High deoxynivalenol and ergot alkaloid levels in wheat grain: effects on growth performance, carcass traits, rumen fermentation, and blood parameters of feedlot cattle

This study was designed to assess the impacts of a mixture of deoxynivalenol (DON) and ergot alkaloids (EAs) on growth performance, rumen function, blood parameters, and carcass traits of feedlot cattle. Forty steers (450 ± 6.0 kg) were stratified by weight and randomly allocated to 1 of 4 treatments; control-low (CON-L), control-high (CON-H) which contained low or high wheat screenings that lacked mycotoxins at the same level as the mycotoxin-low (MYC-L; 5.0 mg/kg DON, 2.1 mg/kg EA), and mycotoxin-high (MYC-H: 10 mg/kg DON, 4.2 mg/kg EA) diets that included wheat screening with mycotoxins. Steers were housed in individual pens for a 112-day finishing trial. Intake was 24.8% lower (P < 0.001) for MYC steers compared to CON steers. As a result, average daily gains of MYC steers were 42.1% lower (P < 0.001) than CON steers. Gain to feed ratio was also lower (P < 0.001) for MYC steers compared to CON steers. Platelets, alanine aminotransferase, globulins, and blood urea nitrogen were lower (P ≤ 0.008), and lymphocytes, glutathione peroxidase activity (GPx), and interleukin-10 (IL-10) were elevated (P ≤ 0.002) in MYC steers compared to CON steers. Hot carcass weights and backfat thickness were reduced (P < 0.001) in MYC steers, resulting in leaner (P < 0.001) carcasses and higher (P < 0.007) meat yield compared to CON steers. Results suggest that a mixture of DON and EAs negatively impacted health, performance, and carcass traits of feedlot steers, with the majority of this response likely attributable to EAs. However, more research is needed to distinguish the relative contribution of each mycotoxin to the specific responses observed.

Enterococci as a One Health Indicator of Antimicrobial Resistance

The rapid increase of antimicrobial resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial resistant bacteria. Globally, antimicrobial resistance is recognized as an One-health problem affecting humans, animals and environment. Enterococcal species are gram positive bacteria that are widely distributed in nature. Their occurrence, prevalence and persistence across the One-health continuum make them an ideal candidate to study antimicrobial resistance from a One-health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One-health sectors. We also briefly address the prevalence of enterococci in human, animal and environmental settings. In addition, a 16S RNA gene based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and if they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in Enterococcal species across the One Health Continuum.

Antimicrobial Activities of α-Helix and β-Sheet Peptides against the Major Bovine Respiratory Disease Agent, Mannheimia haemolytica

Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in cattle raised in North America. At the feedlot, cattle are subject to metaphylactic treatment with macrolides to prevent BRD, a practice that may promote antimicrobial resistance and has resulted in an urgent need for novel strategies. Mannheimia haemolytica is one of the major bacterial agents of BRD. The inhibitory effects of two amphipathic, α-helical (PRW4, WRL3) and one β-sheet (WK2) antimicrobial peptides were evaluated against multidrug-resistant (MDR) M. haemolytica isolated from Alberta feedlots. WK2 was not cytotoxic against bovine turbinate (BT) cells by the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. All three peptides inhibited M. haemolytica, with WK2 being the most efficacious against multiple isolates. At 8-16 µg/mL, WK2 was bactericidal against Mh 330 in broth, and at 32 µg/mL in the presence of BT cells, it reduced the population by 3 logs CFU/mL without causing cytotoxic effects. The membrane integrity of Mh 330 was examined using NPN (1-N-phenylnaphthylamine) and ONPG (o-Nitrophenyl β-D-galactopyranoside), with both the inner and outer membranes being compromised. Thus, WK2 may be a viable alternative to the use of macrolides as part of BRD prevention and treatment strategies.

Evaluating the liver abscess microbiota of beef cattle during a reduction in tylosin supplementation shows differences according to abscess size and fraction

Liver abscesses (LA) resulting from bacterial infection in cattle pose a significant global challenge to the beef and dairy industries. Economic losses from liver discounts at slaughter and reduced animal performance drive the need for effective mitigation strategies. Tylosin phosphate supplementation is widely used to reduce LA occurrence, but concerns over antimicrobial overuse emphasize the urgency to explore alternative approaches. Understanding the microbial ecology of LA is crucial to this, and we hypothesized that a reduced timeframe of tylosin delivery would alter LA microbiomes. We conducted 16S rRNA sequencing to assess severe liver abscess bacteriomes in beef cattle supplemented with in-feed tylosin. Our findings revealed that shortening tylosin supplementation did not notably alter microbial communities. Additionally, our findings highlighted the significance of sample processing methods, showing differing communities in bulk purulent material and the capsule-adhered material. Fusobacterium or Bacteroides ASVs dominated LA, alongside probable opportunistic gut pathogens and other microbes. Moreover, we suggest that liver abscess size correlates with microbial community composition. These insights contribute to our understanding of factors impacting liver abscess microbial ecology and will be valuable in identifying antibiotic alternatives. They underscore the importance of exploring varied approaches to address LA while reducing reliance on in-feed antibiotics.

The Science of Shiga Toxin-Producing (Verotoxin-Producing) Escherichia coli (STEC): An Ongoing One Health Journey toward Improved Health and Food Safety-Editorial Summary

Verotoxigenic Escherichia coli (VTEC), also termed Shiga toxin-producing Escherichia coli (STEC), is a human pathogen transmitted by food, water, animals, and their environment, and from one person to another [...].

In Silico Analysis of Shiga Toxin-Producing Escherichia coli O157:H7 Strains from Presumptive Super- and Low-Shedder Cattle

Cattle are the primary reservoir for STEC O157, with some shedding >104 CFU/g in feces, a phenomenon known as super-shedding (SS). The mechanism(s) responsible for SS are not understood but have been attributed to the environment, host, and pathogen. This study aimed to compare genetic characteristics of STEC O157 strains from cattle in the same commercial feedlot pens with SS or low-shedding (LS) status. Strains from SS (n = 35) and LS (n = 28) collected from 11 pens in three feedlots were analyzed for virulence genes, Shiga toxin-carrying bacteriophage insertion sites, and phylogenetic relationships. In silico analysis showed limited variation regarding virulence gene profiles. Stx-encoding prophage insertion sites mrlA and wrbA for stx1a and stx2a, respectively, were all occupied, but two isolates had fragments of the stx-carrying phage in mrlA and wrbA loci without stx1a and stx2a. All strains screened for lineage-specific polymorphism assay (LSPA-6) were 111111, lineage I. Of the isolates, 61 and 2 were clades 1 and 8, respectively. Phylogenetic analysis revealed that pens with more than one SS had multiple distantly related clusters of SS and LS isolates. Although virulence genes and lineage were largely similar within and across feedlots, multiple genetic origins of strains within a single feedlot pen illustrate challenges for on-farm control of STEC.

Effect of continuous or intermittent feeding of ergot contaminated grain in a mash or pelleted form on the performance and health of feedlot beef steers

This study evaluated the effect of feeding ergot contaminated grain continuously or intermittently through backgrounding (BG) and finishing (FN) in a mash or pelleted supplement on the growth performance, health and welfare parameters, and carcass characteristics of feedlot beef steers. Sixty black Angus steers (300 ± 29.4 kg BW) were used in a complete randomized 238-d study. Steers were stratified by weight and randomly assigned to four different diets (15 steers/treatment) and individually housed. Treatments included: (1) control [CON; no added ergot alkaloids (EA)], (2) continuous ergot mash (CEM; fed continuously at 2 mg total EA/kg of DM), (3) intermittent ergot mash (IEM; fed at 2 mg total EA/kg of DM, during the first week of each 21-d period and CON for the remaining 2 wk, this feeding pattern was repeated in each period), and (4) intermittent ergot pellet (IEP; fed at 2 mg of total EA/kg of DM as a pellet during the first week of each 21-d period and CON for the remaining 2 wk as described for IEM). Steers were fed barley based BG diets containing 40% concentrate:60% silage (DM basis) for 84 d (four 21-d periods), transitioned over 28 d (no ergot fed) to an FN diet (90% concentrate:10% silage DM basis) and fed for 126 d (six 21-d periods) before slaughter. In the BG phase, steer DMI (P < 0.01, 7.45 vs. 8.05 kg/d) and ADG (P < 0.01) were reduced for all EA diets compared to CON. The CEM fed steers had lower ADG (P < 0.01, 0.735 vs. 0.980 kg) and shrunk final BW (P < 0.01, 350 vs. 366 kg) than CON. CEM had lower gain:feed (P < 0.07, 0.130 vs. 0.142) than CON. In the FN phase, steer DMI (P < 0.01, 9.95 vs. 11.05 kg/d) and ADG (P = 0.04) were also decreased for all EA fed steers compared to CON. Total shrunk BW gain (P = 0.03, 202.5 vs. 225.2 kg), final BW (P = 0.03, 617.9 vs. 662.2 kg), and carcass weight (P = 0.06) decreased for all EA fed steers compared to CON. The percentage of AAA carcasses decreased for all EA fed steers (P < 0.01, 46.7 vs. 93.3%) compared to CON. EA fed steers had increased rectal temperatures (P < 0.01, 39.8 vs. 39.4 °C) compared to CON. Pelleting ergot contaminated grain did not reduce the impact of ergot alkaloids on any of the measured parameters during BG or FN. Continuously or intermittently feeding ergot contaminated diets (2 mg total EA/kg of DM) significantly reduced intake, growth performance, and carcass weight, with minimal impact on blood parameters in feedlot steers. Pelleting was not an effective method of reducing ergot toxicity.

Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome

Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.

The Isolation and Characterization of Bacteriophages Infecting Avian Pathogenic Escherichia coli O1, O2 and O78 Strains

Avian pathogenic Escherichia coli (APEC), such as O1, O2 and O78, are important serogroups relating to chicken health, being responsible for colibacillosis. In this study, we isolated and characterized bacteriophages (phages) from hen feces and human sewage in Alberta with the potential for controlling colibacillosis in laying hens. The lytic profile, host range, pH tolerance and morphology of seven APEC-infecting phages (ASO1A, ASO1B, ASO2A, ASO78A, ASO2B, AVIO78A and ASO78B) were assessed using a microplate phage virulence assay and transmission electron microscopy (TEM). The potential safety of phages at the genome level was predicted using AMRFinderPlus and the Virulence Factor Database. Finally, phage genera and genetic relatedness with other known phages from the NCBI GenBank database were inferred using the virus intergenomic distance calculator and single gene-based phylogenetic trees. The seven APEC-infecting phages preferentially lysed APEC strains in this study, with ECL21443 (O2) being the most susceptible to phages (n = 5). ASO78A had the broadest host range, lysing all tested strains (n = 5) except ECL20885 (O1). Phages were viable at a pH of 2.5 or 3.5-9.0 after 4 h of incubation. Based on TEM, phages were classed as myovirus, siphovirus and podovirus. No genes associated with virulence, antimicrobial resistance or lysogeny were detected in phage genomes. Comparative genomic analysis placed six of the seven phages in five genera: Felixounavirus (ASO1A and ASO1B), Phapecoctavirus (ASO2A), Tequatrovirus (ASO78A), Kayfunavirus (ASO2B) and Sashavirus (AVIO78A). Based on the nucleotide intergenomic similarity (<70%), phage ASO78B was not assigned a genus in the siphovirus and could represent a new genus in class Caudoviricetes. The tail fiber protein phylogeny revealed variations within APEC-infecting phages and closely related phages. Diverse APEC-infecting phages harbored in the environment demonstrate the potential to control colibacillosis in poultry.

Evaluation of metagenomic assembly methods for the detection and characterization of antimicrobial resistance determinants and associated mobilizable elements

Antimicrobial resistance genes (ARGs) can be transferred between members of a bacterial population by mobile genetic elements (MGE). Understanding the risk of these transfer events is important in monitoring and predicting antimicrobial resistance (AMR), especially in the context of a One Health Continuum. However, there is no universally accepted method for detection of ARGs and MGEs, and especially for determining their linkages. This study used publicly available shotgun metagenomic DNA short-read (Illumina, 100 bp paired-end) sequence data from samples across the One Health Continuum (including beef cattle composite feces from feedlots, catch basin water at feedlots, agricultural soil from feedlot manured surrounding fields, and urban/municipal sewage influent from two municipal wastewater treatment plants) to develop a workflow to identify and associate ARGs and MGEs. ARG- and MGE-based targeted-assemblies with available short-read data were unable to meet this analysis goal. In contrast, de novo assembly of contigs provided enough sequence context to associate ARGs and MGEs, without compromising discovery rate. However, to estimate the relative abundance of these elements, unassembled sequence data must still be used.

Prevalence and antimicrobial susceptibility of Mycoplasma bovis from the upper and lower respiratory tracts of healthy feedlot cattle and those diagnosed with bovine respiratory disease

Mycoplasma bovis is an important respiratory pathogen of cattle. In this study, the prevalence and antimicrobial susceptibility of M. bovis were evaluated from two Cohorts of feedlot cattle spanning an 8-year period. In the first study conducted in 2008-2009, nasopharyngeal swabs from cattle sampled at feedlot entry and after 60 days on feed were collected (Cohort 1). In a second study conducted in 2015-2016, nasopharyngeal and trans-tracheal samples were collected from cattle diagnosed with bovine respiratory disease (BRD) and matching healthy controls (Cohort 2). For Cohort 1, the prevalence of M. bovis was lower in cattle at entry compared to when the same individuals were sampled ≥60 days later (P < 0.05). For Cohort 2, the prevalence of M. bovis was greater in both nasopharyngeal and tracheal samples from cattle diagnosed with BRD, compared to controls (P < 0.05). In both Cohorts, almost all isolates were resistant to tilmicosin. Compared to M. bovis from Cohort 1, isolates of Cohort 2 exhibited increased resistance to clindamycin, enrofloxacin, florfenicol, tylosin, and tulathromycin, with the latter showing resistance levels >90 %. These data suggest that antimicrobials used to prevent and treat BRD selected for resistance in M. bovis over the 8-year period. For macrolides, cross-resistance occurred and M. bovis can retain resistance even when antimicrobial selection pressure is removed. Within 9 years of commercial availability of tulathromycin, the majority of M. bovis displayed resistance. Therefore, longitudinal evaluation of resistance in respiratory pathogens is important to ensure efficacious treatment of BRD.

Bacteriophages for the Targeted Control of Foodborne Pathogens

Foodborne illness is exacerbated by novel and emerging pathotypes, persistent contamination, antimicrobial resistance, an ever-changing environment, and the complexity of food production systems. Sporadic and outbreak events of common foodborne pathogens like Shiga toxigenic E. coli (STEC), Salmonella, Campylobacter, and Listeria monocytogenes are increasingly identified. Methods of controlling human infections linked with food products are essential to improve food safety and public health and to avoid economic losses associated with contaminated food product recalls and litigations. Bacteriophages (phages) are an attractive additional weapon in the ongoing search for preventative measures to improve food safety and public health. However, like all other antimicrobial interventions that are being employed in food production systems, phages are not a panacea to all food safety challenges. Therefore, while phage-based biocontrol can be promising in combating foodborne pathogens, their antibacterial spectrum is generally narrower than most antibiotics. The emergence of phage-insensitive single-cell variants and the formulation of effective cocktails are some of the challenges faced by phage-based biocontrol methods. This review examines phage-based applications at critical control points in food production systems with an emphasis on when and where they can be successfully applied at production and processing levels. Shortcomings associated with phage-based control measures are outlined together with strategies that can be applied to improve phage utility for current and future applications in food safety.

Genomic Characterization of Carbapenem-Resistant Bacteria from Beef Cattle Feedlots

Carbapenems are considered a last resort for the treatment of multi-drug-resistant bacterial infections in humans. In this study, we investigated the occurrence of carbapenem-resistant bacteria in feedlots in Alberta, Canada. The presumptive carbapenem-resistant isolates (n = 116) recovered after ertapenem enrichment were subjected to antimicrobial susceptibility testing against 12 different antibiotics, including four carbapenems. Of these, 72% of the isolates (n = 84) showed resistance to ertapenem, while 27% of the isolates (n = 31) were resistant to at least one other carbapenem, with all except one isolate being resistant to at least two other drug classes. Of these 31 isolates, 90% were carbapenemase positive, while a subset of 36 ertapenem-only resistant isolates were carbapenemase negative. The positive isolates belonged to three genera; Pseudomonas, Acinetobacter, and Stenotrophomonas, with the majority being Pseudomonas aeruginosa (n = 20) as identified by 16S rRNA gene sequencing. Whole genome sequencing identified intrinsic carbapenem resistance genes, including blaOXA-50 and its variants (P. aeruginosa), blaOXA-265 (A. haemolyticus), blaOXA-648 (A. lwoffii), blaOXA-278 (A. junii), and blaL1 and blaL2 (S. maltophilia). The acquired carbapenem resistance gene (blaPST-2) was identified in P. saudiphocaensis and P. stutzeri. In a comparative genomic analysis, clinical P. aeruginosa clustered separately from those recovered from bovine feces. In conclusion, despite the use of selective enrichment methods, finding carbapenem-resistant bacteria within a feedlot environment was a rarity.

