Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes.

We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in the liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR < 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella, and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. In conclusion, our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in the relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared to high-RFI steers.

Effects of dietary supplementation of peanut skins (Arachis hypogaea) on performance, digestibility, and rumen fermentation of cattle: a meta-analysis.

This study aimed to estimate the magnitude of the effects of dietary inclusion of peanut skins (PS) byproduct (Arachis hypogea L.) on intake, total-tract digestibility, and rumen fermentation of cattle via meta-analysis. Data were collected following the PRISMA methodology. Nine manuscripts and a graduate thesis met the inclusion criteria from 1983 to 2010. The effect size was estimated by calculating the weighted raw mean differences (RMD) between PS vs. control diets. The RMD was compared with a robust variance estimation method followed by a meta-regression and a dose-response analysis fitting the diet characteristics like crude protein content (CP), NDF content, ether extract content (EE), tannin content, and PS level in diet (0 to 40%) as covariates. Dietary PS decreased (P < 0.01) total-tract CP digestibility (52.0 vs. 64.3%), final body weight (371.5 vs. 397.9 kg), and average daily gain (1.14 vs. 1.44 kg/day) among treatment comparisons. Likewise, PS decreased total VFA (92.6 vs. 107.6 mmol/L) and NH3-N (8.22 vs. 12.1 mg/dL), but no effects were observed on rumen pH (6.47 vs. 6.14) and VFA molar proportions. Despite the between-cluster variance, dietary PS increased the ether extract digestibility (77.5 vs. 70.2%) among treatment comparisons. The subset and dose-response analysis revealed that PS should not exceed 8% (DM basis) in the diet to prevent negative effects on CP digestibility and animal performance. In conclusion, the results of this meta-analysis do not support the dietary inclusion of PS in cattle diets beyond 8%.

Copy number variant-based genome wide association study reveals immune-related genes associated with parasite resistance in a heritage sheep breed from the United States.

Florida Native is a heritage sheep breed in the United States and expresses superior ability to regulate gastrointestinal nematodes. The objective of the present study was to investigate the importance of copy number variants (CNVs) on resistance to natural Haemonchus contortus infections. A total of 300 Florida Native sheep were evaluated. Phenotypic records included fecal egg count (FEC, eggs/gram), FAMACHA© score, percentage cell volume (PCV, %), body condition score (BCS) and average daily gain (ADG, kg). Sheep were genotyped using the GGP Ovine 50K single nucleotide polymorphism (SNP) chip. Log ratios from 45.2 k SNP markers spanning the entire genome were utilized for CNV detection. After quality control, 261 animals with CNVs and phenotypic records were used for the association testing. Association tests were carried out using correlation-trend test and principal component analysis correction to identify CNVs associated with FEC, FAMACHA©, PCV, BCS and ADG. Significant CNVs were detected when their adjusted p-value was <.05 after FDR correction. A total of 8124 CNVs were identified, which gave 246 non-overlapping CNVs. Fourteen CNVs were significantly associated with FEC and PCV. CNVs associated with FEC overlapped 14 Quantitative Trait Locus previously associated with H. contortus resistance. Our study demonstrated for the first time that CNVs could be potentially involved with parasite resistance in Florida Native sheep. Immune-related genes such as CCL1, CCL2, CCL8, CCL11, NOS2, TNF, CSF3 and STAT3 genes could play an important role for controlling H. contortus resistance. These genes could be potentially utilized as candidate markers for selection of parasite resistance in this breed.

Meta-analysis of effects of inoculation with Lactobacillus buchneri, with or without other bacteria, on silage fermentation, aerobic stability, and performance of dairy cows.

A meta-analysis of 158 peer-reviewed articles was conducted to examine effects of inoculation with Lactobacillus buchneri (LB)-based inoculants (LBB) that did or did not include homolactic or obligate heterolactic bacteria on silage fermentation and aerobic stability. A complementary meta-analysis of 12 articles examined LBB inoculation effects on dairy cow performance. Raw mean differences between inoculant and control treatment means weighted by inverse variance were compared with a hierarchical effects model that included robust variance estimation. Meta-regression and subgrouping analysis were used to identify effects of covariates including forage type, application rate (≤104, 105, 106, or ≥ 107 cfu/g as fed), bacteria type (LB vs. LB plus other bacteria), enzyme inclusion, ensiling duration, and silo type (laboratory or farm scale). Inoculation with LBB increased acetate (62%), 1, 2 propanediol (364%) and propionate (30%) concentration and aerobic stability (73.8%) and reduced lactate concentration (7.2%), yeast counts (7-fold) and mold counts (3-fold). Feeding inoculated silage did not affect milk yield, dry matter intake, and feed efficiency in lactating dairy cows. However, forage type, inoculant composition, and dose effects on silage quality measures were evident. Inoculation with LBB increased aerobic stability of all silages except tropical grasses. Adding obligate homolactic or facultative heterolactic bacteria to LB prevented the small increase in DM losses caused by LB alone. The 105 and 106 cfu/g rates were most effective at minimizing DM losses while aerobic stability was only increased with 105, 106, and ≥ 107 cfu/g rates. Inoculation with LBB increased acetate concentration, reduced yeast counts and improved aerobic stability but did not improve dairy cow performance.

