Bovine respiratory microbiota of feedlot cattle and its association with disease

Bovine respiratory disease (BRD), as one of the most common and costly diseases in the beef cattle industry, has significant adverse impacts on global food security and the economic stability of the industry. The bovine respiratory microbiome is strongly associated with health and disease and may provide insights for alternative therapy when treating BRD. The niche-specific microbiome communities that colonize the inter-surface of the upper and the lower respiratory tract consist of a dynamic and complex ecological system. The correlation between the disequilibrium in the respiratory ecosystem and BRD has become a hot research topic. Hence, we summarize the pathogenesis and clinical signs of BRD and the alteration of the respiratory microbiota. Current research techniques and the biogeography of the microbiome in the healthy respiratory tract are also reviewed. We discuss the process of resident microbiota and pathogen colonization as well as the host immune response. Although associations between the microbiota and BRD have been revealed to some extent, interpreting the development of BRD in relation to respiratory microbial dysbiosis will likely be the direction for upcoming studies, which will allow us to better understand the importance of the airway microbiome and its contributions to animal health and performance.

Comparative Microbiomes of the Respiratory Tract and Joints of Feedlot Cattle Mortalities

A comparative study of microbiota of the respiratory tract and joints of bovine respiratory disease (BRD) cattle mortalities was undertaken. Nasopharynx, trachea, lung and joint samples were collected from 32 cattle that died of BRD, “cases”, and 8 that died of other causes, “controls”. Bacterial diversity was lower (p < 0.05) in the nasopharynx, trachea and lungs of cases as compared to controls. In cases, alpha-diversity (p < 0.05) was lower in the lungs and joints than the nasopharynx. Proteobacteria, Tenericutes, Bacteroidetes, Firmicutes and Actinobacteria were the most abundant phyla in all samples. Relative abundances of Mycoplasma spp. in the lung, Pasteurella spp. in the trachea and lung, and Histophilus spp. in the lung, trachea and nasopharynx of cases were higher (p < 0.001) than controls. Mycoplasma spp. comprised 20.5% of bacterial flora in the joint, 36.0% in the lung, 22.4% in the trachea and 8.8% in the nasopharynx. Mannheimia spp. (21.8%) and Histophilus spp. (10.4%) were more abundant in lungs. Cattle that died of BRD possessed less diverse respiratory microbiomes with a higher abundance of respiratory pathogens. Mycoplasma spp. were prominent members of pneumonic lungs and joints displaying septic arthritis.

Kinome Analysis of Cattle Peripheral Lymph Nodes to Elucidate Differential Response to Salmonella spp.

Salmonella spp., contained within the peripheral lymph nodes (PLNs) of cattle, represents a significant source of contamination of ground beef. Herein is the first report where species-specific kinome peptide arrays designed for bovine biology were used to further the understanding of Salmonella spp. within these PLNs. For the purpose of this research, multiple comparisons of sub-iliac lymph nodes were made to include nodes from feedlot cattle that were infected with Salmonella spp. to those that were non-infected; seasonal differences in feedlot cattle harvested in either August or January; cull dairy cows compared to feedlot cattle; and PLNs from cattle experimentally inoculated with Salmonella spp. versus naturally infected animals. The first comparison of Salmonella-positive and -negative PLNs found that considering the kinotypes for these animals, the major distinguishing difference was not the presence or absence of Salmonella spp. in the PLNs but the concentration. Further, the majority of pathways activated were directly related to immune responses including innate immunity, thus Salmonella spp. within the PLNs activates the immune system in that node. Results from the comparison of feedlot cattle and cull dairy cows suggests that a Salmonella spp.-negative animal, regardless of type, has a more consistent kinome profile than that of a Salmonella spp.-positive animal and that the differences between feedlot and cull dairy cattle are only pronounced when the PLNs are Salmonella spp. positive. PLNs collected in the winter showed a much more consistent kinome profile, regardless of Salmonella status, suggesting that in the winter these cattle are similar, and this is not affected by the presence of Salmonella spp., whereas significant variability among kinotypes was observed for PLNs collected in the summer. The most distinct clustering of kinotypes observed in this study was related to how the animal was infected with Salmonella spp. There were significant differences in the phosphorylation state of the immune response peptides between experimentally and naturally infected animals, suggesting that the immune system is activated in a significantly different manner when comparing these routes of infection. Increasing our understanding of Salmonella spp. within cattle, and specifically within the PLNs, will ultimately help design effective pre-harvest intervention strategies as well as appropriate experimentation to validate those technologies.

