Journal of Dairy Science最新文献

{"title":"Comparison of 4 calculators for milk carbon footprint assessment on dairy farms in eastern Canada.","authors":"F Nadon, J-P Matteau, S Binggeli, S Delmotte, R Kroebel, É Charbonneau","doi":"10.3168/jds.2026-28559","DOIUrl":"https://doi.org/10.3168/jds.2026-28559","url":null,"abstract":"<p><p>Assessing the milk carbon footprint (MCF) is essential for understanding greenhouse gas emissions associated with dairy production and for guiding mitigation strategies on dairy farms. The objective of this study was to compare 4 commonly used MCF calculators in Québec (Holos-ULaval, Agriclimat, Logiag, and the Cool Farm Tool) across 20 dairy farms. The average MCF values were 1.02 ± 0.15 kg CO₂ equivalent/kg of fat- and protein-corrected milk (FPCM) for Holos-ULaval, 1.05 ± 0.16 for Agriclimat, 1.13 ± 0.14 for Logiag, and 1.16 ± 0.27 for the Cool Farm Tool. The comparison revealed differences in methodology, data requirements, and applicability to Canadian dairy systems. Enteric fermentation was consistently identified as the main source of emissions across all 4 calculators. Soil carbon sequestration, considered by 3 of the calculators, was treated differently, resulting in contrasting effects on the MCF: the inclusion of soil carbon sequestration reduced MCF in Holos-ULaval (-5.5% on average) and slightly decreased it in the Cool Farm Tool (-1.8%), while increasing it in Agriclimat (+10.2%). This highlights the uncertainty associated with soil carbon modeling and supports its separation from whole-farm MCF assessments. Overall, these results underscore the importance of carefully selecting an MCF calculator according to assessment objectives and highlight opportunities to harmonize methodological approaches, improving consistency and relevance for both research and on-farm decision-making.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of feeding hybrid rye silage as a replacement for barley silage on feed intake, milk production, ruminal fermentation characteristics, and omasal nutrient flow in lactating Holstein dairy cows.","authors":"Bianca P Rusawo, Gregory B Penner, Timothy Mutsvangwa","doi":"10.3168/jds.2026-28709","DOIUrl":"https://doi.org/10.3168/jds.2026-28709","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The objective of this study was to evaluate the effects of feeding graded levels of hybrid rye silage (HRS) as a replacement for barley silage (BARS) on DMI, milk yield and composition, ruminal fermentation characteristics, omasal nutrient flow, total-tract nutrient digestibility, and nitrogen (N) utilization in dairy cows. Twelve lactating Holstein cows (4 primiparous and 8 multiparous; 670 ± 68 kg BW and 104 ± 14 DIM at the beginning of the study) were used in a replicated 4 × 4 Latin square design with 28-d periods consisting of 18 d for dietary adaptation and 10 d for data and sample collection. Four multiparous cows in one Latin square were ruminally cannulated to facilitate ruminal and omasal sampling. Experimental diets consisted of a control diet containing 46.4% (DM basis; designated CON) BARS as the major forage source, and diets containing 15.3% (LOW), 31.1% (MED), and 46.4% (HIGH) HRS as a partial or complete replacement for BARS. Increasing the dietary inclusion of HRS linearly decreased DMI, and milk and ECM yields. Milk fat and lactose concentrations were unaffected by diet; however, milk protein concentration decreased linearly as the dietary inclusion level of HRS increased. Milk yields of fat, protein, and lactose decreased linearly as the dietary inclusion of HRS increased. Increasing dietary inclusion of HRS linearly decreased ruminal acetate concentration, but ruminal concentrations of propionate and valerate, and the acetate:propionate ratio were not affected by diet. The ruminal concentrations of butyrate, isovalerate, isobutyrate, and total branched short-chain fatty acids changed quadratically as the dietary inclusion of HRS increased. There was a tendency for a linear decrease in ruminal total short-chain fatty acid concentrations with increasing HRS; however, mean ruminal pH was not affected by diet. Ruminal ammonia-N concentration increased linearly with increasing dietary inclusion of HRS. When expressed as absolute amounts, apparent ruminal digestion of DM and OM and true ruminal digestion of