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Extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli have been widely described as the cause of treatment failures in humans around the world. The origin of human infections with these microorganisms is discussed controversially and in most cases hard to identify. Since they pose a relevant risk to human health, it becomes crucial to understand their sources and the transmission pathways. In this study, we analyzed data from different studies in Germany and grouped ESBL-producing E. coli from different sources and human cases into subtypes based on their phenotypic and genotypic characteristics (ESBL-genotype, E. coli phylogenetic group and phenotypic antimicrobial resistance pattern). Then, a source attribution model was developed in order to attribute the human cases to the considered sources. The sources were from different animal species (cattle, pig, chicken, dog and horse) and also from patients with nosocomial infections. The human isolates were gathered from community cases which showed to be colonized with ESBL-producing E. coli. We used the attribution model first with only the animal sources (Approach A) and then additionally with the nosocomial infections (Approach B). We observed that all sources contributed to the human cases, nevertheless, isolates from nosocomial infections were more related to those from human cases than any of the other sources. We identified subtypes that were only detected in the considered animal species and others that were observed only in the human population. Some subtypes from the human cases could not be allocated to any of the sources from this study and were attributed to an unknown source. Our study emphasizes the importance of human-to-human transmission of ESBL-producing E. coli and the different role that pets, livestock and healthcare facilities may play in the transmission of these resistant bacteria. The developed source attribution model can be further used to monitor future trends. A One Health approach is necessary to develop source attribution models further to integrate also wildlife, environmental as well as food sources in addition to human and animal data.

Background Cattle have been identified as a major reservoir of E. coli O157:H7 for human infection; the ecology of the organism in sheep and goats is less understood. This study was carried out to determine prevalence, source of infection, antibiotic resistance and molecular characterization of Escherichia coli O157: H7 isolated from sheep and goat. Methods Systematic random sampling was carried out at Modjo export abattoir, Ethiopia, from November 2012 to April 2013 to collect 408 samples from 72 sheep and 32 goats. Samples collected were skin swabs, fecal samples, intestinal mucosal swabs and the inside and outside part of carcasses as well as carcass in contacts such as workers hands, knife, hook and carcass washing water. Then, samples were processed following standard bacteriological procedures. Non-Sorbitol fermenting colonies were tested on latex agglutination test and the positives are subjected to PCR for detection of attaching and effacing genes (eaeA) and shiga toxin producing genes (stx1 and stx2). All E. coli O157:H7 isolates were checked for their susceptibility pattern towards 15 selected antibiotics. Results E. coli O157:H7 were detected in only 20/408 samples (4.9%). Among these 20 positive samples, 70% (14/20), 25% (5/20) and 5% (1/20) were from sheep, goats and knife samples, respectively. No significant associations were found between carcasses and the assumed sources of contaminations. Of all the 20 isolates virulence genes were found in 10 (50%) of them; 3 (15%) with only the eaeA gene and 7(35%) expressing eaeA and stx2 genes. All the isolates were susceptible to Norfloxacin (NOR) (100%). Conclusions The presence of virulence genes shows E. coli O157:H7 is a potential source of human infection in Ethiopia.

Sickness behaviour has been suggested as an applicable indicator for monitoring disease. Deviating feeding behaviour and activity can provide information about animals' health and welfare status. Recent advances in sensor technology enable monitoring of such behaviours and could potentially be utilized as an indicator of gastrointestinal nematode (GIN) infections. This study investigated activity and rumination patterns in first-season grazing steers exposed to subclinical infection levels of the GIN Ostertagia ostertagi and Cooperia oncophora. At turnout, animals were allocated to one of four experimental groups and were faced with "high" (H1, n = 15; H2, n = 17) or "low" (L1, n = 17; L2, n = 11) levels of parasite exposure by grazing in similar enclosures contaminated with overwintering third stage (13) GIN larvae. Animals in H1 and H2 (HP) received a 1:1 mix of approximately 10,000 0. ostertagi and C. oncophora L3 at turnout; whereas the animals in Ll and L2 (LP) were treated monthly with ivermectin. Activity and rumination patterns were monitored by fitting animals with leg- (IceQube) and neck-mounted (Heatime) sensors. BW was recorded every fortnight, whereas faecal and blood samples were examined every four weeks for nematode faecal egg count and serum pepsinogen concentrations (SPCs). There was an interaction effect of exposure level and period (P < 0.0001) on average lying daily time across the entire grazing time. A higher mean daily lying time (P = 0.0037) was found in HP compared with LP during the first 40 days on pasture. There was also interaction effects of treatment and day since turnout on rumination time (P < 0.0001) and rumination change (P = 0.0008). Also mean daily steps (P < 0.0001) and mean daily motion index (P < 0.0001) were markedly higher in HP during days 62-69, coinciding with peaking SPC in HP. Strongyle eggs were observed both in HP and LP from 31 days after turnout. Eggs per gram (EPG) differed between parasite exposure levels (P < 0.0001), with mean EPG remaining low in LP throughout the experiment. Similarly, an increase in SPC was observed (P < 0.0001), but only in HP where it peaked at day 56. In contrast, no difference in BW gain (BWG) (P = 0.78) between HP and LP was observed. In conclusion, this study shows that behavioural measurements monitored with sensors were affected even at low infection levels not affecting BWG. These combined results demonstrate the potential of automated behavioural recordings as a tool for detection of subclinical parasitism.

