Genome-wide analysis of fermentation and probiotic trait stability in Lactobacillus plantarum during continuous culture Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): Cuijiao Feng, Fuxin Zhang, Bini Wang, Liyuan Zhang, Yushan Dong, Yuyu Shao ABSTRACT Trait stability of Lactobacillus plantarum was studied following daily subculture over a 90-d period. Acid and bile tolerance, self-aggregation ability, cell hydrophobicity, pathogen inhibition activity, and cholesterol removal ability of cultures subcultured 30 (Lp30), 60 (Lp60), or 90 (Lp90) times were not significantly different from the original strain (Lp0). However, carbohydrate metabolism patterns did change; the Lp0 culture was unable to use d-sorbitol, α-methyl-d-mannose, and d-raffinose, whereas Lp30, Lp60, and Lp90 cultures could. Furthermore, gluconate and gentiobiose were fully used by the Lp0 culture but only poorly used by the Lp30, Lp60, and Lp90 cultures. Milk fermentation test confirmed that L. plantarum was unable to use lactose throughout laboratory evolution. Six non-synonymous mutations in genome of the Lp30, Lp60, and Lp90 cultures were identified by whole-genome sequencing, including mutant gene encoding the phosphoglycerate mutase, which is closely related to the transport and metabolism of carbohydrates. These mutations may play an important role in changes of carbohydrate metabolism patterns observed. Understanding the evolutionary characteristics of L. plantarum will help in development for food industry.

Association of transient, persistent, or delayed subclinical hypocalcemia with early lactation disease, removal, and milk yield in Holstein cows Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): J.A.A. McArt, R.C. Neves ABSTRACT Our objectives were to evaluate the association of subclinical hypocalcemia (SCH) dynamics with the risk of early lactation disease, removal, and milk production. We conducted a prospective observational cohort study in 407 Holstein cows in 2 dairy herds in New York. Cows were stratified by parity group (144 primiparous, 263 multiparous) and classified into 1 of 4 groups based on postpartum plasma Ca concentrations previously associated with improved milk production or increased risk of disease: normocalcemic (NC; primiparous [Ca] >2.15 mmol/L at 1 and 2 d in milk, n = 67; multiparous [Ca] >1.77 at 1 d in milk and 2.20 mmol/L at 4 d in milk, n = 109); transient SCH (tSCH; primiparous [Ca] ≤2.15 at 1 d in milk and >2.15 mmol/L at 2 d in milk, n = 25; multiparous [Ca] ≤1.77 at 1 d in milk and >2.20 mmol/L at 4 d in milk, n = 50); persistent SCH (pSCH; primiparous [Ca] ≤2.15 mmol/L at 1 and 2 d in milk, n = 33; multiparous [Ca] ≤1.77 at 1 d in milk and ≤2.20 mmol/L at 4 d in milk, n = 34); or delayed SCH (dSCH; primiparous [Ca] >2.15 at 1 d in milk and ≤2.15 mmol/L at 2 d in milk, n = 19; multiparous [Ca] >1.77 at 1 d in milk and ≤2.20 mmol/L at 4 d in milk, n = 70). Evaluated outcomes were development of an adverse event [hyperketonemia (blood β-hydroxybutyrate concentration ≥1.2 mmol/L at 3, 5, 7, or 10 d in milk), metritis, displaced abomasum, or herd removal in the first 60 d in milk] and average milk yield per day across the first 10 wk of lactation. Multivariable Poisson regression was used to analyze the adverse event outcome and generalized linear mixed models for milk yield analysis. Primiparous cows with tSCH were no more likely to have an adverse event than NC cows [risk ratio = 1.3; 95% confidence interval (CI) = 0.5 to 3.2], whereas multiparous cows tended to have a higher risk for an adverse event than NC cows (risk ratio = 1.4; 95% CI = 0.9 to 2.1). However, pSCH cows were 4.1 (95% CI = 2.1 to 7.9, primiparous) and 1.8 (95% CI = 1.2 to 2.7, multiparous) times more likely, and dSCH cows 3.2 (95% CI = 1.5 to 7.0, primiparous) and 1.9 (95% CI = 1.3 to 2.6, multiparous) times more likely, to have an adverse event than NC cows. Primiparous and multiparous cows with tSCH made more milk per day than NC, pSCH, or dSCH cows across the first 10 wk of lactation. Primiparous cows averaged 28.5 ± 0.7, 31.9 ± 1.1, 29.7 ± 0.9, and 28.7 ± 1.2 kg/d, and multiparous cows averaged 44.6 ± 0.7, 49.1 ± 1.1, 46.4 ± 1.3, and 41.4 ± 0.9 kg/d for NC, tSCH, pSCH, and dSCH cows, respectively. Our results suggest that cows with tSCH adapt well to early lactation, develop fewer disease or removal events than pSCH or dSCH cows, and make more milk than NC, pSCH, or dSCH cows. Cows with pSCH or dSCH, regardless of parity group, are at an increased risk for early lactation disease or removal events.