Comparative analysis of macroalgae supplementation on the rumen microbial community: Asparagopsis taxiformis inhibits major ruminal methanogenic, fibrolytic, and volatile fatty acid-producing microbes in vitro

Seaweeds have received a great deal of attention recently for their potential as methane-suppressing feed additives in ruminants. To date, Asparagopsis taxiformis has proven a potent enteric methane inhibitor, but it is a priority to identify local seaweed varieties that hold similar properties. It is essential that any methane inhibitor does not compromise the function of the rumen microbiome. In this study, we conducted an in vitro experiment using the RUSITEC system to evaluate the impact of three red seaweeds, A. taxiformis, Palmaria mollis, and Mazzaella japonica, on rumen prokaryotic communities. 16S rRNA sequencing showed that A. taxiformis had a profound effect on the microbiome, particularly on methanogens. Weighted Unifrac distances showed significant separation of A. taxiformis samples from the control and other seaweeds (p &lt; 0.05). Neither P. mollis nor M. japonica had a substantial effect on the microbiome (p &gt; 0.05). A. taxiformis reduced the abundance of all major archaeal species (p &lt; 0.05), leading to an almost total disappearance of the methanogens. Prominent fiber-degrading and volatile fatty acid (VFA)-producing bacteria including Fibrobacter and Ruminococcus were also inhibited by A. taxiformis (p &lt; 0.05), as were other genera involved in propionate production. The relative abundance of several other bacteria including Prevotella, Bifidobacterium, Succinivibrio, Ruminobacter, and unclassified Lachnospiraceae were increased by A. taxiformis suggesting that the rumen microbiome adapted to an initial perturbation. Our study provides baseline knowledge of microbial dynamics in response to seaweed feeding over an extended period and suggests that feeding A. taxiformis to cattle to reduce methane may directly, or indirectly, inhibit important fiber-degrading and VFA-producing bacteria.

Comparative Genomic Analysis of Enterococci across Sectors of the One Health Continuum

Enterococci are Gram-positive bacteria that can be isolated from a variety of environments including soil, water, plants, and the intestinal tract of humans and animals. Although they are considered commensals in humans, Enterococcus spp. are important opportunistic pathogens. Due to their presence and persistence in diverse environments, Enterococcus spp. are ideal for studying antimicrobial resistance (AMR) from the One Health perspective. We undertook a comparative genomic analysis of the virulome, resistome, mobilome, and the association between the resistome and mobilome of 246 E. faecium and 376 E. faecalis recovered from livestock (swine, beef cattle, poultry, dairy cattle), human clinical samples, municipal wastewater, and environmental sources. Comparative genomics of E. faecium and E. faecalis identified 31 and 34 different antimicrobial resistance genes (ARGs), with 62% and 68% of the isolates having plasmid-associated ARGs, respectively. Across the One Health continuum, tetracycline (tetL and tetM) and macrolide resistance (ermB) were commonly identified in E. faecium and E. faecalis. These ARGs were frequently associated with mobile genetic elements along with other ARGs conferring resistance against aminoglycosides [ant(6)-la, aph(3′)-IIIa], lincosamides [lnuG, lsaE], and streptogramins (sat4). Study of the core E. faecium genome identified two main clades, clade ‘A’ and ‘B’, with clade A isolates primarily originating from humans and municipal wastewater and carrying more virulence genes and ARGs related to category I antimicrobials. Overall, despite differences in antimicrobial usage across the continuum, tetracycline and macrolide resistance genes persisted in all sectors.

Soil antibiotic resistance genes accumulate at different rates over four decades of manure application

Manure can be a source of antibiotic resistance genes (ARGs) that enter the soil. However, previous studies assessing ARG persistence in soil have generally lacked continuity over sampling times, consistency of location, and assessing the impact of discontinuing manure application. We evaluated both short- and long-term ARG accumulation dynamics in soil with a 40-year known history of manure use. Manure application caused a greater abundance of tetracycline, macrolide, and sulfonamide ARGs in the soil. There was an initial spike in ARG abundance resulting from manure bacteria harboring ARGs being introduced to soil, followed by resident soil bacteria out-competing them, which led to ARG dissipation within a year. However, over four decades, annual manure application caused linear or exponential ARG accumulation, and bacteria associated with ARGs differed compared to those in the short term. Eleven years after discontinuing manure application, most soil ARG levels declined but remained elevated. We systematically explored the historical accumulation of ARGs in manured soil, and provide insight into factors that affect their persistence.

Effect of increasing concentration of ergot alkaloids in the diet of feedlot cattle: performance, welfare, and health parameters

This study was designed to evaluate the effects of feeding increasing dietary concentrations of ergot alkaloids from cereal grains (EA; 0, 0.75, 1.5, 3.0 mg/kg of dietary DM) to feedlot cattle over backgrounding (BG) and finishing (FS) phases on health, welfare, and growth performance. Two hundred and forty commercial steers (280 ± 32 kg BW) were stratified by weight and randomly allocated to 16 pens (15 steers/pen), 4 of which were equipped with the GrowSafe system (1 pen/treatment) to measure individual feed intake. Each pen was randomly assigned to a treatment (n = 4/treatment). Treatments included 1) control (CTRL), no added EA; 2) CTRL + 0.75 mg/kg EA (EA075); 3) CTRL + 1.5 mg/kg EA (EA150); and 4) CTRL + 3.0 mg/kg EA (EA300). Steers were fed barley-based BG diets containing 40% concentrate: 60% silage (DM basis) for 84 d. Steers were then transitioned over 28 d to an FS diet (90% concentrate: 10% silage DM basis) and fed for 119 d before slaughter. The diet fed to EA300 steers was replaced with the CTRL diet after 190 d on feed (DOF), due to EA-induced hyperthermia starting at 165 DOF. In the BG phase, average meal length (P = 0.01) and size (P = 0.02), daily feeding duration (P = 0.03), final body weight (BW; P = 0.03), and total BW gain (P = 0.02) linearly decreased with increasing EA levels, while gain to feed (G:F) responded quadratically (P = 0.04), with EA150 having the poorest value. Increasing concentrations of EA in the diet linearly increased rectal temperature (P < 0.01) throughout the trial. Over the full FS phase, a quadratic response was observed for ADG (P = 0.05), final BW (P = 0.05), total BW gain (P = 0.02), and carcass weight (P = 0.05) with steers fed EA150 having the lowest performance, as EA300 steers were transferred to CTRL diet after 190 DOF. Dressing percentage (P = 0.02) also responded quadratically, with the lowest values observed for EA300. Thus, EA reduced ADG during BG and FS phases, although more prominently in FS, likely due to increased ambient temperatures and high-energy diet in FS triggering hyperthermia. When EA300 steers were transferred to the CTRL diet, compensatory gain promoted higher hot carcass weight (HCW) when compared with steers fed EA150. In conclusion, feeding feedlot steers diets with > 0.75 mg/kg EA caused reductions in performance and welfare concerns, although this breakpoint may be affected by duration of feeding, environmental temperatures, and EA profiles in the feed.

Effect of physically effective neutral detergent fiber and undigested neutral detergent fiber on eating behavior, ruminal fermentation and motility, barrier function, blood metabolites, and total tract digestibility in finishing cattle

This study evaluated the effects of physically effective neutral detergent fiber (peNDF) and undigested neutral detergent fiber (uNDF) on eating behavior, ruminal fermentation and motility, barrier function, blood metabolites, and total tract nutrient digestibility for finishing cattle. Six Simmental heifers (668 ± 28.4 kg BW) were used in a replicated 3 × 3 Latin square (21 d periods) balanced for carry-over effects. Treatments included a control (CON; Table 1) with no forage peNDF and minimal uNDF (peNDF: 0.0%, and uNDF: 4.88 ± 0.01; 95.15% barley grain, 4.51% vitamin and mineral supplement, and 0.34% urea on a DM basis). Pelleted wheat straw (PELL) was included at 10% of dietary DM by replacing barley grain to provide added uNDF but no forage peNDF (peNDF: 0.00%, and uNDF: 6.78 ± 0.02%). Finally, chopped wheat straw (STR) was included as a replacement for pelleted wheat straw to provide forage peNDF and uNDF (peNDF: 1.74 ± 0.06%, and uNDF: 6.86 ± 0.03%). Dry matter intake was not affected (P = 0.93) by treatments. Cattle fed CON spent less time ruminating (P = 0.010) and had less meals/d (P = 0.035) when compared with cattle fed STR, with those fed PELL being intermediate but not different from other treatments. Cattle fed CON had lesser ruminal pH (P = 0.020), and a greater duration that pH was < 5.5 (P = 0.020) as compared to cattle fed STR, with those fed PELL being intermediate but not different. Cattle fed CON and PELL had greater total short-chain fatty acid concentration (P = 0.003) and molar proportion of propionate (P < 0.001) when compared with cattle fed STR. Cattle fed STR had greater (P = 0.010) total ruminal pool size when compared with cattle fed CON and PELL. Cattle fed CON had greater (P = 0.043) duration between ruminal contractions when compared with cattle fed STR, with those fed PELL being intermediate. Cattle fed CON had greater serum amyloid A (P = 0.003) and haptoglobin (P < 0.001) concentration when compared with the other treatments. Cattle fed CON had greater dry matter (P < 0.001) digestibility when compared with the other treatments. In conclusion, inclusion of PELL and STR impacted eating behavior, but only STR affected ruminal fermentation, ruminal motility, systemic inflammation, and total tract nutrient digestibility in finishing cattle. These results are interpreted to suggest that the combination of peNDF and uNDF may be better than uNDF alone to adequately capture biological effects of NDF in high-concentrate diets.

