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ABSTRACT: The objectives of this study were to determine if weaning would induce behavioral and physiological indicators of a negative affective state, and if supplementation of inactivated Lactobacillus helveticus (ILH) to dairy calves would reduce those indicators of negative affect during weaning. Male Holstein calves (n = 23) were enrolled in the study on d 1 of life. The calves were housed in individual pens in 1 of 4 rooms for the 42-d study. Calves began a step-down weaning from 9 L/d of milk replacer (MR), at 150 g of MR powder/L, on d 35 and received 6 L/d on d 35 to 36, 3 L/d on d 37 to 38, and 0.4 L/d on d 39 to 42. The MR was divided between 3 meals/d until the last 0.4 L/d phase, which was divided between 2 meals/d. Calves had ad libitum water access throughout the study and calf starter from d 28 onward. Within room, calves were assigned to 1 of 2 treatments: (1) control (CON; n = 11) and (2) 5 g of ILH/d split over and mixed into the 0800 h and 2000 h milk feedings from d 3 to 42 (ILH; n = 12). Lying behavior was recorded using HOBO data loggers from d 21 to 41. On d 33, 37, and 41, infrared eye images were taken to determine maximum eye temperature (MET), saliva samples were collected to determine cortisol concentration, and play assessments were conducted to quantify play behavior. On d 34, 38, and 42, blood samples were collected to determine blood serotonin concentration, whereas on d 38 and 39, calves were tested with a cognitive task. A subset of calves (n = 5/treatment) were euthanized to collect gut and brain tissue samples for serotonin concentration on d 43. Weaning resulted in fewer (d 37–41; tendency: d 36), but longer (d 38–41; tendency: d 37), lying bouts and reduced play (d 41), although no changes in lying time, MET, saliva cortisol, nor blood serotonin were detected with initiation of weaning. Supplementation of ILH was associated with less lying time throughout the study, and reduced play duration and higher salivary cortisol during weaning. No differences in lying bouts, play count, blood and tissue (colon, ileum, prefrontal cortex and brain stem) serotonin concentration, and time to complete the cognitive task were detected between the treatments. Overall, weaning induced behavioral changes indicative of negative affective state, and some behavioral differences were observed with ILH supplementation both before and during weaning, with some physiological changes observed during weaning.

ABSTRACT: The gastrointestinal microbial consortium in dairy cattle is critical to determining the energetic status of the dairy cow from birth through her final lactation. The ruminant's microbial community can degrade a wide variety of feedstuffs, which can affect growth, as well as production rate and efficiency on the farm, but can also affect food safety, animal health, and environmental impacts of dairy production. Gut microbial diversity and density are powerful tools that can be harnessed to benefit both producers and consumers. The incentives in the United States to develop Alternatives to Antibiotics for use in food-animal production have been largely driven by the Veterinary Feed Directive and have led to an increased use of probiotic approaches to alter the gastrointestinal microbial community composition, resulting in improved heifer growth, milk production and efficiency, and animal health. However, the efficacy of direct-fed microbials or probiotics in dairy cattle has been highly variable due to specific microbial ecological factors within the host gut and its native microflora. Interactions (both synergistic and antagonistic) between the microbial ecosystem and the host animal physiology (including epithelial cells, immune system, hormones, enzyme activities, and epigenetics) are critical to understanding why some probiotics work but others do not. Increasing availability of next-generation sequencing approaches provides novel insights into how probiotic approaches change the microbial community composition in the gut that can potentially affect animal health (e.g., diarrhea or scours, gut integrity, foodborne pathogens), as well as animal performance (e.g., growth, reproduction, productivity) and fermentation parameters (e.g., pH, short-chain fatty acids, methane production, and microbial profiles) of cattle. However, it remains clear that all direct-fed microbials are not created equal and their efficacy remains highly variable and dependent on stage of production and farm environment. Collectively, data have demonstrated that probiotic effects are not limited to the simple mechanisms that have been traditionally hypothesized, but instead are part of a complex cascade of microbial ecological and host animal physiological effects that ultimately impact dairy production and profitability.

ABSTRACT: This graduate student literature review provides an examination of the ontological adaptations of the calf's immune system and how the intestinal microbiota influences calf immune function in health and disease. Within dairy rearing systems, various nutritional and management factors have emerged as critical determinants of development influencing multiple physiological axes in the calf. Furthermore, we discuss how multiple pre- and postnatal maternal factors influence the trajectory of immune development in favor of establishing regulatory networks to successfully cope with the new environment, while providing early immune protection via immune passive transfer from colostrum. Additionally, our review provides insights into the current understanding of how the intestinal microbiota contributes to the development of the intestinal and systemic immune system in calves. Lastly, we address potential concerns related to the use of prophylactic antimicrobials and waste milk, specifically examining their adverse effects on intestinal health and metabolic function. By examining these factors, we aim to better understand the intricate relationship between current management practices and their long-term effect on animal health.

ABSTRACT: This study aimed to characterize the development of systemic and colon tissue resident B and γδ T cells in newborn calves from birth until weaning. At birth, calves have limited capacity to initiate immune responses, and the immune system gradually matures over time. Gamma delta (γδ) T cells are an important lymphocyte subset in neonatal calves that confer protection and promote immune tolerance. A total of 36 newborn calves were enrolled in a longitudinal study to characterize how systemic and colon tissue resident B and γδ T cells develop from birth until weaning. Blood and colon biopsy samples were collected on d 2, 28, and 42 to determine the proportions of various B and γδ T cell subsets by flow cytometry. We classified γδ T cells into different functional subsets according to the level of expression intensity of the coreceptors WC1.1 (effector function) and WC1.2 (regulatory function). Furthermore, naive B cells were classified based on the expression IgM receptor, and activation state was determined based on expression of CD21 and CD32, 2 receptors with opposing signals involved in B cell activation in early life. Additional colon biopsy samples were used for 16S sequencing, and microbial diversity data are reported. At birth, γδ T cells were the most abundant lymphocyte population in blood, accounting for 58.5% of the lymphocyte pool, after which the proportions of these cells declined to 38.2% after weaning. The proportion of γδ T cells expressing WC1.1 decreased by 50% from d 2 to d 28, whereas no change was observed in the expression of WC1.2. In the colon, there was a 50% increase of γδ T cells after weaning and the proportion of WC1.2+ γδ T cells doubled from d 28 to 42. The proportion of IgM+ B lymphocytes in blood increased from 23.6% at birth to 30% after weaning, were the proportion of B cells expressing CD21 increased by 25%, while the proportion of B cells expressing CD32 decreased by 30%. While no changes were observed for the overall proportion of IgM+ B lymphocytes in the colon, there was a 6-fold increase in the proportion of CD21+ B cells from pre- (d 28) to postweaning (d 42). Microbial diversity increased from d 2 of life to 28 and declined abruptly after weaning. The reduction in microbial diversity during weaning was negatively correlated with the increase in all γδ T cell subsets and CD21+ B cells. These data suggest that developmental adaptations after birth coordinate expansion of γδ T cells to provide early systemic protection, as well as to steer immune tolerance, while B cells mature over time. Additionally, the increase of colonic γδ T cells on d 42 suggests a protective role of these cells during weaning.