OM responded quadratically as the dietary inclusion of HRS increased, but ruminal digestion of NDF was unaffected by diet. Intake, apparent ruminal digestion (expressed as absolute amounts), and omasal flow of starch all decreased linearly as the dietary inclusion of HRS increased. Replacing BARS with HRS did not affect apparent total-tract digestibilities of DM, CP, OM, and ether extract; however, apparent total-tract digestibilities of NDF and starch linearly increased with increasing dietary levels of HRS. Increasing the dietary inclusion of HRS linearly decreased N intake and RDP supply and tended to linearly decrease RUP supply. Omasal flow of total microbial NAN linearly decreased as dietary inclusion level of HRS increased. Urinary N excretion tended to decrease, whereas fecal N excretion (g/d) and milk N secretion (g/d) linearly decreased as dietary inclusion of HRS increased. In conclusion, the partial or complete","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of select emulsifying salts on pepsin-mediated casein hydrolysis of acidified skim milk.","authors":"Z D Datt, A M Mrozinski, A Fuchs, K Gannaway, A DeMeyer, G E Lewis","doi":"10.3168/jds.2026-28780","DOIUrl":"https://doi.org/10.3168/jds.2026-28780","url":null,"abstract":"<p><p>In milk, casein proteins are oriented into spherical micellar structures. During gastric digestion, casein is destabilized via the pepsin-induced cleavage of κ-casein, forming a clot that certain populations (e.g., infants, elderly) have a difficult time digesting. Emulsifying salts (ES), such as sodium citrate (SC) and sodium hexametaphosphate (SHMP), are used in some dairy products (e.g., protein-fortified beverages, infant formula) and serve several beneficial functions including protein stabilization. As an investigative study, this research aims to determine whether SC or SHMP addition (1-100 mM) impact the pepsin-mediated hydrolysis of casein proteins by monitoring the interaction between milk proteins and pepsin in 2 distinct acidification stages: (1) high pH, reflecting infant or early-stage adult digestion, and (2) low pH, representing late-stage adult digestion. The high pH stage (pH 6.0), represented by the initial interaction of milk within the infant or adult gastrointestinal tract, is characterized by protein destabilization and clotting. During this stage, rheology was used to determine clotting kinetics, protein clots were periodically extracted and weighed, and gel electrophoresis was used to monitor κ-casein hydrolysis. The low pH stage (pH 2.2) corresponds to when the milk system has reached typical gastric acidity, and the rate of protein hydrolysis during this stage was monitored by gel electrophoresis. During the high pH stage, the control acidified skim milks formed a strong clot with a relative strength of 304.9 ± 40.6 Pa after 30 min. However, the acidified skim milks containing 10 or 100 mM SC failed to form any pepsin-induced clot, reflected by consistently low storage modulus values (<0.70 Pa) and lack of clot separation. In the low pH stage, pepsin-induced hydrolysis occurred in all samples, yet the 100 mM SC-containing sample had a reduced level of casein hydrolysis after 15 min. In contrast, samples with SHMP (10 and 100 mM) had severely inhibited hydrolysis rates compared with the control skim milks, reflecting SHMP-induced pepsin inactivation. Specifically, all of the casein was hydrolyzed in the control skim milks after 60 min, while 40.5 ± 14.5% and 43.5 ± 6.7% intact casein remained in the samples containing 10 mM and 100 mM of SHMP, respectively. These results indicate that SC and SHMP impact the pepsin-induced hydrolysis of acidified skim milk systems, and these differences are dependent on ES type and concentration. By resisting clotting, ES addition might allow for a faster transit rate through the gastric digestion phase and offer options for populations that struggle to metabolize casein clots, but there is a need to further investigate digestion and nutrient absorption using more advanced digestion protocols (e.g., INFOGEST).