calving and randomly assigned to one of 3 treatments in the same barn: 5-min interval (30s on, 5 min off) cooling periods with shade, fans, and soakers (CL; n = 14); Agpro smart cooling with shade, fans, and soakers (SS; n = 14); and heat stress with only shade and natural ventilation and no active cooling system (HT; n = 14) during the dry period until parturition. Daily DMI of individual cows, pen water intake, and pen water usage from soakers were measured daily. Blood samples for hematocrit were taken weekly. Respiration rate (in breaths per minute [bpm]) and rectal temperature (RT) were measured 3 times weekly. Calf birth weight and gestation length were recorded upon parturition. No differences were observed for gestation length, calf birth weight, dry period length, or hematocrit among the treatments. However, HT cows had lower overall DMI than SS (8.6 vs. 10.1 ± 0.4 kg/d; P = 0.01) and tended to be lower than CL (8.6 vs. 9.5 ± 0.4 kg/d; P = 0.11). Water usage per cow was lowest in the HT group compared with the CL and SS groups (89.6 vs. 225.3 vs. 80.6 ± 156.5 L/cow per day). Respiration rate (68 vs. 53 vs. 48 ± 1.2 bpm; P < 0.01), RT (38.8°C vs. 38.4°C vs. 38.3°C ± 0.03°C; P < 0.01), and vaginal temperatures (38.9°C vs. 38.6°C vs. 38.7°C ± 0.09°C) were affected by treatment with HT, having the higher values relative to CL and SS, respectively. Compared with conventional cooling, the SS system effectively cooled the animals, decreased the estimated total water usage per cow, and maintained adequate animal welfare.
Nutritional grouping (NG), where cows are fed in groups based on similar nutrient requirements, has been used as a strategy to improve the precision of nutrition delivery and thus economic returns. Enteric methane, one of the largest on-farm sources of greenhouse gas emissions, is strongly influenced by diet formulation. With growing concerns about climate change, it is important to evaluate whether NG can also help reduce enteric methane emissions. To address this, we developed an open-source linear optimization model to assess the impact of NG on both feed cost and enteric methane emissions. We conducted a case study with 675 cows from the University of Wisconsin's Arlington Agricultural Research Station. Diets were formulated using the farm's actual feed ingredients and prices and were constrained according to current dairy cattle feeding guidelines. Without NG, optimization alone reduced feed cost by $2.52/cow per day (32%) under the cost-minimization objective, and reduced methane emissions by 57 g/cow per day (12%) under the methane-minimization objective, relative to the on-farm diet used during the study period. Under a dual-objective approach that simultaneously considered feed cost and enteric methane emissions, the model identified a pragmatic compromise solution. By placing greater emphasis on economic performance to reflect the current US production context, methane emissions decreased by 55 g/cow per day compared with the cost-minimization scenario while maintaining similarly low feed costs. Nutritional grouping did not consistently outperform the optimized single-group diet, but it modestly improved the nontarget outcome (lower methane when minimizing cost and lower cost when minimizing methane). These findings indicate that well-optimized rations using existing feeds can deliver meaningful economic and environmental benefits, and NG offers an additional layer of management refinement that may not only reduce the feed cost as suggested by literature, but also offer complementary benefits when methane is considered as a secondary performance dimension.
The goal of this observational study was to compare the prepartum vitamin E and selenium concentrations of multiparous cows based on herd incidence of retained placenta membranes (RP). Within a database of 50 herds enrolled by convenience for a previous study and followed for a whole year, 5 herds with no incidence of RP and 5 herds with high incidence (≥6.5%) of RP were randomly selected. In each farm, 10 multiparous cows were randomly selected. Vitamin E and selenium were analyzed by HPLC in serum collected from 21 to 7 d before predicted calving. No significant difference was observed in the concentration of vitamin E or selenium between cows from herds with no incidence of RP and herds with high incidence of RP. Our results suggest that prepartum concentrations of vitamin E and selenium are not good indicators of herd RP incidence status, and perhaps other predictors should be explored.