A Single Intranasal Dose of Bacterial Therapeutics to Calves Confers Longitudinal Modulation of the Nasopharyngeal Microbiota

To address the emergence of antimicrobial-resistant pathogens in livestock, microbiome-based strategies are increasingly being sought to reduce antimicrobial use. Here, we describe the intranasal application of bacterial therapeutics (BTs) for mitigating bovine respiratory disease (BRD) and used structural equation modeling to investigate the causal networks after BT application. Beef cattle received i) an intranasal cocktail of previously characterized BT strains, ii) an injection of metaphylactic antibiotic tulathromycin or iii) intranasal saline. Despite being transient colonizers, inoculated BT strains induced longitudinal modulation of the nasopharyngeal bacterial microbiota while showing no adverse effect on animal health. The BT-mediated changes in bacteria included reduced diversity and richness and strengthened cooperative and competitive interactions. In contrast, tulathromycin increased bacterial diversity and antibiotic resistance, and disrupted bacterial interactions. Overall, a single intranasal dose of BTs can modulate the bovine respiratory microbiota, highlighting that microbiome-based strategies have the potential in being utilized to mitigate BRD in feedlot cattle.

Supplementing a blend of magnesium oxide to feedlot cattle: effects on ruminal, physiological, and productive responses

This experiment evaluated ruminal, physiological, and productive responses of feedlot cattle consuming a corn-based finishing diet that included different levels of a magnesium oxide (MG) blend. Yearling cattle (58 heifers and 62 steers) were ranked by sex and initial body weight (BW; 407 ± 3.1 kg), and allocated to 4 groups of 30 animals each. Groups were housed in 1 of 4 drylot pens (30 × 12 m) equipped with GrowSafe automated feeding systems (Model 6000E, 4 bunks/pen) during the experiment (d -14 to 117). On d 0, groups were randomly assigned to receive a total-mixed ration without (CON; n = 30) or with the inclusion (as-fed basis) of MG at 0.25% (MG25; n = 30), 0.50% (MG50; n = 30), or 0.75% (MG75; n = 30) until slaughter on d 118. Individual feed intake was recorded daily, and BW were recorded every 14 d and prior to slaughter (d 117). Blood samples were collected on d 0, 28, 56, 84 and 112, and hair samples were collected on d 0, 56 and 112 from the tail-switch. On d 42, 8 rumen-cannulated steers (BW = 492 ± 8.0 kg) were housed with yearling cattle (1 pair/pen). Pairs rotated among groups every 14 d, resulting in a replicated 4 × 4 Latin square design (n = 8/treatment; d 42 to 98). Rumen pH was measured on d 7 and 14 of each period (0800, 1200, 1600 and 2000 h). Orthogonal contrasts were used to determine if inclusion of MG (0, 0.25, 0.50, or 0.75% of the diet) yielded linear or quadratic effects, and to explore overall effect of MG supplementation (CON vs. MG25 + MG50 + MG75). No treatment differences were noted (P ≥ 0.31) for BW gain, feed intake, or feed efficiency. Cattle supplemented with MG tended have less carcass marbling (P = 0.07) compared with CON. Inclusion of MG linearly increased (P &lt; 0.01) mean plasma concentrations of magnesium, and tended to linearly decrease (P = 0.09) mean plasma concentrations of haptoglobin. Cattle supplemented with MG had greater (P &lt; 0.01) mean plasma concentrations of cortisol compared with CON. Hair cortisol concentration did not differ between treatments on d 56 (P ≥ 0.25), and linearly decreased (P &lt; 0.01) with MG inclusion on d 112 (treatment × day; P = 0.02). Inclusion of MG linearly increased (P = 0.03) mean rumen pH, but these outcomes were mostly noted during the last two sampling of the day (treatment × hour; P = 0.02). Collectively, supplemental MG was effective in controlling rumen pH in cattle receiving a corn-based finishing diet, but without improvements in feedlot performance and carcass merit.

Understanding the transmission dynamics of Escherichia coli O157:H7 super-shedding infections in feedlot cattle

