Publications

As global demand for animal protein rises, improving feed efficiency in beef cattle has become a central focus for sustainable livestock production. Feed efficiency, often quantified through residual feed intake (RFI), is a complex trait influenced by genetic, physiological, and environmental factors. Among these, skeletal muscle plays a pivotal role due to its central function in growth, metabolism, and nutrient utilization. This mini-review explores the molecular and metabolic mechanisms linking muscle development to feed efficiency, highlighting recent advances in gene expression profiling, hormone signaling, and energy metabolism. Studies have identified key genes and pathways, such as those involved in the electron transport chain and insulin-like growth factor 1 (IGF1) signaling, that contribute to muscle growth and efficient energy use. Additionally, the role of the rumen microbiome in modulating nutrient absorption and its interaction with host muscle metabolism is discussed. Integrating these insights with genomic selection tools provides a promising avenue for enhancing feed efficiency while maintaining production goals. Understanding the biological foundations of muscle development offers valuable opportunities to refine genetic selection and management practices for a more profitable and environmentally sustainable beef industry.

Abstract Tall fescue [Schedonorus arundinaceus (Shreb.) Dumort.; (TF)] is the primary forage species used by cow-calf producers in grazing systems in Tennessee. It is an excellent cool-season perennial grass due to its great forage mass (FM), nutritive value, and extensive growing season. Orchardgrass [Dactylis glomerata L.; (OG)] is also a widely used cool-season grass in the U.S. This study compared TF and OG cultivars under continuous stocking in terms of FM, nutritive value, and animal performance over two grazing seasons (2022 to 2023) in Spring Hill, Tennessee, U.S. Treatments were: 1) OG cv. Persist I (OG-P1), 2) OG cv. Persist II (OG-P2), 3) TF cv. Kentucky 31’ (TF-K31), and 4) a novel endophyte TF cv. Max Q (TF-NE). Forage mass was not affected by treatments (P = 0.0519), with an average of 2979 kg DM ha−1. Crude protein (CP) and neutral detergent fiber (NDF) concentrations were also unaffected by treatments (P = 0.6728, P = 0.1300), averaging 106 and 687 g kg–1, respectively. However, TF-NE had the lowest acid detergent fiber (ADF) (P = 0.0258; 380 g kg–1) and the greatest in vitro dry matter digestibility in 48 hours (INVDMD48) (P < 0.0001; 680 g kg–1), while OG-P2 had the greatest ADF (400 g kg–1) and the lowest INVDMD48 (661 g kg–1). Total gain and average daily gain (ADG) were affected by treatment × year interaction (P = 0.0314 and P = 0.0161, respectively). In 2022, TF-NE, TF-K31, and OG-P1 outperformed OG-P2, but no differences were observed in 2023 (total gain: 78.6 kg animal–1; ADG: 0.78 kg animal–1 day–1). Ergovaline concentrations in TF-K31 were low, which likely minimized its negative effects. These findings indicate that both TF and OG can sustain beef cattle production under continuous stocking, with TF offering potential advantages in botanical composition and forage nutritive value over time.

Beef cattle is the most consumed red meat in the United States, and the United States is the largest producer and consumer of beef cattle globally. Feed is one of the largest input costs for the beef cattle industry, accounting for 40–60% of the total input costs. Identifying methods for improving feed efficiency in beef cattle herds could result in decreased cost to both producers and consumers, as well as increased animal protein available for global consumption. Identification of feed efficiency biomarkers could aid in the selection of more feed-efficient animals. To identify potential biomarkers of feed efficiency, rumen fluid was collected from low- (n = 14) and high-RFI (n = 15) Angus steers based on RFI ± 0.5 SD around the mean following a 70d feed efficiency trial to determine rumen metabolites associated with variations in feed efficiency. Steers were 7 months of age, weighing 264±2.7 kg. Rumen fluid was collected via gastric tubing, filtered through a 0.22 µM syringe filter, extracted for metabolomic analysis using 0.1% formic acid in acetonitrile:water:methanol (2:2:1), and injected into the Dionex UltiMate 3000 UHPLC system with an Exactive Plus Orbitrap MS. Peaks for known metabolites were identified using MAVEN and analyzed using MetaboAnalyst 4.0 and SAS. Significance was determined using an α ≤ 0.05. Based on fold change (high/low RFI), eight metabolites were greater in low-RFI steers compared to high-RFI steers, including 3,4-dihydroxyphenylacetate, 4-pyridoxate, citraconate, hypoxanthine, succinate/methylmalonate, thymine, uracil, and xylose (P ≤ 0.05), while 12 metabolites differed by ≥ 2-fold. These metabolites were predominantly involved in amino acid and lipid metabolism. Rumen fluid metabolomes differed in steers of varying feed efficiencies. These metabolites may be used as biomarkers of feed efficiency and may provide insight as to factors contributing to differences in feed efficiency that may be exploited to improve feed efficiency in beef cattle herds.