Tropical plant supplementation effects on the performance and parasite burden of goats.

OBJECTIVE: Examine the effects of supplementing bahiagrass hay (BG) with potentially anthelmintic quantities of hays of perennial peanut (PEA) or sericea lespedeza (LES) or seeds of velvet bean (Mucuna pruriens L.; MUC) or papaya (PAP) on the intake and nutritive value (Experiment 1), and the performance and parasite burden (Experiment 2) of goats. METHODS: In Experiment 1, 38 male goats (27.4±5.7 kg body weight) were randomly assigned to each of 5 treatments: i) BG alone and BG plus; ii) PEA; iii) LES; iv) MUC; and v) PAP. Goats were fed for ad libitum consumption and adapted to the diets for 14 d followed by 7 d of measurement. The PEA, LES, MUC (50%, 50%, and 10% of the diet dry matter [DM], respectively), and PAP (forced-fed at 10 g/d) were fed at rates that would elicit anthelmintic effects. In Experiment 2, goats remained in the same treatments but were allocated to 15 pens (3 pens per treatment) from d 22 to 63. All goats were infected with parasites by grazing an infected bahiagrass pasture from 0800 to 1500 h daily and then returned to the pens. RESULTS: Dry matter intake tended to be greater in goats fed PEA and LES than those fed BG (757 and 745 vs 612 g/d, respectively). Digestibility of DM (59.5% vs 54.9%) and organic matter (60.8% vs 56.0%) were greater in goats fed MUC vs BG, respectively. In Experiment 2, feeding PAP, LES, and PEA to goats reduced nematode fecal egg counts by 72%, 52%, and 32%, reduced abomasal adult worm counts by 78%, 52%, and 42%, and decreased plasma haptoglobin concentrations by 42%, 40%, and 45% relative to feeding BG alone, respectively. CONCLUSION: Supplementation with PEA, LES, and PAP decreased the parasite burden of goats but did not increase their performance. PAP was the most effective anthelmintic supplement.

Meta-analysis of effects of inoculation with homofermentative and facultative heterofermentative lactic acid bacteria on silage fermentation, aerobic stability, and the performance of dairy cows.

Forages are usually inoculated with homofermentative and facultative heterofermentative lactic acid bacteria (LAB) to enhance lactic acid fermentation of forages, but effects of such inoculants on silage quality and the performance of dairy cows are unclear. Therefore, we conducted a meta-analysis to examine the effects of LAB inoculation on silage quality and preservation and the performance of dairy cows. A second objective was to examine the factors affecting the response to silage inoculation with LAB. The studies that met the selection criteria included 130 articles that examined the effects of LAB inoculation on silage quality and 31 articles that investigated dairy cow performance responses. The magnitude of the effect (effect size) was evaluated using raw mean differences (RMD) between inoculated and uninoculated treatments. Heterogeneity was explored by meta-regression and subgroup analysis using forage type, LAB species, LAB application rate, and silo scale (laboratory or farm-scale) as covariates for the silage quality response and forage type, LAB species, diet type [total mixed ration (TMR) or non-TMR], and the level of milk yield of the control cows as covariates for the performance responses. Inoculation with LAB (≥105 cfu/g as fed) markedly increased silage fermentation and dry matter recovery in temperate and tropical grasses, alfalfa, and other legumes. However, inoculation did not improve the fermentation of corn, sorghum, or sugarcane silages. Inoculation with LAB reduced clostridia and mold growth, butyric acid production, and ammonia-nitrogen in all silages, but it had no effect on aerobic stability. Silage inoculation (≥105 cfu/g as fed) increased milk yield and the response had low heterogeneity. However, inoculation had no effect on diet digestibility and feed efficiency. Inoculation with LAB improved the fermentation of grass and legume silages and the performance of dairy cows but did not affect the fermentation of corn, sorghum, and sugar cane silages or the aerobic stability of any silage. Further research is needed to elucidate how silage inoculated with homofermentative and facultative heterofermentative LAB improves the performance of dairy cows.

Effects of dietary supplementation of a blend of Saccharomyces cerevisiae, multiple live probiotic bacteria, and their fermentation products on performance, health, and rumen bacterial community of newly weaned beef steers during a 56-d receiving period.