Short communication: Anesthetic residues in milk after topical application during treatment of hoof lesions in dairy cows Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): G. Stilwell, A.M. Ferrador, M.S. Santos, J.M. Domingues ABSTRACT Hoof lesions in dairy cows are usually treated by trimming the hoof. However, trimming by itself can cause severe pain or exacerbate already existing pain. Hoof trimming is usually not carried out by trained veterinarians, and pain management is not provided. Pain control during trimming is not only an ethical obligation but also allows for better manipulation and more meticulous treatment. Tri-Solfen (Bayer Animal Health, Pymble, Australia) is a spray gel containing lidocaine, bupivacaine, and cetrimide that is easily applied topically and has demonstrated pain-mitigation effects during and after hoof trimming. In the European Union, these local anesthetics are not approved for use in food-producing animals because of a lack of residue data and concerns about genotoxic effects in cattle and humans. The aim of this study was to assess lidocaine, bupivacaine, and 2,6-xylidine residues in milk after Tri-Solfen application in dairy cows. Five dairy cattle in the dry-off period were enrolled in the study based on clinical evidence of lameness (score ≥3 on a 5-point scale). After cleaning and superficial trimming, we applied 3 to 14 mL of Tri-Solfen to the lesions before continuing treatment. Two milk samples were collected per animal in the following 4 milkings and analyzed in a reference laboratory. Residues of lidocaine above the limits of quantification (0.2 µg/L) were found in milk samples in the first milking 6 h after treatment in only 2 cows. This study shows that excretion of local anesthetics and their metabolites in milk after topical application of Tri-Solfen is negligible and even undetectable after the first milking 6 h post-treatment.

Dietary supplementation of Saanen goats with dried licorice root modifies chemical and textural properties of dairy products Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): Francesca Bennato, Andrea Ianni, Camillo Martino, Alessio Di Luca, Denise Innosa, Armando Marco Fusco, Francesco Pomilio, Giuseppe Martino ABSTRACT The aim of the present study was to evaluate the effect of dietary integration with dried licorice root on the chemical-nutritional qualities of goat milk and cheeses. The study was conducted for 60 d, during which 30 Saanen goats were divided into 2 groups: a control group (CG) that received a standard diet and an experimental group (LG+) whose diet was supplemented with licorice. At the end of the study, milk samples were collected to determine chemical-nutritional compositions and fatty acid (FA) profiles. Cheeses produced with CG and LG+ bulk milk were analyzed for chemical-physical parameters after 3 (T3) and 30 (T30) d of ripening. A different FA profile and a significant increase in protein and casein were observed in LG+ milk samples compared with CG milk. Regarding cheeses, an increase of proteins and fat was found in LG+ cheeses, which also were harder, more elastic, and more gummy than the CG samples after both 3 and 30 d of ripening. A different protein profile was detected in the 2 groups without significant variations in casein fractions (αs2-casein and β-casein) during ripening. Moreover, greater oxidative stability was found in LG+ cheeses at both T3 and T30. Different families of volatile compounds were detected in T30 cheeses obtained from both groups. A significant reduction of octanoic acid and an increase in nonanal and ketones were found in LG+ T3 cheeses, whereas the LG+ T30 cheeses were characterized by a significant decrease of hexanoic acid an increase of 3-methyl-1-butanol and acetoin. We concluded that it is possible to assert that dietary integration with dried licorice root modified chemical and technological properties of goat cheeses, reducing lipid oxidation during ripening and inducing changes in texture that could improve consumer acceptability, although further studies are needed from this point of view.

