bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSII-9 Whole genome sequences of two nitrate-reducing strains of Selenomonas ruminantium isolated from the rumen
Authors: Costello Margaret K , Ricke Steven C , McClure Jennifer , Anderson Robin C 
Published: May 2024

Abstract
Selenomonas ruminantium is a functionally diverse, non-fibrolytic member of the rumen microbial community with two subspecies: lactilytica and ruminantium. Some strains of S. ruminantium can reduce nitrate and nitrite, which may be associated with ruminal fiber degradation and, thus, greater forage diets. Most work done with S. ruminantium has been culture-based, with less genomic and functional data. Here, we performed whole genome sequencing with an Oxford Nanopore GridION on two isolated, nitrate-reducing strains of S. ruminantium to provide complete genomic data and determine the nitrogen usage functional capacities of these novel strains. The two isolated strains, 223 and 231, were shipped on dry ice to the University of Wisconsin-Madison, where they were grown, pelleted, and observed under a microscope to determine purity. The samples were processed with a 3 min bead-beating step before extraction with the Zymo Quick-DNA High Molecular Weight MagBead Kit. Subsequently, the extracted samples underwent a quality assessment step before moving into library preparation for Oxford Nanopore sequencing. The two libraries were then loaded onto two R9.4.1 flow cells per library and were sequenced on an Oxford Nanopore GridION for 72 h. The data were extracted from the GridION, and the combined passed reads from each of the two flow cells per library were assembled with Canu and Flye, long-read de novo genome assemblers designed for noisy, single-molecule sequences. The assembled genomes were compared with a reference S. ruminantium genome with Quast, a quality assessment tool that evaluates assembly accuracy. Finally, the assembled genomes with the highest accuracy were analyzed with prodigal to generate protein-coding gene predictions and then with BLAST to assign functional predictions. For each strain, a different assembly was used. The Canu assembly of strain 223 had greater accuracy rates at 3205.23 mismatches per 100 kbp, while the Flye assembly of strain 231 had 2494.40 mismatches per 100 kbp. The two strains had similar genome sizes: 3,098,553 base pairs for strain 223 and 3,138,614 base pairs for strain 231. Strain 223 had less GC content than strain 231 of 51.02%, while strain 231 had a GC content of 52.80%, which were both less than the 50.68% GC content of the reference genome. These genomes provide a resource for understanding nitrate reduction in the rumen and work to build a better database for analyzing the rumen microbiome.
PSV-6 The additive effect of hormonal implant and inclusion of beta-agonists in carcass quality in beef cattle
Authors: Tollefson Rebecca L , Winebold Deedra M , Deaton Claire , King Adam , Case Riley , Robertson Joel , Church Emily R , Holder Amanda 
Published: May 2024

Abstract
The objective of this study was to determine what additive effect hormonal implants and inclusion of beta-agonists in the diet have on carcass quality in yearling beef steers. Twenty-one Hereford-cross steers (450 ± 15 kg) were assigned to one of three drylot pens based on initial body weight (BW) and sire so that each pen had an equal starting BW and sires were equally represented in each pen. Each drylot pen was assigned to one of three treatments: receiving a hormonal implant (IMP), consuming a beta-agonist (BAG), or receiving both of the previous treatments (AND). All steers were fed a mixed ration consisting of 30.0% rye silage, 28.0% DDGS, 30.0% rolled corn, 10.5% soybean meal, and 1.5% mineral supplement (22.0% CP, 2.90 Mcal ME/kg DM). Animals were fed daily at 0700 and 1700 and weighed weekly at 0630. For the duration of the trial, animals were housed in drylot pens with ad libitum access to feed and water and had shade structures in each pen. Following a 15-d adaptation period, feed intake was recorded for 45 d. Weight gain for each treatment group were 1.26, 1.28, and 1.48 kg/d for IMP, BAG, and AND, respectively. After the intake portion of the study was completed, an animal from each pen was slaughtered and evaluated for carcass quality. Hot carcass weights for diets IMP, BAG, and AND were 347.4, 352.9, and 394.8 kg, respectively. Following 14 d aging, samples from the ribeye area were collected from each animal and subjected to sensory analysis and other assessments of quality. Data were analyzed as a completely random design in SAS v9.4. There was not a significant difference between the IMP treatment and the AND treatment based on assessment from Warner-Bratzler shear force, carcass yield, marbling score, and sensory assessment (P &lt; 0.05); however, the BAG treatment had significantly less marbling than the other two treatments. It was concluded that the additive effect of using both a hormonal implant and a beta-agonist can produce carcass of good quality without detrimental effects on meat quality when compared with a beta-agonist only inclusion.