ABSTRACT: This study was designed to develop a protocol for repeated intramuscular indomethacin injections to replicate leaky-gut-like symptoms in male Holstein calves to model and study the detrimental effects of leaky gut on gut tissue function and inflammatory response. A generalized randomized block design was used to evaluate how repeated indomethacin intramuscular injections affected the development of leaky gut in 18 male Holstein calves. Animals were enrolled at 3 ± 1 d of life, and after 21 d of adaptation, they were randomly assigned to 1 of 3 treatments consisting of intramuscular saline or indomethacin injections every 12 h for 48 h: (1) control (CTL), saline injection, (2) low intramuscular indomethacin (INDO-L) dosed at 1.2 mg/kg of body weight (BW), and (3) high intramuscular indomethacin (INDO-H) dosed at 2.4 mg/kg of BW. During the challenge, milk intake, starter intake, fecal scores, and rectal temperature were measured daily, and BW was measured at the beginning and at the end of the challenge. Plasma samples were used to measure the recovery of markers of intestinal permeability before and after the challenge by dosing lactulose, d-mannitol, and chromium-EDTA. In addition, several cytokines were measured in plasma during the challenge. Calves were dissected at the end of the challenge to obtain tissue and digesta samples from the gastrointestinal tract and liver. No treatment differences were observed for starter and milk intakes, fecal scores, BW, and rectal temperature. The difference in marker concentrations between pre and post challenges was higher for INDO calves compared with CTL calves in the case of lactulose and chromium-EDTA. In addition, chemokine ligand 2 and 4 and IL-6 were higher for INDO-H calves compared with CTL. Both doses of indomethacin resulted in reductions in villus length and surface area in the distal jejunum and ileum and reductions in crypt depth and width in the colon. We showed that repeated indomethacin injections over a 48-h period induced leaky-gut-like symptoms in a region-specific manner, affecting mainly the distal section of the intestine. This outcome was characterized by histomorphological changes in the distal jejunum, ileum, and colon and by increased gut permeability. Interestingly, changes in liver morphology and immune function also occurred, possibly due to the increased translocation of foreign antigens breaching the epithelial cell wall. The leaky gut challenge model described here could be used to improve understanding of the pathogenesis of intestinal disorders in cattle and provide a reliable alternative for testing feed additives with intestinal health benefits.

ABSTRACT: The objectives of this study were to examine the effects of pelleted starter diets differing in starch and neutral detergent fiber (NDF) content when fed differing levels of milk replacer (MR) on nutrient digestibility, whole gastrointestinal tract fermentation, pH, and inflammatory markers in dairy calves around weaning. Calves were randomly assigned to 1 of 4 dietary treatments (n = 12 per treatment) in a 2 × 2 factorial design based on daily MR allowance and amount of starch in pelleted starter (SPS): 0.691 kg of MR per day [dry matter (DM) basis] with starter containing low or high starch (12.0% and 35.6% starch on DM basis, respectively), and 1.382 kg of MR per day (DM) with starter containing low or high starch. All calves were housed in individual pens with straw bedding until wk 5 when bedding was covered. Calves were fed MR twice daily (0700 and 1700 h) containing 24.5% crude protein (DM) and 19.8% fat (DM), and had access to pelleted starter (increased by 50 g/d if there were no refusals before weaning and then 200 g/d during and after weaning) and water starting on d 1. Calves arrived between 1 and 3 d of age and were enrolled into an 8-wk study, with calves undergoing step-down weaning during wk 7. Starting on d 35, an indwelling pH logger was inserted orally to monitor rumen pH until calves were dissected at the end of the study in wk 8. Higher SPS calves showed an increase in rumen pH magnitude (1.46 ± 0.07) compared with low SPS calves (1.16 ± 0.07), a decrease in rumen pH in wk 8 (high SPS: 5.37 ± 0.12; low SPS: 5.57 ± 0.12), and a decrease in haptoglobin in wk 8 (high SPS: 0.24 ± 0.06 g/L; low SPS: 0.49 ± 0.06 g/L). The majority of differences came from increased starter intake in general, which suggests that with completely pelleted starters the differences in starch and NDF do not elicit drastic changes in fermentation, subsequent end products, and any resulting inflammation in calves around weaning.

This research aimed: (i) to evaluate on-farm (FARM data) multiparametric models developed under controlled experiment (INRAE data) and based on non-invasive indicators to detect subacute ruminal acidosis (SARA) in dairy cows. We also aimed to recover high discrimination capacity, if needed, by (ii) building new models with combined INRAE and FARM data; and (iii) enriching the models increasing from 2 to 5 indicators per model. For model enrichment, we focused on indicators determinable on-farm by quick and inexpensive routine analysis. Fifteen commercial dairy farms were selected to cover a wide range of SARA risk. In each farm, four Holstein early-lactating healthy primiparous cows were selected based on their last on-farm recording of milk yield and somatic cell count analysis. Cows were equipped with a reticulo-rumen pH sensor. The pH kinetics were analysed over a subsequent 7-day period. Relative pH indicators were used to classify cows with or without SARA. Milk, blood, faeces, and urine were collected for analysis of the indicators included in the models developed by Villot et al. (2020) on INRAE data that were externally evaluated using FARM data. Then, new models based on the same indicators were developed combining INRAE and FARM data to test whether a possible loss in performance was due to a limited validity domain of model by Villot et al (2020). Finally, the models developed combining INRAE and FARM data were adapted to the on-farm application and enriched by increasing indicators from 2 to 5 per model using linear discriminant analysis and leave-one-out cross-validation. The sensitivities (true-positive rate) in external evaluation on FARM data were substantially lower than those from cross-validation by Villot et al. (2020) (range: 0.1–0.75 vs 0.79–0.96, respectively), and the specificities (true-negative rate) showed a larger range with lower minimum values (range: 0.18–1.0 vs 0.62–0.97, respectively). The sensitivities of new models developed combining INRAE and FARM data ranged from 0.63 to 0.77. Models involving blood cholesterol, β-hydroxybutyrate, haptoglobin, milk and blood urea, and models involving milk fat/protein ratio, dietary starch proportion, and milk fatty acids had the highest performances, whereas models including sieved faecal residues and urine pH had the lowest. Enriching models to three indicators per model improved sensitivity and specificity, but the inclusion of more indicators was less or not effective. Larger field trials are required to validate our results and to increase variability and validity domain of models.

High-starch diets (HSDs) fed to high-producing ruminants are often responsible for rumen dysfunction and could impair animal health and production. Feeding HSDs are often characterized by transient rumen pH depression, accurate monitoring of which requires costly or invasive methods. Numerous clinical signs can be followed to monitor such diet changes but no specific indicator is able to make a statement at animal level on-farm. The aim of this pilot study was to assess a combination of non-invasive indicators in dairy cows able to monitor a HSD in experimental conditions. A longitudinal study was conducted in 11 primiparous dairy cows fed with two different diets during three successive periods: a 4-week control period (P1) with a low-starch diet (LSD; 13% starch), a 4-week period with an HSD (P2, 35% starch) and a 3-week recovery period (P3) again with the LSD. Animal behaviour was monitored throughout the experiment, and faeces, urine, saliva, milk and blood were sampled simultaneously in each animal at least once a week for analysis. A total of 136 variables were screened by successive statistical approaches including: partial least squares-discriminant analysis, multivariate analysis and mixed-effect models. Finally, 16 indicators were selected as the most representative of a HSD challenge. A generalized linear mixed model analysis was applied to highlight parsimonious combinations of indicators able to identify animals under our experimental conditions. Eighteen models were established and the combination of milk urea nitrogen, blood bicarbonate and feed intake was the best to detect the different periods of the challenge with both 100% of specificity and sensitivity. Other indicators such as the number of drinking acts, fat:protein ratio in milk, urine, and faecal pH, were the most frequently used in the proposed models. Finally, the established models highlight the necessity for animals to have more than 1 week of recovery diet to return to their initial control state after a HSD challenge. This pilot study demonstrates the interest of using combinations of non-invasive indicators to monitor feed changes from a LSD to a HSD to dairy cows in order to improve prevention of rumen dysfunction on-farm. However, the adjustment and robustness of the proposed combinations of indicators need to be challenged using a greater number of animals as well as different acidogenic conditions before being applied on-farm.

