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Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide-lincosamide-streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the β-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause-effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms' records (tetracyclines and macrolides in feedlots, β-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the "resistance potential" of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.

Nutrient composition of beef offal was evaluated to expand availability of nutrient data for the following beef items: beef heart, liver, kidney, tongue, honeycomb tripe, oxtail, marrow bones, testicles, and blood. These items are consumed both domestically and internationally, with significant regional variations that can be contributed to unique cultural meals and dietary patterns. Standardized procedures were used to dissect and homogenize beef offal samples. Nutrient analysis occurred at United States Department of Agriculture Agricultural Research Service-approved laboratories using validated methods and standards. Each of the offal items in the study qualified for at least one "Good Source" or "Excellent Source" nutrient labeling claim as defined by the United States Food and Drug Administration, based on composition of the separable lean component. This study provides analytically derived nutrient information for U.S. beef offal items. The results reflect that these products could be beneficial in providing essential nutrients as a component of a healthy diet. [ABSTRACT FROM AUTHOR]

Nutrient composition data that accurately represent available beef products are critical to understanding beef's role in healthy dietary patterns. The quality of beef products has changed over the past several decades, and updated nutrient data are warranted as USDA Prime beef cuts become more available. In an effort to provide a complete nutrient profile for frequently purchased USDA Prime beef cuts, five USDA Prime cuts; strip loin steak, tenderloin steak, ribeye steak, top sirloin steak, and rib roast were collected from retail stores in six geographical locations over three collections for macro- and micronutrient analysis in both the raw and cooked state. The separable lean portion of all analyzed USDA Prime cuts qualified as a good or excellent source, providing 10–19% or at least 20% of the daily value, respectively, for protein, niacin, vitamin B12, selenium, phosphorus, and zinc per FDA labeling claim standards. There was not a significant difference in cholesterol content between any of the cuts, raw or cooked (p ≥ 0.44 and 0.34, respectively). The percent lipid in raw, separable lean portions of the rib roast and strip loin steak was significantly greater than the lipid portion in tenderloin and top sirloin steaks (p ≤ 0.01). Per USDA standards, the separable lean portions of tenderloin steak and top sirloin steak qualify as lean beef, containing less than 10 g total fat, less than 4.5 g saturated fat, and less than or equal to 95 mg cholesterol. The current study provides the most up-to-date nutrient analysis for USDA Prime beef cuts, helping consumers and health professionals better identify the role of high-quality beef cuts in healthy dietary patterns. [ABSTRACT FROM AUTHOR]

Treatment of food-producing animals with antimicrobial drugs (AMD) is controversial because of concerns regarding promotion of antimicrobial resistance (AMR). To investigate this concern, resistance genes in metagenomic bovine fecal samples during a clinical trial were analyzed to assess the impacts of treatment on beef feedlot cattle resistomes. Four groups of cattle were exposed, using a 2-by-2 factorial design, to different regimens of antimicrobial treatment. Injections of ceftiofur crystalline-free acid (a third-generation cephalosporin) were used to treat all cattle in treatment pens or only a single animal, and either chlortetracycline was included in the feed of all cattle in a pen or the feed was untreated. On days 0 and 26, respectively, pre- and posttrial fecal samples were collected, and resistance genes were characterized using shotgun metagenomics. Treatment with ceftiofur was not associated with changes to β-lactam resistance genes. However, cattle fed chlortetracycline had a significant increase in relative abundance of tetracycline resistance genes. There was also an increase of an AMR class not administered during the study, which is a possible indicator of coselection of resistance genes. Samples analyzed in this study had previously been evaluated by culture characterization (Escherichia coli and Salmonella) and quantitative PCR (qPCR) of metagenomic fecal DNA, which allowed comparison of results with this study. In the majority of samples, genes that were selectively enriched through culture and qPCR were not identified through shotgun metagenomic sequencing in this study, suggesting that changes previously documented did not reflect changes affecting the majority of bacterial genetic elements found in the predominant fecal resistome.IMPORTANCE Despite significant concerns about public health implications of AMR in relation to use of AMD in food animals, there are many unknowns about the long- and short-term impact of common uses of AMD for treatment, control, and prevention of disease. Additionally, questions commonly arise regarding how to best measure and quantify AMR genes in relation to public health risks and how to determine which genes are most important. These data provide an introductory view of the utility of using shotgun metagenomic sequencing data as an outcome for clinical trials evaluating the impact of using AMD in food animals.

It has been proposed that livestock production effluents such as wastewater, airborne dust and manure increase the density of antimicrobial resistant bacteria and genes in the environment. The public health risk posed by this proposed outcome has been difficult to quantify using traditional microbiological approaches. We utilized shotgun metagenomics to provide a first description of the resistome of North American dairy and beef production effluents, and identify factors that significantly impact this resistome. We identified 34 mechanisms of antimicrobial drug resistance within 34 soil, manure and wastewater samples from feedlot, ranch and dairy operations. The majority of resistance-associated sequences found in all samples belonged to tetracycline resistance mechanisms. We found that the ranch samples contained significantly fewer resistance mechanisms than dairy and feedlot samples, and that the resistome of dairy operations differed significantly from that of feedlots. The resistome in soil, manure and wastewater differed, suggesting that management of these effluents should be tailored appropriately. By providing a baseline of the cattle production waste resistome, this study represents a solid foundation for future efforts to characterize and quantify the public health risk posed by livestock effluents.

Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads for Salmonella enterica,Listeria monocytogenes,Escherichia coli,Staphylococcus aureus, Clostridium spp. (C. botulinum and C. perfringens), and Campylobacter spp. (C. jejuni,C. coli, and C. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts for S. enterica,E. coli, and C. botulinumwere greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes.

This preliminary study aimed to estimate the heritability of liver abscess incidence in fed, beef on dairy crossbred progeny. Liver abscesses affect approximately 20% to 30% of livers at slaughter. They are commonly identified during viscera inspection at slaughter due to difficulty with antemortem diagnosis. All livers with abscesses are condemned, causing a profit loss for producers. This loss is increased when the abscesses are ruptured or adhered to the gut due to additional condemnation of the gut. The most common prevention techniques include antimicrobial feed additives and nutritional management; however, mitigation has not been highly effective. Few studies have attempted to ascertain if a genetic component for liver abscess incidence exists. Determining if there is a genetic component to liver abscess occurrence could enable the ability to utilize genetic selection as a preventative measure. Liver abscess scores were collected on 1,492 crossbred beef on dairy heifers at slaughter. Cattle were harvested in Kansas. Individual livers were scored using the Elanco scoring system of 0, A-, A, A+. Scores of A+, A+AD, and A+O were combined into the A+ category. A score of 0 indicates a normal liver, as scores of A-, A, and A+ indicate increasing severity of abscesses. Scores of A+AD and A+O represent animals with adhesion to the gut or ruptured abscesses, respectively. In the dataset, the distribution was 903, 168, 69, and 352 for scores of 0, A-, A, and A+, respectively. Overall, the prevalence of liver abscesses was 39.5% in this sample. All 1,492 heifers had recorded sire information, but no dam information existed other than knowing they were of dairy origin. In total, 19 unique sires were represented in the data, with six of the sires producing 89.4% of the heifers. A 3-generation sire pedigree was built from the data, and heritability was estimated using a sire model and the statistical software package ASReml 3.0. Fixed effects included the number of bovine respiratory disease treatments, age in days, and a contemporary group consisting of kill lot and treatment type. These cattle were part of an additional study evaluating the effectiveness of various treatment regimens for mitigating the incidence of liver abscesses. There were three treatment groups, one control and two treatments. Genetic and phenotypic variation for this model was estimated to be 2.70 × 10-7 ± 9.99 × 10-9 and 1.58 ± 5.86 × 10-2, respectively. With such a small genetic variance estimate, the heritability of liver abscesses was effectively 0 (1.70 × 10-7), which suggests the lack of a genetic component for liver abscesses in these data. This was a preliminary study that had limited sire variation. Currently, dam information is being accumulated in an attempt to account for dam genetic variation. [ABSTRACT FROM AUTHOR]

The effects of a Nutritional Packet offered to beef steers during the final 64 d of the feedlot-finishing phase on growth performance, carcass characteristics, nutrient digestibility, and feeding behavior were evaluated. Angus-crossbred steers (N = 120; initial body weight = 544 ± 52 kg) were assigned to 30 pens (4 steers per pen; 15 pens per treatment) in a randomized complete block design where pen was the experimental unit. A steam-flaked corn-based finishing diet was offered to ad libitum, and the treatments were as follows: 1) control and 2) 30 g per steer-daily (dry matter basis) of the Nutritional Packet. The Nutritional Packet was formulated to provide 1.7 × 1010 CFU per steer-daily of Saccharomyces cerevisiae, 162 mg per steer-daily of vitamin C; 400 mg per steer-daily of vitamin B1; 2.4 g per steer-daily of NaCl, and 2.4 g per steer-daily of KCl. Data were analyzed using the GLIMMIX procedure of SAS with the fixed effect of treatment and the random effect of block. The average daily gain (P = 0.89), dry matter intake (P = 0.57), and gain efficiency (P = 0.82) were not affected by the inclusion of the Nutritional Packet. Digestibility of dry and organic matter, and neutral and acid detergent fiber increased (P ≤ 0.02) for steers offered the Nutritional Packet, while a trend for the same response was observed for hemicellulose (P = 0.08). The 12th rib backfat thickness increased (P = 0.02) for carcasses of steers offered the Nutritional Packet, followed by a greater (P = 0.03) calculated yield grade, whereas other carcass traits were not affected (P ≥ 0.32). While the steers under the control diet decreased behavior activities on day 63, a consistent pattern of feeding behavior measurements (activity min/d and min/kg of dry and organic matter, fiber fractions, and digestible nutrients) were observed for steers consuming the Nutritional Packet during both feeding behavior assessment periods (treatment × period interactions, P ≤ 0.03). Overall time (min/d) spent on rumination, drinking, active, chewing, and resting were not affected (P ≥ 0.28) by treatments. The Nutritional Packet offered to steers during the final 64 d on feed induced an improvement in apparent digestibility of nutrients and carcass fat deposition, without affecting growth performance or other carcass quality indices. Such effects associated with the more consistent feeding behavior of steers receiving the Nutritional Packet may warrant a shorter time on feed during the final portion of the finishing phase. [ABSTRACT FROM AUTHOR]