PSV-3 Effects of maternal early gestational weight gain on multigenerational skeletal muscle gene regulation in offspring
Authors: Ramirez-Zamudio German D , Dahlen Carl R , Baumgaertner Friederike , Menezes Ana Clara B , Hurlbert Jennifer L , Bochantin Kerri A , Underdahl Sarah R , McCarthy Kacie L , Reynolds Lawrence P P , Ward Alison , Borowicz Pawel P P , Sedivec Kevin K , Caton Joel S , Diniz Wellison J j S 
Published: May 2024

Abstract
Maternal nutrition during the periconceptional period may have multigenerational effects on the gene regulation of fetal skeletal muscle. This study aimed to investigate the impact of maternal rate of body weight gain (F0) during early gestation on the differential gene expression in the skeletal muscle of newborn (F1) and second-generation fetuses (F2) female offspring. To this end, crossbred Angus heifers (F0) were assigned to either a low gain (LG; 0.28 kg/d; n = 8) or moderate gain (MG; 0.79 kg/d; n = 8) group during the first 84 d of gestation. Subsequently, heifers (F0) were managed as a single group on a forage-based diet until the weaning of the F1 offspring (8 mo). The F1 heifers were estrus synchronized and bred via AI at 15 mo, and F2 fetuses were harvested on d 84 of gestation. Longissimus dorsi muscle was collected at birth (F1) and the 84-d harvest in F1 heifers and their F2 fetuses for multigenerational RNA-Seq analysis. Differentially expressed genes (DEGs) were identified using the DESeq2 R-package. Significant genes were retrieved based on P - value ≤ 0.05 and log2 fold change|0.5|. We previously reported that F1 heifers from MG dams at birth were ~2 kg heavier (P &lt; 0.03), and herein we report the impact on the gene regulation of skeletal muscle in the F1 and F2 generations. At birth, F1 heifers from MG cows exhibited 275 DEGs, of which 98 were downregulated, and 177 genes were upregulated, related to the immune system (TNFAIP3, TLR5), cellular signaling and transduction (RASGRP2, NFE2), and extracellular matrix (TGM3, MMP17). Changes in gene expression persisted in F1 heifers through development, breeding, and until the evaluation at d 84 of gestation. At this time point, we identified 75 upregulated genes out of 177 DEGs. These genes were underlying cellular functions (USP43, PASK), hematopoiesis (THPO), metabolism, and enzymatic activity (SMOX, OAT) as possible metabolic adaptations. Similarly, 102 genes were downregulated, mainly associated with immune and inflammatory response (CHI3L1, LDAF1). Regarding the F2 fetuses, 151 DEGs were differentially expressed. Among them, 63 were upregulated in the MG group and involved with biological functions such as ion channels and transport (KCNAB1, SLC9A3), transcriptional regulation, and signaling (ZNF75D, TMEM106B, DPP6), enzymatic activity, and metabolism (B3GNT4, FAM20A, ALDH5A1, and PRSS23). Likewise, 88 downregulated genes were associated with the cell cycle and proliferation (APOOL, CIR1, and STIL). In conclusion, periconceptional maternal nutrition aimed at moderate weight gains can have multigenerational effects on the gene regulation of fetal muscle tissue.
