This study investigated plasma metabolic responses to microfused essential oil blend (MEO) supplementation and identified candidate biomarkers associated with growth performance in Katahdin ewes. Eighteen Katahdin ewes (26.34 kg) were randomly assigned to a basal diet (CON; n = 9) or the basal diet supplemented with 4 g/head/day of a microfused essential oil blend containing oregano (Origanum vulgare), cinnamon (Cinnamomum spp.), and white thyme (Thymus vulgaris) (MEO; n = 9) for 35 days. Growth performance was evaluated, and plasma metabolomic profiling was performed using chemical isotope labeling liquid chromatography–mass spectrometry. MEO supplementation increased final body weight, total weight gain, and average daily gain (ADG) while reducing feed:gain (p < 0.05). Untargeted metabolomics identified 12 differentially abundant metabolites (FDR < 0.05), predominantly showing lower circulating concentrations in MEO-supplemented ewes. Pathway analysis revealed significant enrichment of linoleic acid metabolism, α-linolenic acid metabolism, and biosynthesis of unsaturated fatty acids (p ≤ 0.05). Receiver operating characteristic (ROC) analysis identified four candidate plasma biomarkers: γ-amino-γ-cyanobutanoic acid, Nocardicin A/Isonocardicin A, 2-propylmalic acid, and isoleucine that discriminated MEO from CON ewes (AUC > 0.85), while a combined four-metabolite panel achieved an AUC of 0.943 (95% CI: 0.778 to 1.000). Correlation and regression analyses further identified γ-amino-γ-cyanobutanoic acid and isoleucine as independent predictors of ADG and feed efficiency. Microfused essential oil supplementation improved growth performance and induced coordinated remodeling of the plasma metabolome in Katahdin ewes. The identified metabolic pathways and candidate biomarkers provide mechanistic insight into the physiological responses to phytogenic supplementation and represent promising targets for monitoring nutritional interventions in sheep.

This study employed hepatic transcriptional changes to catalogue signature genes associated with divergent residual average daily gain (RADG) phenotypes in crossbred beef steers. A total of 108 crossbred beef steers (average body weight = 495 ± 32kg) were fed a high-forage total mixed ration for 49 d in five dry-lot pens equipped with GrowSafe8000 intake nodes to determine RADG. Steers were ranked based on RADG coefficients, and liver biopsies were collected under local anesthesia from the most efficient (positive RADG; n = 8; 0.73 kg/d) and least efficient (negative RADG; n = 8; −0.69 kg/d) animals. Differential gene expression analysis identified a total of 16,735 genes, based on FDR ≤ 0.05 and an absolute log2 fold change (|log2FC|) ≥ 1.0, 6 genes were upregulated in positive-RADG steers, including COL2A1, IL32, FBLN2 and MR1, while 9 genes, including SMO, ABCB4 and RPS3A were downregulated. Gene Ontology enrichment indicated that positive RADG steers exhibited over-representation of biological processes related to regulation of extrinsic apoptotic signaling, DNA-dependent DNA replication, signal transduction in the absence of ligand, and transmembrane transport. Enriched cellular components included the sarcolemma, while enriched molecular functions were associated with carbohydrate transmembrane transporter activity, monosaccharide binding, and antioxidant activity. In contrast, negative RADG steers showed enrichment of biological processes related to immune activation, stress responsiveness, and regulation of ossification. Gene Ontology gene network analysis highlighted COL2A1, E2F8, SLC2A5, and GZMA as highly connected nodes within interaction networks derived from DEGs in positive RADG steers. Pathway enrichment analysis further identified pathways associated with protein digestion and absorption, cytoskeletal organization in muscle cells, and carbohydrate digestion and absorption as over-represented in positive RADG steers. Collectively, these findings describe hepatic transcriptional signatures associated with divergent RADG phenotypes and provide candidate genes and pathways for future studies aimed at functionally validating mechanisms underlying feed efficiency in beef cattle.