</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reduced pancreatic responsiveness to glucose plus amino acids and incretins in early versus late lactation dairy cows.","authors":"G C Reyes, G Z Wang, M K Fox, B Li, J P Cant","doi":"10.3168/jds.2026-29115","DOIUrl":"https://doi.org/10.3168/jds.2026-29115","url":null,"abstract":"<p><p>The action of insulin that influences partitioning of nutrients to milk in early lactation and to the body in later lactation is controlled by the effect of insulin on an array of insulin-dependent tissues and by pancreatic responsiveness to insulin secretagogues. To examine differences in pancreatic responsiveness between stages of lactation, pairs of cows in early (39 ± 24.3 DIM; n = 11) and late lactation (316.5 ± 77.3 DIM; n = 11) were feed restricted for 24 h and then subjected to a 2-h hyperglycemic, hyperaminoacidemic clamp (HGHAC) where glucose + 9 essential amino acids were infused intravenously to reach plasma concentration targets of 5 mM for glucose and 800 μM for branched-chain amino acids. Glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide 1 (GLP-1) were then added to the HGHAC for 2 more hours to isolate the pancreatic responsiveness to these incretins. Baseline, feed-restricted glucose and insulin concentrations before infusion were lower in the early-lactation group compared with late lactation, while baseline branched-chain amino acid and lysine concentrations were higher. Early-lactation cows needed 147 mmol/h more glucose to maintain hyperglycemia than those in late lactation, indicating a higher glucose disposition. The physiological basis for this response and for the low baseline glucose concentration is likely the high glucose uptake of the mammary glands of early lactation. In contrast, 224 mmol/h less amino acid was infused in early lactation to maintain hyperaminoacidemia, suggesting a faster endogenous entry of amino acid from body stores. Insulin concentrations during both sets of clamps showed that cows in early lactation exhibited reduced pancreatic responsiveness to glucose + amino acids and to incretins, compared with cows in late lactation. The opposing effects of stage of lactation on glucose and amino acid infusion rates reveal the existence of differences between glucose and amino acids in how the insulin sensitivities of their production and utilization are affected. Blunted pancreatic responsiveness may be more important than a decrease in insulin sensitivity for directing glucose and amino acids toward milk.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of colostrum volume at birth on growth, live carcass ultrasound, and feed efficiency in Holstein and Holstein-Angus steers.","authors":"T Chapelain, M Kovacs, H McCarthy, J Yu, J P Cant, K M Wood, M S Duarte, D L Renaud, M A Steele","doi":"10.3168/jds.2026-28957","DOIUrl":"https://doi.org/10.3168/jds.2026-28957","url":null,"abstract":"<p><p>Dairy-beef calves represent a growing proportion of the beef supply, yet little is known about how early-life nutrition affects long-term performance. This study evaluated the effects of breed and colostrum replacer (CR) volume at birth on growth, feed intake, feed efficiency, and carcass-related traits in Holstein and Holstein-Angus calves from birth to slaughter at 13 mo of age. Male Holstein (n = 20) and Holstein-Angus calves (n = 20) were enrolled at birth and assigned to receive either 2.5 or 5.0 g of IgG/kg of birth BW from CR (n = 10 per breed and CR treatment), divided into equal meals at 0 and 12 h after birth. Thereafter, calves were managed similarly and fed the same diets until slaughter. Individual intake was recorded daily, whereas BW, frame measurements, and live carcass ultrasound traits were collected monthly. Apparent total-tract digestibility was estimated at wk 28 and 55, and ruminal VFA concentrations were measured at wk 28 and 48. Data were analyzed using linear mixed models for repeated measures, and a nonlinear mixed model was used to fit a growth function to cumulative intake. Breed was the primary factor affecting performance across the rearing, growing, and finishing phases. Holstein-Angus steers grew faster, consumed more feed, and had greater feed efficiency at a common BW than Holstein steers. At wk 48, fiber digestibility and acetate-to-propionate ratio were greater in Holstein steers. Holstein-Angus steers also had greater ribeye area and greater rump and rib fat thickness during the growing and finishing phases. Colostrum replacer volume had limited effects on most growth and intake outcomes; however, steers receiving the high CR volume had greater rump and rib fat thickness during the growing and finishing phases, suggesting that early-life nutrition may influence later body composition. Holstein steers receiving the low CR volume had a lower predicted final BW and required greater DMI to reach 650 kg BW, as estimated using the Richards function, whereas Holstein-Angus steers were not affected. These findings emphasize the dominant role of breed in lifetime performance while indicating that colostrum volume fed at birth may have long-term effects on intake and adipose tissue deposition.