PSV-4 Exposure to prenatal tributyrin improved pre-weaning growth performance and reduced fat deposition in the muscle of market age pigs
Authors: Cooper Elizabeth , Murray Robert , Palou Rousset , Markley Grace I , Stahl Chad H 
Published: May 2024

Abstract
Organic acids, including short chain fatty acids, medium chain fatty acids, and tricarboxylic acid, are used as alternatives to antibiotics for the purpose of growth promotion in livestock species. Butyric acid has been used extensively for its various functions in intestinal health and barrier function, as well as its actions as a histone deacetylase inhibitor. Many of the issues relating to using butyric acid as a feed supplement are overcome by utilizing tributyrin (TB), a butyrate prodrug. Dietary supplementation of TB to sows during gestation was able to improve pre-weaning litter performance. Sows (n = 52, 42 gestational days) were randomly assigned to either a control diet or control diet supplemented with 2% TB. All diets were made isocaloric with the addition of oil and wheat flour. Dietary treatments continued until 112 d of gestation. After farrowing, piglet growth performance was monitored. Once offspring reached 6 mo of age, 30 gilts from the most median performing litters were identified for tissue collection and evaluation of meat characteristics. Sows that received tributyrin during gestation tended to have greater total litter weights at birth (P &lt; 0.1); however, average individual birthweights were not statistically different between control and TB litters. The TB piglets tended to be heavier at weaning (P &lt; 0.1). Pre-weaning average daily gains were higher in piglets exposed to prenatal TB (P &lt; 0.01). Body weights and hot carcass weights did not differ significantly in gilts at market age. There was, however, a trend of increased dressing percentage from TB treated offspring, accompanied by significantly reduced back fat at the 10th rib (P &lt; 0.1 and P &lt; 0.05 respectively). These data suggest that TB supplementation results in both temporary and permanent improvements to growth and development. This study provides further evidence that prenatal TB can have long term effects on muscle growth and meat quality. Further studies are needed to ultimately determine whether prenatal or postnatal supplementation is ideal for improving long-term growth performance.
PSV-2 Digestible indispensable amino acid scores (DIAAS) in pork products
Authors: Martins Juliana Carolina Florencio Ravagnani , Fanelli Natalia Dos Santos , Stein Hans H 
Published: May 2024

Abstract
The “Digestible Indispensable Amino Acid Score” (DIAAS) method measures protein quality in human foods. However, values for DIAAS are not available for some pork products. Therefore, this study aimed to determine DIAAS values for nine pork products. Nine diets contained one pork product (i.e., back ribs, shoulder butt, tenderloin, Coppa ham, prosciutto ham, speck ham, chorizo, Italian sausage, and bratwurst) as the only source of crude protein (CP) and amino acids (AA). Nine ileal cannulated gilts with an initial average body weight of 50.3 ± 3.8 kg were used in a 9 × 6 incomplete Latin square with 9 diets and six 7-d periods. Ileal digesta were collected on d 6 and 7 of each period. There were, therefore, six replicate pigs per diet, but no pig was fed the same diet twice. A nitrogen-free diet was used to measure basal endogenous losses of CP and AA, and this diet was fed to all pigs in one separate 7-d period. The standardized ileal digestibility (SID) and DIAAS of each pork product were calculated. Reference ratios were used for children from 6 mo to 3 yr old and individuals older than 3 yr. Data were analyzed by ANOVA using the MIXED procedure of SAS with pig as the experimental unit. Diet was the fixed effect and replicate pig was the random effect. Results indicated that for both age groups, prosciutto ham had greater (P &lt; 0.05) DIAAS than all other pork products (Table 1), which may be because prosciutto is from the hind leg of the pig, which contains less connective tissue. Prosciutto was also not smoked, which may contribute to the greater DIAAS values for this protein because smoking may reduce DIAAS. For children from 6 mo to 3 yr old, tenderloin, Coppa ham, and Italian sausage had greater (P &lt; 0.05) DIAAS than chorizo and bratwurst sausages, back ribs, and shoulder butt. However, for individuals older than 3 yr, Coppa ham had greater (P &lt; 0.05) DIAAS than all other pork cuts and sausages. The observation that back ribs and shoulder butt had decreased DIAAS than tenderloin is likely because tender cuts with less connective tissues tend to have greater concentrations of indispensable AA with less non-nitrogen content. In addition, for both age groups, there was no limiting AA for all pork products, except that chorizo sausage was limiting in sulfur AA for children from 6 mo to 3 yr old. In conclusion, data from this experiment demonstrated that all pork products have “good” or “excellent” protein quality for individuals older than 6 mo of age, indicating that these food ingredients may be used to complement lower-quality proteins and provide a meal with all indispensable AA.