Total mixed rations (TMR) based on grass silage (GS), triticale silage (TS), mixture of GS and TS, barley silage (BS) and mixture of GS and BS were fed to fifty Hereford (HF) and fifty Charolais (CH) bulls. The proportion (g kg-1 dry matter [DM]) of the silages in the TMRs were as follows: (1) GS (600); (2) TS (600); (3) GS (300) and TS (300); (4) BS (600); (5) GS (300) and BS (300). Concentrate proportion was 400 g kg-1 DM. According to feed analyses, the GS had 15 and 8% higher metabolizable energy (ME) concentration as well as 51 and 49% higher crude protein (CP) concentration compared to TS and BS, respectively. Average DM intake (DMI) on TS and BS containing diets was higher compared to GS as a sole forage (p=0.001). Compared to the TS based rations the use of BS rations increased daily DMI by 5% (p

Background The current large spectrum of sheep phenotypic diversity results from the combined product of sheep selection for different production traits such as wool, milk and meat, and its natural adaptation to new environments. In this study, we scanned the genome of 25 Sasi Ardi and 75 Latxa sheep from the Western Pyrenees for three types of regions under selection: (1) regions underlying local adaptation of Sasi Ardi semi-feral sheep, (2) regions related to a long traditional dairy selection pressure in Latxa sheep, and (3) regions experiencing the specific effect of the modern genetic improvement program established for the Latxa breed during the last three decades. Results Thirty-two selected candidate regions including 147 annotated genes were detected by using three statistical parameters: pooled heterozygosity H, Tajima’s D, and Wright’s fixation index Fst. For Sasi Ardi sheep, chromosomes Ovis aries (OAR)4, 6, and 22 showed the strongest signals and harbored several candidate genes related to energy metabolism and morphology (BBS9, ELOVL3 and LDB1), immunity (NFKB2), and reproduction (H2AFZ). The major genomic difference between Sasi Ardi and Latxa sheep was on OAR6, which is known to affect milk production, with highly selected regions around the ABCG2, SPP1, LAP3, NCAPG, LCORL, and MEPE genes in Latxa sheep. The effect of the modern genetic improvement program on Latxa sheep was also evident on OAR15, on which several olfactory genes are located. We also detected several genes involved in reproduction such as ESR1 and ZNF366 that were affected by this selection program. Conclusions Natural and artificial selection have shaped the genome of both Sasi Ardi and Latxa sheep. Our results suggest that Sasi Ardi traits related to energy metabolism, morphological, reproductive, and immunological features have been under positive selection to adapt this semi-feral sheep to its particular environment. The highly selected Latxa sheep for dairy production showed clear signatures of selection in genomic regions related to milk production. Furthermore, our data indicate that the selection criteria applied in the modern genetic improvement program affect immunity and reproduction traits. Electronic supplementary material The online version of this article (10.1186/s12711-018-0378-x) contains supplementary material, which is available to authorized users.

International audience; Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp-773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining. We observed higher differentiation among breeds for deletions in some genic-regions, such as ABCA12, TTC1, VWA3B, TSHR, DST/BPAG1, and CD1D. The genes overlapping deletions are on average evolutionarily less conserved compared with known mouse lethal genes (P-value = 2.3 × 10-6). We report 167 natural gene knockouts in cattle that are apparently nonessential as live homozygote individuals are observed. These genes are functionally enriched for immunoglobulin domains, olfactory receptors, and MHC classes (FDR = 2.06 × 10-22, 2.06 × 10-22, 7.01 × 10-6, respectively). We also demonstrate that deletions are enriched for health and fertility related quantitative trait loci (2-and 1.5-fold enrichment, Fisher's P-value = 8.91 × 10-10 and 7.4 × 10-11, respectively). Finally, we identified and confirmed the breakpoint of a ∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8), causing stillbirth in Nordic Red Cattle.