Although hay is the foundation of most equine diets, horse owners rarely ask for biochemical analysis and the routine practice is to choose hay based on its ‘perceived‘ nutritional value. The present study aimed at exploring the relationship between sensory properties as perceived by sight, touch and smell, and the nutritional value of hay measured by biochemical analysis using a ‘free sorting task’ method. Fifty-four non-expert participants were asked individually to: (1) observe 21 hays samples, (2) group together hays that they perceived as similar for each of the three modalities (hay appearance, odour or texture) and (3) characterize each formed group with a maximum of five descriptive terms. For each modality, results were recorded in a contingency matrix (hays × terms) where only terms cited at the minimum five times for at least one sample, were kept for data analysis. A correspondence analysis (CA) was performed on the contingency matrix to plot both samples and descriptive terms on a χ2 metric map. Then, a Hierarchical Ascending Classification (HAC) was performed on the coordinates of samples in the CA space. Clusters were identified by truncating the HAC tree-diagrams. The attributes that defined the best resulting clusters were identified by computing their probability of characterizing a cluster. Correlations were computed between each biochemical parameter on one hand, and the first two dimensions of the CA map on the other. Finally, correlations between the values of each hay on the first dimension of the three CA maps (appearance, odour and texture) were computed. Hedonic descriptive terms were primarily used for describing odour and texture modalities. For describing hay appearance, participants spontaneously used visual cues referring to colour or aspect. Based on the tree-diagrams resulting from the HAC, 3, 5 and 2 groups were clustered, respectively for appearance, odour and texture description. Digestible energy was correlated to the first dimension on the three CA maps, whereas CP was correlated to the first dimension of the CA appearance map only. While NDF value was correlated to the first and second dimensions on the CA odour map only, ADF content was correlated to the first dimension on the three CA maps. Non-fibre carbohydrates were correlated to the first dimension of the CA appearance map only. The similarity-based approach which is part of the standard toolbox of food sensory evaluation by untrained consumers was well adapted to animal feeds evaluation by non-experts.

Subacute ruminal acidosis (SARA) is usually characterized by abnormal and intermittent drops in rumen pH. Nevertheless, high individual animal variability in rumen pH and the difference in measurement methods for pH data acquisition decrease the sensitivity and accuracy of pH indicators for detecting SARA in ruminants. The aim of this study was to refine rumen pH indicators in long-term SARA based on individual dairy cow reticulo-rumen pH kinetics. Animal performances and rumen parameters were studied weekly in order to validate SARA syndrome and rumen pH was continuously measured using reticulo-rumen sensors. In total, 11 primiparous dairy cows were consecutively fed two different diets for 12 successive weeks: a control diet as low-starch diet (LSD; 13% starch for 4 weeks in period 1), an acidotic diet as high-starch diet (HSD; 32% starch for 4 weeks in period 2), and again the LSD diet (3 weeks in period 3). There was a 1-week dietary transition between LSD and HSD. Commonly used absolute SARA pH indicators such as daily average, area under the curve (AUC) and time spent below pH

Long-distance transport can cause stress to beef cattle impairing health and growth performances. This study aimed to deepen the knowledge of the effects of long-distance transport on young bulls' metabolic profile to identify reliable blood parameters for monitoring their health and welfare. Eighty Charolais young bulls, transported for 12 hours to the final fattening unit, were weighed and blood sampled at three time intervals: before leaving the commingling centre (day -1), upon arrival at the fattening unit (day 0), and 7 days post-arrival (day 7). These bulls were part of a larger study aimed at testing whether the animals have some benefit from the supplementation of live yeast and selenium through slow-release rumen boluses that were administered to half of them before departure from France ('Yeast' vs 'Control' group). The effect of the supplementation on the parameters considered in this study was included in the statistical analysis to account for the structure of the experimental design. Transport affected the initial body weight of the animals, which dropped on day 0 and it was not fully recovered on day 7. Most plasma traits of protein, energy, hepato-muscle, and mineral profiles were affected by transport. Cortisol was also assessed and peaked at day 0. The footprint of the long-distance transport on bulls' metabolic profile indicated a combination of stress, energy deficit, and muscle damage, with a certain degree of dehydration and liver impairment. Plasma traits measured on day -1 highlighted that stressful conditions and physiological responses of the bulls to recover homeostasis already started during the commingling phase before departure. No effect of supplementation was detected, except for higher selenium plasma level in Yeast bulls at day 7. Among blood parameters, non-esterified fatty acids, total protein, cortisol, glucose, and iron were those responsible for most of the variation in metabolic profile of bulls undergoing long journey. Therefore, these traits might be used as major biomarkers to assess stress in transported beef cattle, helping to identify critical situations for which proper mitigating actions should be taken. The outcomes of this study suggested that preventive measures against transport stress in beef cattle should start at the commingling of the animals in the collection centers, thus before departure., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Matteo Santinello, Isabella Lora, Giulio Cozzi, Mauro Penasa, Alberto Guerra, Federico Righi, Massimo De Marchi have no conflicts of interest. Clothilde Villot, Eric Chevaux, and Bruno Martin are employed by Lallemand SAS, (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