PSV-5 Influence of an oregano-based essential oil on growth performance and carcass traits of beef steers
Authors: DeBruin Bergin M , Bakker Christina , Smith Zachary K , Underwood Keith , Grubbs Judson K , Blair Amanda , Rusche Warren C 
Published: May 2024

Abstract
The objective of this study was to determine the influence of an oregano-based essential oil on growth performance, health outcomes, and carcass characteristics of yearling beef steers finished in an all-natural program. Single-sourced yearling steers [n = 128; initial body weight (BW) = 335 ± 7.98 kg] were allotted to 16 pens (n = 8 pens/treatment with 8 steers/pen). Steers were blocked by initial BW grouping in a Randomized Complete Block Design (n = 8 blocks total). Groups consisted of 1) control group fed no oregano-based essential oil product (CON) and 2) group fed 4 g/steer daily of By-O-Reg+ Beef (Advanced Ag Products, Canton, SD; OEO). Steers were individually weighed on d 0 (arrival), d 38, d 66, d 108, and d 149 for growth performance measures. Steers were transitioned from a 70% concentrate diet to a diet that contained 90% concentrate over 14 d and remained on the finishing diet until harvest on d 149. The finishing diet provided 1.37 Mcal/kg of NEg. Steers were evaluated daily for indications of disease or visible digestive disorders by a trained technician blinded to the treatments. Steers were fed until visually assessed to have 1.27 cm rib fat and were shipped for harvest at a commercial processing facility. Liver scores and hot carcass weights were recorded at the time of harvest and steer identity was maintained throughout the harvest process. Following an approximately 24 h chilling period, carcass data were recorded, and USDA Yield and Quality Grade were determined. Health outcomes were not influenced by dietary treatment (P ≥ 0.18). Inclusion of OEO did not influence (P ≥ 0.73) carcass-adjusted final BW, DMI, average daily gain (ADG), gain:feed, observed dietary NEm or NEg, observed-to-expected dietary NEm or NEg. In addition, no differences (P ≥ 0.30) were observed between treatment groups for hot carcass weight, dressing percentage, ribeye area, rib fat thickness, calculated yield grade, marbling score, estimated empty body fat percentage, or distribution of USDA Yield and Quality Grades. The OEO treatment tended (P = 0.11) to have a decreased percentage of normal liver scores compared with CON. Collectively, growth performance and carcass traits of yearling steers finished in an all-natural program in this experiment were not influenced by dietary inclusion of an oregano-based essential oil.
PSI-17 Effect of timing of high dietary zinc supplementation on the microbiome of gestating sows and their piglets
Authors: Hammers Kelsey L , Urriola Pedro E , Schwartz Mark , Ryu Moon-Suhn , Gomez Andres , Huma Noor , Johnston Lee J 
Published: May 2024

Abstract
The objective of this study was to assess if high dietary zinc (Zn) fed to gestating sows modulates the microbiome of the sow and that of their offspring. Sows were fed 1 of 3 dietary treatments: 1) Control: a corn-soybean meal-based diet containing 125 ppm total supplemental zinc, 2) Breed-to-Farrow: as Control + 141 ppm supplemental Zn as ZnSO4 fed from 5 d post-breeding to farrowing; and 3) Day 110-to-Farrow: as Control + 2,715 ppm supplemental Zn as ZnSO4 starting on d 110 of gestation until farrowing. A subset of third parity sows (n = 30; 10 per treatment) were selected to assess the microbiome of colostrum, milk, and rectal and vaginal surfaces of sows. At farrowing, 4 pigs per litter (n = 120) were selected based on birthweight (BiW; 2 average BiW pigs and 2 pigs with BiW below the litter average) were selected to assess the piglet gut microbiome on the day of birth (d 0) and d5 of age. 16S rRNA sequencing was implemented for colostrum and milk samples while all other sample types were sequenced using shotgun metagenomics to determine taxonomic and functional profiles. Measures of alpha and beta diversity were conducted along with determination of differentially abundant taxa and pathways in tandem with generalized linear mixed models. Greater dietary concentrations of Zn fed to gestating sows minimally affected their colostrum, milk, and vaginal microbiome. However, fecal samples of Breed-to-Farrow sows showed decreased abundance of potentially pathogenic bacteria such as Salmonella enterica and Shigella flexneri and greater abundance of bacteria typically involved in fiber fermentation compared with Control sows (Figure 1a). Piglets born to Day 110-to-Farrow sows also showed greater abundance of some taxa typically involved in fiber breakdown and short chain fatty acid (SCFA) generation on d 5 compared with Control pigs (Figure 1b). At d 0, Breed-to-Farrow piglets showed less abundance of methanogenic archaea and differential abundance of taxa with potentially pathogenic roles, compared with Control pigs (Figure 1c). Gene families and pathways playing roles in central metabolic functions (starch, pyruvate, sucrose, amino acid metabolism) were more abundant in Breed-to-Farrow piglets compared with pigs born to Control sows on d 0 and 5 of age. In conclusion, greater Zn fed to gestating sows impacted the abundance of gut taxa with potential roles in SCFA-production and pathogenicity in both sow and piglet, despite overall minor effects. However, the physiological significance of these findings for the sow and piglet remains unclear.