This study characterized the peripheral blood mononuclear cell (PBMC) transcriptomic responses to in vitro lipopolysaccharide (LPS) stimulation in beef steers with divergent residual average daily gain (RADG), a residual-based index of feed efficiency. Positive-RADG (n = 6; RADG = +0.53 kg/d) and negative-RADG (n = 6; RADG = −0.46 kg/d) crossbred steers were selected from a cohort of 41 steers (average body weight = 384 ± 5.8 kg) following a 50-d performance testing period on a high-forage total mixed ration. PBMCs were isolated from positive-RADG and negative-RADG steers and assigned to LPS stimulation (20 μg/mL for 2 hours) or untreated control. RNA was extracted, sequenced and differentially expressed genes (DEGs; FDR ≤ 0.01, |log2FC| ≥ 1) were identified by comparison with unstimulated controls. Gene ontology (GO) enrichment analysis was performed to characterize associated biological processes (P < 0.05). Prior to LPS stimulation, one DEG was identified between RADG groups, indicating near-equivalent baseline PBMC transcriptomes. Following stimulation, 2,739 DEGs were identified in positive-RADG steers (1,484 upregulated; 1,255 downregulated), and 3,299 DEGs in negative-RADG steers (1,555 upregulated; 1,744 downregulated). GO enrichment analysis revealed activation of canonical innate immune pathways in both groups, including cytokine production, positive regulation of IL-1 and IL-1β production, and immune response. However, positive-RADG steers exhibited a broader cytokine network enrichment profile, with the highest enrichment score for positive regulation of cytokine production, encompassing genes involved in effector activation, leukocyte trafficking, and inflammatory resolution, including NOS2, STAT3, PTX3, TGFB1, and SOD1. In contrast, negative-RADG steers exhibited disproportionate enrichment of IL-1β- and IL-6-centered inflammatory pathways, with SAA3 as the most highly upregulated DEG (log2FC = 9.18 vs. 6.80 in positive-RADG steers), consistent with a more pronounced acute-phase transcriptional response. These findings demonstrate that while RADG-divergent steers share conserved LPS-responsive signaling pathways, they differ in the architecture of their immune transcriptional responses. The broader, more integrated cytokine network activation in positive-RADG steers, compared with the concentrated IL-1β/IL-6-driven inflammatory signature in negative-RADG steers, suggests that superior feed efficiency is associated with a more coordinated immunoregulatory capacity that may reduce the energetic cost of innate immune activation and facilitate return to metabolic homeostasis.

Background/Objectives: Direct-fed microbials (DFMs) are widely used in dairy calves to improve gut health and mitigate neonatal disorders, yet their systemic metabolic effects remain poorly defined. This study evaluated the impact of DFM supplementation on the plasma metabolome of pre-weaned dairy calves using untargeted liquid chromatography–mass spectrometry (LC–MS). Methods: Eighty-six Holstein bull calves (2 to 5 days old) were assigned to one of four treatments in a 2 × 2 factorial randomized complete block design: Lactobacillus plantarum in starter (CLP), a culture mix of Bifidobacterium animalis and Lactobacillus animalis in milk replacer (BBCM), and a combination of both (CMLP), or no supplementation (CON). Blood samples collected on days 0 and 56 were subjected to metabolomic profiling, and metabolites were annotated using Human Metabolome Database and Kyoto Encyclopedia of Genes and Genomes databases. Results: A total of 231 plasma metabolites were detected. Compared with CON, 24 metabolites were differentially abundant in DFM-treated calves (fold change ≥ 1.2 or ≤ 0.83; p ≤ 0.05). Supplemented calves exhibited increased abundances of ketone functional groups, aldehydes and amino acid-related metabolites. Metabolite set enrichment analysis identified 11 significantly enriched pathways. Branched-chain amino acid degradation pathways (valine, leucine, and isoleucine) were enriched in CLP and CMLP calves, whereas carbohydrate metabolism pathways, including pentose and glucuronate interconversions, were enriched in the CLP and BBCM groups. Conclusions: These findings demonstrate that DFM supplementation modulates systemic metabolism in dairy calves, particularly pathways involved in amino acid and carbohydrate utilization, suggesting enhanced metabolic efficiency during early life.