Drylot beef cow-calf systems are viable alternative management systems to traditional forage-based systems. In such confinement, adding ionophores such as monensin to the diets of beef cattle is common, and has been shown to improve feed efficiency and increase average daily gain. The addition of monensin is also commonly utilized as a strategy for methane mitigation, as this ionophore class antimicrobial acts to interfere with ion flux primarily within Gram-positive cells through its action as an ion carrier. It is widely accepted that suppression of these ruminal organisms results in the reduction of substrates for rumen methanogenic archaea, reducing methane production. However, several studies have indicated that cattle may adapt to monensin, and within weeks of feeding, may return to prior levels of methane production. Our hypothesis is that feeding monensin to bred beef heifers in confinement will temporarily decrease methane production from shifts in the methanogenic archaeal and bacterial communities. Sixteen fall-born bred heifers were randomly assigned to 2 treatment groups (n = 8 per treatment) and were fed a control diet or a diet containing monensin for 70 days using headgates. In vivo gas exchange of oxygen consumption, carbon dioxide and methane production were measured for 24-h periods throughout the trial using individual calorimeter head boxes. Rumen content sampling was conducted on day 0, 18 and 53 of the trial through oral lavage. Upon completion of sampling, DNA was isolated for ruminal bacteriome composition utilizing deep, next-generation sequencing of the V1-V3 hypervariable regions of the 16S bacterial rRNA gene. Level of methanogen 16S rRNA was quantified using qPCR. There was a significant reduction in phylum SR1 (P < 0.05). The abundance of several OTUs was reduced between treatment with monensin, including Anaerofustis (P < 0.0001), Shuttleworthia (P < 0.0001) and Order Bacteroidales (P = 0.003). No significant shifts in key ruminal methanogenic archaeal groups as a percentage of total methanogen 16S rRNA occurred (P > 0.05). Heifers fed monensin did not produce significantly less methane than the control (P > 0.05) on a liters per day basis, which was consistent throughout the study. These data suggest methane production is not reduced long-term when animals are fed monensin in confinement. Additionally, the data suggest that monensin supplementation does not suppress all classical Gram-positive populations, rather it influences finer shifts in bacterial species that may be key in ruminant function. Determining the stability of the ruminal microbiome over time in heifers fed monensin may provide further insights to long-term methane mitigation in cow-calf systems.

The activity of the immune system in the reproductive tract has been proven to be crucial in the response to uterine diseases, normal reproductive functions, and tolerance to the allogeneic fetus during pregnancy. The objectives of the current study were to (1) evaluate uterine and vaginal cytokine concentrations in postpartum cows undergoing estrus synchronization followed by timed artificial insemination (TAI) and (2) correlate bacterial communities with cytokine concentrations. Postpartum Angus cows ( n = 20) were subjected to a 7-Day Co-Synch protocol with pre-synchronization beginning 21 days prior (d −21) to TAI (d 0). Uterine and vaginal flushes were collected on d −21 and −2. Pregnancy was determined by transrectal ultrasound on d 30. Cytokines include interleukin (IL)-1b, IL-6, IL-10, transforming growth factor beta (TGF-β), and immunoglobin A (IgA) and concentrations were determined by commercial ELISA kits. No differences by day or pregnancy status in cytokine concentrations were detected in vaginal samples. No differences by day or pregnancy status in IgA, IL-10, or IL-1b concentrations were detected in uterine samples. Overall TGF-β concentrations in the uterus were greater in resulting pregnant than non-pregnant cows (44.0 ± 13.4 pg/mL vs. 14.7 ± 4.9 pg/mL; P = 0.047). Uterine TGF-β was correlated with the relative abundance of genera Treponema ( r = −0.668; P = 0.049) in resulting non-pregnant cows on d −21 and with the relative abundance of genera Ureaplasma ( r = 0.901; P = 0.0004) in resulting pregnant cows on d −2. In resulting pregnant animals, a tendency for a strong correlation was detected between d −2 progesterone concentrations and uterine TGF-β concentrations ( r = 0.591, P = 0.07). Overall IL-6 concentrations in the uterus were greater in resulting non-pregnant than pregnant cows (198.7 ± 21.8 pg/mL vs. 144.3 ± 16.1 pg/mL; P = 0.045). A correlation was also detected between uterine IL-6 concentrations and the relative abundance of genera Butyrivibrio ( r = 0.742; P = 0.022) in resulting non-pregnant cows on d −21. These results suggest possible relationships between different bacterial communities and cytokine concentrations within the uterus of beef cattle prior to TAI that may ultimately affect fertility outcomes.

Virus-host associations. A listing of all associations (Hi-C linkage or long-read alignment) between predicted viral contigs and non-viral contigs. (XLSX 24 kb)

No abstract is provided for this article.