The objective of this study was to determine the association of single nucleotide polymorphisms (SNPs) in selected candidate genes with fattening performance traits in a commercial cattle herd. Fifteen SNPs in 12 candidate genes (LEP, FABP4, DGAT1, TG, IGF1, IGF1R, MYF5, LGB, CAPN1, CAST, GHR, and OLR1) were evaluated in 296 purebred Holstein–Friesian bulls using PCR-RFLP (polymerase chain reaction – restriction fragment length polymorphism). Associations between each segregating SNP and genetic merit for fattening performance were quantified using linear mixed models. Traits included in the study were fattening period, final weight, dry matter intake, feed conversion rate, and average daily weight gain. Apart from the general determination of the above-mentioned traits, each trait was evaluated based on the fattening periods between five selected target body weights (W1 = 100 kg, W2 = 200 kg, W3 = 300 kg, W4 = 400 kg, W5 = 450 kg). All markers with the exception of CAPN1 530, IGF1R, TG, and DGAT1 were associated with at least one of the traits. Furthermore, novel associations were observed for LEP × GHR, IGF1 × LEP, FABP4 3691 × FABP4 2834, and FAP4 3533 × LEP interactions. The results of this study confirm some previously reported associations. Moreover, novel associations have been identified, which may be incorporated into breeding programs to improve fattening performance.

Salmonellosis is a leading cause of foodborne illnesses in humans with cattle being one of the reservoirs for Salmonella. We estimated a pooled prevalence of Salmonella in apparently healthy cattle and examined serotype diversity through systematic review and meta-analysis of studies published between 2000 and 2017. Peer reviewed publications reporting the prevalence of Salmonella in cattle were searched through five electronic databases (PubMed, Google scholar, Agricola, Scopus, CAB direct) and through manual search. We obtained 71 publications with 75 datasets consisting a total of 52,766 animals examined and 5,010 Salmonella positive cattle from 29 countries in six continents (except from Antarctica). Pooled prevalence of Salmonella in cattle was 9% (95% confidence interval: 7–11%). Significantly high heterogeneity (I2 = 98.7%, P < 0.01) was observed among all studies as well as within continents. Prevalence varied from 2% (Europe) to 16% (North America). Overall, 143 different serotypes were reported with the most diverse serotypes being reported from Africa (76 different serotypes) followed by North America (49 serotypes). The 10 most frequently reported serotypes (Montevideo, Typhimurium, Kentucky, Meleagridis, Anatum, Cerro, Mbandaka, Muenster, Newport, and Senftenberg) accounted for 65% of the isolates for which specific serotype information was reported. Salmonella Montevideo and S. Dublin are the most frequently reported serotypes in North America and Europe, respectively, while S. Typhimurium was the most frequent in Africa, Asia and Australasia. Our results indicated variability both in the prevalence and serotype diversity of Salmonella in cattle across continents. Although all Salmonella serotypes are potentially pathogenic to humans, five (Montevideo, Typhimurium, Anatum, Mbandaka, and Newport) of the top 10 serotypes identified in this study are among the serotypes most commonly associated with clinical illnesses in humans.

De intensivering van de moderne landbouw wordt geassocieerd met een toename van Clostridium perfringens-gerelateerde, gastro-intestinale problemen bij intensief gevoede runderen, zoals “hemorrhagic bowel disease” bij hoogproductief melkvee en enterotoxemie bij kalveren. Waar de pathogenese van hemorrhagic bowel disease nog grotendeels ongekend is, werden er de laatste jaren nieuwe inzichten in de pathogenese van enterotoxemie bekomen die een belangrijke repercussie op de aanpak van deze ziekte onder praktijkomstandigheden hebben. Ook andere clostridiumgeassocieerde maagdarminfecties, zoals “overeating disease” en neonatale clostridiose, worden regelmatig gediagnosticeerd. Overvoedering met structuurarme, eiwitrijke voeders is een overkoepelende risicofactor bij zowel HBD, enterotoxemie als overeating disease. Een goed uitgebalanceerd dieet dat zo stabiel mogelijk gehouden wordt, is dan ook het belangrijkste aandachtspunt op bedrijven die problemen hebben met clostridiose. Daarnaast dient bij jonge kalveren voldoende aandacht gegeven te worden aan een correcte en hygiënische biestverstrekking om problemen met neonatale clostridiose te vermijden.

Marker assisted selection (MAS) have been using to determine the associations between the genes and economic traits of livestock animals. However, phenotypic values do not generally indicate the real genotypic values of animals. However, using MAS approaches in selection of animals can increase the accuracy of selection. From this point of view, validation of candidate gene markers for marker assisted selection is very important to increase genetic gains in breeding. Leptin is a 16 kDa protein which is highly expressed in adipose tissue. Leptin is one of the most significant candidate gene marker for MAS studies. Therefore, bubaline leptin gene exon 2, part of the intron 1 and intron 2 region were amplified and sequenced to identify nucleotide variations in Anatolian water buffaloes. Sequence analysis were revealed seven polymorphic site (G1072A, T1081C, T1131G, T1143C, T1145G, T1151G and C1221T) and one monomorphic site (C1071T) in Anatolian water buffaloes. To the best of my knowledge, this is the first study that fully describes seven polymorphic sites of bubaline leptin gene in Anatolian water buffaloes.

