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Bovine respiratory disease (BRD) is the primary animal health concern facing feedlot producers. Many antimicrobial mitigation strategies are available, but few studies have compared feedlot performance during both the receiving and finishing periods following application of different antimicrobials used as metaphylaxis at arrival. The objective of this study was to compare antimicrobial metaphylaxis methods on clinical health and growth performance across both the receiving and finishing periods. A total of 238 multiple-sourced steers in two source blocks were used in a generalized complete block design. The four treatments included: 1) a negative control, 5 mL of sterile saline injected subcutaneously (CON); 2) subcutaneous administration of florfenicol at 40 mg/kg of BW (NUF); 3) subcutaneous administration of ceftiofur in the posterior aspect of the ear at 6.6 mg/kg of BW (EXC); and 4) subcutaneous administration of tulathromycin at 2.5 mg/kg of BW (DRA). The morbidity rate for the first treatment of BRD was decreased for the DRA and EXC treatments compared to CON and NUF (P <  0.01). Additionally, average daily gain (ADG), dry matter intake (DMI), and gain-to-feed (G:F) were greater (P  ≤ 0.02) in the DRA treatment during the receiving period compared to all other treatments. The ADG was also greater (P  < 0.05) for EXC than the CON treatment throughout the finishing period. Nonetheless, other growth performance variables did not differ among metaphylactic treatments during the finishing period (P ≥  0.14). Likewise, no differences in carcass characteristics or liver abscess score were observed (P ≥  0.18). All complete blood count (CBC) variables were affected by day (P ≤  0.01) except mean corpuscular hemoglobin concentration (P  = 0.29). Treatment × time interactions were observed for platelet count, white blood cell (WBC) count, monocyte count and percentage, and lymphocyte percentage (P ≤  0.03). However, there were no observed hematological variables that differed among treatment (P ≥  0.10). The results indicate that some commercially available antimicrobials labeled for metaphylactic use are more efficacious than others in decreasing morbidity rate. [ABSTRACT FROM AUTHOR]

Aims: Our objective was to determine how injectable antimicrobials affected populations of Salmonella enterica, Escherichia coli and Enterococcus spp. in feedlot cattle. Methods and Results: Two arrival date blocks of high‐risk crossbred beef cattle (n = 249; mean BW = 244 kg) were randomly assigned one of four antimicrobial treatments administered on day 0: sterile saline control (CON), tulathromycin (TUL), ceftiofur (CEF) or florfenicol (FLR). Faecal samples were collected on days 0, 28, 56, 112, 182 and study end (day 252 for block 1 and day 242 for block 2). Hide swabs and subiliac lymph nodes were collected the day before and the day of harvest. Samples were cultured for antimicrobial‐resistant Salmonella, Escherichia coli and Enterococcus spp. The effect of treatment varied by day across all targeted bacterial populations (p ≤ 0.01) except total E. coli. Total E. coli counts were greatest on days 112, 182 and study end (p ≤ 0.01). Tulathromycin resulted in greater counts and prevalence of Salmonella from faeces than CON at study end (p ≤ 0.01). Tulathromycin and CEF yielded greater Salmonella hide prevalence and greater counts of 128ERYRE. coli at study end than CON (p ≤ 0.01). No faecal Salmonella resistant to tetracyclines or third‐generation cephalosporins were detected. Ceftiofur was associated with greater counts of 8ERYREnterococcus spp. at study end (p ≤ 0.03). By the day before harvest, antimicrobial use did not increase prevalence or counts for all other bacterial populations compared with CON (p ≥ 0.13). Conclusions: Antimicrobial resistance (AMR) in feedlot cattle is not caused solely by using a metaphylactic antimicrobial on arrival, but more likely a multitude of environmental and management factors. [ABSTRACT FROM AUTHOR]

Our objective was to evaluate the use of a novel direct-fed microbial as an alternative to antimicrobials to decrease liver abscesses in feedlot cattle. Angus beef steers (n = 240; initial BW = 263 ± 18.0 kg) were used in a randomized complete block design comprised of 3 BW blocks and 3 pen replications per treatment. Experimental treatments were randomly assigned to pen within BW block and consisted of: 1) negative control, dietary supplement contained no tylosin phosphate (NCON); 2) positive control, dietary supplement contained tylosin phosphate (PCON); 3) positive control with tylosin phosphate removed the last 65 d of the feeding period (PCONW); and 4) novel direct-fed microbial fed at 1 g mixture/animal with 1 × 1011 CFU/g (DFM). By design, initial BW did not differ (P = 0.79) among treatments, and at the end of the 59-d receiving period, there were no differences in final BW (P = 0.25). From d 0 to d 30, ADG, DMI, DMI as a percentage of BW, and G:F did not differ (P = 0.21). Likewise, ADG, DMI, DMI as a percentage of BW, and G:F, from d 31 to d 59, were not different (P = 0.30). From d 0 to d 59, there were no differences in ADG, DMI, DMI as a percentage of BW, nor G:F (P = 0.20). During the finishing period, live- and carcassadjusted final BW did not differ (P = 0.57) among treatments. During the finishing period, there were also no differences in ADG, DMI, DMI as a percentage of BW, or G:F (P = 0.17). Carcass-adjusted ADG, DMI as a percentage of BW, and G:F also did not differ (P = 0.16). Across treatments, no differences in HCW were noted (P = 0.84). Dressing percentage, marbling score, longissimus dorsi (LM) area, 12th-rib fat thickness, and calculated yield grade (YG) were not different among dietary treatments (P = 0.32). Liver abscess incidence and severity were not affected by dietary treatments (P = 0.13). The inclusion of a novel direct-fed microbial in finishing cattle diets did not affect growth performance, carcass characteristics, nor the prevalence of liver abscesses. However, the removal of tylosin phosphate 65 d before harvest numerically resulted in the lowest frequency of severe liver abscesses when compared with steers not fed tylosin phosphate. [ABSTRACT FROM AUTHOR]