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prioritization of candidate genomic regions for milking speed in Holstein cattle using international evaluations.","authors":"M Šimon, S Bogićević, B Luštrek, K Potočnik, T Kunej","doi":"10.3168/jds.2026-28464","DOIUrl":"https://doi.org/10.3168/jds.2026-28464","url":null,"abstract":"<p><p>Milking speed (MSPD) is an economically important trait in dairy cattle affecting labor efficiency, animal welfare and milking parlor productivity. This complex quantitative trait has been investigated to characterize its genetic basis and support genomic selection. Previous genome-wide association studies (GWAS) have reported genomic regions potentially related to MSPD; however, results vary considerably among studies and often provide limited functional interpretation. This study aimed to prioritize candidate genomic regions for MSPD based on the ranking of estimated SNP effects from the InterGenomics Holstein genomic evaluation coordinated by Interbull. The data set included genotypic and estimated breeding value information from 14,668 Holstein bulls, including 486 from Slovenia. Bioinformatic analyses were performed using Variant Effect Predictor, Animal QTLdb, STRING, KEGG and Haploview. The highest-ranked SNPs were selected for downstream genomic characterization and functional analyses. The 30 highest-ranked SNPs were located within protein-coding or long non-coding RNA genes or in intergenic regions. Thirteen SNPs had previously been reported for MSPD, including variants within ANKFN1, TRIM25, NDUFA9, YPEL2 and PPP2R2C, whereas 17 SNPs mapped to regions not previously linked to MSPD, including MAPRE2, MSI2 and ANGPT4. Three SNPs located within or near ANKFN1 were among the 4 highest-ranked variants. The highest number of prioritized SNPs was observed on BTA19, BTA13 and BTA6. Nine of the highest-ranked SNPs overlapped with production, fertility and conformation traits, potentially indicating pleiotropy. These findings provide a prioritized set of candidate genomic regions for further investigation of the genetic basis of MSPD.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Saccharomyces cerevisiae boulardii CNCM I-1079 on immune phenotype during the periparturient period.","authors":"T Fernandez Wallace, S Cartwright, S Jantzi, A Pineda, S Kvidera, C Villot, M A Steele, L R Cangiano","doi":"10.3168/jds.2026-28535","DOIUrl":"https://doi.org/10.3168/jds.2026-28535","url":null,"abstract":"<p><p>This study aims to characterize systemic and colonic intestinal mucosal immune phenotype in dairy cows across the periparturient period, and to determine whether Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB) supplementation affects those components. Holstein cows (n = 83) were blocked by parity and randomly assigned to either control (CON; n = 43) or SCB (n = 40; targeted supplementation: 1.0 × 10¹⁰ cfu/cow/d of SCB top dressed) dietary treatments from d -28 prepartum to d 70 postpartum. Blood samples were collected on d -30, -7, 7, 21 and 70 relative to calving and colon biopsies at d -30, 7 and 70. Peripheral blood mononuclear cells (PBMCs) and intraepithelial leukocytes (IELs) were isolated from blood and colon biopsies, respectively, and analyzed by flow cytometry to assess T and B cell subsets, macrophages and dendritic cells. Pre and postpartum data were analyzed separately using linear mixed effect models, with fixed effects of treatment, day and its interaction, and the random effect of cow within block, and day -30 as covariable. Independent of treatment, several myeloid and lymphoid populations changed during early lactation. In blood, the proportion of CD4⁺ T cells declined from d 7 to d 21 and then recovered by d 70, whereas CD28 expression on CD4⁺ T cells peaked