We examined the effects of a blend of Saccharomyces cerevisiae, multiple live probiotic bacteria, and their fermentation products on performance, health, and the ruminal bacterial community of newly weaned beef steers during a 56-d receiving period. Forty newly weaned Angus crossbred steers (221 ±â€…25.6 kg BW; 180 ±â€…17 d of age) were stratified by body weight (BW) into four pens (10 steers per pen) such that each pen had a similar average BW at the beginning of the experiment. The pens were randomly assigned to receive a corn silage basal diet (CON; n = 20) or the basal diet supplemented with 9 g/steer/d of PRO feed additive (PRO; n = 20). The PRO additive is a blend of S. cerevisiae and the fermentation products of Enterococcus faecium, Bacillus licheniformis, B. subtilis, Lactobacillus animalis, and Propionibacterium freudenreichii. The DMI and water consumed were monitored using the GrowSafe intake nodes and custom flow meters, respectively. BWs were recorded weekly to calculate average daily gain (ADG). Before morning feeding, 10 mL of blood was taken from each steer on days 0-7, and thereafter weekly for analyses of immune cells, plasma glucose, and NEFAs. On day 56, rumen fluid samples (200 mL each) were collected from all the steers for microbiome analysis. Over the 56-d receiving period, the supplemental PRO had no effects on DMI, water intake, or ADG. However, compared to CON, beef steers fed supplemental PRO tended to have greater ADG (P = 0.08) and BW (P = 0.07) during the first 14 d of the study. There was a treatment × day interaction (P ≤ 0.05) for WBC, neutrophils and monocytes over the 56 d such that beef steers fed supplemental PRO had lower blood concentrations on certain days during the first 7 d after weaning, indicating reduced inflammation or stress response. The results of the rumen microbiome analysis revealed that the relative abundance of complex fiber degrading or obligate proton-reducing bacterial genera such as Bacteroides, Ruminococcus gauvreauii group, Desulfovibrio, Syntrophococcus, and Acetitomaculum were greater (P ≤ 0.05) in beef steers fed supplemental PRO compared to CON. This study demonstrated that dietary supplementation of PRO improved the growth performance, reduced stress or inflammatory response during the initial days after weaning, and altered the ruminal bacterial community toward increased relative abundance of bacterial genera associated with improved rumen function.

Effects of rumen-bypass protein supplement on growth performance, hepatic mitochondrial protein complexes, and hepatic immune gene expression of beef steers with divergent residual feed intake.

We investigated the impact of a rumen-bypass protein (RBP) supplement on growth performance, plasma and urinary N (UN) concentration, hepatic mitochondrial protein complexes, and hepatic mRNA expression of immune genes of beef steers with negative or positive residual feed intake (RFI) phenotype. Forty crossbred beef steers with an average body weight (BW) of 492 ± 36 kg were subjected to a generalized randomized block design over a 42-day experimental period. This study followed a 2 × 2 factorial arrangement of treatments. The factors evaluated were: 1) RFI classification (low-RFI (-2.12 kg/d) vs. high-RFI (2.02 kg/d), and 2) rumen-bypass protein supplement: RBP supplement (RBP; 227 g/steer/d) vs. control diet (CON; 0 g/d), resulting in four distinct treatments: LRFI-CON (n = 10), LRFI-RBP (n = 10), HRFI-CON (n = 10), and HRFI-RBP (n = 10). The RBP supplement (84% crude protein) is a mixture of hydrolyzed feather meal, porcine blood meal, and DL-methionine hydroxy analogue. The beef steers were stratified by BW, randomly assigned to treatments, and housed in four pens (1 treatment/pen) equipped with two GrowSafe feed bunks each to measure individual dry mater intake (DMI). Body weight was measured every 7 d. Liver tissue samples were collected on d 42 from all the beef steers. These samples were used for mRNA expression analysis of 16 immune-related genes and for evaluating the mitochondrial protein complexes I - V. No significant effects due to RBP supplementation or RFI × RBP interactions (P > 0.05) were observed for average daily gain (ADG) and DMI. However, compared to high-RFI steers, low-RFI steers showed a trend towards reduced DMI (12.9 vs. 13.6 kg/d; P = 0.07) but ADG was similar for the two RFI groups. Regardless of RFI status, supplemental RBP increased blood urea nitrogen (BUN) (P = 0.01), with a lower BUN concentration in low-RFI steers compared to high-RFI ones. A tendency for interaction (P = 0.07) between RFI and RBP was detected for the UN concentrations; feeding the dietary RBP increased the UN concentration in high-RFI beef steers (209 vs. 124 mM), whereas the concentration was lower than that of the CON group for low-RFI beef steers (86 vs. 131 mM). Interactions of RBP and RFI were observed (P ≤ 0.05) for mitochondrial activities of complexes IV, V, and mRNA expressions of some immune genes such as TLR2, TLR3, and IL23A. In conclusion, while RBP supplementation did not alter growth performance, its observed effects on hepatic immune gene expression, mitochondrial protein complexes, BUN, and UN depended on the beef steers' RFI phenotype. Therefore, the RFI status of beef steers should be considered in future studies evaluating the effects of dietary protein supplements.