The objectives of this study were to determine if weaning would induce behavioral and physiological indicators of a negative affective state, and if supplementation of inactivated Lactobacillus helveticus (ILH) to dairy calves would reduce those indicators of negative affect during weaning. Male Holstein calves (n = 23) were enrolled in the study on d 1 of life. The calves were housed in individual pens in 1 of 4 rooms for the 42 d study. Calves began a stepdown weaning from 9 L/d of milk replacer (MR), at 150 g of MR powder/L, on d 35 and received 6 L/d on d 35 - 36, 3 L/d on d 37 - 38, and 0.4 L/d on d 39 - 42. The MR was divided between 3 meals/d until the last 0.4 L/d phase which was divided between 2 meals/d. Calves had ad libitum water access throughout the study and calf starter from d 28 onwards. Within room, calves were assigned to 1 of 2 treatments: 1) control (CON; n = 11) and 2) 5 g of ILH/d split over and mixed into the 0800 h and 2000 h milk feedings from d 3-42 (ILH; n = 12). Lying behavior was recorded using HOBO data loggers from d 21-41. On d 33, 37 and 41, infrared eye images were taken to determine maximum eye temperature (MET), saliva samples were collected to determine cortisol concentration, and play assessments were conducted to quantify play behavior. On d 34, 38, and 42, blood samples were collected to determine blood serotonin concentration, whereas on d 38 and 39, calves were tested with a cognitive task. A subset of calves (n = 5/treatment) were euthanized to collect gut and brain tissue samples for serotonin concentration on d 43. Weaning resulted in fewer (d 37-41, tendency: d 36), but longer (d 38-41, tendency: d 37), lying bouts and reduced play (d 41), although no changes in lying time, MET, saliva cortisol, nor blood serotonin were detected with initiation of weaning. Supplementation of ILH was associated with lower lying time throughout the study, and reduced play duration and higher salivary cortisol and MET during weaning. No differences in lying bouts, play count, blood and tissue (colon, ileum, prefrontal cortex and brain stem) serotonin concentration, and time to complete the cognitive task were detected between the treatments. Overall, weaning induced behavioral changes indicative of negative affective state, and some behavioral differences were observed with ILH supplementation both before and during weaning, with some physiological changes observed during weaning., (© 2024, The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Background: As Holstein calves are susceptible to gastrointestinal disorders during the first week of life, understanding how intestinal immune function develops in neonatal calves is important to promote better intestinal health. Feeding probiotics in early life may contribute to host intestinal health by facilitating beneficial bacteria colonization and developing intestinal immune function. The objective of this study was to characterize the impact of early life yeast supplementation and growth on colon mucosa-attached bacteria and host immune function., Results: Twenty Holstein bull calves received no supplementation (CON) or Saccharomyces cerevisiae boulardii (SCB) from birth to 5 d of life. Colon tissue biopsies were taken within 2 h of life (D0) before the first colostrum feeding and 3 h after the morning feeding at d 5 of age (D5) to analyze mucosa-attached bacteria and colon transcriptome. Metagenome sequencing showed that there was no difference in α and β diversity of mucosa-attached bacteria between day and treatment, but bacteria related to diarrhea were more abundant in the colon mucosa on D0 compared to D5. In addition, qPCR indicated that the absolute abundance of Escherichia coli (E. coli) decreased in the colon mucosa on D5 compared to D0; however, that of Bifidobacterium, Lactobacillus, and Faecalibacterium prausnitzii, which could competitively exclude E. coli, increased in the colon mucosa on D5 compared to D0. RNA-sequencing showed that there were no differentially expressed genes between CON and SCB, but suggested that pathways related to viral infection such as "Interferon Signaling" were activated in the colon mucosa of D5 compared to D0., Conclusions: Growth affected mucosa-attached bacteria and host immune function in the colon mucosa during the first 5 d of life in dairy calves independently of SCB supplementation. During early life, opportunistic pathogens may decrease due to intestinal environmental changes by beneficial bacteria and/or host immune function. Predicted activation of immune function-related pathways may be the result of host immune function development or suggest other antigens in the intestine during early life. Further studies focusing on the other antigens and host immune function in the colon mucosa are required to better understand intestinal immune function development., (© 2024. The Author(s).)

In this work, we utilize our recently developed machine learning (ML)-corrected ab initio dispersion (aiD) potential, known as D3-ML, which is based on the comprehensive SAPT10K dataset and relies solely on Cartesian coordinates as input, to address the dispersion deficiencies in second-order Møller-Plesset perturbation theory (MP2) by replacing its problematic dispersion and exchange-dispersion terms with D3-ML. This leads to the development of a new dispersion-corrected MP2 method, MP2+aiD(CCD), which outperforms other spin-component-scaled and dispersion-corrected MP2 methods as well as popular ML models for predicting noncovalent interactions across various datasets, including S66 × 8, NAP6 (containing 6 naphthalene dimers), L7, S12L, DNA-ellipticine, the C60 dimer, and C60[6]CPPA. In addition, MP2+aiD(CCD) exhibits comparable or even superior performance compared to the contemporary ωB97M-V functional. The limited performance of pure ML models for systems outside the training set or larger than those in the training set highlights their instability and unpredictability. Conversely, the outstanding performance and transferability of the hybrid MP2+aiD(CCD) method can be attributed to the fusion of the physical electronic structure method and a data-driven ML model, combining the strengths of both sides. This investigation firmly establishes MP2+aiD(CCD) as one of the most accurate and reliable fifth-order scaling correlated wave function methods currently available for modeling noncovalent interactions, even for large complexes. MP2+aiD(CCD) is expected to be reliably applicable in investigating real-life complexes at the hundred-atom scale., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this study, we introduce SAPT10K, a comprehensive dataset comprising 9982 noncovalent interaction energies and their binding energy components (electrostatics, exchange, induction, and dispersion) for diverse intermolecular complexes of 944 unique dimers. These complexes cover significant portions of the intermolecular potential energy surface and were computed using higher-order symmetry-adapted perturbation theory, SAPT2+(3)(CCD), with a large aug-cc-pVTZ basis set. The dispersion energy values in SAPT10K serve as crucial inputs for refining the ab initio dispersion potentials based on Grimme's D3 and many-body dispersion (MBD) models. Additionally, Δ machine learning (ML) models based on newly developed intermolecular features, which are derived from intermolecular histograms of distances for element/substructure pairs to simultaneously account for local environments as well as long-range correlations, are also developed to address deficiencies of the D3/MBD models, including the inflexibility of their functional forms, the absence of MBD contributions in D3, and the standard Hirshfeld partitioning scheme used in MBD. The developed dispersion models can be applied to complexes involving a wide range of elements and charged monomers, surpassing other popular ML models, which are limited to systems with only neutral monomers and specific elements. The efficient D3-ML model, with Cartesian coordinates as the sole input, demonstrates promising results on a testing set comprising 6714 dimers, outperforming another popular ML model, component-based machine-learned intermolecular force field (CLIFF), by 1.5 times. These refined D3/MBD-ML models have the capability to replace the time-consuming dispersion components in symmetry-adapted perturbation theory-based calculations and can promptly illustrate the dispersion contribution in noncovalent complexes for supramolecular assembly and chemical reactions., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

This graduate student literature review provides an examination of the ontological adaptations of the calf's immune system and how the intestinal microbiota influences calf immune function in health and disease. Within dairy rearing systems, various nutritional and management factors have emerged as critical determinants of development influencing multiple physiological axes in the calf. Furthermore, we discuss how multiple pre- and postnatal maternal factors influence the trajectory of immune development in favor of establishing regulatory networks to successfully cope with the new environment, while providing early immune protection via immune passive transfer from colostrum. Additionally, our review provides insights into the current understanding of how the intestinal microbiota contributes to the development of the intestinal and systemic immune system in calves. Lastly, we address potential concerns related to the use of prophylactic antimicrobials and waste milk, specifically examining their adverse effects on intestinal health and metabolic function. By examining these factors, we aim to better understand the intricate relationship between current management practices and their long-term effect on animal health., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

The gastrointestinal microbial consortium in dairy cattle is critical to determining the energetic status of the dairy cow from birth through her final lactation. The ruminant's microbial community can degrade a wide variety of feedstuffs, which can affect growth, as well as production rate and efficiency on the farm, but can also affect food safety, animal health, and environmental impacts of dairy production. Gut microbial diversity and density are powerful tools that can be harnessed to benefit both producers and consumers. The incentives in the United States to develop Alternatives to Antibiotics for use in food-animal production have been largely driven by the Veterinary Feed Directive and have led to an increased use of probiotic approaches to alter the gastrointestinal microbial community composition, resulting in improved heifer growth, milk production and efficiency, and animal health. However, the efficacy of direct-fed microbials or probiotics in dairy cattle has been highly variable due to specific microbial ecological factors within the host gut and its native microflora. Interactions (both synergistic and antagonistic) between the microbial ecosystem and the host animal physiology (including epithelial cells, immune system, hormones, enzyme activities, and epigenetics) are critical to understanding why some probiotics work but others do not. Increasing availability of next-generation sequencing approaches provides novel insights into how probiotic approaches change the microbial community composition in the gut that can potentially affect animal health (e.g., diarrhea or scours, gut integrity, foodborne pathogens), as well as animal performance (e.g., growth, reproduction, productivity) and fermentation parameters (e.g., pH, short-chain fatty acids, methane production, and microbial profiles) of cattle. However, it remains clear that all direct-fed microbials are not created equal and their efficacy remains highly variable and dependent on stage of production and farm environment. Collectively, data have demonstrated that probiotic effects are not limited to the simple mechanisms that have been traditionally hypothesized, but instead are part of a complex cascade of microbial ecological and host animal physiological effects that ultimately impact dairy production and profitability., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

