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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.

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]

Microbiome research has gained significant momentum in the last decade. Although many studies have investigated livestock microbiome to improve animal health and productivity, only a few microbiome manipulation approaches are currently used in the industry. This is partly due to the limited understanding of livestock microbiome and how such knowledge can be applied to improve animal health and performance. Additionally, the potential role of the microbiome is poorly characterized, limiting the opportunities available to improve animal health and productivity through microbiome manipulation. Here we describe and demonstrate how current microbiome theory such as "colonization history" can be utilized to establish beneficial microbiomes in livestock species. Our data suggest that the sow microbiome greatly impacts the early microbiome establishment in piglets and represents as much as 67% of the community even after 21 days following birth. This suggests early colonization provides unique opportunities to establish "beneficial" microbiomes. Additionally, we describe how microbiome-wide association studies (MWAS) can be used to quantify the microbial role in animal performance using a cattle population consisting of more than 750 animals. Finally, we describe how livestock animal models can be used to understand key concepts of microbial establishment and how such models can be used to investigate the human microbiome using germ free pig models. USDA is an equal opportunity provider and employer. [ABSTRACT FROM AUTHOR]

In light of recent host-microbial association studies, a consensus is evolving that species composition of the gastrointestinal microbiota is a polygenic trait governed by interactions between host genetic factors and the environment. Here, we investigated the effect of host genetic factors in shaping the bacterial species composition in the rumen by performing a genome-wide association study. Using a common set of 61,974 single-nucleotide polymorphisms found in cattle genomes (n = 586) and corresponding rumen bacterial community composition, we identified operational taxonomic units (OTUs), Families and Phyla with high heritability. The top associations (1-Mb windows) were located on 7 chromosomes. These regions were associated with 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) associated with both related and unrelated taxa. The annotated genes associated with identified genomic regions suggest the associations observed are directed toward selective absorption of volatile fatty acids from the rumen to increase energy availability to the host. This study demonstrates that host genetics affects rumen bacterial community composition. [ABSTRACT FROM AUTHOR]