Short communication: Herd-level analysis of antimicrobial use and mortality in veal calves: Do herds with low usage face higher mortality? Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): J. Bokma, R. Boone, P. Deprez, B. Pardon ABSTRACT The veal calf sector fears that a too-rapid and large decrease in antimicrobial use (AMU) as demanded by European authorities would increase mortality, causing economic and welfare issues. To determine whether this concern is justified, the relationship between AMU (total and different classes) and mortality in dairy-type white veal calves, managed by 2 large veal companies, was explored. A retrospective cohort study was performed on electronically collected antimicrobial consumption and mortality data from the largest Belgian veal practice during the period 2014 to 2016. Mixed linear [mortality (%) as continuous outcome] and generalized linear mixed models with binary outcome for event and trial approach were built to identify factors associated with mortality. Data consisted of 76 production cycles from 29 farms managed by 2 veal companies (1 and 2) and covering 45,001 calves. Average AMU was 30.1 ± 10.4 defined daily doses for animals per year (± standard deviation) and was higher in veal company 2 than in veal company 1 (35.9 ± 9.3 and 22.4 ± 5.7 defined daily doses for animals per year, respectively). In contrast, mean mortality was lower in veal company 2 (2.3 ± 1.4%) than in veal company 1 (4.1 ± 1.4%). Both models showed a positive association between AMU and mortality in veal company 1 and no association in veal company 2. The final linear model identified increasing herd size and the use of third- or fourth-generation cephalosporins as risk factors for mortality and the use of long-acting macrolides as a protective factor. The final logistic model identified an increased mortality risk with increased use of third- or fourth-generation cephalosporins and sulfonamides–trimethoprim and decreased mortality when using long-acting macrolides. Based on these data, at the current levels of AMU in Belgian veal calves, an increase in mortality when reducing AMU could not be evidenced. Differences in herd size and factors other than AMU likely better explain why one veal company faces almost double the mortality of another one. Abandoning the use of long-acting macrolides might have negative consequences for mortality under the current state of the industry. The most ethical way to further reduce AMU in veal calves is likely simultaneously monitoring AMU and animal welfare parameters, starting with, but not limited to, mortality.

Predicting survival in dairy cattle by combining genomic breeding values and phenotypic information Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): E.M.M. van der Heide, R.F. Veerkamp, M.L. van Pelt, C. Kamphuis, B.J. Ducro ABSTRACT Advances in technology and improved data collection have increased the availability of genomic estimated breeding values (gEBV) and phenotypic information on dairy farms. This information could be used for the prediction of complex traits such as survival, which can in turn be used in replacement heifer management. In this study, we investigated which gEBV and phenotypic variables are of use in the prediction of survival. Survival was defined as survival to second lactation, plus 2 wk, a binary trait. A data set was obtained of 6,847 heifers that were all genotyped at birth. Each heifer had 50 gEBV and up to 62 phenotypic variables that became gradually available over time. Stepwise variable selection on 70% of the data was used to create multiple regression models to predict survival with data available at 5 decision moments: distinct points in the life of a heifer at which new phenotypic information becomes available. The remaining 30% of the data were kept apart to investigate predictive performance of the models on independent data. A combination of gEBV and phenotypic variables always resulted in the model with the highest Akaike information criterion value. The gEBV selected were longevity, feet and leg score, exterior score, udder score, and udder health score. Phenotypic variables on fertility, age at first calving, and milk quantity were important once available. It was impossible to predict individual survival accurately, but the mean predicted probability of survival of the surviving heifers was always higher than the mean predicted probability of the nonsurviving group (difference ranged from 0.014 to 0.028). The model obtained 2.0 to 3.0% more surviving heifers when the highest scoring 50% of heifers were selected compared with randomly selected heifers. Combining phenotypic information and gEBV always resulted in the highest scoring models for the prediction of survival, and especially improved early predictive performance. By selecting the heifers with the highest predicted probability of survival, increased survival could be realized at the population level in practice.