This study aimed to characterize the development of systemic and colon tissue resident B and γδ T cells in newborn calves from birth until weaning. At birth, calves have limited capacity to initiate immune responses, and the immune system gradually matures over time. Gamma delta (γδ) T cells are an important lymphocyte subset in neonatal calves that confer protection and promote immune tolerance. A total of 36 newborn calves were enrolled in a longitudinal study to characterize how systemic and colon tissue resident B and γδ T cells develop from birth until weaning. Blood and colon biopsy samples were collected on d 2, 28, and 42 to determine the proportions of various B and γδ T cell subsets by flow cytometry. We classified γδ T cells into different functional subsets according to the level of expression intensity of the coreceptors WC1.1 (effector function) and WC1.2 (regulatory function). Furthermore, naive B cells were classified based on the expression IgM receptor, and activation state was determined based on expression of CD21 and CD32, 2 receptors with opposing signals involved in B cell activation in early life. Additional colon biopsy samples were used for 16S sequencing, and microbial diversity data are reported. At birth, γδ T cells were the most abundant lymphocyte population in blood, accounting for 58.5% of the lymphocyte pool, after which the proportions of these cells declined to 38.2% after weaning. The proportion of γδ T cells expressing WC1.1 decreased by 50% from d 2 to d 28, whereas no change was observed in the expression of WC1.2. In the colon, there was a 50% increase of γδ T cells after weaning and the proportion of WC1.2 + γδ T cells doubled from d 28 to 42. The proportion of IgM + B lymphocytes in blood increased from 23.6% at birth to 30% after weaning, were the proportion of B cells expressing CD21 increased by 25%, while the proportion of B cells expressing CD32 decreased by 30%. While no changes were observed for the overall proportion of IgM + B lymphocytes in the colon, there was a 6-fold increase in the proportion of CD21 + B cells from pre- (d 28) to postweaning (d 42). Microbial diversity increased from d 2 of life to 28 and declined abruptly after weaning. The reduction in microbial diversity during weaning was negatively correlated with the increase in all γδ T cell subsets and CD21 + B cells. These data suggest that developmental adaptations after birth coordinate expansion of γδ T cells to provide early systemic protection, as well as to steer immune tolerance, while B cells mature over time. Additionally, the increase of colonic γδ T cells on d 42 suggests a protective role of these cells during weaning., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Neonatal calves have a limited capacity to initiate immune responses due to a relatively immature adaptive immune system, which renders them susceptible to many on-farm diseases. At birth, the mucosal surfaces of the intestine are rapidly colonized by microbes in a process that promotes mucosal immunity and primes the development of the adaptive immune system. In a companion study, our group demonstrated that supplementation of a live yeast probiotic, Saccharomyces cerevisiae boulardii (SCB) CNCM I-1079, to calves from birth to 1 week of age stimulates secretory IgA (sIgA) production in the intestine. The objective of the study was to evaluate how SCB supplementation impacts the intestinal microbiota of one-week-old male calves, and how changes in the bacterial community in the intestine relate to the increase in secretory IgA. A total of 20 calves were randomly allocated to one of two treatments at birth: Control (CON, n  = 10) fed at 5 g/d of carrier with no live yeast; and SCB ( n  = 10) fed at 5 g of live SCB per day (10 × 109 CFU/d). Our study revealed that supplementing calves with SCB from birth to 1 week of age had its most marked effects in the ileum, increasing species richness and phylogenetic diversity in addition to expediting the transition to a more interconnected bacterial community. Furthermore, LEfSe analysis revealed that there were several differentially abundant taxa between treatments and that SCB increased the relative abundance the family Eubacteriaceae , Corynebacteriaceae , Eggerthellaceae , Bacillaceae , and Ruminococcaceae . Furthermore, network analysis suggests that SCB promoted a more stable bacterial community and appears to reduce colonization with Shigella . Lastly, we observed that the probiotic-driven increase in microbial diversity was highly correlated with the enhanced secretory IgA capacity of the ileum, suggesting that the calf's gut mucosal immune system relies on the development of a stable and highly diverse microbial community to provide the necessary cues to train and promote its proper function. In summary, this data shows that supplementation of SCB promoted establishment of a diverse and interconnected microbiota, prevented colonization of Escherichia Shigella and indicates a possible role in stimulating humoral mucosal immunity., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Rostoll Cangiano, Villot, Amorin-Hegedus, Malmuthuge, Gruninger, Guan and Steele.)

In this work, we develop an accurate and efficient XGBoost machine learning model for predicting the global-density-dependent range-separation parameter, ωGDD, for long-range corrected functional (LRC)-ωPBE. This ωGDDML model has been built using a wide range of systems (11 466 complexes, ten different elements, and up to 139 heavy atoms) with fingerprints for the local atomic environment and histograms of distances for the long-range atomic correlation for mapping the quantum mechanical range-separation values. The promising performance on the testing set with 7046 complexes shows a mean absolute error of 0.001 117 a0-1 and only five systems (0.07%) with an absolute error larger than 0.01 a0-1, which indicates the good transferability of our ωGDDML model. In addition, the only required input to obtain ωGDDML is the Cartesian coordinates without electronic structure calculations, thereby enabling rapid predictions. LRC-ωPBE(ωGDDML) is used to predict polarizabilities for a series of oligomers, where polarizabilities are sensitive to the asymptotic density decay and are crucial in a variety of applications, including the calculations of dispersion corrections and refractive index, and surpasses the performance of all other popular density functionals except for the non-tuned LRC-ωPBE. Finally, LRC-ωPBE (ωGDDML) combined with (extended) symmetry-adapted perturbation theory is used in calculating noncovalent interactions to further show that the traditional ab initio system-specific tuning procedure can be bypassed. The present study not only provides an accurate and efficient way to determine the range-separation parameter for LRC-ωPBE but also shows the synergistic benefits of fusing the power of physically inspired density functional LRC-ωPBE and the data-driven ωGDDML model., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