A multi-species direct-fed microbial supplement alters the milk lipidome of dairy cows.

The study evaluated the effects of supplementing a multi-species direct-fed microbial (DFM) on the milk lipidome of lactating dairy cows. Twenty-four multiparous Holstein cows (41 ± 7 d in milk) were used in a randomized complete block design with experimental duration of 91 d. Cows were blocked based on energy-corrected milk yield from a 14-d pretreatment period, and were assigned randomly within each block to the following treatments: (1) control (CON): corn silage-based total mixed ration without DFM; or (2) BOV+: basal diet top-dressed with a DFM containing a mixture of Lactobacillus animalis (LA-51), Propionibacterium freudenreichii (PF-24), Bacillus subtilis (CH201), and Bacillus licheniformis (CH200) at 11.8 × 109 cfu/d. Milk samples were taken from morning and evening milkings on 2 consecutive days of each week of the pretreatment and treatment periods. Separate composites of pretreatment period and treatment period samples were prepared for individual cows and used for lipidome analysis. Lipidome analysis of the milk samples was performed using an ultra-high-performance liquid chromatograph linked to a quadrupole time-of-flight mass spectrometer in both positive and negative ionizations. The relative concentrations of 14 lipid species, including long-chain polyunsaturated fatty acids (LC-PUFA) such as FA 20:8 and FA 28:7 and triacylglycerides (TG) such as TG 40:3 and TG 54:2, were increased [false discovery rate (FDR) ≤0.05], whereas 13 lipid species, including saturated FA 24:0 and TG 40:0 were decreased (FDR ≤0.05) by supplemental BOV+. The relative concentration of de novo FA in milk was greater, whereas that of preformed FA was lower in dairy cows supplemented with BOV+. Results from this study demonstrate the potential of a DFM containing L. animalis, P. freudenreichii, Bacillus subtilis, and B. licheniformis to alter the milk lipidome in lactating dairy cows toward increased relative concentration of LC-PUFA, which might offer a healthier profile of FA to consumers with its associated health benefits.

Effects of bovine respiratory disease on the plasma metabolome of beef steers during the receiving period.

The study aimed to investigate the impact of Bovine Respiratory Disease (BRD) on the metabolism of beef steers during a 35-d receiving period using plasma metabolomics. In this study, 77 newly weaned crossbred (Angus × Hereford) beef steers (BW = 206 ± 12 kg and age = 180 ± 17 days) were categorized into two groups: Healthy and Sick groups. The Sick group comprised beef steers diagnosed with BRD at any time during the 35-day period (n = 31), while the Healthy group did not show any signs of BRD (n = 46). Blood samples were collected from the coccygeal vessels on day 35, and plasma samples were subjected to targeted metabolomics analysis using Nuclear Magnetic Resonance spectroscopy. Data and statistical analyses, including biomarker and pathway enrichment analyses, were performed using Metaboanalyst 5.0. Results of the growth performance showed that sick steers had lower (p ≤ 0.05) ADG (1.44 vs. 1.64 kg/d) and higher (p = 0.01) feed:gain ratio (3.57 vs. 3.13) compared to healthy steers. A total of 50 metabolites were quantified. The partial least squares discriminant scores plot showed a slight separation between the two groups of steers, indicating some metabolic differences. Furthermore, the plasma concentrations of four metabolites (sarcosine, methionine, dimethyl sulfone, and L-histidine) were greater (p ≤ 0.05) in healthy steers compared to sick steers. Among these metabolites, sarcosine and methionine qualified as candidate biomarkers associated with BRD infection based on an area under the curve >0.70. Additionally, quantitative enrichment analysis revealed that cysteine and methionine metabolism was enriched in healthy steers compared to sick steers. This suggests that these metabolic pathways may play a role in the response to BRD infection. The findings of this study highlight the altered plasma metabolome in steers with BRD during the receiving period. Understanding these metabolic changes can contribute to the development of effective management strategies and nutritional interventions to mitigate the negative impact of BRD on beef cattle health and immune function.

The differential plasma and ruminal metabolic pathways and ruminal bacterial taxa associated with divergent residual body weight gain phenotype in crossbred beef steers.