The environmental footprint of dairy production is one of the most pressing challenges faced by the industry globally. Our study aimed to develop and validate a cost-effective sensing solution for real-time monitoring of dairy farms' GHG emissions and microclimatic conditions. Each of the integrated sensing nodes was equipped with carbon dioxide (CO2), methane (CH4), and ammonia (NH3) gas sensors, along with an all-in-one weather sensor. Sensing nodes were validated against gold-standard measurements using open-circuit respiration chambers with individual cows under controlled conditions. The CH4 emissions (133.0 ± 22.5 ppm, mean ± SD) showed an overall correlation (r = 0.46) with the gold-standard respiration chamber (166.0 ± 32.8 ppm) across all 3 d. However, the correlation changed over time, with a strong correlation on d 1 (r = 0.62), a moderate correlation on d 2 (r = 0.35), and a weak correlation on d 3 (r = 0.11). In contrast, sensor node quantified CO2 emissions (905 ± 779 ppm) showed a weaker correlation (r = 0.019, 2,461 ± 346 ppm), indicating the need for further improvements to the sensing node. A wireless network of calibrated sensing nodes was deployed in 3 different locations within a dairy farm: dry cow pen (DCP), feed bunk (FB), and freestall beds (FSB) at a research dairy farm. The CH4 emissions were greater in the DCP (12.5 ± 6.65 ppm) compared with FB (2.80 ± 0.61 ppm) and FSB (2.34 ± 0.62 ppm). The CO2 emissions at the FB were greater (1,498 ± 1,020 ppm) compared with the DCP (534 ± 222 ppm) and FSB (724 ± 517 ppm). The NH3 emissions were highest in the FSB (4.24 ± 0.91 ppm) compared with DCP (2.93 ± 1.35 ppm) and FB (1.10 ± 0.44 ppm). The differences in GHG emissions across the different areas of the dairy farm may be influenced by ambient temperature, humidity, housing conditions, and manure management practices. Our sensing nodes may provide a low-cost, scalable sensing network that can offer a practical solution for continuous GHG monitoring.
The objective of this study was to evaluate the effects of Beef Quality Assurance (BQA) certification on relevant traits of cull dairy cows. This study compared BCS, lameness scores, hot carcass weight, and carcass damage of cull dairy cows originating from BQA and non-BQA certified farm operations at the slaughter facility. A blinded observational study was completed to visually score 611 cows from 15 different dairy operations upon arrival at the holding pens of a slaughter facility. Of the 15 farms, 9 were BQA certified. Dairy cows from BQA-certified operations had improved BCS, were less lame, had greater hot carcass weight (346 vs. 283 kg), and had less carcass damage when compared with dairy cows from noncertified farms. If we assume that the difference in hot carcass weight and damage loss can be fully attributed to BQA certification, then the certification led to an additional value of US$251/cow. These findings indicate that BQA certification is associated with improved BCS, mobility, carcass outcomes, and profit potential in cull dairy cows.
The aim of this study was to evaluate the use of 3 different genomic relationship matrices built from SNPs, haplotypes (HAP), and runs of homozygosity (ROH), on phenotype predictive ability and estimated genetic variance of milk yield, SCS, and days open in Mexican Holstein cattle. The analyses included the use of the genomic relationship matrices as kernel-based models fitting either one or multiple sources of information. The SNPs and HAP matrices were built as linear kernels, and the ROH matrix as a Gaussian kernel. Also, we used as a reference the performance of the single-step GBLUP. Predictive ability was evaluated in 10-fold cross-validation. The highest predictive correlation was obtained using SNPs (0.63 for SCS, 0.57 for milk yield, and 0.20 for days open). The use of multigenomic relationships, including HAP and ROH, did not outperform the use of only SNPs in predictive ability, but the highest genetic variance was estimated using ROH (0.39 for milk yield, 0.26 for SCS, and 0.22 for days open).
The US dairy calving ease (CE) genetic evaluation is based on a threshold sire-maternal grandsire (SMGS) model and includes 2 genetic components: one reflecting the sire's direct genetic effect on calving, and the other capturing the maternal influence, modeled through either the dam or the maternal grandsire. This study compared 2 CE evaluation models-SMGS and sire-maternal (SMAT)-using different solving algorithms: Newton-Raphson (NR) and expectation maximization (EM). The analysis used over 24 million CE records provided by the Council on Dairy Cattle Breeding. Correlations of GEBV for phenotyped sires and maternal grandsires were highly consistent across algorithms, exceeding 0.99 within models. The NR algorithm was the most computationally efficient solver, requiring fewer iterations and less computing time than EM. Both SMGS and SMAT models are suitable for routine genetic evaluation of CE in US dairy cattle, with NR and EM offering reliable and efficient solutions for single-trait analysis.