The ruminal papillae morphology characteristics of feedlot beef on dairy non-spayed heifers with liver abscess to those with non-abscessed liver were evaluated. Heifers were sourced from 27 lots which were harvested on six dates between November 2022 and February 2023. Upon harvest, a total of 94 rumen tissue samples from animals presenting liver abscesses and 110 rumen tissue samples from animals with non-abscessed livers were collected in pairs, as abscesses were identified within the harvesting facility viscera inspection line, following a randomized complete block design (block = lot within harvest date). Individual fragments (6 cm²) from the cranial sac epithelium of the rumen were collected, rinsed with deionized water, immersed in 70% alcohol, and preserved under refrigeration (4°C) until analysis. Ruminal tissues were trimmed (1 cm²), in which the number of papillae was counted by three trained personnel, followed by the removal of 12 representative papillae specimens for further area electronic scanning (The University of Texas Health Science Center of San Antonio, Image Tool) to determine average papillae area, number per cm² (AVP), average papillae area in cm² (APA), absorptive surface area in cm² /fragment cm² (ASA), and papillae absorptive surface area, % (ASA). Data were analyzed using the GLIMMIX procedures of SAS, with individual animal ruminal tissue used as the experimental unit, the fixed effect of ruminal condition, and the random effect of lot within the harvesting date. Average papillae number (P = 0.27), average papillae area (P = 0.74), absorptive surface area (P = 0.48), and papillae absorptive surface area (P = 0.43) were not affected by the presence of liver abscess. Severity of liver abscess distinguished as A -, A, or A+ scores compared with non-abscessed liver showed no difference on papillae number (P = 0.34), papillae area (P = 0.89), and absorptive area (P = 0.62). The presence of small or large liver abscesses did not affect the papillae area, size, or absorptive area (P ≥ 0.41). The liver lobe location of abscesses (cranial, caudal, both) did not affect (P ≥ 0.17) any of the ruminal morphological variables measured. The presence of liver abscesses, whether diffuse or localized, in beef on dairy heifers, did not affect (P ≥ 0.58) the development of ruminal papillae. The presence, severity, or location of liver abscess was not connected with ruminal papillae number, area, or absorptive surface area of beef on dairy heifers measured upon harvest time. The absence of ruminal papillae morphological changes in animals committed with liver abscesses may be further investigated with the characterization of potential cellular physical changes of the ruminal tissue and the integrity of the primary barrier in the digestive tract. [ABSTRACT FROM AUTHOR]

Beef carcasses with non-normal color costs the United States industry billions of dollars annually. While dark cutters have long been attributed to long-term stress and glycogen depletion, few studies have aimed to understand other potential metabolomic markers of dark and light-colored beef. The objective of this study was to determine the metabolomic profile of carcasses possessing dark, intermediate, normal, and light lean according to RGB instrumental color evaluation. Over 9 consecutive months, 216 carcasses (n = 24/ mo) from 4 color categories were collected from 2 commercial abattoirs. Carcasses were identified using L* values from industry grading cameras. Carcasses were classified into categories based on the least L* value from either side: dark (L* ≤ 55; n = 53), intermediate (55 < L* < 60; n = 54), normal (60 ≤ L* < 80; n = 54), or light (L* ≥ 80; n = 54). A 5.08 cm steak was collected from the longissimus lumborum from both carcass sides. Steaks were aged until 5 d postmortem, snapfrozen and homogenized into a powder. Metabolites were extracted by weighing 50 mg of sample into a tube with 50 μL of ribitol and 1.5 mL of 80% methanol and homogenized using a bead beater. Sample extract was dried with nitrogen gas before being reconstituted with 50 μL of methoxyamine hydrochloride and 50 μL of N-methyl-N-trimethylsilyltrifluoroacetamide with 1% trimethylchlorosilane. Untargeted metabolomics was conducted via gas chromatography-mass spectrometry. Mass spectral data were deconvoluted, aligned, and annotated using MS-DIAL. Total ion counts were normalized by the internal standard and log10 transformed prior to analysis. Data were analyzed using MetaboAnalyst by analysis of variance. Pathway analyses were conducted using the KEGG Bos taurus pathway library. Significance for all analyses was declared at FDR P < 0.05. Metabolite analyses identified 137 total features with 74 identified by the reference library and 45 were differentially expressed between carcass color categories. Malic acid was greatest in dark carcasses and least in normal and light carcasses (FDR P < 0.05). 1-methylgalactose, beta-D-galactose, sorbose, and phosphohexonoic acid was greatest in light carcasses, second in normal, third in intermediate, and least in dark carcasses (FDR P < 0.05). [ABSTRACT FROM AUTHOR]