at d 7 and subsequently decreased, indicating early transient activation. Cytotoxic CD8⁺ T cells increased in proportion from d 7 to d 21 and remained elevated through d 70. Class-switched (IgG⁺) B cells progressively upregulated CD21 expression from d 7 through d 70, suggesting maturation and enhanced complement-responsiveness later in lactation. Within the colonic intestinal mucosa, dendritic cells were most abundant at d 7, consistent with heightened early postpartum antigen presentation. Supplementation with SCB selectively enhanced humoral activation postpartum, reflected by increased CD86 expression on both naïve (IgM⁺) and class-switched (IgG⁺) B cells. Together, these findings indicate that immune changes during the periparturient period reflect a transient immune activation at immediate postpartum rather than overall suppression, and that SCB supplementation may enhance B cell activation and support immune function during early lactation.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Invited review: Herd-level udder health indices derived from repeated individual somatic cell count measurements.","authors":"E Molgat, D F Kelton, J P Roy, S Dufour","doi":"10.3168/jds.2026-28531","DOIUrl":"https://doi.org/10.3168/jds.2026-28531","url":null,"abstract":"<p><p>Subclinical mastitis persists as a challenge in dairy production, contributing to significant economic losses, compromising animal health and welfare, and driving antimicrobial use. It adversely affects milk quality, farm productivity, and overall profitability. This narrative review synthesizes historical literature, knowledge, and tools for herd-level udder health monitoring, with a focus on indices derived from repeated individual cow SCC measurements. Grounded in epidemiological principles, this review is structured around the life cycle of dairy cattle, using SCC data collected through routine milk recording tests to support meaningful interpretation of udder health dynamics across different physiological stages, not solely the lactation period. While SCC measurements are exclusively obtained during lactation, they may also be used to infer udder health status and dynamics around nonlactating periods; however, this approach may not fully represent the entire nonlactating stage or capture infectious events occurring between widely spaced tests or long before a cow's first SCC measurement. This framework also acknowledges that udder health is influenced by age, parity, and physiological and production stages, and that effective monitoring requires thoughtful interpretation of available data across the entire lactational trajectory. It supports more comprehensive and sustainable udder health herd-level management strategies. The review presents key herd-level udder health indices, discusses considerations for their use, and highlights the importance of standardized definitions and thresholds to ensure consistency and comparability. It also provides a curated selection of indices, including definitions, calculation methods, strengths and limitations, and reference values reported in the literature. This review aims to support veterinarians and dairy producers who routinely use summarized SCC reports generated through milk recording systems in implementing robust mastitis monitoring strategies throughout the cow's life cycle. The objective is to provide conceptual guidance and practical considerations that can be applied across a wide range of dairy production systems and herd sizes.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive evaluation of metabolite imputation methods and the effect of imputation accuracy on the performance of metabolite-trait association using large-scale metabolite datasets in cattle.","authors":"Zhujun Chen, Jun Teng, Chongwei Duan, Xinyi Zhang, Jian Yang, Fen Pei, Xiuxin Zhao, Guanghui Xue, Yan Liu, Huiming Liu, Hongding Gao, Rongling Li, Yundong Gao, Jianbin Li, Qin Zhang, Xiao Wang","doi":"10.3168/jds.2026-28962","DOIUrl":"https://doi.org/10.3168/jds.2026-28962","url":null,"abstract":"<p><p>As metabolomics data are typically acquired across multiple batches over months or even years, the integrated metabolite data sets often face complex missing-value challenges arising from fluctuations in instrument performance, variation in detection windows, and heterogeneity among