This research aimed: (i) to evaluate on-farm (FARM data) multiparametric models developed under controlled experiment (INRAE data) and based on non-invasive indicators to detect subacute ruminal acidosis (SARA) in dairy cows. We also aimed to recover high discrimination capacity, if needed, by (ii) building new models with combined INRAE and FARM data; and (iii) enriching the models increasing from 2 to 5 indicators per model. For model enrichment, we focused on indicators determinable on-farm by quick and inexpensive routine analysis. Fifteen commercial dairy farms were selected to cover a wide range of SARA risk. In each farm, four Holstein early-lactating healthy primiparous cows were selected based on their last on-farm recording of milk yield and somatic cell count analysis. Cows were equipped with a reticulo-rumen pH sensor. The pH kinetics were analysed over a subsequent 7-day period. Relative pH indicators were used to classify cows with or without SARA. Milk, blood, faeces, and urine were collected for analysis of the indicators included in the models developed by Villot et al. (2020) on INRAE data that were externally evaluated using FARM data. Then, new models based on the same indicators were developed combining INRAE and FARM data to test whether a possible loss in performance was due to a limited validity domain of model by Villot et al (2020). Finally, the models developed combining INRAE and FARM data were adapted to the on-farm application and enriched by increasing indicators from 2 to 5 per model using linear discriminant analysis and leave-one-out cross-validation. The sensitivities (true-positive rate) in external evaluation on FARM data were substantially lower than those from cross-validation by Villot et al. (2020) (range: 0.1-0.75 vs 0.79-0.96, respectively), and the specificities (true-negative rate) showed a larger range with lower minimum values (range: 0.18-1.0 vs 0.62-0.97, respectively). The sensitivities of new models developed combining INRAE and FARM data ranged from 0.63 to 0.77. Models involving blood cholesterol, β-hydroxybutyrate, haptoglobin, milk and blood urea, and models involving milk fat/protein ratio, dietary starch proportion, and milk fatty acids had the highest performances, whereas models including sieved faecal residues and urine pH had the lowest. Enriching models to three indicators per model improved sensitivity and specificity, but the inclusion of more indicators was less or not effective. Larger field trials are required to validate our results and to increase variability and validity domain of models., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the "gold standard" coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller-Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.

The objectives of this study were to examine the effects of pelleted starter diets differing in starch and neutral detergent fiber (NDF) content when fed differing levels of milk replacer (MR) on nutrient digestibility, whole gastrointestinal tract fermentation, pH, and inflammatory markers in dairy calves around weaning. Calves were randomly assigned to 1 of 4 dietary treatments (n = 12 per treatment) in a 2 × 2 factorial design based on daily MR allowance and amount of starch in pelleted starter (SPS): 0.691 kg of MR per day [dry matter (DM) basis] with starter containing low or high starch (12.0% and 35.6% starch on DM basis, respectively), and 1.382 kg of MR per day (DM) with starter containing low or high starch. All calves were housed in individual pens with straw bedding until wk 5 when bedding was covered. Calves were fed MR twice daily (0700 and 1700 h) containing 24.5% crude protein (DM) and 19.8% fat (DM), and had access to pelleted starter (increased by 50 g/d if there were no refusals before weaning and then 200 g/d during and after weaning) and water starting on d 1. Calves arrived between 1 and 3 d of age and were enrolled into an 8-wk study, with calves undergoing step-down weaning during wk 7. Starting on d 35, an indwelling pH logger was inserted orally to monitor rumen pH until calves were dissected at the end of the study in wk 8. Higher SPS calves showed an increase in rumen pH magnitude (1.46 ± 0.07) compared with low SPS calves (1.16 ± 0.07), a decrease in rumen pH in wk 8 (high SPS: 5.37 ± 0.12; low SPS: 5.57 ± 0.12), and a decrease in haptoglobin in wk 8 (high SPS: 0.24 ± 0.06 g/L; low SPS: 0.49 ± 0.06 g/L). The majority of differences came from increased starter intake in general, which suggests that with completely pelleted starters the differences in starch and NDF do not elicit drastic changes in fermentation, subsequent end products, and any resulting inflammation in calves around weaning., (© 2022, The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

This study was designed to develop a protocol for repeated intramuscular indomethacin injections to replicate leaky-gut-like symptoms in male Holstein calves to model and study the detrimental effects of leaky gut on gut tissue function and inflammatory response. A generalized randomized block design was used to evaluate how repeated indomethacin intramuscular injections affected the development of leaky gut in 18 male Holstein calves. Animals were enrolled at 3 ± 1 d of life, and after 21 d of adaptation, they were randomly assigned to 1 of 3 treatments consisting of intramuscular saline or indomethacin injections every 12 h for 48 h: (1) control (CTL), saline injection, (2) low intramuscular indomethacin (INDO-L) dosed at 1.2 mg/kg of body weight (BW), and (3) high intramuscular indomethacin (INDO-H) dosed at 2.4 mg/kg of BW. During the challenge, milk intake, starter intake, fecal scores, and rectal temperature were measured daily, and BW was measured at the beginning and at the end of the challenge. Plasma samples were used to measure the recovery of markers of intestinal permeability before and after the challenge by dosing lactulose, d-mannitol, and chromium-EDTA. In addition, several cytokines were measured in plasma during the challenge. Calves were dissected at the end of the challenge to obtain tissue and digesta samples from the gastrointestinal tract and liver. No treatment differences were observed for starter and milk intakes, fecal scores, BW, and rectal temperature. The difference in marker concentrations between pre and post challenges was higher for INDO calves compared with CTL calves in the case of lactulose and chromium-EDTA. In addition, chemokine ligand 2 and 4 and IL-6 were higher for INDO-H calves compared with CTL. Both doses of indomethacin resulted in reductions in villus length and surface area in the distal jejunum and ileum and reductions in crypt depth and width in the colon. We showed that repeated indomethacin injections over a 48-h period induced leaky-gut-like symptoms in a region-specific manner, affecting mainly the distal section of the intestine. This outcome was characterized by histomorphological changes in the distal jejunum, ileum, and colon and by increased gut permeability. Interestingly, changes in liver morphology and immune function also occurred, possibly due to the increased translocation of foreign antigens breaching the epithelial cell wall. The leaky gut challenge model described here could be used to improve understanding of the pathogenesis of intestinal disorders in cattle and provide a reliable alternative for testing feed additives with intestinal health benefits., (© 2022, The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

In this work, we report the benchmark binding energies of the seven complexes within the L7 data set, six host-guest complexes from the S12L data set, a C 60 dimer, the DNA-ellipticine intercalation complex, and the largest system of the study, the HIV-indinavir system, which contained 343 atoms or 139 heavy atoms. The high-quality values reported were obtained via a focal point method that relies on the canonical form of second-order Møller-Plesset theory and the domain-based local pair natural orbital scheme for the coupled cluster with single double and perturbative triple excitations [DLPNO-CCSD(T)] extrapolated to the complete basis set (CBS) limit. The results in this work not only corroborate but also improve upon some previous benchmark values for large noncovalent complexes albeit at a relatively steep cost. Although local CCSD(T) and the largely successful fixed-node diffusion Monte Carlo (FN-DMC) have been shown to generally agree for small- to medium-size systems, a discrepancy in their reported binding energy values arises for large complexes, where the magnitude of the disagreement is a definite cause for concern. For example, the largest deviation in the L7 data set was 2.8 kcal/mol (∼10%) on the low end in C3GC. Such a deviation only grows worse in the S12L set, which showed a difference of up to 10.4 kcal/mol (∼25%) by a conservative estimation in buckycatcher-C 60 . The DNA-ellipticine complex also generated a disagreement of 4.4 kcal/mol (∼10%) between both state-of-the-art methods. The disagreement between local CCSD(T) and FN-DMC in large noncovalent complexes shows that it is urgently needed to have the canonical CCSD(T), the Monte Carlo CCSD(T), or the full configuration interaction quantum Monte Carlo approaches available to large systems on the hundred-atom scale to solve this dilemma. In addition, the performances of cheaper popular computational methods were assessed for the studied complexes with respect to DLPNO-CCSD(T)/CBS. r 2 SCAN-3c, B97M-V, and PBE0+D4 work well in large noncovalent complexes in this work, and GFN2-xTB performs well in π-π stacking complexes. B97M-V is the most reliable computationally efficient approach to predicting noncovalent interactions for large complexes, being the only one to have binding errors within the so-called 1 kcal/mol "chemical accuracy". The benchmark interaction energies of these host-guest complexes, molecular materials, and biological systems with electronic and medicinal implications provide crucial reference data for the improvement of current and future lower-cost methods.