How globalization impacts native land cover has become an important issue in studies addressing environmental change, which draw explicit attention to processes of cause and effect operating over significant distances. The literature shows that globalization constitutes an important underlying driver of both deforestation and forest transition via demographic and economic phenomena such as migration and remittance flows. Yet, little is known about how global forces mold the spatial structure of agro-commodity production and how this impacts the balance of forces affecting land change at the meso-scale, within the boundaries of the nation-state. The research presented here fills this gap by examining production networks for Mexico, a large OECD country with complex land change dynamics that has recently experienced a dramatic opening to the world economy. Specifically, we consider how maize and beef commodity chains evolved over the past few decades into a highly interdependent maize-cattle complex, and suggest linkages to patterns of land change at the national scale. Using land cover maps for 1993, 2002, and 2012, at the national scale, governmental statistics and datasets, interviews with key informants, and field observations the article provides an analysis of the impact of neoliberal reforms on the changing geography of beef and maize production, and argues that this process underlies the evolution of Mexico’s land change regime, both before and after the NAFTA reforms. As such, the article presents an account, and a case for further research on the topic of how teleconnections are constituted by spatially-extensive food production networks.

The objective of this study was to determine the association of single nucleotide polymorphisms ( SNPs) with carcass characteristics and meat quality traits in selected candidate genes in Holstein bulls. Five SNPs in four genes, i.e. calpain 1 (CAPN1), calpastatin (CAST), leptin (LEP) and growth hormone receptor (GHR), were genotyped in 400 purebred bulls using PCR-RFLP. Statistically significant associations were as follows: CAPN1 G316A with live weight, carcass weight, back fat thickness, m. longissimus thoracis et lumborum area and carcass measurements; CAPN1 V530I with pH and L *; CAST S20T with live weight, inner chest depth and b * value; and GHR with ph, a * and h *. In addition, significant genotypic interactions were observed for dressing percentage (LEP A80V x CAST S20T), pH (CAPN1 V530I x GHR S555G and LEP A80V x GHR S555G) and rump width (CAPN1 V530I * CAST S20T). There was no association between the LEP A80V marker and any of the traits evaluated, nor was there any association of the tested SNPs with chest width, C* and marbling score. The present results could therefore be indicative for future studies on meat yield and quality.

Background Residual feed intake (RFI) was investigated as a measure of feed efficiency in a breeding population of Litopenaeus vannamei. Shrimp from 34 families were housed individually and feed efficiency and growth traits were recorded during two successive growth periods. The objectives of this study were (1) to estimate the heritability of RFI and related traits, including feed efficiency ratio (FER), average daily gain (ADG) and daily feed intake (DFI), (2) to determine the relationships between RFI and other traits, and (3) to evaluate the variation of these traits across two growth periods. Results Shrimp displayed large inter-individual variation in RFI, FER, ADG and DFI during each growth period. Heritability estimates of all these traits during both periods reached high values (0.577 ± 0.232 to 0.707 ± 0.252). RFI showed weak and no genetic correlations with ADG during the two growth periods between days 1 to 21 (0.135 ± 0.204) and 22 to 42 (–0.018 ± 0.128), respectively, but high positive genetic correlations with DFI (>0.8). Weak and moderate negative genetic correlations were observed between RFI and FER during the two periods (–0.126 ± 0.208 and –0.387 ± 0.183). As evidenced by the high genetic correlations between the two periods for each trait (>0.6), trait performance of the shrimp tended to be consistent across periods. Conclusions For the first time, accurate measurement of individual feed efficiency on a large scale was achieved in shrimp. Although the estimated heritability reported here for RFI may be overestimated, it is a heritable trait in L. vannamei that can be improved by genetic improvement. For L. vannamei, the biggest potential advantage in using RFI as a measure of feed efficiency is that it is independent of growth rate, and thus genetic selection on RFI has the potential to improve feed efficiency and reduce feed intake, without compromising growth performance. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0334-1) contains supplementary material, which is available to authorized users.

The aim of this study was to investigate the effects of single nucleotide polymorphisms (SNPs) at six candidate genes (LEP, CAST, CAPN1, GHR, FABP4 and DGAT1) on fattening performance and carcass traits of Simmental bulls in Turkey. The analysis covered a total of 81 Simmental bulls grown on a private farm that were randomly selected for their fattening period for use in this study. Genotyping was performed using the PCRRFLP method. The S20T polymorphism at the CAST gene and the G316A polymorphism at the CAPN1 gene were associated with variation in final weight, fattening period, weight gain and average daily gain (P < 0.05). In addition, LEP A80V had a significant effect on hot and chilled carcass weight and dressing percentage (P < 0.05). There was no association between GHR S555G, FABP4 V110M and DGAT1 K232A markers with the traits analysed. These results suggested that focusing on the novel effects of LEP, CAST and CAPN1 gene polymorphisms on meat production traits might be useful for marker-assisted selection in Simmental cattle.