Statistical modeling of ruminal pH parameters from dairy cows based on a meta-analysis Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): A. Mensching, J. Hummel, A.R. Sharifi ABSTRACT Adequate feeding of high-performance dairy cows is extremely important to avoid the digestive disorder subacute ruminal acidosis. Subacute ruminal acidosis is defined as a status with a below-average ruminal pH that does not cause direct clinical symptoms at the individual level but is relevant for animal welfare due to a higher risk of secondary health problems at the herd level. The main objective of this study was to apply meta-analytical methods in an exploratory approach to investigate the association between pH parameters of the ventral rumen with milk and diet parameters. Data from 32 studies using continuous pH measurement in the ventral rumen of lactating cows were included in the meta-analysis. Available information extracted from all studies was categorized into parameters associated with management, cow, diet, milk, and pH. The statistical analysis was divided into 4 sections. First, a multiple imputation procedure based on a principal component model was applied, since approximately 19% of the data set consisted of missing values due to heterogeneity in provided information between the studies included in the analysis. In a second step, all potential predictors for the pH parameters, including the daily mean pH, the time with a pH below 5.8, and the pH range, were examined for their prediction suitability using multi-level mixed effects meta-regression models. These analyses were performed on the raw and the imputed data. Because the results of both approaches were consistent, the imputing procedure was considered to be appropriate. Third, automated variable selection was applied to all 3 pH parameters separately for the predictor groups milk and diet using the imputed data set. Thereby, multi-model inference was used to estimate the relative importance of the selected variables. Finally, a functional relationship between the 3 pH parameters was established. The fat to protein ratio of milk, milk fat, and milk protein showed significant associations in meta-regression analysis for all 3 pH parameters when used as a single predictor. Out of the group of diet-specific variables, the acid detergent fiber, neutral detergent fiber, nonfiber carbohydrate, starch content, as well as the forage to concentrate ratio, showed the highest significance in the models. In particular, the multi-model inference showed that the protein, fat, and lactose content of the milk can best quantify the association to the daily mean pH and the time with a pH below 5.8 in a multiple regression model.

Effect of milk types on the attributes of the glutinous rice wine-fermented yogurt-like product Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): Shaoying Gong, Peng Fei, Aslam Ali, Xiaolin Cai, Wei Xue, Wen Jiang, Ling Guo ABSTRACT This study was conducted to analyze the effect of milk types on the attributes of the glutinous rice wine-fermented yogurt-like product named Kouwan Lao (KWL). Four types of raw milks were used in this study, including high temperature, long time (HTLT: H milk), HTLT milk supplemented with 3% skim milk powder (S milk), pasteurized milk (P milk), and ultra-high temperature milk (U milk). Microbiological compositions of the fermented glutinous rice and KWL at different stages were analyzed using PCR-denaturing gradient gel electrophoresis and gene sequencing based on 16S rRNA and 26S rRNA. The physicochemical properties of KWL samples were determined, and textural properties of those were analyzed using a texture analyzer (Jiawei Innovation and Technology Co. Ltd., Zhejiang Province, China). The microstructure of KWL samples was observed using scanning electron microscopy. The results showed that the milk types had significant influences on the bacterial composition of KWL. In the curdling process, the predominant bacteria of H, S, P, and U KWL samples were Lactobacillus brevis, Janthinobacterium sp., Lactobacillus casei, and Streptococcus agalactiae, respectively. In the ripening process, the main strains in H KWL were Enterococcus faecium and Pediococcus pentosaceus. Lactobacillus casei and Lactobacillus paracasei were the dominant bacteria of U KWL. Lactobacillus casei was the main strain of P KWL, and no bacteria were detected in S KWL. Saccharomyces cerevisiae was the dominant fungus of KWL, and no significant effect of milk types on fungal composition of KWL was found. The results of physicochemical properties showed that significant differences in protein contents were found in the KWL samples, and P KWL had the highest protein content. The fat content of U KWL was significantly higher than that of samples from the other 3 groups. The U KWL and P KWL showed lower moisture than that of the other 2 KWL samples. In addition, no significant difference in pH value was found in all samples. The results of texture analysis and microstructure showed that compared with other 3 types of KWL samples, the related mass parameters of U KWL were more advantageous and improved significantly with the increase of the heat treatment temperature of raw milk and the addition of skim milk powder. Our findings revealed the effects of milk types on microbial composition, physicochemical properties, textural properties, and microstructure of KWL, and provided a basic theory for the optimization and industrial production of KWL.