Background The presence of Escherichia coli O157:H7 (E. coli O157:H7) super-shedding cattle in feedlots has the potential to increase the overall number (bio-burden) of E. coli O157:H7 in the environment. It is important to identify factors to reduce the bio-burden of E. coli O157 in feedlots by clarifying practices associated with the occurrence of super-shedders in feedlot cattle. Methods The objective of this study is to (1) identify host, pathogen, and management risk factors associated with naturally infected feedlot cattle excreting high concentrations of E. coli O157:H7 in their feces and (2) to determine whether the ingested dose or the specific strain of E. coli O157:H7 influences a super-shedder infection within experimentally inoculated feedlot cattle. To address this, (1) pen floor fecal samples and herd parameters were collected from four feedlots over a 9-month period, then (2) 6 strains of E. coli O157:H7, 3 strains isolated from normal shedder steers and 3 strains isolated from super-shedder steers, were inoculated into 30 one-year-old feedlot steers. Five steers were assigned to each E. coli O157:H7 strain group and inoculated with targeted numbers of 102, 104, 106, 108, and 1010 CFU of bacteria respectively. Results In the feedlots, prevalence of infection with E. coli O157:H7 for the 890 fecal samples collected was 22.4%, with individual pen prevalence ranging from 0% to 90% and individual feedlot prevalence ranging from 8.4% to 30.2%. Three samples had E. coli O157:H7 levels greater than 104 MPN/g feces, thereby meeting the definition of super-shedder. Lower body weight at entry to the feedlot and higher daily maximum ambient temperature were associated with increased odds of a sample testing positive for E. coli O157:H7. In the experimental inoculation trial, the duration and total environmental shedding load of E. coli O157:H7 suggests that the time post-inoculation and the dose of inoculated E. coli O157:H7 are important while the E. coli O157:H7 strain and shedding characteristic (normal or super-shedder) are not. Discussion Under the conditions of this experiment, super-shedding appears to be the result of cattle ingesting a high dose of any strain of E. coli O157:H7. Therefore strategies that minimize exposure to large numbers of E. coli O157:H7 should be beneficial against the super-shedding of E. coli O157:H7 in feedlots.

Factors associated with Bovine Respiratory Disease case fatality in feedlot cattle

Bovine Respiratory Disease (BRD) is the primary cause of morbidity and mortality in cattle feedlots. There is a need to understand what animal health and production factors are associated with increased mortality risk due to BRD. The aim of the present study was to explore factors associated with BRD case fatality in feedlot cattle. Four pens totalling 898 steers were monitored daily for visual signs of BRD such as difficult breathing and coughing, and animals exhibiting signs of BRD were taken to the hospital shed for further examination and clinical measures. Blood samples were obtained at feedlot entry and at time of first BRD pull from animals diagnosed with BRD (n=121) and those that died due to BRD confirmed by post-mortem examination (n=16; 13.2% case fatality rate). Mixed-effects linear regression models were used to estimate differences in animal health and production factors and the relative concentrations of 34 identified blood metabolites between animals that survived versus those that died. Generalised linear mixed-effects models were used to obtain the odds of being seronegative (at both feedlot entry and first BRD pull) to five BRD viruses and having a positive nasal swab result at the time of first pull in died and survived animals. Animals that died from BRD had lower average daily gain (ADG), reduced weight at first BRD pull, higher visual BRD scores and received more treatments for BRD compared to animals that survived BRD (P &lt; 0.05). The odds of being seronegative for bovine viral diarrhea virus 1 (BVDV-1) was 5.66 times higher for animals that died compared to those that survived (P = 0.013). The odds of having a positive bovine coronavirus nasal swab result were 13.73 times higher in animals that died versus those that survived (P = 0.007). Animals that died from BRD had higher blood concentrations of α glucose chain, β-hydroxybutyrate, leucine, phenylalanine and pyruvate compared to those that survived (P &lt; 0.05). Animals that died from BRD had lower concentrations of acetate, citrate and glycine compared to animals that survived (P &lt; 0.05). The results of the current study suggest that ADG to first BRD pull, weight at first BRD pull, visual BRD score, the number of BRD treatments, seronegativity to BVDV-1, virus positive to BCoV nasal swab, and that certain blood metabolites are associated with BRD case fatality risk. The ability of these measures to predict the risk of death due to BRD needs further research.

Fecal Microbiome Modulation of Bacterial Communities Associated With the Administration of Probiotic Lactic Acid Bacteria to Feedlot Cattle

Modulation of animal gut microbiota is a prominent function of probiotics to improve the health and performance of livestock. In this study, a large-scale survey to evaluate the effect of lactic acid bacteria probiotics on shaping the fecal bacterial community structure of 126 feedlot cattle during three experimental periods of the fattening cycle (163 days) was conducted. A feedlot industry located in northwestern Argentina was enrolled with cattle fed mixed rations (forage and increasing grain diet). High-throughput sequencing (HTS) of 16S rDNA amplicons was applied to characterize the fecal microbiota and explore its modulation as affected by the administration of five probiotic groups and experimental administration periods. The microbial diversity of fecal samples was significantly affected (p < 0.05) by the administration period compared with probiotic group supplementation. The fecal microbiome of samples was dominated by the Firmicutes (72-98%) and Actinobacteria (0.8-27%) phyla, while a lower abundance of Bacteroidetes (0.08-4.2%) was present. At the family level, probiotics were able to modulate the fecal microbiota with a convergence of Clostridiaceae, Lachnospiraceae, Ruminococcaceae and Bifidobacteriaceae associated with health and growth benefits as core microbiome members. Metabolic functional prediction comparing experimental administration periods showed an enrichment of metabolic pathways related to complex plant-derived polysaccharide digestion as well as amino acids and derivatives during the first 40 days of probiotic supplementation. Genomic-based knowledge on the benefits of autochthonous probiotics on cattle gastrointestinal tract (GIT) microbiota composition and functions will contribute to their selection as antibiotic alternatives for the feedlot industry.

