The fecal microbiome of cattle plays a critical role not only in animal health and productivity but also in food safety, pathogen shedding, and the performance of fecal pollution detection methods. Unfortunately, most published molecular surveys fail to provide adequate detail about variability in the community structures of fecal bacteria within and across cattle populations. Using massively parallel pyrosequencing of a hypervariable region of the rRNA coding region, we profiled the fecal microbial communities of cattle from six different feeding operations where cattle were subjected to consistent management practices for a minimum of 90 days. We obtained a total of 633,877 high-quality sequences from the fecal samples of 30 adult beef cattle (5 individuals per operation). Sequence-based clustering and taxonomic analyses indicate less variability within a population than between populations. Overall, bacterial community composition correlated significantly with fecal starch concentrations, largely reflected in changes in the Bacteroidetes, Proteobacteria, and Firmicutes populations. In addition, network analysis demonstrated that annotated sequences clustered by management practice and fecal starch concentration, suggesting that the structures of bovine fecal bacterial communities can be dramatically different in different animal feeding operations, even at the phylum and family taxonomic levels, and that the feeding operation is a more important determinant of the cattle microbiome than is the geographic location of the feedlot.The enteric microbiota of cattle affects animal health and food safety and is used as an indicator of fecal pollution, which can affect the types and concentrations of indicator organisms in recreational surface waters. The presence of pathogenic bacteria such as Escherichia coli O157:H7 in the bovine gastrointestinal tract has been linked to disease outbreaks due to the consumption of contaminated beef, milk, and drinking water (3). The average feedlot steer produces 1.62 kg of feces (dry matter) per day (2), resulting in more than 18 million metric tons of feces (dry matter) per year in the United States alone. When bovine fecal waste is moved from feedlot operations for land application as fertilizer or is accidentally discharged into the environment due to severe storms, hazardous events, or failure of onsite waste management practices, pathogenic members of this microbial community, such as E. coli O157:H7, Campylobacter jejuni, Salmonella spp., Leptospira interrogans, and Cryptosporidium parvum (5,14,22,41,44), can pose a serious public health risk.Because of the enormous influence the fecal bacterial community of cattle has on the beef and dairy industry, the economy, and public health, a great deal of research has been conducted to characterize the effects of animal age, disease state, feeding practices, and antibiotic treatments on cattle fecal microorganisms. Many of the most comprehensive studies use DNA-based methodologies, such as sequencing of the full-length 16S rRNA gen...

Methane production from enteric fermentation in cattle is one of the major sources of anthropogenic greenhouse gas emission in the United States and worldwide. National estimates of methane emissions rely on mathematical models such as the one recommended by the Intergovernmental Panel for Climate Change (IPCC). Models used for prediction of methane emissions from cattle range from empirical to mechanistic with varying input requirements. Two empirical and 2 mechanistic models (COWPOLL and MOLLY) were evaluated for their prediction ability using individual cattle measurements. Model selection was based on mean square prediction error (MSPE), concordance correlation coefficient, and residuals vs. predicted values analyses. In dairy cattle, COWPOLL had the lowest root MSPE and greatest accuracy and precision of predicting methane emissions (correlation coefficient estimate = 0.75). The model simulated differences in diet more accurately than the other models, and the residuals vs. predicted value analysis showed no mean bias (P = 0.71). In feedlot cattle, MOLLY had the lowest root MSPE with almost all errors from random sources (correlation coefficient estimate = 0.69). The IPCC model also had good agreement with observed values, and no significant mean (P = 0.74) or linear bias (P = 0.11) was detected when residuals were plotted against predicted values. A fixed methane conversion factor (Ym) might be an easier alternative to diet-dependent variable Ym. Based on the results, the 2 mechanistic models were used to simulate methane emissions from representative US diets and were compared with the IPCC model. The average Ym in dairy cows was 5.63% of GE (range 3.78 to 7.43%) compared with 6.5% +/- 1% recommended by IPCC. In feedlot cattle, the average Ym was 3.88% (range 3.36 to 4.56%) compared with 3% +/- 1% recommended by IPCC. Based on our simulations, using IPCC values can result in an overestimate of about 12.5% and underestimate of emissions by about 9.8% for dairy and feedlot cattle, respectively. In addition to providing improved estimates of emissions based on diets, mechanistic models can be used to assess mitigation options such as changing source of carbohydrate or addition of fat to decrease methane, which is not possible with empirical models. We recommend national inventories use diet-specific Ym values predicted by mechanistic models to estimate methane emissions from cattle.