The use of agroindustrial byproducts in ruminant nutrition is gaining increased attention because of economic and environmental benefits and their potential to enhance ruminal function and animal performance. However, the effect of these byproducts on ruminal microbiome and fermentation has been scarcely investigated. This study aimed to evaluate the effects of replacing conventional feeds with agroindustrial byproducts (18:18:8 mixture of corn dried distillers grains with solubles, dry citrus pulp, and exhausted olive cake) on the ruminal microbiome and fermentation parameters of sheep. Four rumen-fistulated Lacaune sheep were used in 2 experimental periods, receiving mixed diets composed of 50% alfalfa hay and 50% of either a control concentrate (CON diet) or a concentrate with agroindustrial byproducts (BYP diet). Ruminal samples were collected at 0, 3, and 6 h postfeeding to assess microbial composition and fermentation parameters. Diet significantly influenced the ruminal microbiome, but the effect of individual sheep was more pronounced than that of the diet. Sampling time also influenced the ruminal microbiome. The inclusion of agroindustrial byproducts in the concentrate did not significantly alter ruminal fermentation parameters. However, the BYP diet led to more steady ruminal fermentation, preventing large fluctuations in total VFA and ammonia concentrations, likely the result of a broader range of fermentable substrates present in the BYP concentrate and changes in ruminal microbiome. These results may indicate improved synchronization of nutrient availability for ruminal microorganisms. Overall, replacing conventional feed ingredients with agroindustrial byproducts promoted microbial diversity and improved ruminal fermentation, potentially leading to increased dairy ruminant performance.
A recent study found that 30% of all dairy farms in British Columbia (BC) were positive for Salmonella Dublin, which has prompted a need to determine how to properly manage and mitigate Salmonella Dublin within the province. The overarching goal of this study is to use the components of a Danish Salmonella Dublin risk scoring tool to perform a cross-sectional, exploratory study to evaluate whether the tool, or components therein, can differentiate between Salmonella Dublin bulk tank milk (BTM)-positive versus BTM-negative BC dairy farms. A total of 70 BC dairy producers completed the survey and were classified as positive or negative based of BTM surveillance results. Overall, the components outlined in the modified Danish tool failed to differentiate herds that were positive or negative for Salmonella Dublin on BTM, with only 2 risk factors being identified. Farms that reported housing more than one adult dairy cow in the maternity pen were 4 times more likely to be positive for Salmonella Dublin on BTM than farms that only kept one adult in the maternity pen at a time. Future research should seek to determine if further modifications to the risk factor survey would be useful, especially the inclusion of questions on factors that target introduction of Salmonella Dublin versus on-farm transmission of Salmonella Dublin.
The occurrence of mycotoxins in ruminant feeds has been traditionally linked to corn silage, but alternative forages such as cereal straw, grass silages, sorghum, and legume hays may also contribute to exposure. We investigated the main regulated mycotoxins in 977 forage samples from Italian farms, including 642 silages (wheat, grasses, sorghum) and 335 hays (wheat straw, grasses, alfalfa). Samples were analyzed for deoxynivalenol, zearalenone (ZEN), and total fumonisins (FUM) using accredited methods. Noncorn forages were not exempt from contamination, showing variable prevalence and concentrations depending on forage type and botanical origin. Deoxynivalenol was the most prevalent, ZEN showed moderate prevalence with rising concentrations in recent years, and FUM occurred less frequently but with occasional and not significant high levels. These findings highlight the need for continuous monitoring of all forage types, suggesting that mycotoxin risk assessment in dairy diets should extend beyond corn silage.
Artificial intelligence is increasingly applied in livestock farming and offers valuable tools for monitoring animal health and welfare. Among these, facial expressions have emerged as informative indicators of well-being in animals. In this context, the main objective of this study was to evaluate the accuracy of pose estimation models for extracting facial features in North American Holstein calves. Three YOLOv8-based models were trained using 10, 16, and 30 facial keypoints, and their performance was evaluated using training metrics (loss, precision, recall, F1 score, training time, and number of epochs) and keypoint accuracy measures (object keypoint similarity, average precision, average recall). The 10-keypoint model outperformed the others, requiring less training time, achieving lower loss, and yielding the highest prediction accuracy. This model enabled reliable extraction of facial phenotypes, including nostril distance, eye opening, and ear angles and movements. These findings demonstrate the potential of pose estimation models for automated phenotyping and welfare monitoring in dairy calves.