We applied ruminal and plasma metabolomics and ruminal 16S rRNA gene sequencing to determine the metabolic pathways and ruminal bacterial taxa associated with divergent residual body weight gain phenotype in crossbred beef steers. A group of 108 crossbred growing beef steers (average BW = 282.87 ± 30 kg) were fed a forage-based diet for a period of 56 d in a confinement dry lot equipped with GrowSafe intake nodes to determine their residual body weight gain (RADG) phenotype. After RADG identification, blood and rumen fluid samples were collected from beef steers with the highest RADG (most efficient; n = 16; 0.76 kg/d) and lowest RADG (least efficient; n = 16; -0.65 kg/d). Quantitative untargeted metabolome analysis of the plasma and rumen fluid samples were conducted using chemical isotope labelling/liquid chromatography-mass spectrometry. Differentially abundant metabolites in each of the plasma and rumen fluid samples between the two groups of beef steers were determined using a false discovery rate (FDR)-adjusted P-values ≤ 0.05 and area under the curve (AUC) > 0.80. Rumen and plasma metabolic pathways that were differentially enriched or depleted (P ≤ 0.05) in beef steers with positive RADG compared to those with negative RADG were determined by the quantitative pathway enrichment analysis. A total of 1,629 metabolites were detected and identified in the plasma of the beef steers; eight metabolites including alanyl-phenylalanine, 8-hydroxyguanosine, and slaframine were differentially abundant (FDR ≤ 0.05; AUC > 0.80) in beef steers with divergent RADG; five metabolic pathways including steroid hormone biosynthesis, thiamine metabolism, propanoate metabolism, pentose phosphate pathway, and butanoate metabolism were enriched (P ≤ 0.05) in beef steers with positive RADG, relative to negative RADG steers. A total of 1,908 metabolites were detected and identified in the rumen of the beef steers; results of the pathway enrichment analysis of all the metabolites revealed no metabolic pathways in the rumen were altered (P > 0.05). The rumen fluid samples were also analyzed using 16S rRNA gene sequencing to assess the bacterial community composition. We compared the rumen bacterial community composition at the genus level using a linear discriminant analysis effect size (LEfSe) to identify the differentially abundant taxa between the two groups of beef steers. The LEfSe results showed greater relative abundance of Bacteroidetes_vadinHA17 and Anaerovibrio in steers with positive RADG compared to the negative RADG group, while steers in the negative RADG group had greater relative abundance of Candidatus_Amoebophilus, Clostridium_sensu_stricto_1, Pseudomonas, Empedobacter, Enterobacter, and Klebsiella compared to the positive RADG group. Our results demonstrate that beef steers with positive or negative RADG exhibit differences in plasma metabolic profiles and some ruminal bacterial taxa which probably explain their divergent feed efficiency phenotypes.

Meta-analysis of the effects of the dietary application of exogenous alpha-amylase preparations on performance, nutrient digestibility, and rumen fermentation of lactating dairy cows.

Several studies have evaluated the effects of the dietary application of exogenous alpha-amylase preparations (AMA) as a strategy to increase total tract starch digestibility (TTSD) and milk yield (MY) in dairy cows, but the results have been inconsistent. Thus, the objective of this study was to evaluate the effects of the dietary application of AMA on the performance, digestibility, and rumen fermentation of lactating dairy cows using a meta-analytic method. A total of 18 peer-reviewed manuscripts (N = 32 treatment comparisons) from 2003 to 2019 were systematically identified following the PRISMA method. The weighted raw mean differences between dietary AMA and control treatments were compared with a robust variance estimation. Likewise, diet characteristics like crude protein (CP) content, NDF content, starch content, days in milk (DIM), experimental design (Latin square and continuous), and AMA dose (0 to 732 Kilo Novo units [KNU]/kg TMR) were used as covariates in a meta-regression, subgrouping, and dose-response analysis. Compared to the control, dietary AMA increased (P < 0.05) DM digestibility (69.32% vs. 68.30%), TTSD (94.62% vs. 94.10%), milk protein concentration and yield (3.11% vs. 3.08%; 1.14 vs. 1.10 kg/d) and tended to increase (P = 0.09) fat-corrected milk (35.96 vs. 35.10 kg/d), but no effects were observed on DM intake (22.99 vs. 22.90 kg/d) and feed efficiency (1.50 vs. 1.48). Dietary AMA tended (P = 0.10) to reduce rumen pH (6.27 vs. 6.30). Both the enzyme dose and DIM strongly influenced (P < 0.05) the effects of AMA on digestibility and performance. The dose-response analysis revealed that feeding 600 KNU/kg to high-producing early lactation (< 70 DIM) dairy cows increased FCM and milk protein. Accounting for the type of experimental design was associated with a lower between-studies-variance among comparisons. Overall, this meta-analysis supports the hypothesis that dietary AMA supplementation is associated with a better lactational performance in dairy cows. However, these effects are only suitable for high-producing early lactation dairy cows.

For more than a decade, starch-degrading enzymes (amylolytic enzymes) have been used as a strategy to increase total-tract starch degradation to increase milk yield of dairy cows. Therefore, we conducted a meta-analysis to evaluate the effectiveness of starch-degrading enzymes on starch digestion and milk yield in dairy cows. Collectively, results across the literature suggest that feeding starch-degrading enzymes increased the degradation of starch in the rumen of dairy cows and tended to increase milk yield. Our results suggest that starch-degrading enzymes could increase milk yield in high-producing early lactation dairy cows.