Behavioural tests for cattle take time to perform and can be stressful for the animals but are currently the only way of assessing behavioural reactions to fear-causing stimuli in a standardised manner. It may be possible to use behavioural data collected remotely in the home pen environment through the use of activity monitors and robotic milkers to identify fearful cattle without testing. In this study eighty five dairy cows were given a novel arena novel object (NANO) test and 79 of these were also human approach (HAP) tested, both thought to reflect fear. All animals had their activity recorded for 40 days prior to the testing period using a tri-axial accelerometer activity monitor. High numbers of novel object contacts in the test was associated with younger animals with fewer lying bouts per day and were less variable in their lying bout duration (Radj2=0.13, F 3,75 = 4.65, P = 0.005). Cows with a higher tolerance for human approach had fewer lying bouts per day, a shorter average standing bout duration and presented themselves to the robot milker more often (Radj2=0.08, F 3,69 = 3.12, P = 0.032). Personality traits constructed from a principle components analysis of the observed NANO behaviours were also associated with home pen activity. Cows which scored highly on the first component termed ‘neophobia’ were older, had more lying bouts and a greater variation in the duration of their average lying bout (Radj2=0.15, F 3,75 = 5.32, P = 0.002) while cows which scored highly on the second component termed ‘boldness’ were older cows with less variation in their average lying bout duration (Radj2=0.11, F2,75 = 5.63, P = 0.005). To conclude, significant relationships exist between behaviours in short-term personality tests and home pen activity recorded over several weeks. As fearfulness is reflected in spontaneous home pen behaviours, activity databases could be incorporated into models predicting fearfulness and welfare assessment protocols.

In livestock, many studies have reported the results of imputation to 50k single nucleotide polymorphism (SNP) genotypes for animals that are genotyped with low-density SNP panels. The objective of this paper is to review different measures of correctness of imputation, and to evaluate their utility depending on the purpose of the imputed genotypes. Across studies, imputation accuracy, computed as the correlation between true and imputed genotypes, and imputation error rates, that counts the number of incorrectly imputed alleles, are commonly used measures of imputation correctness. Based on the nature of both measures and results reported in the literature, imputation accuracy appears to be a more useful measure of the correctness of imputation than imputation error rates, because imputation accuracy does not depend on minor allele frequency (MAF), whereas imputation error rate depends on MAF. Therefore imputation accuracy can be better compared across loci with different MAF. Imputation accuracy depends on the ability of identifying the correct haplotype of a SNP, but many other factors have been identified as well, including the number of genotyped immediate ancestors, the number of animals with genotypes at the high-density panel, the SNP density on the low- and high-density panel, the MAF of the imputed SNP and whether imputed SNP are located at the end of a chromosome or not. Some of these factors directly contribute to the linkage disequilibrium between imputed SNP and SNP on the low-density panel. When imputation accuracy is assessed as a predictor for the accuracy of subsequent genomic prediction, we recommend that: (1) individual-specific imputation accuracies should be used that are computed after centring and scaling both true and imputed genotypes; and (2) imputation of gene dosage is preferred over imputation of the most likely genotype, as this increases accuracy and reduces bias of the imputed genotypes and the subsequent genomic predictions.

Charolais bulls are selected for their crossbreed performance when mated to Montbéliard or Holstein dams. To implement genomic prediction, one could build a reference population for each crossbred population independently. An alternative could be to combine both crossbred populations into a single reference population to increase size and accuracy of prediction. The objective of this study was to investigate the accuracy of genomic prediction by combining different crossbred populations. Three scenarios were considered: 1) using 1 crossbred population as reference to predict phenotype of animals from the same crossbred population, 2) combining the 2 crossbred populations into 1 reference to predict phenotype of animals from 1 crossbred population, and 3) using 1 crossbred population as reference to predict phenotype of animals from the other crossbred population. Traits studied were bone thinness, height, and muscular development. Phenotypes and 45,117 SNP genotypes were available for 1,764 Montbéliard × Charolais calves and 447 Holstein × Charolais calves. The population was randomly spilt into 10 subgroups, which were assigned to the validation one by one. To allow fair comparison between scenarios, size of the reference population was kept constant for all scenarios. Breeding values were estimated with BLUP and genomic BLUP. Accuracy of prediction was calculated as the correlation between the EBV and the phenotypic values of the calves in the validation divided by the square root of the heritability. Genomic BLUP showed higher accuracies (between 0.281 and 0.473) than BLUP (between 0.197 and 0.452). Accuracies tended to be highest when prediction was within 1 crossbred population, intermediate when populations were combined into the reference population, and lowest when prediction was across populations. Decrease in accuracy from a prediction within 1 population to a prediction across populations was more pronounced for bone thinness (–27%) and height (–29%) than for muscular development (–14%). Genetic correlation between the 2 crossbred populations was estimated using pedigree relationships. It was 0.70 for bone thinness, 0.80 for height, and 0.99 for muscular development. Genetic correlation indicates the expected gain in accuracy of prediction when combining different populations into 1 reference population. The larger the genetic correlation is, the larger the benefit is to combine populations for genomic prediction.