We hypothesized that stearoyl-CoA desaturase (SCD) enzyme activity would not correlate with fatty acid indices of SCD activity in steers fed different grains. Forty-five Angus steers (358 +/- 26 kg BW) were individually fed for 107 d diets differing in whole cottonseed (WCS) supplementation (0, 5, or 15% of DM) and grain source (rolled corn, flaxseed plus rolled corn, or ground sorghum grain) in a 3 x 3 factorial arrangement. Flaxseed- and corn-fed steers had greater (P < 0.01) G:F (0.119 and 0.108, respectively) than sorghum-fed steers (0.093). Marbling score was decreased by WCS (P = 0.04), and LM area was decreased (P < 0.01) by sorghum. Plasma 14:0, 16:0, 16:1n-7, and 18:2n-6 were greatest in corn-fed steers, whereas plasma 18:3n-3 and 20:5n-3 were greatest in the flax-seed-fed steers (P < 0.01). Plasma 18:1trans-11 was least in sorghum-fed steers, and plasma cis-9,trans-11 CLA was barely detectable, in spite of high intestinal mucosal SCD enzyme activity (118 to 141 nmol*g tissue(-1).7 min(-1)). Interfascicular (i.f.) and s.c. cis-9,trans-11 CLA remained unchanged (P > or = 0.25) by treatment, although 18:1trans-11 was increased (P < or = 0.02) in steers fed corn or flaxseed. Steers fed flaxseed also had greater (P < 0.01) i.f. and s.c. concentrations of 18:3n-3 than steers fed the other grain sources. Oleic acid (18:1n-9) was least and total SFA were greatest (P < 0.01) in i.f. adipose tissue of steers fed 15% WCS. Lipogenesis from acetate in s.c. adipose tissue was greater (P < 0.01) in flaxseed-fed steers than in the corn- or sorghum-fed steers. Steers fed flaxseed or corn had larger i.f. mean adipocyte volumes (P < 0.01) than those fed sorghum and tended (P = 0.07) to have larger s.c. adipocyte volumes. Several fatty acid indices of SCD enzyme activity were decreased (P < or = 0.03) by WCS in i.f. adipose tissue, including the 18:2cis-9,trans-11/ 18:1trans-11 ratio. The 18:2cis-9,trans-11/18:1trans-11 ratio also tended to be decreased (P = 0.09) in s.c. adipose tissue by flaxseed; however, SCD enzyme activities in i.f. and s.c. adipose tissue were not affected by dietary WCS (P > or = 0.47) or grain source (P > or = 0.37). Differences in SFA seemed to be independent of SCD enzyme activity in both adipose tissues, suggesting that duodenal concentrations of fatty acids were more important in determining tissue fatty acid concentrations than endogenous desaturation by SCD.

Nitrogen was recognized over 200 yr ago as an element essential for normal function of farm animals. During the first half of the 19th century, the roles of proteins and urea in N metabolism were discovered. By the middle of the 20th century, the substrates, products, and enzymes of the urea cycle were elucidated. Work since then has quantified dietary crude protein requirements for specific production goals, protein synthesis and breakdown, ruminal ammonia production, endogenous urea synthesis, and urea recycling. In ruminants fed conventional diets, N absorbed as ammonia can be several times the amount of N absorbed in the form of amino acids or peptides. Nitrogen recycled to the digestive tract as urea in saliva or urea transported from blood ranges from 10 to 40% of N consumed in feed. Under production conditions, from 0 to 20% of N consumed by ruminants is retained as tissue N or excreted as milk protein. This review describes the quantitative aspects of urea and ammonia metabolism in ruminants and it relates the metabolic or economic costs of that metabolism to practical feeding situations. The review concludes with a discussion of conflicts and considerations among three main priorities in ruminant N metabolism: 1) maximizing microbial function in the rumen; 2) optimizing amino acid supply to the host ruminant; and 3) minimizing negative environmental effects of cycling N through ruminant production systems.

The effects of two forage species and N levels on urea kinetics and whole-body N metabolism were evaluated in eight Angus steers (initial BW 217+/-15 kg). In a replicated, 4 x 4 Latin square design, steers were fed gamagrass (Tripsacum dactyloides L.) or switchgrass (Panicum virgatum L.), each of which had 56.2 (LO) or 168.5 (HI) kg of N fertilization per hectare. Diets provided adequate energy for 0.5 kg ADG. Nitrogen balance and urea kinetics were measured from d 22 to 27 of each period. Urine samples collected during intravenous infusion of bis 15N urea were used to calculate production and recycling of urea N from relative abundance of urea isotopomers. Jugular blood serum was analyzed for serum urea N (SUN). Gamagrass differed from switchgrass (P < 0.05) in daily DMI (4,273 vs 4,185 g), N intake (72 vs 67 g), DM digestibility (61.0 vs 63.6%), fecal N (30.6 vs 28.3 g/d), urine urea N (10.5 vs 8.0 g/d), and percentage of urinary N present as urea N (53.5 vs 40.0%). After adjustment for differences in N intake, fecal N still tended to be greater (P < 0.09) for gamagrass than for switchgrass. The LO differed from the HI (P < 0.01) in daily N intake (63 vs 76 g), DM digestibility (61.3 vs 63.3%), urine N (13.6 vs 25.9 g/d), and N retained as a percentage of N digested (57.3 vs 43.5%). Compared to switchgrass, gamagrass had greater SUN, N digestibility, and N digested as N level increased (forage x N level interactions, P < 0.05). As N level increased, N retention increased from 19.5 to 23.5 g/d in gamagrass and decreased from 20.5 to 18.1 g/d in switchgrass (interaction, P < 0.07). The HI group was greater than the LO intake group (P < 0.03) in endogenous production of urea N (44.4 vs 34.0 g/d), gut entry rate of urea N (31.6 vs 28.2 g/d), and the amount of urea N that re-entered the ornithine cycle (9.4 vs 7.9 g/d). However, the percentage of urea N entering the gastrointestinal tract that was recycled was constant among treatments (29.1%), indicating that almost 70% of the urea N that entered the gastrointestinal tract was potentially available for anabolic purposes of the steers as a component of microbial products that were absorbed or excreted in the feces. In summary, N levels affected N metabolism of steers more when they were fed gamagrass than when they were fed switchgrass. Although the absolute amounts of N moving through the system changed with variations in intake, the proportions remained similar, with a greater efficiency of N use at low N intakes.