This study evaluated for the first time the effects of H. contortus infection on hematological and parasitological parameters, as well as on the composition, metabolomic, and lipidomic profiles of colostrum in periparturient Florida Cracker ewes. Twenty pregnant Florida Cracker ewes were allocated to infected (INF, n = 10) or control (CTL, n = 10) groups at 90 days of pregnancy. Then, at 120 days of gestation, the INF group received an oral dose of 10,000 L3 H. contortus larvae, while the CTL group received 3 mL of distilled water. Fecal egg counts (FEC) and FAMACHA scoring were performed before infection (−1 h), and at 7-, 14-, 21-, 28- and 35- days post-infection (pi). Blood was collected by jugular venipuncture before infection (−1 h) and at 3-, and 6-h, and at 7-, 14-, 21- and 28-days pi from all ewes for full hematology analysis. Colostrum samples were collected at lambing from each ewe. The FEC data was log transformed [log10(FEC + 100)] for analysis (LFEC). A mixed-effects model with repeated measures was used to analyze the hematological and parasitological data. Colostrum chemical composition was analyzed using a t-test, while metabolomic and lipidomic data were processed using MetaboAnalyst 5.0. Parasitological analysis revealed significant differences for LFEC and FAMCHA score, at 21-, 28- and 35-days pi and at 14–21-, 28- and 35-days pi, respectively. For hematological data, significant differences (p ≤ 0.05) were observed for white blood cell count (WBC), lymphocyte count (LYM), neutrophil count (NEU), monocyte count (MON) and mean corpuscular volume (MCV). No significant differences were observed for the chemical composition of colostrum. For colostrum metabolomics, 23 differentially abundant metabolites (p ≤ 0.05, FC ≥ 1.5 or ≤ 0.67) were observed between the experimental groups. Lipidome analysis identified 4,702 lipid species in the colostrum samples. Biomarker analysis identified 3 lipid species (FA 15:1; O, MG 20:5, PE 41:6) as potential biomarkers between the INF and CTL groups. These lipids support cellular integrity and energy biogenesis. These findings highlight the impact of H. contortus infections on colostrum composition in Florida Cracker ewes, suggesting the need for further research to understand how these changes impact the metabolism and performance of lambs.

This study investigates different physical responses of St. Croix (STC) and Suffolk (SUF) sheep in response to lipopolysaccharide (LPS) challenge. Through a multidisciplinary approach encompassing physiological, immunological, and metabolic analyses, we aim to explore the mechanisms underlying disease susceptibility and resilience in small ruminants. Sheep were intravenously administered LPS at a dose of 2.5 mu g/kg; blood and body temperature data were collected hourly. Behavioral observations were recorded during sampling and videos within pens were obtained 30 min after blood collection. An increase of body temperature by 1 degrees C was observed in all groups (P >= 0.05). Significant variances were observed in leukocyte and neutrophil counts, wherein STC sheep displayed elevated cell concentrations compared to SUF sheep from 6 h following LPS injection until the conclusion of the sampling period (P <= 0.05). Additionally, SUF sheep exhibited greater hemolysis to acute LPS injury, as evidenced by higher optical density at 540 nm (P = 0.02). Behavioral assessment revealed a more pronounced grimace response in SUF sheep following LPS exposure, with an average sheep grimace score (SGS) of 2.67 compared to 1.25 in STC sheep (P < 0.0001). Metabolomic analysis demonstrated significant alterations in serum metabolite profiles between the two breeds, with 28 metabolites showing differential abundance (FDR <= 0.05). These findings contribute to a better understanding of host immunity and offer insights for targeted interventions to enhance disease resistance in small ruminants.

This study aimed to investigate breed-specific differences in the liver transcriptomic response to lipopolysaccharide (LPS) in St. Croix (STC) and Suffolk (SUF) sheep. A total of 18 sheep (9 STC and 9 SUF) were administered LPS (E. coli O111), at a dosage of 2.5 mg/kg via I.V. After euthanasia, liver samples were collected at three time points: HR0 (n = 3 per breed; no LPS), HR2 (n = 3 per breed; 2 hours after LPS), and HR6 (n = 3 per breed; 6 hours after LPS). RNA sequencing and pathway enrichment analysis were conducted to assess differentially expressed genes (DEG; FDR ≤ 0.05) and associated biological processes. At baseline (HR0), 141 DEGs were identified between STC and SUF. SUF sheep upregulated pathways related to immune readiness, including defense responses and innate immune responses. At HR2, STC had 1,719 DEGs with top upregulated genes including SELE and CCL20. Alternatively, SUF had 2,742 DEGs at HR2, with similar immune response genes expressed but at lower magnitudes. At HR6, STC had a significant shift in gene expression, with 5,568 DEGs. Notably, STC shifted from immunity-related pathways to metabolic processes. In contrast, SUF had 5,862 DEGs at HR6, continuing to express pathways related to cytokine signaling and cellular responses. Overall, STC exhibited a more intense initial response to LPS, followed by a shift towards increased differential expression of genes associated with metabolism rather than immunity. SUF, however, maintained heightened immune activity even after 6 hours, suggesting a less effective resolution of the LPS-induced challenge.

