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Additional File 1. Supplementary Results. Figure S1. Top 10 most abundant genera present in the DNA extraction negative controls used as a negative control in the DNA extraction and sequencing step. Figure S2. Holstein steer nasal microbiome alpha diversity relative to the date of collection. Figure S3. Variation in the cattle���s nasal alpha diversity estimated relative to the average daily temperature (��F). Figure S4. Average relative abundance of the 10 most abundant phyla (a), family (b), and genera (c) present in the nasal microbiome of BRD and healthy animals. Figure S5. Variable importance measured by random forest indicated by the mean decrease accuracy. Figure S6. Visual representation of the positive ASV co-occurrence analysis in the healthy group (n = 74) with a probability of occurrence in the same sample > 0.9. Figure S7. Visual representation of the positive ASV co-occurrence analysis in the BRD group (n = 57) with a probability of occurrence in the same sample > 0.9. Figure S8. Visual representation of the negative ASV co-occurrence analysis of the healthy group (n = 74) with a probability of occurrence in the same sample < 0.05. Figure S9. Visual representation of the negative ASV co-occurrence analysis in the BRD group (n = 57) with a probability of occurrence in the same sample < 0.05. Table S1. Variation in the cattle���s nasal alpha diversity relative to the animal age (months) analyzed using General Linear Mixed Model. Table S2. Sample average distance to the centroids of the BRD and healthy groups. Table S3. Prevalence of ASVs assigned as P. multocida, H. somni and M. bovis the nasal cavity of BRD (n = 75) and healthy (n = 74) groups based on 16S rRNA gene sequencing. Table S4. Prevalence of the genera Pasteurella, Histophilus, Mannheimia or Mycoplasma in the nasal cavity of Holstein steers (n=131) and between BRD (n = 75) and healthy (n = 74) animals based on 16S rRNA gene sequencing. Table S5. Positive ASV pair combinations present in 73 out of 74 healthy samples with a probability of occurrence in the same sample > 0.9. Table S6. Co-occurrence analysis with positive ASV pair combinations present in 56 out of 57 BRD samples with a probability of occurrence in the same sample of 1. Table S7. Co-occurrence analysis showing negative ASV pair combinations that are not likely to co-exist in the heathy group with a probability < 0.04. Table S8. Co-occurrence analysis showing negative ASV pair combinations that are not likely to co-exist in the BRD group with a probability < 0.04. Table S9. Evaluation of Pasteurella multocida, Histophilus somni, Mannheimia haemolytica and Mycoplasma bovis using qPCR assays.

One hundred twenty Angus × Simmental steers [322 ± 4.8 kg initial body weight (BW)] were blocked by BW and randomly allocated to 4 treatments arranged as a 2 × 2 factorial to evaluate the effects of supplemental arginine (none or 63 g/d of a 15.6% metabolizable arginine), supplemental lysine (none or 40 g/d of a 25% metabolizable lysine), and their interaction on performance and carcass composition of feedlot steers during a 170-d feeding period. The basal diet [dry matter (DM) basis] contained 52% dry-rolled corn, 22% dried distillers grains with solubles, 20% corn silage, and 6% vitamin-mineral supplement. Lysine balance was estimated to be -10.3 to -10.8 g for diets that did not contain supplemental lysine, and arginine supply was estimated to be +9.7 g for diets that did not contain supplemental arginine during period 1 (days 0 to 87). Lysine and arginine supplies met or exceeded requirements in period 2 (days 88 to 170). Rumen-protected arginine and lysine were top dressed daily until slaughter at a common BW (622 ± 5.5 kg). Data were analyzed using the MIXED procedure of SAS. Body weight, average daily gain, and DM intake were not affected (P ≥ 0.14) by arginine or lysine supplementation. However, lysine increased gain:feed (P = 0.05) during period 1. Lysine decreased serum urea nitrogen (P = 0.03) on day 87, increased (P = 0.01) longissimus muscle (LM) area, decreased (P ≤ 0.01) fat thickness and yield grade, and tended (P = 0.06) to increase moisture content of LM steaks. There tended to be an interaction for moisture content of steaks (P = 0.09), where arginine supplementation increased moisture content to a greater extent in steaks from cattle supplemented with lysine compared with steaks from cattle not fed supplemental lysine. Arginine tended to increase the proportion of Choice grade carcasses (P = 0.09) but did not change lipid content of steaks (P = 0.59). Arginine tended to decrease serum glutamate (P = 0.09) and lysine (P = 0.07) after 87 d of feeding. In conclusion, supplemental rumen-protected arginine and lysine did not improve performance, but lysine can increase carcass muscle and leanness, and although arginine did not increase lipid content of steaks, it may favorably shift carcasses to a greater quality grade.