Identification of Key Pathways Associated With Residual Feed Intake of Beef Cattle Based on Whole Blood Transcriptome Data Analyzed Using Gene Set Enrichment Analysis.

We applied whole blood transcriptome analysis and gene set enrichment analysis to identify pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, whole blood samples were collected from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.

Effects of a multicomponent microbial feed additive containing prebiotics and probiotics on health, immune status, metabolism, and performance of newly weaned beef steers during a 35-d receiving period.

We examined the effects of dietary supplementation of a multicomponent blend of prebiotics and probiotics on health, immune status, metabolism, and performance of newly weaned beef steers during a 35-d receiving period. Eighty newly weaned crossbred steers (12-hour postweaning; 206 ± 12 kg of body weight [BW]) from a single source were stratified by BW into four pens (20 steers per pen) such that each pen had similar BW at the beginning of the experiment. The pens were randomly assigned to receive a corn silage-based diet with no additive (CON; two pens; n = 40 steers) or a basal diet supplemented with SYNB feed additive at an average of 28 g/steer/d (SYNB; two pens; n = 40 steers). The SYNB additive is a blend of live Saccharomyces cerevisiae and the fermentation products of S. cerevisiae, Enterococcus lactis, Bacillus licheniformis, and Bacillus subtilis and was supplemented for the first 21 d only. Percentage of steers treated for bovine respiratory disease (BRD) was calculated for each dietary treatment. Daily dry matter intake (DMI) and meal events (meal frequency and duration) were measured. Weekly BWs were measured to calculate average daily gain (ADG). Blood samples collected on days 0, 14, 21, 28, and 35 were used for ex-vivo tumor necrosis factor alpha (TNF-α) release assay following lipopolysaccharides (LPS) stimulation, plasma metabolome analysis, and mRNA expression analysis of 84 innate and adaptive immune-related genes. Compared with CON, supplemental SYNB increased (P ≤ 0.05) ADG, DMI, and meal events during the first 7 d. At d 21, there was no treatment effect (P > 0.05) on final BW, DMI, ADG, and meal events; however, beef steers fed supplemental SYNB had greater (P = 0.02) meal duration. Over the entire 35-d receiving period, beef steers fed supplemental SYNB had greater (P = 0.01) ADG and feed efficiency, tended to have greater (P = 0.08) meal duration, and had lower percentage (35 vs. 50%) of animals treated for BRD and lower percentage of sick animals treated for BRD more than once (7.15 vs. 45%). Whole blood expression of pro-inflammatory genes was downregulated while that of anti-inflammatory genes was upregulated in beef steers fed supplemental SYNB. Beef steers fed supplemental SYNB had lower (P = 0.03) plasma concentration of TNF-α after LPS stimulation. Six nutrient metabolic pathways associated with health benefits were enriched (false discovery rate ≤ 0.05) in beef steers fed supplemental SYNB. This study demonstrated that dietary supplementation of SYNB during the first 21 d of arrival reduced BRD morbidity, improved the performance, immune, and metabolic status of beef steers over a 35-d receiving period thereby extending the SYNB effect by a further 14 days post supplementation.

Dietary fenugreek seed extract improves dry matter intake, apparent total tract nutrient digestibility, and alters whole blood transcriptome of Holstein dairy heifers.

This study was conducted to evaluate the effects of dietary supplementation of a fenugreek seed extract (SAP) as a source of saponins on dry matter intake, blood metabolites, apparent total tract nutrient digestibility, and whole blood transcriptome of Holstein dairy heifers. Eight heifers (BW = 477 ± 23.8 kg) were stratified by BW and then randomly assigned to one of two treatments in a cross-over design with two 35-d experimental periods and a 14-d wash-out between the two periods. The heifers were housed individually in eight dry lot pens. Each pen was equipped with one GrowSafe intake node. Treatments were 1) corn silage-based diet with no additive (CON) and 2) corn silage-based diet plus 2 g per hd per d of SAP. Dairy heifers fed supplemental SAP had higher (P ≤ 0.05) DMI and apparent total tract digestibility of dry matter, crude protein, and neutral detergent fiber compared to CON. Dairy heifers fed supplemental SAP had lower (P = 0.03) blood urea nitrogen and higher (P = 0.01) blood glucose concentration compared to CON. Pathway analysis via gene set enrichment analysis revealed increased (FDR ≤ 0.05) transcript levels for gene sets belonging to ISG15 antiviral mechanism, metabolism of proteins, citric acid cycle and respiratory electron transport, ATP synthesis by chemiosmotic coupling, and complex I biogenesis in dairy heifers fed supplemental SAP compared to CON. Decreased (FDR ≤ 0.05) transcript levels for gene sets associated with erythrocytes take up/release carbon dioxide, release/take up oxygen, and O2/CO2 exchange in erythrocytes were also observed with SAP supplemental group. Taken together, our results revealed that fenugreek seed extract can be used as an effective dietary supplement for dairy heifers to improve intake and digestibility, and alter the host transcriptome toward improved energy and amino acid metabolism, improved antiviral immune status, and reduced oxidative stress damage.