The milk microbiome in swine has been recently demonstrated to develop and alter the growing gut microbiome in offspring. Milk is the primary nutritional source for piglets and the established microbial communities from initial diet remain stable over time, thus being critical for long-term effects on the animal. Since little is known about the ontogeny of the milk microbiome, the objective of this study was to determine differences in the sow milk microbiome among multiple parities and days in lactation. A total of 32 sows were grouped by parity, 1–4, with 8 sows per parity. Sows were on the same diet and had ad libitum access to water. At sampling, teats were cleaned and stripped. Milk samples were manually collected on one side from a fore, mid, and hind teat, then combined for one whole milk sample per animal. Milk was sampled on days 2 and 16 to determine differences between days in lactation. Samples were sequenced using an Illumina MiSeq for V1-V3 regions of the bacterial 16S rRNA gene and downstream analyses were conducted in the R environment using ‘phyloseq’ and ‘DADA2’ packages. Statistical analyzes utilized a completely randomized design and a mixed model analysis of variance, with fixed effects of parity and days in lactation and examining a parity by day interaction. The genera Corynebacterium were greater (P &amp;lt; 0.05) abundance in parity 4. There was an increase (P &amp;lt; 0.05) in Staphylococcus at day 2 compared to day 16. Core microbial communities, Lactobacillus and Romboutsia increased (P &amp;lt; 0.05) by day 16. Identifying microbial communities present in the milk microbiome in sows can allow producers to understand how these microbes may influence the gut microbiome in growing piglets to augment gain. USDA is an equal opportunity provider and employer.

Beef cattle is the most consumed red meat in the United States, and the United States is the largest producer and consumer of beef cattle globally. Feed is one of the largest input costs for the beef cattle industry, accounting for 40–60% of the total input costs. Identifying methods for improving feed efficiency in beef cattle herds could result in decreased cost to both producers and consumers, as well as increased animal protein available for global consumption. Identification of feed efficiency biomarkers could aid in the selection of more feed-efficient animals. To identify potential biomarkers of feed efficiency, rumen fluid was collected from low- (n = 14) and high-RFI (n = 15) Angus steers based on RFI ± 0.5 SD around the mean following a 70-d feed efficiency trial to determine rumen metabolites associated with variations in feed efficiency. Steers were 7 mo of age, weighing 264±2.7 kg. Rumen fluid was collected via gastric tubing, filtered through a 0.22 µM syringe filter, extracted for metabolomic analysis using 0.1% formic acid in acetonitrile:water:methanol (2:2:1), and injected into the Dionex UltiMate 3000 UHPLC system with an Exactive Plus Orbitrap MS. Peaks for known metabolites were identified using MAVEN and analyzed using MetaboAnalyst 4.0 and SAS. Significance was determined using an α ≤ 0.05. Based on fold change (high/low RFI), eight metabolites were greater in low-RFI steers compared to high-RFI steers, including 3,4-dihydroxyphenylacetate, 4-pyridoxate, citraconate, hypoxanthine, succinate/methylmalonate, thymine, uracil, and xylose (P ≤ 0.05), while 12 metabolites differed by ≥ 2-fold. These metabolites were predominantly involved in amino acid and lipid metabolism. Rumen fluid metabolomes differed in steers of varying feed efficiencies. These metabolites may be used as biomarkers of feed efficiency and may provide insight as to factors contributing to differences in feed efficiency that may be exploited to improve feed efficiency in beef cattle herds.

The effects of growth-promoting implants have been well-defined for their ability to impact growth performance in beef cattle. Production-relevant microbes and microbiomes in the rumen have also been associated with growth traits. However, the role of implants on the rumen microbiome has not been determined. The objective of this study was to determine if different doses of implant hormones cause gain-associated ruminal microbial community changes. To assess this, a completely randomized design was used and 336 fall-born steers 450 to 470 days of age from the germplasm evaluation population at the US Meat Animal Research Center (Clay Center, NE) were divided into two treatment groups: 1) a moderate implant strategy ( n = 167) of Revalor-IS (80 mg trenbolone acetate and 16 mg estradiol) followed by Revalor-S (120 mg trenbolone acetate and 24 mg estradiol) or 2) an aggressive implant strategy ( n = 169) of Revalor-IS followed by Revalor-200 (200 mg trenbolone acetate and 20 mg estradiol). Steers were fed the same diet (57.0% dry-rolled corn, 30% wet distiller’s grains with solubles, 8.0% alfalfa hay, 4.25% vitamin and mineral supplement, and 0.75% urea, on a DM basis). On d 85 after implants administration, rumen contents were collected via orogastric tubing. Samples were sequenced to target and identify bacteria, archaea, and protozoa. Untargeted metabolomics was performed on rumen content using ultra high performance liquid chromatography high resolution mass spectrometry. Production data between implant strategies was analyzed using a mixed model ANOVA (SASv9.4, Cary, NC) followed by separation of least squares means. Microbial diversity between strategies did not differ for archaea or protozoa ( P &amp;gt; 0.05). Average daily gain was different ( P = 0.01; 1.72 vs 1.66 ± 0.02 kg, aggressive vs moderate, respectively); however, large microbial community shifts were not associated with implant strategy. Two metabolites, N- acetyllysine and N -acetylornithine, were found in greater abundance in the moderate implant strategy ( P ≤ 0.04). Understanding associations between the rumen microbiome and implant strategies may allow improvement of growth efficiency in beef cattle.