The bovine ocular microbiome is of interest because of its potential role in ocular disease, such as infectious bovine keratoconjunctivitis. The ocular bacterial community of 223 pre-weaned beef calves from a single cohort were sampled four times; day 0, day 21, day 41, and day 139 (mean calf ages 65, 86, 99, and 204 days, respectively). The bacterial community was phenotyped using the V4 region of the 16S rRNA gene and were grouped into amplicon sequence variants (ASV) which were taxonomically classified at the phylum and family level. Heritability was estimated for the log transformed relative abundance of each phylum, family, and ASV at each time point using ASReml v. 4.2. The model included calf age at time of sampling, calf sex, pinkeye vaccination treatment group, breed fractions, and retained heterosis as fixed effects. The random effect of animal had a (co)variance structure given by an H matrix comprised of 3,025 animals of which 1,207 were genotyped including all of the sampled animals. Heritability estimates ranged from 0.16 to 0.95 at the ASV level, 0.18 to 0.91 at the family level, and 0.18 to 0.81 at the phylum level. Standard errors were approximately 0.20 on average. The number of features (ASV, family, or phylum) with estimates greater than their standard error changed across time points (Table 1). Overall, time point 1 had the largest number of features with estimates greater than their standard error, followed by time point 4. Time point 3 had a greater number ASV with estimates greater than their standard error than time point 2; however, time point 2 had greater numbers of families and phyla with estimates greater than their standard errors. This trend likely stems from the fact that time points 1 and 4 had the greatest diversity of features while time point 2 had the least diversity. Average Chao1 index diversity estimates of ASV were 144.6, 28.1, 64.7, and 194.6, for time points 1 through 4, respectively. We hypothesize this is due to the perturbation of the ocular microbiome at sampling and the fact that overall diversity in the microbiome recovered by the final sampling, although, species composition differed compared with time point 1. While no ASV, family, or phylum had a heritability estimate greater than its standard error across all time points, certain features had heritabilities greater than their standard errors at multiple time points. The phylum Armatimonadota had heritability estimates greater than their standard error at time points 1, 2, and 4 (0.52, 0.18, and 0.37, respectively). Additionally, an ASV of the Streptococcus genus had estimates of 0.26, 0.45, and 0.26 at time points 1, 2, and 3, respectively. These estimates demonstrate that certain features of the ocular microbiome are influenced by host genetics. [ABSTRACT FROM AUTHOR]

Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum , commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F. necrophorum to invade the bloodstream and colonize the liver. The objective of this study was to determine the changes in gene expression in the rumen epithelium and microbial populations adherent to the rumen epithelium and in the rumen contents of beef cattle with liver abscesses compared with those with no liver abscesses. Rumen epithelial tissue and rumen content were collected from 31 steers and heifers with liver abscesses and 30 animals with no liver abscesses. Ribonucleic acid (RNA) sequencing was performed on the rumen epithelium, and a total of 221 genes were identified as differentially expressed in the animals with liver abscesses compared with animals with no abscesses, after removal of genes that were identified as a result of interaction with sex. The nuclear factor kappa-light-chain enhancer of activated B cells signaling and interferon signaling pathways were significantly enriched in the differentially expressed gene (DEG) set. The majority of the genes in these pathways were downregulated in animals with liver abscesses. In addition, RNA translation and protein processing genes were also downregulated, suggesting that protein synthesis may be compromised in animals with liver abscesses. The rumen content bacterial communities were significantly different from the rumen wall epimural bacterial communities. Permutational multivariate analysis of variance (PERMANOVA) analysis did not identify global differences in the microbiome of the rumen contents but did identify differences in the epimural bacterial communities on the rumen wall of animals without and with liver abscesses. In addition, associations between DEG and specific bacterial amplicon sequence variants of epimural bacteria were observed. The DEG and bacterial profile on the rumen papillae identified in this study may serve as a method to monitor animals with existing liver abscesses or to predict those that are more likely to develop liver abscesses. [ABSTRACT FROM AUTHOR]