The study aimed to investigate the effects of short-term heat stress on physiological, hematological, immunological, and metabolomic responses in Florida Cracker ewes. Fourteen Florida Cracker ewes were randomly assigned to either heat stress (HT) or cooling (control, CTL) conditions, respectively, for a duration of six weeks during the summer season. Ambient temperature and relative humidity data for HT and CTL ewes were recorded weekly to estimate temperature humidity index (THI). Respiration rate and rectal temperature were measured for each experimental ewe. Blood samples were collected from each ewe at baseline (week 0) and at week 1, 2, 3, 4, 5 and 6 post-exposure for hematology analysis and plasma extraction. Plasma samples were used for analysis of IgA level and to conduct targeted metabolomics. Targeted metabolomics analyzed a total of 50 metabolites, including organic acids, amino acids, hexoses, lipids, and carnitines. The THI for the HT and CTL groups ranged from 81.3 – 89.5 and from 73.5 – 75.6, respectively. The HT group exhibited a significant increase (P < 0.05) in respiratory rate compared to the CTL group. No significant changes were observed in rectal temperature or IgA levels between the experimental groups. Hematology analysis revealed a significant increase (P < 0.05) in neutrophil count and neutrophil percentage (%) and a decrease in lymphocyte percentage (%) at week 3 in the HT group. Targeted metabolomics analysis identified 19 differentially abundant metabolites between the HT and CTL groups. Pathway enrichment analysis showed upregulation of fatty acid biosynthesis, glutathione metabolism, primary bile biosynthesis, porphyrin metabolism, and glycine, serine, and threonine metabolism (P ≤ 0.05) in the HT group compared to CTL. Our findings highlight that short-term heat stress alters the immunological, hematological, and metabolomic profile of Florida Cracker ewes. Understanding these changes can contribute to developing effective management strategies to mitigate the detrimental impact of heat stress on sheep operations in the southern U.S.

Objective: Our objective was to examine the differences in the whole blood mRNA expression profiles of immune-related genes in Angus bulls with either negative or positive residual feed intake expected progeny differences (RFI-EPD). Materials and Methods: Twenty Angus bulls with the most negative (n = 10; RFI-EPD = -0.29) and most positive (n = 10; RFI-EPD = 0.26) RFI-EPD values were selected from a group of 106 Angus bulls (average BW = 376 f 36 kg; 370 f 1.3 d of age) after a 78-d feed efficiency testing period. At the end of this testing period, blood samples were collected for RNA extraction followed by the mRNA expression analysis of 84 genes involved in innate and adaptive immunity using pathway-focused PCR-based arrays. Differentially expressed genes (DEG) were determined using false discovery rate (FDR) <0.10. Results and Discussion: Results from the analysis revealed a total of 5 DEG (FDR <0.10) in bulls with divergent RFI-EPD values. We found IL23A to be up-regulated, whereas IL18, TRAF6, TLR2, and MX1 were downregulated in negative RFI-EPD bulls, compared with the positive group. Gene ontology analysis of the DEG indicated the enrichment of different biological pathways linked to innate immune response, NF-kappa B signaling, cytokine and T cell regulation, lipopolysaccharide-mediated signaling pathway, and cellular response to bacteria. Implications and Applications: These findings revealed that negative RFI-EPD bulls exhibit mRNA expression of genes directly related to immune cell function and biological pathways involved in the activation of antimicrobial mechanisms, pathogen recognition mechanisms, and inflammatory response.

Florida Cracker sheep is a heritage sheep breed developed under natural selection in Florida, US. This breed is parasite resistant and can tolerate high environmental heat and humidity. The objective of this study was to evaluate the effect of heat stress on the transcriptomic profile of Florida Cracker sheep. A total of fourteen ewes were allocated to heat stress (HT, n = 7) or cooling (CTL, n = 7) conditions for six weeks in the summer season. Treatment groups were grouped in concrete floor pens with similar dimensions and characteristics. The HT pen was exposed to regular ambient temperatures and had access to shelter, feed, and freshwater ad libitum. For the cooling pen, an evaporative cooling fan was used. Data for ambient temperature and relative humidity of HT and CTL pens was recorded on a weekly basis to estimate the temperature humidity index (THI). Blood samples were collected from each experimental ewe by jugular venipuncture using EDTA vacutainer tubes at week 1, 3 and 6. Right after blood collection, an aliquot of 500 uL from each sample was transferred to a RNAprotect Animal Blood Tube (Qiagen, Redwood City, CA). RNA was extracted using RNeasy Protect Animal Blood Kit (Qiagen, Redwood City, CA). RNA Libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (Human, Mouse, Rat) Globin Reduction method (Roche Diagnostics, Basel, Switzerland). RNA-Sequencing was done using an Illumina NovaSeq 6000 platform. Raw fastq data were filtered by removing low-quality reads (Qscore ≤ 5) using fastqc. DESeq2 was employed to compare gene expression at week 1, 3 and 6. Differentially expressed genes (DEGs) were identified based on a False Discovery Rate (FDR) ≤ 0.05. Pathway and functional enrichment analysis of the DEGs was conducted using the SR-plot platform. Differential expression analysis between HT and CTL groups revealed a total of 47 DEGs at week 1, followed by 24 DEGs at week 3, and 4 DEGs (GBP2, GSTT1, ITGB5 and ENSBTAG00000037634 genes) at week 6. In week 1, significant pathway alterations included immune response (both inflammatory and innate), leukocyte cell adhesion, positive regulation of proteolysis, and positive regulation of cysteine-type endopeptidase activity. In week 3, pathways related to amide and peptide metabolism, organonitrogen compound synthesis, positive regulation of cell cycle arrest, and regulation of signal transduction by p53 class mediators were enriched. In week 6, the four DEGs were involved in cell adhesion signaling, detoxification of endogenous and exogenous electrophilic compounds, and the metabolism of compounds formed during oxidative stress. Our results evidence the ability of Florida Cracker sheep to adapt to heat stress in the summer season. More studies are needed to understand the adaptation mechanisms of this thermotolerant sheep breed.