Branched-chain fatty acids (BCFA) have recently been reported to play a role in human gut health during early life. However, little information is available on the fecal BCFA profiles in young ruminants and whether they are associated with the development of neonatal calf diarrhea. The objectives of this study were to (1) characterize BCFA profiles in feces collected from young calves, (2) compare the fecal BCFA composition between diarrheic and nondiarrheic dairy calves, and (3) explore the potential relationships between BCFA and microbiota in the feces. A total of 32 male Holstein dairy calves (13 ± 3 d old) with the same diet management were grouped as diarrheic (n = 16) or healthy (n = 16) based on fecal score (determined by liquid fecal consistency with some solid particles); diarrhea cases were defined as fecal score ≥2 for at least 2 d. Fecal samples were collected on the seventh day after calf arrival, and the fecal BCFA and microbial profiles were assessed using gas chromatograph and amplicon sequencing, respectively. In total, 7 BCFA were detected in the feces of all dairy calves; however, the concentrations of fecal BCFA differed between diarrheic and nondiarrheic calves. Specifically, the concentrations of iso-C16:0, iso-C17:0, anteiso-C17:0, and total even-chain BCFA were significantly higher in the feces of diarrheic calves. When the associations between BCFA and bacteria were studied, the relative abundance of Eggerthella was positively correlated with the concentrations of iso-C16:0 (ρ = 0.67), iso-17:0 (ρ = 0.77), anteiso-C17:0 (ρ = 0.73), and iso-C18:0 (ρ = 0.65), whereas the relative abundance of Subdoligranulum was positively correlated with the concentrations of iso-C14:0 (ρ = 0.62), iso-C15:0 (ρ = 0.78), and anteiso-C15:0 (ρ = 0.63). Use of random forest algorithm showed that BCFA such as anteiso-C15:0, iso-C16:0, iso-C17:0, iso-C18:0, and total even-chain BCFA could be used as biomarkers to differentiate diarrheic calves from healthy ones. Our findings generated fundamental knowledge on the potential roles of BCFA in neonatal calf gut health. Follow-up studies with larger animal populations are warranted to validate the feasibility of using BCFA as indicators of health status in neonatal calves., (Copyright © 2021 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The early development of immunity and microbiota in the gut of newborn calves can have life-long consequences. Gut microbiota and the intestinal barrier interplay after birth, establishing a homeostatic state whereby mucosal cells cohabit with microorganisms to develop a healthy gut. We hypothesized that postnatal codevelopment of gut immunity and microbiota could be influenced by early-life supplementation with live yeast. Starting from birth, calves either received a daily supplementation of Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB, 10 × 10 9 cfu/d, n = 10) in the morning meal for 7 d or no supplementation (n = 10). Each animal received 2 adequate colostrum replacer meals at 2 and 12 h of life (expected total IgG fed = 300 g) before being fed milk replacer twice a day. Passive transfer of immunity (total protein, IgG, and IgA) through colostrum was evaluated and endogenous production of IgA was investigated by measuring IgA-producing plasma cells, IgA relative gene expression (PIGR and CD79A), and secretory IgA concentration in the gut. The concentration of targeted microbial groups was evaluated with quantitative PCR in the gut digesta collected at d 7 of life. Early SCB supplementation did not impair immunoglobulin absorption and all calves had successful passive transfer of immunity (serum IgG concentration >15 mg/mL at d 1 and d 7 of age). Although the expression of IgA relative gene expression (PIGR and CD79A) was not different, SCB calves had higher secretory IgA concentrations in the ileum (1.98 ± 0.12 mg/g of dry matter; DM) and colon (1.45 ± 0.12 mg/g of DM) digesta compared with control animals (1.18 and 0.59 ± 0.12 mg/g of DM, respectively). In addition, the number of IgA-producing plasma cells were greater in both ileum (2.55 ± 0.40 cells/mm 2 ) and colon (3.03 ± 0.40 cells/mm 2 ) tissues for SCB calves compared with control (respectively 1.00 ± 0.40 and 0.60 ± 0.42 cells/mm 2 ). Endogenous IgA production in the gut of SCB calves was enhanced, which could make them less prone to pathogen intrusion. In addition, SCB calves had higher Lactobacillus and tended to have higher Faecalibacterium prausnitzii in the jejunum compared with control calves, which suggests that SCB supplementation during early-life gut colonization may have a positive effect in newborn calves. Direct SCB supplementation or the cross-talk between SCB and bacteria may be responsible for stimulating IgA production and may play a key role in shaping early colonization in the gut of newborn calves., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).)

Perturbations in early life gut microbiota can have long-term impacts on host health. In this study, we investigated antimicrobial-induced temporal changes in diversity, stability, and compositions of gut microbiota in neonatal veal calves, with the objective of identifying microbial markers that predict diarrhea. A total of 220 samples from 63 calves in first 8 weeks of life were used in this study. The results suggest that increase in diversity and stability of gut microbiota over time was a feature of "healthy" (non-diarrheic) calves during early life. Therapeutic antimicrobials delayed the temporal development of diversity and taxa-function robustness (a measure of microbial stability). In addition, predicted genes associated with beta lactam and cationic antimicrobial peptide resistance were more abundant in gut microbiota of calves treated with therapeutic antimicrobials. Random forest machine learning algorithm revealed that Trueperella, Streptococcus, Dorea, uncultured Lachnospiraceae, Ruminococcus 2, and Erysipelatoclostridium may be key microbial markers that can differentiate "healthy" and "unhealthy" (diarrheic) gut microbiota, as they predicted early life diarrhea with an accuracy of 84.3%. Our findings suggest that diarrhea in veal calves may be predicted by the shift in early life gut microbiota, which may provide an opportunity for early intervention (e.g., prebiotics or probiotics) to improve calf health with reduced usage of antimicrobials.

High-starch diets (HSDs) fed to high-producing ruminants are often responsible for rumen dysfunction and could impair animal health and production. Feeding HSDs are often characterized by transient rumen pH depression, accurate monitoring of which requires costly or invasive methods. Numerous clinical signs can be followed to monitor such diet changes but no specific indicator is able to make a statement at animal level on-farm. The aim of this pilot study was to assess a combination of non-invasive indicators in dairy cows able to monitor a HSD in experimental conditions. A longitudinal study was conducted in 11 primiparous dairy cows fed with two different diets during three successive periods: a 4-week control period (P1) with a low-starch diet (LSD; 13% starch), a 4-week period with an HSD (P2, 35% starch) and a 3-week recovery period (P3) again with the LSD. Animal behaviour was monitored throughout the experiment, and faeces, urine, saliva, milk and blood were sampled simultaneously in each animal at least once a week for analysis. A total of 136 variables were screened by successive statistical approaches including: partial least squares-discriminant analysis, multivariate analysis and mixed-effect models. Finally, 16 indicators were selected as the most representative of a HSD challenge. A generalized linear mixed model analysis was applied to highlight parsimonious combinations of indicators able to identify animals under our experimental conditions. Eighteen models were established and the combination of milk urea nitrogen, blood bicarbonate and feed intake was the best to detect the different periods of the challenge with both 100% of specificity and sensitivity. Other indicators such as the number of drinking acts, fat:protein ratio in milk, urine, and faecal pH, were the most frequently used in the proposed models. Finally, the established models highlight the necessity for animals to have more than 1 week of recovery diet to return to their initial control state after a HSD challenge. This pilot study demonstrates the interest of using combinations of non-invasive indicators to monitor feed changes from a LSD to a HSD to dairy cows in order to improve prevention of rumen dysfunction on-farm. However, the adjustment and robustness of the proposed combinations of indicators need to be challenged using a greater number of animals as well as different acidogenic conditions before being applied on-farm.