Effect of protein source and non-roughage NDF content in finishing diets of feedlot cattle fed free-choice hay on growth performance and carcass characteristics

One-hundred twenty crossbreed steers (initial body weight (BW) 566 ± 42 kg) were used to evaluate the interaction of protein source (PS) and non-roughage NDF content (NRFC) in finishing diets of feedlot cattle fed free-choice hay on performance and carcass characteristics. Steers were stratified by BW and randomly assigned to 8 pens (2×2 factorial) and fed for 104 ± 10 d. Four dietary treatments were investigated: 1) distillers’ dry grains with solubles (DDGS) and a low NRFC (DLF), 2) DDGS and a high NRFC (DHF), 3) soybean meal (SBM) and a low NRFC (SLF), 4) SBM and a high NRFC (SHF). Free-choice grass hay and concentrates were offered in a different bunk. Data were analyzed as a randomized complete block design. Do to the confounded effect of PS and protein intake, a linear regression was used to evaluate the effect of protein intake in growth performance. For gain to feed ratio (G:F) an interaction tended to occur (P = 0.10) between PS and NRFC. Steers on the DHF treatment had a lower G:F compared with SLF and SHF. Feeding SBM increased (P = 0.05) final BW, tended to increase (P = 0.06) average daily gain (ADG), and decreased (P = 0.05) hay intake (HI) compared with steers fed DDGS. There was a positive association (P ˂ 0.01) of crude protein intake with ADG and FBW. Dietary NRFC did not change (P ≥ 0.3) final BW, ADG, DMI, and HI. Protein source did not affect (P ≥ 0.16) hot carcass weight (HCW), longissimus muscle (LM) area, dressing, 12th rib fat thickness, or marbling score (MS). No differences were detected between NRFC for dressing, HCW, LM area, or MS (P ≥ 0.18); but diets with greater NRFC decreased (P = 0.03) the 12th rib fat thickness. Steers in the SHF treatment presented the lesser kidney-pelvic-heart fat compared with the remaining treatments (PS×NRFC interaction, P = 0.04). Soybean meal inclusion/increase in protein intake improved growth performance of feedlot steers compared with DDGS, despite protein intake meet the protein requirement. Increasing the NRFC did not affect growth or HI but decreased feed efficiency of steers fed DDGS.

Effects of feeding lubabegron on gas emissions, growth performance, and carcass characteristics of beef cattle housed in small-pen environmentally monitored enclosures during the last 3 months of the finishing period

The development of technologies that promote environmental stewardship while maintaining or improving the efficiency of food animal production is essential to the sustainability of producing a food supply to meet the demands of a growing population. As such, Elanco (Greenfield, IN) pursued an environmental indication for a selective β-modulator (lubabegron; LUB). LUB was recently approved by the United States Food and Drug Administration (FDA) to be fed to feedlot cattle during the last 14 to 91 d of the feeding period for reductions in gas emissions/kg of unshrunk final BW and HCW. A 4 × 2 factorial arrangement of treatments was used with the factors of dose (0.0, 1.38, 5.5 or 22.0 mg·kg-1 DM basis) and sex (steers or heifers). Three 91-d cycles were conducted (112 cattle/cycle) with each dose × sex combination being represented by a single cattle pen enclosure (CPE; 14 cattle/CPE) resulting in a total of 168 steers and 168 heifers (n = 6 replicates/dose). There were no interactions observed between dose and sex for any variable measured in the study (P ≥ 0.063). Five gases were evaluated for all pens based on CPE concentrations relative to ambient air: NH3, CH4, N2O, H2S, and CO2. Cumulative NH3 gas emissions were reduced by feeding cattle 5.5 and 22.0 mg·kg-1 LUB (P ≤ 0.023) and tended (P = 0.076) to be lower for the cattle fed 1.38 mg·kg-1 LUB compared to the negative controls (CON). The cumulative NH3 gas emission reductions of 960 to 1032 g, coupled with HCW increases (P ≤ 0.019) of 15 kg to 16 kg for all LUB doses vs. CON, led to reductions in NH3 gas emissions/kg HCW for all 3 LUB treatments (P ≤ 0.004). Similar to HCW, reductions in NH3 gas emissions/kg of unshrunk final BW were observed for all LUB doses (P ≤ 0.009) and were attributable to both decreases in NH3 gas emissions and numerical increases in BW. Dose had no effect on cumulative emissions or emissions standardized by BW or HCW for the other 4 gases (P ≥ 0.268). Lubabegron is a novel tool to reduce emissions of NH3 gas per kg of unshrunk live BW and hot carcass weight.