A 2-part experiment was conducted to determine the effects of a blend of specialized mannan- and glucan-rich fractions of yeast (Select-TC, Alltech Inc.) on the health status and performance of steers during the first 2 mo of the feedlot period. Eighty crossbred steers were acquired from commercial sale barns in Mississippi and Georgia and transported to Purdue University. All animals were fed a corn silage-based receiving diet and were checked and treated daily for respiratory disease as needed following established treatment protocols. In Exp. 1, 64 steers (246.5 ± 4.7 kg initial weight) were blocked by BW and randomly allocated to 2 treatments to determine the impact of supplementation of a hydrolyzed mannan- and glucan-rich yeast fraction for 56 d on BW, ADG, daily DMI, and G:F: hydrolyzed yeast fed at 13 g (as-fed)/steer daily (TC) or nonsupplemented control (CON). Steers in Exp. 1 were housed in bedded pens with 2 animals per pen [n = 16 pens (32 steers)/treatment]. In Exp. 2, 16 steers (247.1 ± 5.4 kg initial BW) were similarly allotted to 2 treatments (CON and TC), individually penned, and subjected to a lipopolysaccharide (LPS) endotoxin challenge on day 62 or 63 after the start of the study to determine the animal’s response to an inflammatory agent. Serum samples and rectal temperatures were taken every half an hour from −2 to 8 h relative to LPS injection from steers in Exp. 2. Data were analyzed as a complete randomized block design using the MIXED procedure of SAS. Morbidity for both experiments did not differ (P ≥ 0.16). Weight, ADG, DMI, and G:F did not differ among treatments (P ≥ 0.32) in Exp. 1. After the LPS infusion in Exp. 2, rectal temperatures (P = 0.03) and serum NEFA concentration (P = 0.04) were decreased in TC compared with CON steers. Concentrations of blood urea nitrogen (P = 0.31), glucose (P = 0.70), insulin (P = 0.57), and cortisol (P = 0.77) did not differ by treatment after LPS administration. Serum IL-6 concentrations were decreased (P < 0.0001), and interferon-γ concentrations tended to be greater (P = 0.07) in TC compared with CON steers after LPS infusion. Serum cytokine and metabolite results indicate that Select-TC improved health and metabolic status of LPS-challenged cattle, but this did not result in quantifiable improvements in performance in the conditions observed in this study.

Heterotrophic production of microalgae biomass provides a consistent, high-quality source of docosahexaenoic acid (DHA; C22:6 n-3) in triglyceride oils that could be used as a ration supplement for feedlot steers to improve nutritional qualities of beef. Sixty Angus × Simmental steers (438 ± 6.4 kg) were allotted to two treatments (30 steers each, six pens, five steers/pen) to determine the effects of ForPLUS (DHA-rich microalgae Aurantiochytrium limacinum; 63.6% fat; 17.9% DHA; 30 mg/kg Sel-Plex; Alltech Inc.) on performance, insulin sensitivity, LM fatty acid composition, and meat quality. Steers were fed basal diets containing 45% corn, 30% distillers dried grains with solubles, 20% corn silage, and 5% supplement. Basal diets were formulated to contain 16.1% CP and 1.32 Mcal/kg NE(g). Treatments were delivered to steers in a ground corn-based top-dress (454 g total/steer) and contained no microalgae for control steers or 100 g/steer daily of ForPLUS for microalgae steers. A glucose tolerance test (GTT) was performed 10 d prior to slaughter. Steers were slaughtered when a target pen BW of 621 kg was achieved. Fatty acid oxidation potential was determined by measuring thiobarbituric acid reactive substances (TBARS) on LM samples collected 24 h after slaughter and aged for 48 h or 21 d. Weight and BW gain did not differ during the study (P ≥ 0.13); however, steers fed microalgae remained in the feedlot seven more days compared to steers fed the control diet (111 vs. 104 d; P = 0.04). Overall DMI decreased (P = 0.002) and G:F increased during the second half of the study (P = 0.04) in steers fed microalgae compared to steers fed the control diet. Steers fed microalgae secreted less insulin (P = 0.01) and took longer to clear glucose (P = 0.01) during a 2-h GTT. Carcass traits did not differ between treatments (P ≥ 0.23). Microalgae had no effect on n-6 content (P = 0.67), but more than doubled the n-3 fatty acid percentage and the n-3:n-6 ratio of the LM (P < 0.0001). The percentage of n-3 fatty acids C20:5 and C22:6 were increased (P < 0.0001) 4-fold and 6.25-fold, respectively, by microalgae supplementation. Concentration of TBARS did not differ in LM aged for 48 h (P = 0.91); however, when aged for 21 d, steers fed microalgae tended to produce LM with greater TBARS concentration compared to steers fed the control diet (P = 0.08). In conclusion, DHA-rich microalgae decreased DMI of steers, and increased n-3 fatty acids and beef oxidation in steaks aged for 21 d.