Veterinary antimicrobials in cattle feedlot environs and irrigation conveyances in a high-intensity agroecosystem in southern Alberta, Canada

The South Saskatchewan River Basin (SSRB) is considered one of the most intensively farmed regions in Canada, with high densities of livestock and expansive areas of irrigated cropland. We measured concentrations of seven veterinary antimicrobials (VAs) in 114 surface water samples from feedlot environs and 219 samples from irrigation conveyances in the SSRB. Overall, detection frequencies in feedlot environs were 100% for chlortetracycline (CTC) and tetracycline (TC), 94% for monensin (MON), 84% for tylosin (TYL), 72% for lincomycin (LIN), 66% for erythromycin (ERY), and 23% for sulfamethazine (SMZ). For irrigation conveyances, detection frequencies for CTC and TC remained high (94-100%), but dropped to 18% for ERY, 15% for TYL, 10% for MON, and 4% for SMZ. Lincomycin was not detected in irrigation conveyance water. Maximum concentrations of VAs ranged from 1384 µg L^-1 (TC) to 17 ng L^-1 (SMZ) in feedlot environs while those in irrigation conveyances were 155 ng L^-1 (TC) to 29 ng L^-1 (ERY). High detection frequencies and median concentrations of VAs in both feedlot environs and irrigation conveyances were associated with high amounts of precipitation. However, an irrigation district (ID) with high livestock density (Lethbridge Northern) did not exhibit higher concentrations of VAs compared to IDs with less livestock, while levels of VAs in irrigation conveyances were less influenced by the degree of surface runoff. The ubiquity of CTC and TC in our study is likely a reflection of its widespread use in intensive livestock operations. Additional investigation is required to link environmental concentrations of VAs with livestock densities and increase our understanding of potential antimicrobial resistance in high-intensity agroecosystems.

Analysis of Complex Carbohydrate Composition in Plant Cell Wall Using Fourier Transform Mid-Infrared Spectroscopy

Fourier transform mid-infrared spectroscopy (FTIR) is a powerful tool for compositional analysis of plant cell walls. The infrared spectrum generates a fingerprint of a sample with absorption peaks corresponding to the frequency of vibrations between the bonds of the atoms making up the material. Here we describe a method focused on the use of FTIR in combination with principal component analysis (PCA) to characterize the composition of the plant cell wall. The FTIR method described here facilitates high-throughput identification of the major compositional differences across a large set of samples in a low-cost and non-destructive manner.

Isolation and Preparation of Extracellular Proteins from Lignocellulose-Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry

Fungi utilize a unique mechanism of nutrient acquisition involving extracellular digestion. To understand the biology of these microbes, it is important to identify and characterize the function of proteins that are secreted and involved in nutrient acquisition. Mass spectrometry-based proteomics is a powerful tool to study complex mixtures of proteins and understand how the proteins produced by an organism change in response to different conditions. Many fungi are efficient decomposers of plant cell walls, and anaerobic fungi are well recognized for their ability to digest lignocellulose. Here we outline a protocol for the enrichment and isolation of proteins secreted by anaerobic fungi after growth on simple (glucose) and complex (straw and alfalfa hay) carbon sources. We provide detailed instruction on generating protein fragments and preparing these for proteomic analysis using reversed-phase chromatography and mass spectrometry. The interpretation of results and their relevance to a particular biological system is study-dependent and beyond the scope of this protocol.

Predicting fecal composition, intake, and nutrient digestibility in beef cattle consuming high forage diets using near infrared spectroscopy

The objective of this study was to develop near infrared spectroscopy (NIRS) calibrations to predict fecal nutrient composition, intake, and diet digestibility from beef cattle fed high forage diets. Heifers were fed 12 different forage-based diets (>95% forage dry matter basis) in 3 total collection digestibility studies, resulting in individual fecal samples and related spectra (n = 135), corresponding nutrient intake, and apparent total tract digestibility (aTTD) data. Fecal samples were also collected from steers grazing two annual and two perennial forage mixtures over two growing seasons. Samples (n = 13/paddock) were composited by paddock resulting in 30 samples from year 1, and 24 from year 2. The grazing fecal spectra (n = 54) were added to the existing fecal composition spectral library. Dried and ground fecal samples were scanned using a FOSS DS2500 scanning monochromator (FOSS, Eden Prairie, MN). Spectra were mathematically treated for detrend and scatter correction and modified partial least squares (MPLS) regression was performed. The coefficient of determination for cross validation (R²_cv) and standard error of cross validation (SECV) were used to evaluate the quality of calibrations. Prediction equations were developed for fecal composition [organic matter (OM), nitrogen (N), amylase-treated ash-corrected neutral detergent fiber (aNDFom), acid detergent fiber (ADF), acid detergent lignin (ADL), undigestible NDF after 240 h of in vitro incubation (uNDF), calcium (Ca), and phosphorus (P)], digestibility [DM, OM, aNDFom, N], and intake [DM, OM, aNDFom, N, uNDF]. The calibrations for fecal OM, N, aNDFom, ADF, ADL, uNDF, Ca, P resulted in R²_cv between 0.86 and 0.97 and SECV of 1.88, 0.07, 1.70, 1.10, 0.61, 2.00, 0.18, and 0.06, respectively. Equations predicting intake of DM, OM, N, aNDFom, ADL, and uNDF resulted in R²_cv values between 0.59 and 0.91, SECV values of 1.12, 1.10, 0.02, 0.69, 0.06, 0.24 kg·d^-1, respectively, and SECV values between 0.00 and 0.16 when expressed as % body weight (BW). Digestibility calibrations for DM, OM, aNDFom, and N resulted in R²_cv ranging from 0.65 to 0.74 and SECV values from 2.20 to 2.82. We confirm the potential of NIRS to predict fecal chemical composition, digestibility, and intake of cattle fed high forage diets. Future steps include validation of the intake calibration equations for grazing cattle using forage internal marker and modelling energetics of grazing growth performance.

Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics

Lignocellulosic biomass represents an abundant, renewable resource that can be used to produce biofuels, low-cost livestock feed, and high-value chemicals. The potential of this bioresource has led to intensive research efforts to develop cost-effective methods to break down lignocellulose. The efficiency with which the anaerobic fungi (phylum Neocallimastigomycota) degrade plant biomass is well recognized and in recent years has received renewed interest. Transcriptomics has been used to identify enzymes that are expressed by these fungi and are involved in the degradation of a range of lignocellulose feedstocks. The transcriptome is the entire complement of coding and non-coding RNA transcripts that are expressed by a cell under a particular set of conditions. Monitoring changes in gene expression can provide fundamental information about the biology of an organism. Here we outline a general methodology that will enable researchers to conduct comparative transcriptomic studies with the goal of identifying enzymes involved in the degradation of the plant cell wall. The method described will include growth of fungal cultures, isolation and sequencing of RNA, and a basic description of data analysis for bioinformatic identification of differentially expressed transcripts.

Biodegradation of bovine spongiform encephalopathy prions in compost

To reduce the transmission risk of bovine spongiform encephalopathy prions (PrP^BSE), specified risk materials (SRM) that can harbour PrP^BSE are prevented from entering the feed and food chains. As composting is one approach to disposing of SRM, we investigated the inactivation of PrP^BSE in lab-scale composters over 28 days and in bin composters over 106-120 days. Lab-scale composting was conducted using 45 kg of feedlot manure with and without chicken feathers. Based on protein misfolding cyclic amplification (PMCA), after 28 days of composting, PrP^BSE seeding activity was reduced by 3-4 log₁₀ with feathers and 3 log₁₀ without. Bin composters were constructed using ~ 2200 kg feedlot manure and repeated in 2017 and 2018. PMCA results showed that seeding activity of PrP^BSE was reduced by 1-2 log₁₀ in the centre, but only by 1 log₁₀ in the bottom of bin composters. Subsequent assessment by transgenic (Tgbov XV) mouse bioassay confirmed a similar reduction in PrP^BSE infectivity. Enrichment for proteolytic microorganisms through the addition of feathers to compost could enhance PrP^BSE degradation. In addition to temperature, other factors including varying concentrations of PrP^BSE and the nature of proteolytic microbial populations may be responsible for differential degradation of PrP^BSE during composting.

Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle

Introduction

Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle.

Methods

This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics.

Results

Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively).

Discussion

Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.