analytical platforms. Accurate imputation of missing values is therefore a crucial strategy to addressing these challenges and enhancing the performance of downstream metabolomics analyses. In this study, we utilized large-scale authentic plasma and serum metabolite data sets (n = ∼3,000 metabolites) in Holstein cattle (n = ∼3,000 individuals), with each data set consisting of 2 batches, to evaluate the performance of 5 imputation methods (MIRTH, PIXANT, EM, KNN, and RF) to impute missing metabolites within batches and non-overlapping metabolites between batches. We demonstrated that RF yielded the best imputation performance in most cases, with accuracies reaching approximately 0.6 ∼0.7 for within-batch imputation and approximately 0.3 ∼0.4 for cross-batch imputation. Subsequently, we assessed the effect of imputation accuracy on the performance of metabolite-trait association analysis for 5 milk production traits using RF-imputed metabolite data. Compared with significantly associated metabolites identified using the original metabolite data, analysis using the imputed metabolite data resulted in substantial reductions in statistical power as well as increases in false-positive associations, particularly when imputed data from different batches were merged. Further efforts are needed to improve the accuracy for cross-batch imputation by developing new imputation methods and increasing the number of overlapping metabolites across batches.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of coffee lyophilizate addition on the physicochemical properties and bioactive profile of yogurt during storage.","authors":"Aleksander Siger, Dorota Cais-Sokolińska, Paulina Bielska, Marzena Gawrysiak-Witulska, Ewa Bąkowska","doi":"10.3168/jds.2026-29000","DOIUrl":"https://doi.org/10.3168/jds.2026-29000","url":null,"abstract":"<p><p>This study investigated the effect of caffeinated Arabica and decaffeinated coffee lyophilizate (0.6 g/100 g), incorporated either before or after fermentation, on the phenolic compound profile, caffeine and diterpene content, antioxidant activity, and physicochemical properties of yogurt during 20 d of refrigerated storage. Yogurts were produced from commercially available pasteurized and homogenized cow's milk (2.0% fat) using a thermophilic starter culture comprising Streptococcus thermophilus, Lactobacillus acidophilus, and Bifidobacterium animalis ssp. lactis (Lyofast SAB 440B). Total phenolic losses during lyophilization amounted to 14.0% and 19.0% for caffeinated and decaffeinated preparations, respectively, with feruloylquinic acid isomers showing the highest susceptibility to degradation (losses of 55-72%). Coffee enrichment resulted in an approximately 9-10-fold increase in total phenolic content relative to control yogurt, with overall phenolic retention reaching 73-85% of theoretical values. After-fermentation addition yielded higher extractable phenolic content, while before-fermentation addition was associated with lower extractable phenolics but superior hydroxyl radical scavenging capacity (OHSC), potentially reflecting the formation of polyphenol-protein complexes during fermentation. Oxygen radical absorbance capacity (ORAC) increased significantly during storage in before-fermentation variants, suggesting progressive release of bound phenolics through starter culture-mediated proteolysis. Decaffeinated lyophilizate added before fermentation produced the firmest yogurt gel, an effect potentially attributable to polyphenol-casein interactions and possible caffeine-mediated modification of starter culture activity. Addition timing rather than coffee type was the primary determinant of surface optical properties. The majority of bioactive compound profiles and physicochemical parameters showed no systematic changes during the 20-d storage period, although significant storage-related changes were observed for selected antioxidant activity indices, textural parameters, surface gloss, and diterpene content in specific treatment groups. These findings indicate that coffee lyophilizate is a promising functional ingredient for yogurt enrichment, with the timing of addition being a critical process parameter that influences bioactive compound availability, antioxidant functionality, and textural quality.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}