Eighteen pre-weaned female calves from a single beef cattle herd in western France were sampled weekly from birth to 21/2 months of age in order to characterize Gyptosporidium oocyst output. 182 fecal samples were screened for the presence of oocysts after concentration using immunofluorescence analysis. DNA was extracted from positive samples and a PCR-RFLP protocol, with the restriction enzyme SspI and MboII, to amplify the partial SSU rRNA gene was performed. For the subtyping of Cryptosporidium parvum, a gp60 PCR was carried out. All animals excreted oocysts at at least one sampling date and 80% of the calves presented a mild diarrhea at at least one occasion, with no mortality. The prevalence of excretion reached 94% when calves were 17-23 days of age. The mean number of oocysts at the peak of excretion (10-16 days) was 5 x 10(5) oocysts per gram of feces. PCR-RFLP analysis was successful for 61 of 84 positive samples: 14 were identified as C. parvum, 15 as Cryptosporidium bovis, and 22 as Cryptosporidium ryanae. Ten mixed infections with all combinations of these species were also identified. Calves excreted the following Cryptosporidium species: C. parvum between 7 and 27 days of age, C bovis between 11 and 38 days and C ryanae from 19 to 72 days. The IIaA15G2R1 zoonotic subtype of C. parvum subtype was the only subtype identified. We observed the presence of different Cryptosporidium species depending on the age of the animals. This study showed that C parvum and C. bovis can infect beef calf neonates at similar levels of oocyst excretion with or without clinical signs and that C parvum isolates had zoonotic potential. (C) 2013 Elsevier B.V. All rights reserved.

The present study investigated the long-term consistency of individual differences in dairy cattles' responses in tests of behavioural and hypothalamo-pituitary-adrenocortical (HPA) axis reactivity, as well as the relationship between responsiveness in behavioural tests and the reaction to first milking. Two cohorts of heifer calves, Cohorts 1 (N = 25) and 2 (N = 16), respectively, were examined longitudinally from the rearing period until adulthood. Cohort 1 heifers were subjected to open field (OF), novel object (NO), restraint, and response to a human tests at 7 months of age, and were again observed in an OF test during first pregnancy between 22 and 24 months of age. Subsequently, inhibition of milk ejection and stepping and kicking behaviours were recorded in Cohort 1 heifers during their first machine milking. Cohort 2 heifers were individually subjected to OF and NO tests as well as two HPA axis reactivity tests (determining ACTH and/or cortisol response profiles after administration of exogenous CRH and ACTH, respectively) at 6 months of age and during first lactation at approximately 29 months of age. Principal component analysis (PCA) was used to condense correlated response measures (to behavioural tests and to milking) within ages into independent dimensions underlying heifers' reactivity. Heifers demonstrated consistent individual differences in locomotion and vocalisation during an OF test from rearing to first pregnancy (Cohort 1) or first lactation (Cohort 2). Individual differences in struggling in a restraint test at 7 months of age reliably predicted those in OF locomotion during first pregnancy in Cohort 1 heifers. Cohort 2 animals with high cortisol responses to OF and NO tests and high avoidance of the novel object at 6 months of age also exhibited enhanced cortisol responses to OF and NO tests at 29 months of age. Measures of HPA axis reactivity, locomotion, vocalisation and adrenocortical and behavioural responses to novelty were largely uncorrelated, supporting the idea that stress responsiveness in dairy cows is mediated by multiple independent underlying traits. Inhibition of milk ejection and stepping and kicking behaviours during first machine milking were not related to earlier struggling during restraint, locomotor responses to OF and NO tests, or the behavioural interaction with a novel object. Heifers with high rates of OF and NO vocalisation and short latencies to first contact with the human at 7 months of age exhibited better milk ejection during first machine milking. This suggests that low underlying sociality might be implicated in the inhibition of milk ejection at the beginning of lactation in heifers. (C) 2013 Elsevier B.V. All rights reserved.

This study aimed to identify chromosomal regions associated with genetic variation in pre-weaning growth traits in Angora goats. A genome-wide scan was performed by genotyping 1042 offspring from 12 half-sib families using 88 microsatellite caprine markers covering 1368cM. Phenotypes were recorded at birth (BW) and weaning (WW) and analysed using GridQTL software. A total of six putative QTL were detected on six different chromosomes, all at chromosome-wide significance level. Four QTL were identified for BW on CHI 4, 8, 17 and 27 and two QTL for WW on CHI 16 and 19. QTL effects ranged from −0.32 to 0.25 in units of residual standard deviation in different families. Some of these QTL correspond to chromosomes where QTL associated with growth have been identified in other species. These chromosomal segments hold potential to influence weight gain in young goats.