Molecular Evolution and Inheritance Pattern of Sox Gene Family among Bovidae.

Sox genes are an evolutionarily conserved family of transcription factors that play important roles in cellular differentiation and numerous complex developmental processes. In vertebrates, Sox proteins are required for cell fate decisions, morphogenesis, and the control of self-renewal in embryonic and adult stem cells. The Sox gene family has been well-studied in multiple species including humans but there has been scanty or no research into Bovidae. In this study, we conducted a detailed evolutionary analysis of this gene family in Bovidae, including their physicochemical properties, biological functions, and patterns of inheritance. We performed a genome-wide cataloguing procedure to explore the Sox gene family using multiple bioinformatics tools. Our analysis revealed a significant inheritance pattern including conserved motifs that are critical to the ability of Sox proteins to interact with the regulatory regions of target genes and orchestrate multiple developmental and physiological processes. Importantly, we report an important conserved motif, EFDQYL/ELDQYL, found in the SoxE and SoxF groups but not in other Sox groups. Further analysis revealed that this motif sequence accounts for the binding and transactivation potential of Sox proteins. The degree of protein-protein interaction showed significant interactions among Sox genes and related genes implicated in embryonic development and the regulation of cell differentiation. We conclude that the Sox gene family uniquely evolved in Bovidae, with a few exhibiting important motifs that drive several developmental and physiological processes.

Aflatoxin in Dairy Cows: Toxicity, Occurrence in Feedstuffs and Milk and Dietary Mitigation Strategies.

Aflatoxins are poisonous carcinogens produced by fungi, mainly Aspergillus flavus and Aspergillus parasiticus. Aflatoxins can contaminate a variety of livestock feeds and cause enormous economic losses, estimated at between US$52.1 and US$1.68 billion annually for the U.S. corn industry alone. In addition, aflatoxin can be transferred from the diet to the milk of cows as aflatoxin M1 (AFM1), posing a significant human health hazard. In dairy cows, sheep and goats, chronic exposure to dietary aflatoxin can reduce milk production, impair reproduction and liver function, compromise immune function, and increase susceptibility to diseases; hence, strategies to lower aflatoxin contamination of feeds and to prevent or reduce the transfer of the toxin to milk are required for safeguarding animal and human health and improving the safety of dairy products and profitability of the dairy industry. This article provides an overview of the toxicity of aflatoxin to ruminant livestock, its occurrence in livestock feeds, and the effectiveness of different strategies for preventing and mitigating aflatoxin contamination of feeds.

Effects of Multi-Species Direct-Fed Microbial Products on Ruminal Metatranscriptome and Carboxyl-Metabolome of Beef Steers.

We examined the effects of two direct-fed microbial (DFM) products containing multiple microbial species and their fermentation products on ruminal metatranscriptome and carboxyl-metabolome of beef steers. Nine ruminally-cannulated Holstein steers were assigned to 3 treatments arranged in a 3 × 3 Latin square design with three 21-d periods. Dietary treatments were (1) Control (CON; basal diet without additive), (2) Commence (PROB; basal diet plus 19 g/d of Commence), and (3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both S. cerevisiae-based DFM products containing several microbial species and their fermentation products. Mixed ruminal contents collected multiple times after feeding on day 21 were used for metatranscriptome and carboxyl-metabolome analysis. Partial least squares discriminant analysis revealed a distinct transcriptionally active taxonomy profiles between CON and each of the PROB and SYNB samples. Compared to CON, the steers fed supplemental PROB had 3 differential (LDA ≥ 2.0; p ≤ 0.05) transcriptionally active taxa, none of which were at the species level, and those fed SYNB had eight differential (LDA > 2.0, p ≤ 0.05) transcriptionally active taxa, but there was no difference (p > 0.05) between PROB and SYNB. No functional microbial genes were differentially expressed among the treatments. Compared with CON, 3 metabolites (hydroxylpropionic acid and 2 isomers of propionic acid) were increased (FC ≥ 1.2, FDR ≤ 0.05), whereas 15 metabolites, including succinic acid and fatty acid peroxidation and amino acid degradation products were reduced (FC ≤ 0.83, FDR ≤ 0.05) by supplemental PROB. Compared with CON, 2 metabolites (2 isomers of propionic acid) were increased (FC ≥ 1.2, FDR ≤ 0.05), whereas 2 metabolites (succinic acid and pimelate) were reduced (FC ≤ 0.83, FDR ≤ 0.05) by supplemental SYNB. Compared to SYNB, supplemental PROB reduced (FC ≤ 0.83, FDR ≤ 0.05) the relative abundance of four fatty acid peroxidation products in the rumen. This study demonstrated that dietary supplementation with either PROB or SYNB altered the ruminal fermentation pattern. In addition, supplemental PROB reduced concentrations of metabolic products of fatty acid peroxidation and amino acid degradation. Future studies are needed to evaluate the significance of these alterations to ruminal fatty acid and amino acid metabolisms, and their influence on beef cattle performance.