Although hay is the foundation of most equine diets, horse owners rarely ask for biochemical analysis and the routine practice is to choose hay based on its 'perceived' nutritional value. The present study aimed at exploring the relationship between sensory properties as perceived by sight, touch and smell, and the nutritional value of hay measured by biochemical analysis using a 'free sorting task' method. Fifty-four non-expert participants were asked individually to: (1) observe 21 hays samples, (2) group together hays that they perceived as similar for each of the three modalities (hay appearance, odour or texture) and (3) characterize each formed group with a maximum of five descriptive terms. For each modality, results were recorded in a contingency matrix (hays × terms) where only terms cited at the minimum five times for at least one sample, were kept for data analysis. A correspondence analysis (CA) was performed on the contingency matrix to plot both samples and descriptive terms on a χ2 metric map. Then, a Hierarchical Ascending Classification (HAC) was performed on the coordinates of samples in the CA space. Clusters were identified by truncating the HAC tree-diagrams. The attributes that defined the best resulting clusters were identified by computing their probability of characterizing a cluster. Correlations were computed between each biochemical parameter on one hand, and the first two dimensions of the CA map on the other. Finally, correlations between the values of each hay on the first dimension of the three CA maps (appearance, odour and texture) were computed. Hedonic descriptive terms were primarily used for describing odour and texture modalities. For describing hay appearance, participants spontaneously used visual cues referring to colour or aspect. Based on the tree-diagrams resulting from the HAC, 3, 5 and 2 groups were clustered, respectively for appearance, odour and texture description. Digestible energy was correlated to the first dimension on the three CA maps, whereas CP was correlated to the first dimension of the CA appearance map only. While NDF value was correlated to the first and second dimensions on the CA odour map only, ADF content was correlated to the first dimension on the three CA maps. Non-fibre carbohydrates were correlated to the first dimension of the CA appearance map only. The similarity-based approach which is part of the standard toolbox of food sensory evaluation by untrained consumers was well adapted to animal feeds evaluation by non-experts.

The objective of this study was to investigate the effect of one specific strain of yeast, Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB), on the growth performance, health, and fecal bacterial profile of veal calves. A total of 84 animals were enrolled in an experiment at a commercial veal farm for a total of 7 wk. Calves were fed twice a day with a milk replacer meal during the entire experiment and were randomly assigned to receive daily either SCB supplementation (10 × 10 9 cfu/d) or a placebo (CON). Individual feed intake and body weight were monitored on a daily and weekly basis, respectively. Fecal samples were collected at arrival to the veal facility (wk 0) and additional samples were taken on d 14 (wk 2) and d 49 (wk 7). These samples were subjected to 16S rRNA gene amplicon sequencing using Illumina MiSeq (Illumina Inc., San Diego, CA) to examine the bacterial profiles and real-time quantitative PCR to quantify Saccharomyces cerevisiae and specific bacterial groups. The significant increase of S. cerevisiae in the feces of SCB calves at wk 2 and 7 compared with wk 0 (respectively 1.7 × 10 7 , 1.2 × 10 7 , and 2.2 × 10 5 copy number of S. cerevisiae/g of feces) indicates a good survival of that yeast strain along the gastrointestinal tract. Supplementation of SCB did not improve overall growth performance with regard to average daily gain (ADG), final body weight, and feed intake. Nevertheless, a total of 69.1% of nonsupplemented calves had diarrhea and 28.6% experienced severe diarrhea, whereas 50.0% of the calves supplemented with SCB had diarrhea and 9.5% experienced severe diarrhea. With respect to antibiotic use, 89.7% of the diarrheic calves recorded in the CON group were treated, whereas only 66.7% of the SCB diarrheic calves received an antibiotic. In addition, diarrheic calves supplemented with SCB maintained an ADG similar to nondiarrheic animals, whereas the CON diarrheic calves had a significantly lower ADG in comparison with nondiarrheic CON calves. Fecalibacterium was the most predominant bacterial genus in fecal samples of nondiarrheic and diarrheic calves supplemented with SCB, whereas fecal microbiota was predominated by Collinsella in diarrheic calves from the CON group. Live yeast supplementation in milk replacer led to a decrease of diarrhea in milk-fed veal calves and the fecal microbiota of diarrheic calves maintained a healthy community similar to nondiarrheic animals, with Fecalibacterium being the predominant genus., (The Authors. Published by FASS Inc. and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).)

Subacute ruminal acidosis (SARA) is usually characterized by abnormal and intermittent drops in rumen pH. Nevertheless, high individual animal variability in rumen pH and the difference in measurement methods for pH data acquisition decrease the sensitivity and accuracy of pH indicators for detecting SARA in ruminants. The aim of this study was to refine rumen pH indicators in long-term SARA based on individual dairy cow reticulo-rumen pH kinetics. Animal performances and rumen parameters were studied weekly in order to validate SARA syndrome and rumen pH was continuously measured using reticulo-rumen sensors. In total, 11 primiparous dairy cows were consecutively fed two different diets for 12 successive weeks: a control diet as low-starch diet (LSD; 13% starch for 4 weeks in period 1), an acidotic diet as high-starch diet (HSD; 32% starch for 4 weeks in period 2), and again the LSD diet (3 weeks in period 3). There was a 1-week dietary transition between LSD and HSD. Commonly used absolute SARA pH indicators such as daily average, area under the curve (AUC) and time spent below pH<5.8 and pH<6 were processed from absolute (raw) daily kinetics. Then signal processing was applied to raw pH values in order to calculate relative pH indicators by filtering and normalizing data to remove inter-individual variability, sensor drift and sensor noise. Normalized AUC, times spent below NpH<-0.3 and NpH<-0.5, NpH range and NpH standard deviation were calculated. Those relative pH indicators were compared with commonly used pH indicators to assess their ability to detect SARA. This syndrome induced by HSD was confirmed by consistent expected changes in milk quality, dry matter intake and acetate : propionate ratio in the rumen, whereas the ruminal concentration of lipopolysaccharide was increased. Commonly used pH SARA indicators were not able to discriminate SARA syndrome due to high animal variability and sensor drift and noise, whereas relative pH indicators developed in this study appeared more relevant for SARA detection as assessed by receiver operating characteristic tests. This work shows that absolute pH kinetics should be corrected for drift, noise and animal variability to produce relative pH indicators that are more robust for SARA detection. These relative pH indicators could be more relevant for identifying affected animals in a herd and also for comparing SARA risk among studies.