Genomic Profiling of Non-O157 Shiga Toxigenic Escherichia coli-Infecting Bacteriophages from South Africa

Background

Non-O157 Shiga toxigenic Escherichia coli (STEC) are one of the most important food and waterborne pathogens worldwide. Although bacteriophages (phages) have been used for the biocontrol of these pathogens, a comprehensive understanding of the genetic characteristics and lifestyle of potentially effective candidate phages is lacking.

Materials and Methods

In this study, 10 non-O157-infecting phages previously isolated from feedlot cattle and dairy farms in the North-West province of South Africa were sequenced, and their genomes were analyzed.

Results

Comparative genomics and proteomics revealed that the phages were closely related to other E. coli-infecting Tunaviruses, Seuratviruses, Carltongylesviruses, Tequatroviruses, and Mosigviruses from the National Center for Biotechnology Information GenBank database. Phages lacked integrases associated with a lysogenic cycle and genes associated with antibiotic resistance and Shiga toxins.

Conclusions

Comparative genomic analysis identified a diversity of unique non-O157-infecting phages, which could be used to mitigate the abundance of various non-O157 STEC serogroups without safety concerns.

Effects of a mixture of Lentilactobacillus hilgardii, Lentilactobacillus buchneri, Pediococcus pentosaceus and fibrolytic enzymes on silage fermentation, aerobic stability, and growth performance of growing beef cattle

This study evaluated the effects of novel silage inoculants containing lactic acid bacteria (LAB) and fibrolytic enzymes on ensiling, aerobic stability (AS), and the performance of growing beef cattle. Whole-plant corn forage was either uninoculated (CON) or inoculated with a mixture of LAB containing (cfu g -1 fresh forage) 1.5 × 10 5L. hilgardii (CNCM I-4785), 1.5 × 10 5L. buchneri (NCIMB 40788) and 1.0 × 10 5P. pentosaceus (NCIMB 12455) for a total of 4.0 × 10 5 cfu g -1 fresh forage LAB (IB), or a combination of IB plus fibrolytic enzymes (xylanase + β-glucanase) (IC). All treatments were ensiled in mini-silos, whereas CON and IC were also ensiled in silo bags for the growth performance study. Total bacteria (TB) counts were lower (P = 0.02) for IC than CON after 14 d of ensiling, whereas TB counts of IC and IB were greater (P ≤ 0.01) than CON after 60 d of ensiling in mini-silos. The LAB in IC and IB ensiled in mini-silos were greater than CON on d 60 (P ≤ 0.01) and 90 (P ≤ 0.001) of ensiling and after 3 d (P ≤ 0.01) of aerobic exposure (AE). Silage pH of IC ensiled in silo bags was lower than CON on d 3 (P &lt; 0.01), 7 (P &lt; 0.001), and 14 (P = 0.02) of AE. Yeast counts were lower for IC than CON in terminal silage (P &lt; 0.001), and after 3 (P &lt; 0.001) and 7 d (P &lt; 0.01) of AE. Acetate (AC) concentrations were higher (P ≤ 0.02) for IC than CON throughout AE, whereas lactate (LA) concentrations of IC were greater than CON on d 3 (P &lt; 0.001), 7 (P &lt; 0.01), and 14 (P &lt; 0.001) of AE. Greater AC concentration and lower yeast counts resulted in greater (P &lt; 0.001) stability for IC ensiled in silo bags than CON after 14 d of AE. Growth performance of steers was similar (P &gt; 0.05) as the nutrient composition of silage was similar across diets. Improved AS of IC could potentially have a greater impact on DMI, production efficiency, and growth performance in large-scale commercial feedlot operations where silage at the silo face may be exposed to air for longer periods of time.

155 Effect of Forage Inclusion Strategy on Finishing Beef Cattle Performance and Liver Abscesses

This study evaluated different strategies of forage inclusion for finishing beef cattle and their impact on performance, carcass quality, and liver abscesses. Steers (n=360, 400±29 kg) were blocked by weight and randomly assigned to one of four treatments (15 steers/pen, 6 pens/treatment) in a complete randomized experiment. Treatments were: 1) positive control (+CON) fed a diet (7.5% forage on a diet DM basis) with tylosin (11 mg/kg); 2) negative control (–CON; control diet without tylosin); 3) a diet where forage concentration decreased (DECR) every 42 d and was static for the last 84 d (forage represented 15%, 9%, 3%, and 3% of DM, respectively) without tylosin; and 4) a diet where forage concentration increased (INCR), the inverse of the DECR without tylosin. There were no differences in initial BW, DMI, and G:F (P≥0.38). The INCR steers had lower ADG (1.63 vs. 1.74 kg, P=0.05), total BW gain (287 vs. 306 kg, P=0.05), and tended to have lower final BW and carcass weight (P=0.07) compared to +CON, with no differences from the other treatments. No differences were observed for carcass dressing percentage, ribeye area, marbling scores, and quality grades (P≥0.41). Backfat thickness and yield score were lower for INCR steers (14.2 mm and 3.42) compared to –CON (16.9 mm and 3.82, P=0.04), while other treatments did not differ. There was no difference for the percentage of steers with liver abscess or severe abscess (A+; P≥0.17). However, the percentage of steers with minor liver abscesses (A) was numerically less for +CON (51.8%) and DECR (51.8%) compared to –CON (62.2%) and INCR (64.3%, P=0.055). This suggests that higher dietary concentrations of forage in the beginning stages of finishing, with a subsequent decline thereafter has the potential to decrease the proportion of minor liver abscesses, similar to the inclusion of tylosin in a high-grain diet, without impacting growth performance or carcass quality.

159 Effect of dry or Temper Rolling of High or low Protein Wheat and its Impact on Rumen Parameters, Liver Abscesses, and Growth Performance of Feedlot Cattle

The objective of this study was to assess the impact of low (13%, LP) or high protein (18%, HP) wheat grain subjected to dry (DR) vs temper rolling (TR) on growth performance, rumen parameters, and liver abscesses of feedlot steers. A backgrounding (BG) to finishing (FN) feedlot trial was performed using 160 302 ± 34 kg; 24 ruminally cannulated) Angus steers blocked by weight and randomly assigned to 16 pens. Cannulated steers (3 per pen) were housed within 8 pens equipped with a feed intake monitoring system. BG diets contained 35% wheat grain, 60% barley silage, and 5% supplement on a DM basis. Transition (TN) diets included sequential increases to the proportion of wheat grain in the total mixed ration to achieve a FN diet comprised of 85% wheat grain, 10% barley silage, and 5% supplement. Rumen pHs were measured with an indwelling logger and rumen samples were collected in each phase. Steers fed the HP-DR and LP-TR diets had lower (P≤0.03) ruminal pH than HP-TR during the TN phase. Tempering HP wheat reduced (P&lt;0.001) the generation of fine particles during rolling. During BG and TN, steers fed diets containing HP wheat had higher (P&lt;0.001) ruminal NH3 concentrations than the LP treatments. NH3 measurements during the FN phase were higher (P=0.01) for the LP-DR treatment compared to the LP-TR treatment. Greater (P≤0.01) C2:C3 ratios were noted for HP wheat diets during the BG and FN phases whereas the C2:C3 ratio was reduced (P&lt;0.001) with TR wheat during the FN phase. Greater (P= 0.01) NEgs were assessed for FN steers fed LP wheat. Steers fed HP wheat had more severe (P&lt;0.001) abscesses. Results suggest that HP wheat may limit the growth performance of FN cattle and increase the severity of liver abscesses.

163 Assessment of the Methanogenic Archaeal Communities Throughout the Gastrointestinal Tract in Beef Cattle with Different Breeds

Methane mitigation in ruminants is important to reduce greenhouse gas emissions and enhance feed utilization. Methanogenic archaea inhabit the gastrointestinal tract (GIT) of ruminants where they utilize H2 reducing equivalents formed by other microbiota (i.e., bacteria, fungi, and protozoa) to reduce CO2 to methane. This study aimed to assess methanogens in the GIT of beef cattle and evaluate the influence of gut regions and cattle breeds on methanogenic ecology. Digesta were collected from six gut regions (rumen, duodenum, jejunum, ileum, colon, rectum) in forty-two beef steers representing three breeds (Angus n=13, Charolais n=14, Kinsella composite hybrid n=15). Methanogens were characterized using 16S rRNA gene amplicon sequencing with methanogen-specific primers and analyzed using RIM-DB with QIIME2. Total methanogens were quantified using qPCR with universal methanogen primers. Gut region and breed effects were assessed using the non-parametric Kruskal-Wallis test. Estimation of methanogenic populations showed a region effect (P &lt; 0.05), with the highest copy number observed in the rumen and the lowest in the duodenum and jejunum. Ten methanogenic species were identified (with a relative abundance ≥ 0.01% in ≥ 50% of individuals per breed) throughout the GIT with Methanobrevibacter ruminantium (predominant in all regions), Methanobrevibacter gottschalkii, and Methanosphaera sp. ISO3-F5 observed in all regions and in all breeds. Divergent methanogenic compositions were observed among gut regions (P &lt; 0.05) and breed-specific species were identified (e.g., Methanobacterium bryantii in the colon of Charolais). The alpha-diversity index (Chao1) varied among gut regions (P &lt; 0.05), and rumen showed the highest richness over other gut regions. Breed affected the alpha-diversity where Angus was distinct from other breeds (P &lt; 0.05). These results revealed that methanogens in the GIT are region-dependent and breed-specific, highlighting the importance of taking cattle breed and total-tract ecology into consideration to understand the role of methanogens in the GIT.