Effects of a blend of mannan and glucan on growth performance, apparent nutrient digestibility, energy status, and whole-blood immune gene expression of beef steers during a 42-d receiving period.

We examined the effects of dietary supplementation of a blend of mannan and glucan on the growth performance, energy status, and whole-blood immune gene expression of newly weaned beef steers during a 42-d receiving period. Forty-eight newly weaned Angus crossbred steers (2-d post-weaning; 199 ± 13 kg of initial body weight [BW]) from a single source were stratified by BW and randomly assigned to one of the two treatments: basal diet with no additive (CON; n = 24) or a basal diet top-dressed with 5 g of a blend of mannan and glucan (MANGLU; n = 24). Average daily gain (ADG) and feed efficiency (FE) from days 1 to 14, 15 to 42, and 1 to 42 were calculated from daily dry matter intake (DMI) and weekly BW. Blood samples were collected on days 0, 14, and 42 for measurement of plasma glucose and nonesterified fatty acids (NEFA). Blood samples collected on days 14 and 42 were composited for each steer for untargeted carbonyl-metabolome analysis (measurement of carbonyl-containing metabolites). Expression of 84 immune-related genes was analyzed on blood samples collected on day 42. Beginning on days 37 to 42, total mixed ration, refusals, and fecal samples were collected once daily to determine apparent total tract digestibility of DM, CP, NDF, and ADF using indigestible NDF as an internal marker. Over the 42-d feeding trial, supplemental MANGLU tended to increase final BW (P = 0.07) and ADG (P = 0.06). Compared to CON, beef steers fed supplemental MANGLU had greater (P = 0.01) DMI during the first 14 d, greater DM digestibility (P = 0.03), and tended to have greater NDF digestibility (P = 0.09). No treatment effects (P > 0.10) on plasma glucose and NEFA on days 14 and 42 were detected; however, carbonyl-metabolome analysis revealed increased (FDR ≤ 0.05) plasma concentrations of galactose and glyceraldehydes, and altered (FDR ≤ 0.05) concentrations of some microbiome-derived metabolites in beef steers fed MANGLU. Compared with CON, MANGLU increased (P ≤ 0.05) the expression of five immune-related genes involved in recognition of and mounting immune defense against microbial pathogens. In conclusion, the results of this study demonstrated that supplemental MANGLU enhances beef cattle immunocompetence and productivity during feedlot receiving period.

Alteration of the Canine Metabolome After a 3-Week Supplementation of Cannabidiol (CBD) Containing Treats: An Exploratory Study of Healthy Animals.

Despite the increased interest and widespread use of cannabidiol (CBD) in humans and companion animals, much remains to be learned about its effects on health and physiology. Metabolomics is a useful tool to evaluate changes in the health status of animals and to analyze metabolic alterations caused by diet, disease, or other factors. Thus, the purpose of this investigation was to evaluate the impact of CBD supplementation on the canine plasma metabolome. Sixteen dogs (18.2 ± 3.4 kg BW) were utilized in a completely randomized design with treatments consisting of control and 4.5 mg CBD/kg BW/d. After 21 d of treatment, blood was collected ~2 h after treat consumption. Plasma collected from samples was analyzed using CIL/LC-MS-based untargeted metabolomics to analyze amine/phenol- and carbonyl-containing metabolites. Metabolites that differed - fold change (FC) ≥ 1.2 or ≤ 0.83 and false discovery ratio (FDR) ≤ 0.05 - between the two treatments were identified using a volcano plot. Biomarker analysis based on receiver operating characteristic (ROC) curves was performed to identify biomarker candidates (area under ROC ≥ 0.90) of the effects of CBD supplementation. Volcano plot analysis revealed that 32 amine/phenol-containing metabolites and five carbonyl-containing metabolites were differentially altered (FC ≥ 1.2 or ≤ 0.83, FDR ≤ 0.05) by CBD; these metabolites are involved in the metabolism of amino acids, glucose, vitamins, nucleotides, and hydroxycinnamic acid derivatives. Biomarker analysis identified 24 amine/phenol-containing metabolites and 1 carbonyl-containing metabolite as candidate biomarkers of the effects of CBD (area under ROC ≥ 0.90; P < 0.01). Results of this study indicate that 3 weeks of 4.5 mg CBD/kg BW/d supplementation altered the canine metabolome. Additional work is warranted to investigate the physiological relevance of these changes.