Charolais sires can be mated to Montbéliard or Holstein dairy cows to produce crossbred calves sold for meat production. Heritabilities and correlations between traits can differ when they are calculated within Charolais × Montbéliard or within Charolais × Holstein population. Moreover, the genetic correlation between the same trait measured on Charolais × Montbéliard and on Charolais × Holstein crossbred calves is not necessarily unity. The first objective of this study was to estimate heritability and genetic correlation between traits within Charolais × Montbéliard and within Charolais × Holstein population. The second objective was to investigate if those traits are genetically identical between crossbred populations. Traits studied were calving difficulty, birth weight, height, bone thinness, and muscular development. Data included 22,852 Charolais × Montbéliard and 16,012 Charolais × Holstein crossbred calves from 391 Charolais sires. Heritabilities estimated separately within each crossbred population were similar. Stronger genetic correlations were observed in Charolais × Holstein population compared with Charolais × Montbéliard between calving difficulty and height (0.67 vs. 0.54), calving difficulty and bone thinness (0.42 vs. 0.27), birth weight and bone thinness (0.52 vs. 0.20), and birth weight and muscular development (0.41 vs. 0.18). Bivariate analysis considering observations on Charolais × Montbéliard and on Charolais × Holstein as different traits showed that genetic variances and heritabilities were similar for all traits except height. Birth weight and muscular development were genetically identical traits in each crossbred populations, with genetic correlations of 0.96 and 0.99. Genetic correlations were 0.91 for calving difficulty, 0.80 for height, and 0.70 for bone thinness and log-likelihood ratio tests indicated that they were significantly different from 1 (P = 0.01). Results show evidence for reranking of Charolais sires for calving difficulty, height, and bone thinness depending on whether they are mated to Montbéliard or Holstein cows.

Two experiments were conducted to assess the effects of a mixture of dietary additives on enteric methane production, rumen fermentation, diet digestibility, energy balance, and animal performance in lactating dairy cows. Identical diets were fed in both experiments. The mixture of feed additives investigated contained lauric acid, myristic acid, linseed oil, and calcium fumarate. These additives were included at 0.4, 1.2, 1.5, and 0.7% of dietary dry matter, respectively (treatment ADD). Experimental fat sources were exchanged for a rumen inert source of fat in the control diet (treatment CON) to maintain isolipidic rations. Cows (experiment 1, n = 20; experiment 2, n = 12) were fed restricted amounts of feed to avoid confounding effects of dry matter intake on methane production. In experiment 1, methane production and energy balance were studied using open-circuit indirect calorimetry. In experiment 2, 10 rumen-fistulated animals were used to measure rumen fermentation characteristics. In both experiments animal performance was monitored. The inclusion of dietary additives decreased methane emissions (g/d) by 10%. Milk yield and milk fat content tended to be lower for ADD in experiment 1. In experiment 2, milk production was not affected by ADD, but milk fat content was lower. Fat- and protein-corrected milk was lower for ADD in both experiments. Milk urea nitrogen content was lowered by ADD in experiment 1 and tended to be lower in experiment 2. Apparent total tract digestibility of fat, but not that of starch or neutral detergent fiber, was higher for ADD. Energy retention did not differ between treatments. The decrease in methane production (g/d) was not evident when methane emission was expressed per kilogram of milk produced. Feeding ADD resulted in increases of C12:0 and C14:0 and the intermediates of linseed oil biohydrogenation in milk in both experiments. In experiment 2, ADD-fed cows tended to have a decreased number of protozoa in rumen fluid when compared with that in control cows. Total volatile fatty acid concentrations were lower for ADD, whereas molar proportions of propionate increased at the expense of acetate and butyrate.

Mitigation of enteric methane (CH₄) emission in ruminants has become an important area of research because accumulation of CH₄ is linked to global warming. Nutritional and microbial opportunities to reduce CH₄ emissions have been extensively researched, but little is known about using natural variation to breed animals with lower CH₄ yield. Measuring CH₄ emission rates directly from animals is difficult and hinders direct selection on reduced CH₄ emission. However, improvements can be made through selection on associated traits (e.g., residual feed intake, RFI) or through selection on CH₄ predicted from feed intake and diet composition. The objective was to establish phenotypic and genetic variation in predicted CH₄ output, and to determine the potential of genetics to reduce methane emissions in dairy cattle. Experimental data were used and records on daily feed intake, weekly body weights, and weekly milk production were available from 548 heifers. Residual feed intake (MJ/d) is the difference between net energy intake and calculated net energy requirements for maintenance as a function of body weight and for fat- and protein-corrected milk production. Predicted methane emission (PME; g/d) is 6% of gross energy intake (Intergovernmental Panel on Climate Change methodology) corrected for energy content of methane (55.65 kJ/g). The estimated heritabilities for PME and RFI were 0.35 and 0.40, respectively. The positive genetic correlation between RFI and PME indicated that cows with lower RFI have lower PME (estimates ranging from 0.18 to 0.84). Hence, it is possible to decrease the methane production of a cow by selecting more-efficient cows, and the genetic variation suggests that reductions in the order of 11 to 26% in 10 yr are theoretically possible, and could be even higher in a genomic selection program. However, several uncertainties are discussed; for example, the lack of true methane measurements (and the key assumption that methane produced per unit feed is not affected by RFI level), as well as the limitations of predicting the biological consequences of selection. To overcome these limitations, an international effort is required to bring together data on feed intake and methane emissions of dairy cows.