156 Effect of Increasing Levels of Ergot Alkaloids in the Diet of Feedlot Cattle

This study evaluated the effects of feeding ergot alkaloids (EA) at increasing levels (0, 0.75, 1.5, and 3.0 ppm) to feedlot beef cattle over backgrounding (BG) and finishing (FS) phases on growth performance and carcass quality. Steers (n=240; 280±32 kg) were blocked by weight and randomly allocated to 16 pens (4 pens/treatment; 15 steers/pen). Treatments included: no added EA (CTL); or EA added at 0.75 (EA075); 1.50 (EA150); and 3.0 ppm (EA300). Steers were fed barley-based BG diets containing 40% concentrate:60% silage (DM basis) for 84 d, then stepped up over 28 d to a 90% concentrate:10% silage (DM basis) FS diet for 119 d. Steers fed EA300 received CTL in FS after 77 days on feed (DOF). In the BG phase, a quadratic decrease (P=0.05) in ADG and a linear decrease in final BW (P=0.03) and total BW gain (P=0.02) were observed with increasing EA. In the FS phase, up to 77 DOF, there was a linear decrease in steers DMI (P=0.04), ADG (P=0.01), and total BW gain (P=0.01) with increasing levels of EA. Over the full FS phase (119 DOF), a quadratic response was observed for ADG (P=0.05), final BW (P=0.05), total BW gain (P=0.02) and carcass weight (P=0.05) with steers fed EA150 showing the lowest performance. Gain:feed was not affected (P&gt;0.20) by EA in the BG or FS phase. Dressing percentage (P=0.02) showed a quadratic effect with EA300 being the lowest. Additionally, a linear increase in lean meat yield (P&lt; 0.001) was observed with increasing EA. Including EA in the diet promoted a linear increase in rectal temperature (P&lt; 0.01). In conclusion, increasing levels of EA in the diet reduced growth performance, but when EA was removed, steers showed compensatory weight gain.

Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements (MGEs), which facilitate their transfer between lineages. Here, features including resistance determinants, virulence factors and MGEs were profiled in a set of 1273 E. faecium genomes from two disparate geographic locations (in the UK and Canada) from a range of agricultural, clinical and associated habitats. Neither lineages of E. faecium, type A and B, nor MGEs are constrained by geographic proximity, but our results show evidence of a strong association of many profiled genes and MGEs with habitat. Many features were associated with a group of clinical and municipal wastewater genomes that are likely forming a new human-associated ecotype within type A. The evolutionary dynamics of E. faecium make it a highly versatile emerging pathogen, and its ability to acquire, transmit and lose features presents a high risk for the emergence of new pathogenic variants and novel resistance combinations. This study provides a workflow for MGE-centric surveillance of AMR in Enterococcus that can be adapted to other pathogens.

Genomic Analysis of Shiga Toxin-Producing E. coli O157 Cattle and Clinical Isolates from Alberta, Canada

Shiga toxin (stx) is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing Escherichia coli (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates from cattle (n = 125) and clinical (n = 127) samples to characterize virulence genes, stx-phage insertion sites and antimicrobial resistance genes that may segregate strains circulating in the same geographic region. In silico analyses revealed that O157 isolates harboured the toxin subtypes stx1a and stx2a. Most cattle (76.0%) and clinical (76.4%) isolates carried the virulence gene combination of stx1, stx2, eae and hlyA. Characterization of stx1 and stx2-carrying phages in assembled contigs revealed that they were associated with mlrA and wrbA insertion sites, respectively. In cattle isolates, mlrA and wrbA insertion sites were occupied more often (77% and 79% isolates respectively) than in clinical isolates (38% and 1.6% isolates, respectively). Profiling of antimicrobial resistance genes (ARGs) in the assembled contigs revealed that 8.8% of cattle (11/125) and 8.7% of clinical (11/127) isolates harboured ARGs. Eight antimicrobial resistance genes cassettes (ARCs) were identified in 14 isolates (cattle, n = 8 and clinical, n = 6) with streptomycin (aadA1, aadA2, ant(3’’)-Ia and aph(3’’)-Ib) being the most prevalent gene in ARCs. The profound disparity between the cattle and clinical strains in occupancy of the wrbA locus suggests that this trait may serve to differentiate cattle from human clinical STEC O157:H7. These findings are important for stx screening and stx-phage insertion site genotyping as well as monitoring ARGs in isolates from cattle and clinical samples.

Effects of Heating, Pelleting, and Feed Matrix on Apparent Concentrations of Cereal Ergot Alkaloids in Relation to Growth Performance and Welfare Parameters of Backgrounding Beef Steers

As the contamination of cereal grains with ergot has been increasing in Western Canada, studies were undertaken to evaluate the impacts of heating (60, 80, 120, or 190 °C) alone or in combination with pelleting on concentrations of ergot alkaloids. Fifteen samples of ergot-contaminated grain from Alberta and Saskatchewan were assayed for R and S epimers of six alkaloids (ergocryptine, ergocristine, ergocornine, ergometrine, ergosine, and ergotamine) using HPLC MS/MS. Five samples with distinct alkaloid profiles were then selected for heating and pelleting studies. Heating resulted in a linear increase (p < 0.05) of total R and total S epimers with increasing temperature, although some individual R epimers were stable (ergometrine, ergosine, ergotamine). Pelleting also increased (p < 0.05) concentrations of total R and total S epimers detected, although ergometrine concentration decreased (p < 0.05) after pelleting. A feeding study arranged in a 2 × 2 factorial structure used 48 backgrounding Angus-cross steers fed four different diets: (1) Control Mash (CM, no added ergot), (2) Control Pellet (CP), (3) Ergot Mash (EM), or (4) Ergot Pellet (EP). Pelleting heated the ergot to 90−100 °C under 4 bars pressure, but the ergot used in the feeding study was not otherwise heated. Alkaloid concentrations of EM and EP varied by up to 1.1 mg/kg depending on the feed matrix assayed. No differences among treatments were noted for growth performance, feed intake, feed conversion, concentrations of serum prolactin and haptoglobin, hair cortisol, or in temperatures of extremities measured by infrared thermography. The only negative impacts of ergot alkaloids were on blood parameters indicative of reduced immune function or chronic inflammation. Pelleting did not heighten the negative clinical outcomes of ergot, although alkaloid concentrations of pelleted feed increased depending on the matrix assayed. It was hypothesized that the heat and pressure associated with pelleting may enhance the recovery of alkaloids from pelleted feed.

Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum

Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.

Effect of Ergot Alkaloids and a Mycotoxin Deactivating Product on In Vitro Ruminal Fermentation Using the Rumen Simulation Technique (RUSITEC)

The rumen simulation technique (RUSITEC) was used to investigate the effect of ergot alkaloids (EA) and a mycotoxin deactivating product (Biomin AA; MDP) on nutrient digestion, ruminal fermentation parameters, total gas, methane, and microbial nitrogen production. Ruminal fermentation vessels received a feedlot finishing diet of 90:10 concentrate:barley silage (DM basis). Using a randomized complete block design, treatments were assigned (n = 4 vessels/treatment) within two RUSITEC apparatuses in a 2 × 2 factorial arrangement. Treatments included: 1) control (CON) diet (no EA and no MDP); 2) CON diet + 1 g/d MDP; 3) CON diet + 20 mg/kg EA; and 4) CON diet + 20 mg/kg EA + 1 g/d MDP. The study was conducted over 14 d with 7 d of adaptation and 7 d of sample collection. Data were analyzed in SAS using PROC MIXED including fixed effects of EA, MDP, and the EA×MDP interaction. Random effects included RUSITEC apparatus and cow rumen inoculum (n = 4). Ergot alkaloids decreased dry matter (DMD) (P = 0.01; 87.9 vs. 87.2%) and organic matter disappearance (OMD) (P = 0.02; 88.8 vs. 88.4%). Inclusion of MDP increased OMD (P = 0.01; 88.3 vs. 88.9%). Neutral detergent fiber disappearance (NDFD) was improved with MDP; however, an EA×MDP interaction was observed with MDP increasing (P < 0.001) NDFD more with EA diet compared to CON. Acetate proportion decreased (P = 0.01) and isovalerate increased (P = 0.03) with EA. Consequently, acetate:propionate was reduced (P = 0.03) with EA. Inclusion of MDP increased total volatile fatty acid (VFA) production (P < 0.001), and proportions of acetate (P = 0.03) and propionate (P = 0.03), and decreased valerate (P < 0.001), isovalerate (P = 0.04), and caproate (P = 0.002). Treatments did not affect (P ≥ 0.17) ammonia, total gas, or methane production (mg/d or mg/g of organic matter fermented). The inclusion of MDP reduced (P < 0.001) microbial nitrogen (MN) production in the effluent and increased (P = 0.01) feed particle bound MN. Consequently, total MN decreased (P = 0.001) with MDP. In all treatments, the dominant microbial phyla were Firmicutes, Bacteroidota, and Proteobacteria, and the major microbial genus was Prevotella. Inclusion of MDP further increased the abundance of Bacteroidota (P = 0.04) as it increased both Prevotella (P = 0.04) and Prevotellaceae_UCG-003 (P = 0.001). In conclusion, EA reduced OMD and acetate production due to impaired rumen function, these responses were successfully reversed by the addition of MDP.