Immunometabolic traits are increasingly recognized as key determinants of feed efficiency and resilience in beef cattle. This study aimed to identify functional genetic markers associated with these traits by integrating SNP genotyping and gene expression profiling. We evaluated genetic markers for feed efficiency and immunocompetence in 102 crossbred steers (217 ± 8.2 kg) fed a high-forage total mixed ration for 63 days, using GrowSafe8000 intake nodes to calculate residual feed intake (RFI). From the 20 most efficient (low-RFI) and 20 least efficient (high-RFI) animals, we genotyped three metabolic loci (CYP3A4 rs438103222, PLB1 rs456635825, CRAT rs876019788) and profiled blood mRNA levels of these, plus eight innate/adaptive immune genes. Logistic regression revealed that CYP3A4 and PLB1 polymorphisms, but not CRAT, were strongly associated with initial and final body weight, average daily gain, and feed intake: CYP3A4 A/A and PLB1 A-allele carriers achieved superior growth on reduced feed. Haplotype reconstruction across the three loci defined eight multi-SNP combinations, with the C-A-A haplotype enriched in low-RFI steers and combinations harboring CYP3A4 A and PLB1 A alleles linked to low RFI. Intriguingly, these favorable genotypes also overlapped with up-regulation of immune sensors and effectors (e.g., CD14, TLR4, TNF-α), indicating a coordinated metabolic–immune adaptation in efficient cattle. Collectively, our results validate CYP3A4 and PLB1 as high-impact quantitative trait nucleotides for marker-assisted selection aimed at simultaneously improving feed efficiency and immune resilience in beef production.

A 14-day study was conducted to evaluate the effect of litter type (dirty litter, DL; fresh litter, FL) and Salmonella Enteritidis SE challenge (no challenge, NC; challenge, SE) on the growth performance and cecal microbial composition of neonate chicks. Day-old chicks (n = 240, Ross 708 male) were allocated to a 2 × 2 factorial design consisting of four treatments: chicks raised on dirty litter (CONDL), chicks raised on fresh litter (CONFL); and chicks raised on litter types similar to CONDL and CONFL but inoculated with 7.46 × 108 CFU SE/mL at d 1 (CONDLSE and CONFLSE). The performance indices measured included body weight (BW), body weight gain (BWG), feed intake (FI), mortality, and feed conversion ratio (FCR). Cecal SE concentration was assessed on d 3 and 14, and ceca were collected from chicks on day 14 for DNA extraction. The Illumina Miseq platform was used for microbiome analysis of the V3-V4 region of the 16S rRNA gene. The interaction of litter type and SE influenced FCR and FI. CONDL recorded the poorest FCR (1.832). FI was highest and similar in CONFLSE, CONDL, and CONDLSE (0.655, 0.692, and 0.677, respectively). Cecal SE concentration was significantly reduced in CONDLSE at d 3 and 14. Alpha diversity was higher (p < 0.05) in the DL compared to that in NC. Beta diversity showed a separation (p < 0.05) between the DL and the FL. Comparative tree analysis revealed 21 differential significant genera, with 14 prevalent in the DL and 7 in the FL, specifically, bacteria genera such as Lactobacillus, Clostridia_vadinBB60_group, Lachnospira, Oscillospiraceae UCG_005, and Marvinbryantia, which play significant roles relating to improved growth performance, metabolic homeostasis within the gut, energy metabolism, and short-chain fatty acid (SCFA) utilization. Our results concluded that litter management regimen differentially alters the microbiome of chicks, which accounts for the improved performance and exclusion of pathogens in the study.