Stress negatively effects gastrointestinal tract (GIT) barrier function, resulting in compromised animal health. The objective of this study was to evaluate the effectiveness of aspirin to intentionally induce GIT barrier dysfunction in beef cattle. In experiment 1, sixteen crossbred heifers (425 ± 8.6 kg) were enrolled in 2 experimental periods and allotted by BW to 0, 50, 100, or 200 mg/kg BW aspirin. Four heifers per treatment received the same aspirin dose during each period, which were separated by 4 wks. Heifers were fed a 49.4% corn silage, 50.6% concentrate diet. Aspirin was delivered to animals as an oral bolus. The 200 aspirin treatment was dosed as 100 mg/kg BW aspirin 36 and 24 h prior to Cr-EDTA dosing (1 L; 180 mM). The 50 and 100 aspirin treatments were dosed 24 h prior to Cr-EDTA dosing. Urine was collected every 3 h for 48 h and analyzed for Cr using atomic absorption spectrometry. Serum was collected at 0, 24, and 48 h and analyzed for lipopolysaccharide binding protein (LBP) and interleukin-6 (IL-6) using ELISA. In experiment 2, sixteen crossbred steers (576 ± 14.2 kg) fed the same diet were allotted by BW to the 0 and 200 mg/kg BW aspirin treatments (8 steers/treatment) and were slaughtered 24 h after the last dose. Jejunal tissues were collected and tight junction mRNA expression was determined. Data were analyzed using the MIXED procedure of SAS. Aspirin linearly increased Cr absorption (P = 0.02) and elimination (P = 0.04) rate and linearly decreased mean retention time of Cr (P = 0.02). Aspirin tended to increase jejunal claudin-1 mRNA expression (P = 0.10) but did not affect serum IL-6 or LBP or expression of other jejunal tight junction mRNA (P ≥ 0.20). This study indicates that aspirin disrupts GIT barrier function in beef cattle and has potential as a model in GIT permeability research.

Postmortem aging is widely practiced in the beef industry to improve eating quality characteristics. However, the oxidative stability of aged beef muscle could be negatively affected by extending aging period. The use of ruminal bypass amino acids allows levels of crude protein in the diet to be lowered and may also positively impact oxidative stability of aged beef muscle. This study was conducted to evaluate the effects of ruminal bypass arginine (Arg) and lysine (Lys) supplementation on meat quality and oxidative stability of beef loins (M. longissimus lumborum, LL) under two durations of postmortem aging (14 and 28 days). A total of forty cattle fed four different diets (control; regular diet; Arg, additional 6 g Arg per kg feed; Lys, additional 4 g Lys per kg feed; and ArgLys, additional Arg and Lys) were harvested. At 1-day postmortem, paired LL sections were separated, vacuum-packaged, and assigned to 14 and 28 days aging at 2 degrees C. The pH, water-holding capacity (WHC), shear force, color stability, and lipid oxidation of aged beef loins were measured. An increase in aging period decreased shear force (P < 0.05), but negatively impacted color stability as indicated by decreased lean color score and increased discoloration over display (P < 0.05). Arg supplementation reduced discoloration over display (P < 0.05), while Lys supplementation resulted in no positive impact on discoloration (P > 0.05). Dietary treatment had no significant effects on pH, WHC, and shear force (P > 0.05). These findings suggest that extended aging periods could decrease oxidative stability of beef loins, which may be mitigated by Arg supplementation.