Environmental performance of commercial beef production systems utilizing conventional productivity-enhancing technologies

The objective of this study was to evaluate the effects of using conventional productivity-enhancing technologies (PETs) with or without other natural PETs on the growth performance, carcass traits and environmental impacts of feedlot cattle. A total of 768 cross-bred yearling steers (499 ± 28.6 kg; n = 384) and heifers (390 ± 34.9 kg; n = 384) were offered a barley grain-based basal diet and divided into implanted or non-implanted groups. Steers were then allocated to diets that contained either: (i) no additive (control); natural feed additives including (ii) fibrolytic enzymes (Enz), (iii) essential oil (Oleo), (iv) direct fed microbial (DFM), (v) DFM + Enz + Oleo combination; conventional feed additives including (vi) Conv (monensin, tylosin, and beta-adrenergic agonists [βAA]); or Conv with the natural feed additives including (vii) Conv + DFM + Enz; (viii) Conv + DFM + Enz + Oleo. Heifers received one of the first three dietary treatments or the following: (iv) probiotic (Citr); (v) Oleo + Citr; (vi) Melengesterol acetate (MGA) + Oleo + βAA; (vii) Conv (monensin, tylosine, βAA, and MGA); or (viii) Conv + Oleo (ConvOleo). Data were used to estimate greenhouse gas (GHG) and ammonia (NH3) emissions, as well as land and water use. Implant and Conv-treated cattle exhibited improvements in growth and carcass traits as compared to the other treatments (P &lt; 0.05). Improvements in the performance of Conv-cattle illustrated that replacing conventional feed additives with natural feed additives would increase both the land and water required to satisfy the feed demand of steers and heifers by 7.9% and 10.5%, respectively. Further, GHG emission intensity for steers and heifers increased by 5.8% and 6.7%, and NH3 emission intensity by 4.3% and 6.7%, respectively. Eliminating the use of implants in cattle increased both land and water use by 14.6% and 19.5%, GHG emission intensity by 10.5% and 15.8%, and NH3 emission intensity by 3.4% and 11.0% for heifers and steers, respectively. These results demonstrate that use of conventional PETs increased animal performance while reducing environmental impacts of beef production. Restricting use would increase the environmental footprint of beef produced for both domestic and international markets.

Expressions of resistome is linked to the key functions and stability of active rumen microbiome

BACKGROUND

The resistome describes the array of antibiotic resistant genes (ARGs) present within a microbial community. Recent research has documented the resistome in the rumen of ruminants and revealed that the type and abundance of ARGs could be affected by diet and/or antibiotic treatment. However, most of these studies only assessed ARGs using metagenomics, and expression of the resistome and its biological function within the microbiome remains largely unexplored.

RESULTS

We characterized the pools of ARGs (resistome) and their activities in the rumen of 48 beef cattle belonging to three breeds (Angus, Charolais, Kinsella composite hybrid), using shotgun metagenomics and metatranscriptomics. Sixty (including 20 plasmid-associated) ARGs were expressed which accounted for about 30% of the total number of ARGs (187) identified in metagenomic datasets, with tetW and mefA exhibiting the highest level of expression. In addition, the bacterial hosts of 17 expressed ARGs were identified. The active resistome was less diverse in Kinsella composite hybrid than Angus, however, expression of ARGs did not differ among breeds. Although not associated with feed efficiency, the total abundance of expressed ARGs was positively correlated with metabolic pathways and 'attenuation values' (a measurement of stability) of the active rumen microbiome, suggesting that ARGs expression influences the stability and functionality of the rumen microbiome. Moreover, Ruminococcus spp., Prevotella ruminicola, Muribaculaceae spp. and Collinsella aerofaciens were all identified as hosts of expressed ARGs, possibly promoting the dominance of these carbohydrate degraders within the rumen microbiome.

CONCLUSIONS

Findings from this study provide new insight into the active rumen resistome in vivo, which may inform strategies to limit the spread of ubiquitously found ARGs from the rumen to the broader environment without negatively impacting the key functional outcomes of the rumen microbiome.

Bovine Respiratory Disease: Conventional to Culture-Independent Approaches to Studying Antimicrobial Resistance in North America

Numerous antimicrobial resistance (AMR) surveillance studies have been conducted in North American feedlot cattle to investigate the major bacterial pathogens of the bovine respiratory disease (BRD) complex, specifically: Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. While most bacterial isolates recovered from healthy cattle are susceptible to a repertoire of antimicrobials, multidrug resistance is common in isolates recovered from cattle suffering from BRD. Integrative and conjugative elements (ICE) have gained increasing notoriety in BRD-Pasteurellaceae as they appear to play a key role in the concentration and dissemination of antimicrobial resistant genes. Likewise, low macrolide susceptibility has been described in feedlot isolates of M. bovis. Horizontal gene transfer has also been implicated in the spread of AMR within mycoplasmas, and in-vitro experiments have shown that exposure to antimicrobials can generate high levels of resistance in mycoplasmas via a single conjugative event. Consequently, antimicrobial use (AMU) could be accelerating AMR horizontal transfer within all members of the bacterial BRD complex. While metagenomics has been applied to the study of AMR in the microbiota of the respiratory tract, the potential role of the respiratory tract microbiome as an AMR reservoir remains uncertain. Current and prospective molecular tools to survey and characterize AMR need to be adapted as point-of-care technologies to enhance prudent AMU in the beef industry.

Effects of feeding a pine-based biochar to beef cattle on subsequent manure nutrients, organic matter composition and greenhouse gas emissions

Biochar in ruminant diets is being assessed as a method for simultaneously improving animal production and reducing enteric CH₄ emissions, but little is known about subsequent biochar-manure interactions post-excretion. We examined chemical properties, greenhouse gas (GHG) emissions and organic matter (OM) composition during farm scale stockpiling (SP) or composting (CP) of manure from cattle that either received a pine-based biochar in their diet (BM) or did not (RM). Manure piles were monitored hourly for temperature and weekly for top surface CO₂, N₂O and CH₄ fluxes over 90 d in a semiarid location near Lethbridge, AB, Canada. Results indicate that cumulative CO₂, N₂O and CH₄ emissions were not affected by biochar, implying that BM was as labile as RM. The pH, total C (TC), NO₃-N and Olsen P were also not influenced by biochar, although it was observed that NH₄-N and OM extractability were both 13% lower in BM than RM. Solid-state ¹³C nuclear magnetic resonance (NMR) showed that biochar increased stockpile/compost aromaticity, yet it did not alter the bulk C speciation of manure OM. Further analysis by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) revealed that dissolved OM was enriched by strongly reduced chemical constituents, with BM providing more humic-like OM precursors than RM. Inclusion of a pine-based biochar in cattle diets to generate BM is consistent with current trends in the circular economy, "closing the loop" in agricultural supply chains by returning C-rich organic amendments to croplands. Stockpiling/composting the resulting BM, however, may not provide a clear advantage over directly mixing low levels of biochar with manure. Further research is required to validate BM as a tool to reduce the C footprint of livestock waste management.

Hydrogen and formate production and utilisation in the rumen and the human colon

Molecular hydrogen (H₂) and formate (HCOO⁻) are metabolic end products of many primary fermenters in the mammalian gut. Both play a vital role in fermentation where they are electron sinks for individual microbes in an anaerobic environment that lacks external electron acceptors. If H₂ and/or formate accumulate within the gut ecosystem, the ability of primary fermenters to regenerate electron carriers may be inhibited and microbial metabolism and growth disrupted. Consequently, H₂- and/or formate-consuming microbes such as methanogens and homoacetogens play a key role in maintaining the metabolic efficiency of primary fermenters. There is increasing interest in identifying approaches to manipulate mammalian gut environments for the benefit of the host and the environment. As H₂ and formate are important mediators of interspecies interactions, an understanding of their production and utilisation could be a significant entry point for the development of successful interventions. Ruminant methane mitigation approaches are discussed as a model to help understand the fate of H₂ and formate in gut systems.