We evaluated genetic markers for feed efficiency and immunocompetence in 108 crossbred steers (217 ± 8.2 kg) fed a high-forage total mixed ration for 35 days, using GrowSafe8000 intake nodes to calculate residual feed intake (RFI). From the 20 most efficient (low-RFI) and 20 least efficient (high-RFI) animals, we genotyped three metabolic loci (CYP3A4 rs438103222, PLB1 rs456635825, CRAT rs876019788) and profiled blood mRNA levels of these plus eight innate/adaptive immune genes. Logistic regression revealed that CYP3A4 and PLB1 polymorphisms—but not CRAT—were strongly associated with initial and final body weight, average daily gain, and feed intake: CYP3A4 A/A and PLB1 A-allele carriers achieved superior growth on reduced feed. Haplotype reconstruction across the three loci defined eight multi-SNP combinations, with the C-A-A haplotype enriched in low-RFI steers and combinations harboring CYP3A4 A and PLB1 A alleles linked to low RFI. Intriguingly, these favorable genotypes also overlapped with up-regulation of immune sensors and effectors (e.g., CD14, TLR4, TNF-α), indicating a coordinated metabolic–immune adaptation in efficient cattle. Collectively, our results validate CYP3A4 and PLB1 as high-impact quantitative trait nucleotides for marker-assisted selection aimed at simultaneously improving feed efficiency and immune resilience in beef production.

This study aimed to investigate breed-specific differences in the liver transcriptomic response to lipopolysaccharide (LPS) in St. Croix (STC) and Suffolk (SUF) sheep. A total of 18 sheep (9 STC and 9 SUF) were administered LPS (E. coli O111), at a dosage of 2.5 mg/kg via I.V. After euthanasia, liver samples were collected at three time points: HR0 (n = 3 per breed; no LPS), HR2 (n = 3 per breed; 2 hours after LPS), and HR6 (n = 3 per breed; 6 hours after LPS). RNA sequencing and pathway enrichment analysis were conducted to assess differentially expressed genes (DEG; FDR ≤ 0.05) and associated biological processes[IO1]. RNA was sequenced using an Illumina NextSeq2000 with P3 flow then raw data were analyzed using CLC Genomics Workbench 23.0 (QIAGEN) based on General Linear Model with a negative binominal algorithm. Pathway enrichment analysis was completed using the SRplot online platform, where differentially expressed genes (FDR ≤0.05) were applied. At baseline (HR0), 141 DEGs were identified between STC and SUF. SUF sheep upregulated pathways related to immune readiness, including defense responses and innate immune responses. At HR2, STC had 1,719 DEGs with top upregulated genes including SELE and CCL20. Alternatively, SUF had 2,742 DEGs at HR2, with similar immune response genes expressed but at lower magnitudes. At HR6, STC had a significant shift in gene expression, with 5,568 DEGs. Notably, STC shifted from immunity-related pathways to metabolic processes. In contrast, SUF had 5,862 DEGs at HR6, continuing to express pathways related to cytokine signaling and cellular responses. Overall, STC exhibited a more intense initial response to LPS, followed by a shift toward metabolic recovery. SUF, however, maintained heightened immune activity even after 6 hours, suggesting a less effective resolution of the LPS-induced challenge.