Technical note: Development and application of KASP assays for rapid screening of 8 genetic defects in Holstein cattle Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): Yi Zhang, Dong Liang, Hetian Huang, Zhancheng Yang, Yachun Wang, Ying Yu, Lin Liu, Shengli Zhang, Jianlin Han, Wei Xiao ABSTRACT Specific DNA mutations underlying several genetic defects associated with embryo loss or reduced calf survivability have been identified in dairy cattle, and a convenient and cost-effective platform is required for their routine screening. We developed Kompetitive allele-specific PCR (KASP) assays for discrimination of the wild-type alleles from the associated defective alleles at each of 8 common genetic defects in Holstein cattle, involving 5 SNP [HH1, HH3, HH4, bovine leukocyte adhesion deficiency (BLAD), and complex vertebral malformation (CVM)] and 3 insertion or deletion mutations [HH5, haplotype for cholesterol deficiency (HCD), and brachyspina (BS)]. A total of 390 cows from a Chinese Holstein herd were genotyped and the carriers identified at 7 of these 8 loci (except HH4), with the highest carrier frequencies found for CVM (10.5%) and HH1 (10.0%), followed by HH3 (2.6%), BS (2.1%), HCD (1.3%), HH5 (0.8%), and BLAD (0.5%). Surprisingly, 102 cows (26.2%) carried at least 1 of the 7 defective alleles. Our results demonstrate that these KASP assays are simple, rapid, and reliable for the detection of multiple genetic defects. The high carrier frequency of these genetic defects indicates an urgent need for routine molecular testing to eliminate the deleterious alleles from Chinese Holstein cattle.

Behavior of the Linear Regression method to estimate bias and accuracies with correct and incorrect genetic evaluation models Publication date: Available online 6 November 2019 Source: Journal of Dairy Science Author(s): F.L. Macedo, A. Reverter, A. Legarra ABSTRACT Bias in genetic evaluations has been a constant concern in animal genetics. The interest in this topic has increased in the last years, since many studies have detected overestimation (bias) in estimated breeding values (EBV). Detecting the existence of bias, and the realized accuracy of predictions, is therefore of importance, yet this is difficult when studying small data sets or breeds. In this study, we tested by simulation the recently presented method Linear Regression (LR) for estimation of bias, slope, and accuracy of pedigree EBV. The LR method computes statistics by comparing EBV from a data set containing old, partial information with EBV from a data set containing all information (old and new, a whole data set) for the same individuals. The method proposes an estimator for bias (Δpˆ), an estimator of slope (bpˆ) and 3 estimators related to accuracies: the ratio between accuracies (ρˆw,p), the reliability of the partial data set (accp2ˆ), and the ratio of reliabilities (ρp,w2ˆ). We simulated a dairy scheme for low (0.10) and moderate (0.30) heritabilities. In both cases, we checked the behavior of the estimators for 3 scenarios: (1) when the evaluation model is the same as the model used to simulate the data; (2) when the evaluation model uses an incorrect heritability; and (3) when the data includes an environmental trend. For scenarios in which the evaluation model was correct, the LR method was capable of correctly estimating bias, slope, and accuracies, with better performance for higher heritability [i.e., corr(bp,bpˆ) was 0.45 for h2 = 0.10 and 0.59 for h2 = 0.30]. In cases of the use of incorrect heritabilities in the evaluation model, the bias was correctly estimated in direction but not in magnitude. In the same way, the magnitudes of bias and of slope were underestimated in scenarios with environmental trends in data, except for cases in which contemporary groups were random and greatly shrunken. In general, accuracies were well estimated in all scenarios. The LR method is capable of checking bias and accuracy in all cases, if the evaluation model is reasonably correct or robust, and its estimations are more precise with more information (e.g., high heritability). If the model uses an incorrect heritability or a hidden trend exists in the data, it is still possible to estimate the direction and existence of bias and slope but not always their magnitudes.