Effect of sod-seeding bloat-free legumes on pasture productivity, steer performance, and production economics

A five-year experiment evaluated the effects of sod-seeding sainfoin and cicer milkvetch into monoculture grass (Lanigan, SK) or legume (Lethbridge, AB) stands on pasture productivity, steer performance, and economics. At Lanigan, sainfoin decreased (treatment × year P = 0.01) from 13% in yr 1 to 2% in yr 2 (% plant population) and did not differ thereafter, while cicer milkvetch, maintained a proportion of 16% in the stand. Forage yield was greater (treatment × year; P < 0.01) in yr 1 in the sainfoin and cicer milkvetch treatments compared to control. DMI of steers was greater only in yr 5 and ADG was greater (P < 0.01) in sainfoin and cicer milkvetch treatments compared to control. At Lethbridge, sainfoin decreased (treatment × year; P = 0.01) from 46 to 17% (% DM yield), while cicer milkvetch maintained its proportion at 11%. Forage yield increased (treatment × year; P < 0.01) only in yr 2 and 3 of sainfoin, compared to cicer milkvetch or control. ADG gain was not affected by treatment. At Lanigan, sainfoin and cicer milkvetch generated greater gross returns compared to control; however, once establishment costs were applied there were no differences in present value of net returns.

Effects of biochar source, level of inclusion, and particle size on in vitro dry matter disappearance, total gas, and methane production and ruminal fermentation parameters in a barley silage-based diet

This study evaluated the effects of biochar differing in source, inclusion level, and particle size on dry matter disappearance (DMD), total gas and methane (CH4) production, and ruminal fermentation in a barley silage-based diet. The seven biochar products used were coconut (CP001 and CP014) or pine (CP002, CP015, CP016, CP023, CP024)-based. Experiment 1 (Exp. 1) evaluated these biochars at 4.5%, 13.5%, and 22.5% level of diet inclusion, whereas Experiment 2 (Exp. 2) evaluated CP002, CP016, and CP023 at 2.25% and 4.50% of the diet at <0.5, 0.5–2.0, >2.0 mm particle size. Data were analyzed using PROC MIXED in SAS as a randomized complete block design, with biochar source, inclusion level, and particle size (Exp. 2 only) as fixed effects with run and replicate as random effects. Increasing level of biochar inclusion linearly (P < 0.01) decreased DMD in Exp. 1 and did not influence DMD (P > 0.05) in Exp. 2. Total gas, CH4 (mL·g−1 DMD), and ruminal fermentation parameters were not affected by product, inclusion level, or particle size (P > 0.05). In conclusion, biochar of varying source and particle size did not mitigate CH4 production, but reduced DMD at higher inclusion levels in the barley silage-based diet.

Electron flow: key to mitigating ruminant methanogenesis

Disposal of electrons generated during the fermentation of ingested feed is a fundamental feature of anaerobic microbial gut ecosystems. Here, we focus on the well-studied rumen environment to highlight how electrons are transferred through anaerobic fermentation pathways and how manipulating this electron flow is important to reducing methane emissions from ruminants. Priorities for research that can accelerate understanding in this area are highlighted.

Mechanistic insights into the digestion of complex dietary fibre by the rumen microbiota using combinatorial high-resolution glycomics and transcriptomic analyses

There is a knowledge gap regarding the factors that impede the ruminal digestion of plant cell walls or if rumen microbiota possess the functional activities to overcome these constraints. Innovative experimental methods were adopted to provide a high-resolution understanding of plant cell wall chemistries, identify higher-order structures that resist microbial digestion, and determine how they interact with the functional activities of the rumen microbiota. We characterized the total tract indigestible residue (TTIR) from cattle fed a low-quality straw diet using two comparative glycomic approaches: ELISA-based glycome profiling and total cell wall glycosidic linkage analysis. We successfully detected numerous and diverse cell wall glycan epitopes in barley straw (BS) and TTIR and determined their relative abundance pre- and post-total tract digestion. Of these, xyloglucans and heteroxylans were of higher abundance in TTIR. To determine if the rumen microbiota can further saccharify the residual plant polysaccharides within TTIR, rumen microbiota from cattle fed a diet containing BS were incubated with BS and TTIR ex vivo in batch cultures. Transcripts coding for carbohydrate-active enzymes (CAZymes) were identified and characterized for their contribution to cell wall digestion based on glycomic analyses, comparative gene expression profiles, and associated CAZyme families. High-resolution phylogenetic fingerprinting of these sequences encoded CAZymes with activities predicted to cleave the primary linkages within heteroxylan and arabinan. This experimental platform provides unprecedented precision in the understanding of forage structure and digestibility, which can be extended to other feed-host systems and inform next-generation solutions to improve the performance of ruminants fed low-quality forages.

Microbial interaction-driven community differences as revealed by network analysis

Diversity and compositional analysis are the most common approaches in deciphering microbial community differences. However, these approaches neglect microbial structural differences driven by microbial interactions. In this study, the microbiota data were generated from 12 rectal digesta samples collected from steers in which the Shiga toxin 2 gene (stx2) was not expressed (defined as Stx2- group) in the bacteria, and those with stx2 expressed (defined as Stx2+ group) and used to explore whether microbial networks affect gut microbiota and foodborne pathogen virulence in cattle. Although the Shannon and Chao1 indices of rectal digesta microbial communities did not differ between the two groups (P > 0.05), 24 and 13 taxa were identified to be group-specific genera for Stx2- and Stx2+ microbial communities, respectively. The network analysis indicated 12 and 14 generalists (microbes that were densely connected with other taxa) in microbial communities for Stx2- and Stx2+ groups, and 8 out of 12 generalists and 6 out of 14 generalists were designated to Stx2- and Stx2+ group-specific genera, respectively. However, the 66 core genera were not classified as network generalists. Natural connectivity measurements revealed that the higher stability of the Stx2- microbial network in comparison to the Stx2+ network, suggesting that the structure of each microbial community was inherently different even when their diversity and composition were comparable. Group-specific genera intensely interacted with other taxa in the co-occurrence network, indicating that characterizing microbial networks together with group-specific genera could be an alternative approach to identify variation in microbial communities.

Effect of trenbolone acetate, melengestrol acetate, and ractopamine hydrochloride on the growth performance of beef cattle

The effect of trenbolone acetate + estradiol (TBA) implants, melengestrol acetate (MGA), and ractopamine hydrochloride + TBA (RAC + TBA) on growth performance and carcass characteristics in beef cattle (n = 680; 279 ± 10.1 kg) fed barley grain/corn silage was examined in a 4 yr study (four pens per treatment per year; 262 ± 8 d feeding period). In the first 2 yr, treatments were (1) control heifers (H-CON; no growth promoters), (2) TBA-implanted heifers (H-TBA), (3) MGA heifers (H-MGA), (4) control steers (S-CON; no growth promoters), and (5) TBA-implanted steers (S-TBA). A sixth treatment (6) RAC + TBA steers (RAC + TBA) was included in years 3 and 4. Overall dry matter intake (DMI) of heifers was increased (P < 0.001) by TBA but not MGA. Compared with H-CONs, H-TBA had greater average daily gain (ADG) (P < 0.001), gain to feed ratio (G/F) (P < 0.001), and carcass weight (P < 0.001), whereas S-TBA had increased ADG (P < 0.001), G/F (P< 0.001), and carcass weight (P < 0.001) compared with S-CON. Compared with H-CON, H-MGA had increased (P < 0.01) ADG, G/F, and carcass weight. The RAC + TBA had increased (P < 0.01) ADG and carcass weight (3.2%) but not G/F or DMI compared with S-TBA. This 4 yr study showed a consistent positive impact of growth-enhancing technologies on the performance of Canadian feedlot cattle.

A review of the resistome within the digestive tract of livestock

Antimicrobials have been widely used to prevent and treat infectious diseases and promote growth in food-production animals. However, the occurrence of antimicrobial resistance poses a huge threat to public and animal health, especially in less developed countries where food-producing animals often intermingle with humans. To limit the spread of antimicrobial resistance from food-production animals to humans and the environment, it is essential to have a comprehensive knowledge of the role of the resistome in antimicrobial resistance (AMR), The resistome refers to the collection of all antimicrobial resistance genes associated with microbiota in a given environment. The dense microbiota in the digestive tract is known to harbour one of the most diverse resistomes in nature. Studies of the resistome in the digestive tract of humans and animals are increasing exponentially as a result of advancements in next-generation sequencing and the expansion of bioinformatic resources/tools to identify and describe the resistome. In this review, we outline the various tools/bioinformatic pipelines currently available to characterize and understand the nature of the intestinal resistome of swine, poultry, and ruminants. We then propose future research directions including analysis of resistome using long-read sequencing, investigation in the role of mobile genetic elements in the expression, function and transmission of AMR. This review outlines the current knowledge and approaches to studying the resistome in food-producing animals and sheds light on future strategies to reduce antimicrobial usage and control the spread of AMR both within and from livestock production systems.