Haemonchus contortus is a blood-sucking gastrointestinal parasite that significantly impacts productivity and poses a major threat to sustainable sheep production in the southern United States. Infected ewes experience disruptions in their biochemical, hematological, and metabolic profiles, which can compromise their health. The colostrum produced by these ewes is critical for newborn lambs, providing essential nutrients and immunity. The objective of this study was to evaluate the effect of H. contortus infection on the chemical composition, and the metabolomic and lipidomic profile of colostrum in Florida Cracker ewes. Twenty (n=20) pregnant Florida Cracker ewes were allocated to infected (INF, n=10) or control (CTL, n=10) groups at 90 days of pregnancy. Treatment groups were grouped in covered concrete floor pens with similar dimensions and characteristics and had access to shelter, feed, and freshwater ad libitum. Animals were dewormed with a combination of Cydectin (0.2 mg/kg) and Prohibit (8 mg/kg) at 110 days of pregnancy and a fecal egg reduction test was used to ensure that ewes were free of parasite eggs prior infection. At 120 days of pregnancy, the INF group was orally infected with 10,000 L3 of H. contortus. The CTL group received 3 mL of distilled water. Immediately after lambing, colostrum samples were collected from each group to assess their chemical composition (fat, protein, lactose, and total solids), and to analyze the metabolomic and lipidomic profiles. A milk analyzer was used to evaluate the colostrum composition (fat, protein and lactose content, and total solids). The metabolome and lipidome profiles of colostrum were assessed using a mass spectrometry approach. No significant differences were observed for chemical composition of colostrum between the two groups (p< 0.05). For colostrum metabolomics, twenty-three differentially abundant (p< 0.05, FC >1.5) metabolites were observed between the infected and control groups. For colostrum lipidomics, caboxylic acid-based lipidome analysis identified 4,702 lipid species in the colostrum samples. Biomarker analysis identified 3 lipid species (FA 15:1; MG 20:5, PE 41:6) as potential biomarkers between the INF and CTL groups. The differentially abundant metabolites were involved in immune and antioxidant regulation via the tyrosine and ubiquinone terpenoids metabolic pathways. The biomarker lipids support cellular integrity and energy biogenesis. These findings highlight the impact of H. contortus infections on colostrum in Florida Cracker ewes, suggesting the need for further research to understand how these changes impact the metabolism and performance of lambs.

The objective of this study was to determine the metabolic pathway associated with divergent residual body weight gain phenotype in crossbred beef steers. A group of 108 crossbred growing beef steers (average BW = 282.87 ± 30kg) 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 = 20; 0.76 kg/d) and lowest RADG (least efficient; n = 20; -0.65 kg/d). Metabolome analysis of the plasma and rumen fluid samples was conducted using chemical isotope labeling/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 1629 metabolites were detected and identified in the plasma of the beef steers; eight metabolites like 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 1908 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). Our results demonstrate that beef steers with positive or negative RADG exhibit differences in plasma metabolic profiles that probably explain their divergent feed efficiency phenotype.

The rumen microbiome impacts beef cattle feed efficiency, a key economic factor in production systems. This study investigated the rumen microbiome of Charolais bulls with divergent residual feed intake-expected progeny difference (RFI-EPD) values to identify microbial taxa associated with feed efficiency. Forty Charolais bulls were evaluated for feed intake and growth over 60 days, and RFI values were determined. The 10 most efficient (NegRFI) and 10 least efficient (PosRFI) bulls were selected for microbiome analysis. Rumen fluid samples were collected and analyzed via 16S rRNA gene sequencing. Microbial analysis revealed no significant differences in alpha or beta diversity between groups, but differential abundance analysis identified 20 operational taxonomic units (OTUs) as more prevalent in NegRFI bulls, while 15 OTUs were more abundant in PosRFI bulls. Two OTUs from the key genus Prevotella showed different relative abundances in the two RFI-EPD groups. NegRFI bulls had a higher relative abundance of Prevotella OTU 109358, while PosRFI bulls had more Prevotella OTU 626329. Additionally, OTUs from Ruminococcus, a genus involved in fiber degradation and volatile fatty acid (VFA) production, were more abundant in NegRFI bulls. In contrast, PosRFI bulls had a higher abundance of OTUs from Oscillospira and F16, both linked to butyrate production. The results of this study support the need for further exploration into the role of microbial taxa associated with feed efficiency. A deeper understanding of the functional profile of the microbiota could aid in the development of microbiome-informed strategies to enhance nutrient utilization and performance in beef cattle.

We investigated the changes in the PBMC transcriptome profile of beef steers with divergent residual feed intake (RFI) following in vitro LPS stimulation. Negative-RFI beef steers (n =8, RFI= -2.00) and positive-RFI beef steers (n = 8, RFI = +1.59) were identified from a group of 40 crossbred beef steers (average BW = 360 ± 7.3 kg) after a 56-d RFI testing period. Whole blood samples were collected for PBMC extraction and were stimulated for 2 hours with LPS, followed by total RNA extraction and sequencing. The gene expression profiles of LPS-stimulated PBMCs and the LPS-unstimulated control group from negative- or positive- RFI beef steers were compared and analyzed. Differentially expressed genes were determined using FDR ≤ 0.05. In negative-RFI beef steers, there were 37 differentially expressed genes; the expression of 28 genes such as CD14, TREM1, THBS1, S100A12, S100A8, S100A9, CXCL5, IL1RN, and CCL20 were downregulated, whereas expression of 9 genes including CCL22, CD83, TRAF1, NFKBIZ, RSG16, CD60, and IL17A were upregulated in LPS-stimulated PBMC. In positive-RFI beef steers, we found 9 differentially expressed genes (CCL22, CD83, NFKBIZ, E1BK63, TRAF1, BCL2A1, IFNLR1, RSG16, and CD40), all of which were all upregulated. Gene ontology analysis of the differentially expressed genes revealed the enrichment of biological pathways related to defense and innate immune response, cell migration, and cellular response to lipopolysaccharide in negative-RFI beef steers, characteristic of a prompt and efficient immune reaction. In positive-RFI beef steers, biological processes associated with T cell activation and differentiation, positive regulation of adaptive immune response, and immune cell surface receptors were differentially enriched. Taken together, these findings suggest that negative-RFI beef steers may possess a more competent and energy-conserving immune response, marked by a quicker resolution of inflammation and a balanced pro- and anti-inflammatory response. These results enhance the understanding of the molecular mechanisms underlying feed efficiency, highlighting the potential role of immunocompetence in improving livestock productivity.