PSI-19 Growth performance of weaned pigs fed Jerusalem Artichoke tubers
Authors: Erker Natalie A , Everding Talia K , Neujahr Alison C , Paczosa Duncan B , Miller Phillip S , Burkey Thomas E 
Published: May 2024

Abstract
Recent studies have shown that prebiotics have been able to positively affect growth of beneficial bacteria, indices of gut health, and growth performance in pigs. This type of research is important to identify alternative methods for maintaining herd health other than antimicrobial usage. Jerusalem Artichoke tubers were chosen due to their relatively greater amount of inulin (~60%) compared with other prebiotic crops (i.e., chicory pulp - ~20% inulin). The objective of this work was to evaluate growth performance of weaned pigs fed Jerusalem Artichoke tubers. Sixty-four pigs approximately 21 d of age, weighing 6 kg each were used to test four dietary treatments with four pens per treatment (two barrows and two gilts per pen). Dietary treatments were randomly allocated to pens following a completely randomized design in a three-phase feeding trial. Diet treatments consisted of a corn-soybean meal basal diet (control) meeting the nutrient requirements for weanling pigs and three treatment diets with ground Jerusalem Artichoke tubers replacing corn at the rate of 0.05%, 0.5%, and 5.0% (JA-low, JA-mid, and JA-high, respectively) through all three phases. The pigs were allowed 3 d to acclimate to the facility following arrival (d -3 to -1). The trial ran from d 0 to d 35. Growth performance data were collected on d 0, 7, 14, 21, 28, and 35. Blood samples were obtained on d 0, 7, 14, and 28. Fecal samples were collected on d 0, 14, and 28. PROC GLIMMIX in SAS was utilized to analyze the growth performance data. Results indicate greater (P &lt; 0.001) gain to feed ratio (G:F) at wk 2 for JA-high and JA-mid pigs compared with all other treatments. No differences were observed for overall body weight (BW; 25.14, 25.48, 21.8, 22.83 kg), average daily gain (ADG; 0.52, 0.52, 0.51, 0.47 kg/d), or average daily feed intake (ADFI; 0.73, 0.74, 0.71, 0.72 kg/d), respectively, for control, JA-low, JA-mid, and JA-high fed pigs. The growth data suggests that Jerusalem Artichoke tubers may be included in weaned pig diets without negative effects on growth performance; however, these results need to be interpreted in conjunction with the pending analyses to provide a comprehensive look at the role of prebiotic fiber in the gastrointestinal tract of the pig. Future analyses will include evaluation of serum biomarkers (e.g., intestinal fatty acid binding protein as a measure of intestinal epithelial cell damage) and microbiome profiling via 16S microbial sequencing to assess gut health. It is important to note that our study population experienced morbidity and mortality (Trueperella pyogenes was cultured from one pig submitted for necropsy) and the decision was made to prophylactically treat the herd with ceftiofur on d 7 following sample collection to prevent additional loss.