Mycoplasma spp. are highly contagious bacteria that cause chronic, subclinical infections in dairy cattle and are intrinsically resistant to many antimicrobials. This retrospective case control study evaluated whether different calfhood and peripartum variables were associated with postcalving intramammary Mycoplasma spp. infections. We analyzed data from 475 first-lactation animals from one commercial dairy herd, comprising 95 cases with intramammary infections caused by Mycoplasma spp. and 380 culture-negative controls. Data on colostrum Brix%, birth body weight, otitis and pneumonia events, age at first breeding, age at conception, days in the close-up pen, age at calving, days in the fresh cow pen, and calving season were retrospectively extracted from electronic herd records and analyzed using univariable logistic regression models. We found that age at the first otitis event was associated with the occurrence of an intramammary infection with Mycoplasma spp. Cows that experienced an otitis event during calfhood, specifically at ≤23 d of age, had greater odds of postcalving intramammary infection with Mycoplasma spp. No associations were found for other variables. These results suggest that otitis in early life may represent an important predictor of susceptibility to intramammary Mycoplasma spp. infection postcalving and highlight the potential value of calfhood monitoring for mastitis prevention strategies.
Missing pedigrees result in underestimated numerator relationship and inbreeding coefficients in a closed population. Recursive algorithms have been proposed to derive nonzero inbreeding coefficients accounting for unknown parents but can be computationally ineffective with a deep pedigree. In this report, we proposed a pedigree-based metafounder (MF) approach to calculate nonzero inbreeding. Unknown parents were assigned to MF based on the birth year of their offspring. The MF were assumed to have self-relationships equaling twice the average inbreeding coefficients of the animals with both parents known and born in the same year. The relationships between 2 MF were set as a function (i.e., minimum, harmonic mean, or maximum) of their self-relationships. Inbreeding coefficients were then computed using Sargolzaei and Iwaisaki's (2004) algorithm modified to account for MF, and the relationship matrix of MF was constructed iteratively until convergence. The algorithm was tested and compared with a recursive algorithm using a pedigree of 8.6 million Japanese Holsteins (average longest ancestral path = 11) and a simulated pedigree with 11,550,500 animals across 40 generations. For the Holstein pedigree, one iteration took ∼300 s with the recursive algorithm and 70 s with the proposed algorithm. If the relationships between MF were assumed to equal the maximum of their self-relationships, both algorithms converged to the same results. Simulation results further confirmed that the maximum assumption yielded the best correlation between the estimated and true inbreeding. The discussion highlights how different assumptions regarding the relationships between MF affect the resulting numerator relationship and inbreeding coefficients. With the MF approach, the subsets of the numerator relationship matrix accounting for unknown parents can also be derived quickly.
This study assessed the agreement between manual and automatic body condition scoring systems, with a focus on evaluating 2 automated scoring systems by DeLaval (older and newer) for commercial dairy farms. Manual scoring was conducted by experienced assessors using a standardized protocol, and results were compared with data from automated systems. Manual scores showed strong consistency between assessors, supporting the reliability of the method when properly applied. Both automated systems correlated well with manual scores. However, the older system consistently overestimated scores, particularly in thinner cows, whereas the newer system demonstrated closer alignment with manual assessments under the present conditions, though it slightly underestimated early-lactation body condition loss. Despite some limitations in individual cow assessment, especially during early lactation, the newer system represents a potential advancement and both systems are suitable for group-level management. Further refinement is recommended to enhance its precision for individual animal-level monitoring and research applications.
This study evaluated whether a high-IgG colostrum replacer administered at 24 h postpartum (p.p.) influences IgG absorption in neonatal calves. Twelve Holstein and crossbred calves were assigned to 2 groups: CCT (n = 6) received 2.5 L of colostrum replacer (100 mg IgG/mL) at 4 and 12 h p.p., followed by enriched bulk tank milk at 24 h p.p.; CTC (n = 6) received the same colostrum replacer at 4 and 24 h p.p., with enriched bulk tank milk at 12 h p.p. Enriched bulk tank milk was bulk tank milk supplemented with 27 g/L colostrum replacer, mimicking transition feeding. Serum IgG, total protein, γ-glutamyl transferase, and apparent efficiency of absorption (AEA) were measured. The IgG concentrations and AEA were compared at 24 h p.p. in CCT and on d 2 (32-38 h p.p.) in CTC to reflect the status after the second colostrum feeding in each group. At these time points, CTC calves had lower IgG (16.9 ± 1.1 vs. 23.3 ± 1.8 mg/mL) and AEA (11.7% vs. 16.8%), although IgG persisted longer. These findings clearly highlight the superiority of early colostrum feeding for achieving adequate passive immunity, while also revealing that lower initial IgG concentrations were accompanied by a relatively greater persistence during the first week of life.