Distillery byproducts such as brewers grains (BG) have been widely used in dairy cow diets for decades to reduce diet costs and improve nutrient efficiency. Thus, the objective of this study was to evaluate the magnitude of the effects of dietary supplementation with BG on feed intake (DMI), digestibility, milk yield (MY), and feed efficiency (FE) of lactating dairy cows. A total of 12 peer-reviewed articles (n = 472 dairy cows) from 1983 to 2021 were collected systematically with the PRISMA method. The weighted raw mean differences (RMD) between dietary BG and control treatments were estimated with a robust variance estimation. Likewise, diet characteristics, such as CP content, NDF content, type of BG (wet = 1 and dry = 2), DIM, and BG inclusion rate (0 to 75%) were used as covariates in a meta-regression, subset, and dose-response analysis. Compared with the control, dietary BG decreased DMI (19.7 vs. 20.2 kg/d) and tended to increase MY (28.9 vs. 28.4 kg/d), but no effects were observed on FCM yield (29.1 vs. 28.8 kg/d), milk fat (3.8 vs. 3.7%), and milk protein (3.2 vs. 3.2%) concentrations. However, dietary BG increased FE (1.45 vs. 1.34 FCM/DMI) without influencing total-tract DM (61.9 vs. 55.7%) and NDF (49.7 vs. 54.5%) digestibility. Increasing the inclusion rate of BG linearly increased (R2 = 0. 554) dietary NDF. Thus, the dose-response analysis revealed that feeding up to 20% BG (dietary NDF = 39%) to lactating dairy cows increased MY and FE. Overall, this meta-analysis supports the hypothesis that dietary BG improved FE in lactating dairy cows.

We examined the effects of a blend of live Saccharomyces cerevisiae, multiple probiotic bacteria, and their fermentation products on the whole blood transcriptome of newly weaned beef steers during a 56-d receiving period. Forty newly weaned Angus crossbred steers (12-h postweaning; 217 ± 4.6 kg of body weight [BW]; 202 ± 4 d of age) from three different sources were stratified by BW and randomly assigned to one of the two treatments: 1) basal diet with no additive (CON; n = 20), and 2) the basal diet supplemented with 9 g/steer/d of a multi-strain microbial additive (PRO; n = 20). The PRO additive was a blend of S. cerevisiae and the fermentation products of Enterococcus faecium, Bacillus licheniformis, B. subtilis, Lactobacillus animalis, and Propionibacterium freudenreichii. On day 56, 10 mL of blood was collected from 10 randomly selected beef steers from each treatment group prior to morning feeding. Total RNA was isolated from the whole blood samples for the determination of gene expression profiles. Differentially expressed genes (DEGs) were identified using a false discovery rate (FDR) ≤ 0.10. A total of 41 DEGs were detected; 21 genes, including TLR10, GPR183, LGR4, and FCRL1, were upregulated in steers fed the PRO additive compared to CON, while 20 genes, such as C3, DDIT4, and ADCY8 were downregulated. Gene ontology analysis of the DEGs revealed the enrichment (FDR< 0.05) of pathways related to positive regulation of inflammatory response, regulation of cytokine secretion, positive regulation of defense response, and positive regulation of response to external stimuli in beef steers fed PRO additive. No significant differences (P > 0.05) in growth performance (BW, DMI, or ADG) were observed between CON and PRO steers. In conclusion, this study revealed that beef steers fed the PRO additive exhibited differential expression of genes related to immune function and inflammatory response, suggesting an effect on immunity and stress resilience. These findings highlight the potential of multi-strain direct-fed microbials as a nutritional strategy to support immune health, resilience to stress, and overall welfare in beef cattle during the weaning and receiving period.