Among the major sources of methane production, ruminants account for a considerable fraction of the anthropogenic methane produced. Thus, minimizing methane emission in intensive and extensive cattle production systems while maintaining/increasing performance of animals will have a significant impact on the environment and will help develop a sustainable carbon-based market system. We believe that developing science-based dietary intervention strategies using feed additives to manipulate rumen microbial communities is a viable strategy to reduce greenhouse gas emissions. Here we show the potential impact of using an essential oil formulation to reduce methane emissions in cattle. In this study, we used in-vitro fermentation experiments to evaluate the impact of the essential oil mix in reducing methane emissions. Additionally, we evaluated microbial community changes in the presence and absence of the essential oil mix to understand microbial changes that lead to reduced methane emissions. The in-vitro fermentation experiments demonstrated a significant decrease in methane emission in the essential oil mix compared with the control with no essential oil (P < 0.05). This decrease in methane was greater than 50%. Following in-vitro fermentation for 48 hours, the resulting inoculum was evaluated for microbial community changes using 16S rDNA sequencing. Compared with the control, the essential oil mix containing bottles were greater in Anaerovibrio and Succinivibrio and had a reduced abundance of Anaeroplasma and Prevotellaceae at the genus level. Furthermore, the essential oil mix tubes were plated to isolate members that were enriched in this treatment. The isolates obtained include Lysinibacillus halotolerans and Lysinibacillus boronitolerans. Such isolates may have the potential to be effective direct-fed microbial to reduce methane emission. Here we show the potential of the essential oil mix identified to reduce methane invitro and we have an animal study planned for the near future. [ABSTRACT FROM AUTHOR]

The importance of the rumen microbiota on nutrient cycling to the animal is well recognized; however, our understanding of the influence of the rumen microbiome composition on feed efficiency is limited. The rumen microbiomes of two large animal cohorts (125 heifers and 122 steers) were characterized to identify specific bacterial members (operational taxonomic units [OTUs]) associated with feed efficiency traits (ADFI, ADG, and G:F) in beef cattle. The heifer and steer cohorts were fed a forage-based diet and a concentrate-based diet, respectively. A rumen sample was obtained from each animal via esophageal tubing and bacterial community composition was determined through 16S rRNA gene sequencing of the V4 region. Based on a regression approach that used individual performance measures, animals were classified into divergent feed efficiency groups. Within cohort, an extreme set of 16 animals from these divergent groups was selected as a discovery population to identify differentially abundant OTUs across the rumen bacterial communities. The remaining samples from each cohort were selected to perform forward stepwise regressions using the differentially abundant OTUs as explanatory variables to distinguish predictive OTUs for the feed efficiency traits and to quantify the OTUs collective impact on feed efficiency phenotypes. OTUs belonging to the families Prevotellaceae and Victivallaceae were present across models for heifers, whereas OTUs belonging to the families Prevotellaceae and Lachnospiraceae were present across models for steers. Within the heifer cohort, models explained 19.3%, 25.3%, and 19.8% of the variation for ADFI, ADG, and G:F, respectively. Within the steer cohort, models explained 27.7%, 32.5%, and 26.9% of the variation for ADFI, ADG, and G:F, respectively. Overall, this study suggests a substantial role of the rumen microbiome on feed efficiency responses. [ABSTRACT FROM AUTHOR]

In this study, we investigated the degree to which host genetics shape the rumen microbiome. Complex and diverse microbial communities can alter the nutrient profile available to the animal and subsequent performance. Studies of the gut microbiome have demonstrated that host genotype influences gut microbial species composition. Therefore, microbial species composition in the rumen may be a complex trait that manifests through the convergence of host-genetics and environmental factors. To test this hypothesis, we collected rumen contents and blood samples from 586 beef cattle on different diets from two locations. The rumen samples were used to sequence the V4 region of the 16S rDNA on an Illumina MiSeq platform. Animals were genotyped with various platforms and a common set of 61,974 SNP were used to conduct a genome-wide association study (GWAS) using the microbiome (OTUs, families and phyla) as response variables. The GWAS was performed using Bayesian GBLUP fitting fixed effects of cohort (location and date), and the first 2 principle components to account for population stratification. Median posterior genomic heritability estimates were 0.110, 0.124, and 0.141 at the OTU, family and phylum taxonomic level, respectively. The top 8 1-Mb windows for OTUs, families and phyla were located on 7 different chromosomes. These regions affect the rumen microbiota in multiple ways; some (chromosome 19; position 3.0–4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae , and RF16), some (chromosome 27; position 3.0–4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae , RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0–1.0) controlling both related and unrelated taxa. Overall, the 8 regions identified control 11 different families and 6 different phyla. This study shows that host genetics can affect rumen bacterial community members and points towards the possibility that genomics can be used to manipulate the rumen microbiome. [ABSTRACT FROM AUTHOR]