Multiple demands are placed on farming systems today. Society, national legislation and market forces seek what could be seen as conflicting outcomes from our agricultural systems, e.g. food quality, affordable prices, a healthy environmental, consideration of animal welfare, biodiversity etc., Many of these demands, or desirable outcomes, are interrelated, so reaching one goal may often compromise another and, importantly, pose a risk to the economic viability of the farm. SIMS DAIRY , a farm-scale model, was used to explore this complexity for dairy farm systems. SIMS DAIRY integrates existing approaches to simulate the effect of interactions between farm management, climate and soil characteristics on losses of nitrogen, phosphorus and carbon. The effects on farm profitability and attributes of biodiversity, milk quality, soil quality and animal welfare are also included. SIMS DAIRY can also be used to optimise fertiliser N. In this paper we discuss some limitations and strengths of using SIMS DAIRY compared to other modelling approaches and propose some potential improvements. Using the model we evaluated the sustainability of organic dairy systems compared with conventional dairy farms under non-optimised and optimised fertiliser N use. Model outputs showed for example, that organic dairy systems based on grass-clover swards and maize silage resulted in much smaller total GHG emissions per l of milk and slightly smaller losses of NO 3 leaching and NO x emissions per l of milk compared with the grassland/maize-based conventional systems. These differences were essentially because the conventional systems rely on indirect energy use for ‘fixing’ N compared with biological N fixation for the organic systems. SIMS DAIRY runs also showed some other potential benefits from the organic systems compared with conventional systems in terms of financial performance and soil quality and biodiversity scores. Optimisation of fertiliser N timings and rates showed a considerable scope to reduce the (GHG emissions per l milk too).

Two similar experiments were conducted to assess the effect of diallyl disulfide (DADS), yucca powder (YP), calcium fumarate (CAFU), an extruded linseed product (UNSAT), or a mixture of capric and caprylic acid (MCFA) on methane production, energy balance, and dairy cow performance. In experiment 1, a control diet (CON1) and diets supplemented with 56 mg of DADS/kg of dry matter (DM), 3g of YP/kg of DM, or 25 g of CAFU/kg of DM were evaluated. In experiment 2, an inert saturated fat source in the control diet (CON2) was exchanged isolipidically for an extruded linseed source (100g/kg of DM; UNSAT) or a mixture of C8:0 and C10:0 (MCFA; 20.3g/kg of DM). In experiment 2, a higher inclusion level of DADS (200mg/kg of DM) was also tested. Both experiments were conducted using 40 lactating Holstein-Friesian dairy cows. Cows were adapted to the diet for 12 d and were subsequently kept in respiration chambers for 5 d to evaluate methane production, diet digestibility, energy balance, and animal performance. Feed intake was restricted to avoid confounding effects of possible differences in ad libitum feed intake on methane production. Feed intake was, on average, 17.5 and 16.6 kg of DM/d in experiments 1 and 2, respectively. None of the additives reduced methane production in vivo. Methane production in experiment 1 was 450, 453, 446, and 423 g/d for CON1 and the diets supplemented with DADS, YP, and CAFU, respectively. In experiment 2, methane production was 371, 394, 388, and 386 g/d for CON2 and the diets supplemented with UNSAT, MCFA, and DADS, respectively. No effects of the additives on energy balance or neutral detergent fiber digestibility were observed. The addition of MCFA increased milk fat content (5.38% vs. 4.82% for control) and fat digestibility (78.5% vs. 59.8% for control), but did not affect milk yield or other milk components. The other products did not affect milk yield or composition. Results from these experiments emphasize the need to confirm methane reductions observed in vitro with in vivo data.

In animal breeding, recording of correct pedigrees is essential to achieve genetic progress. Markers on DNA are useful to verify the on-farm pedigree records (parental verification) but can also be used to assign parents retrospectively (parental identification). This approach could reduce the costs of recording for traits with low incidence, such as those related to diseases or mortality. In this study, SNP were used to assign the true sires of 368 purebred animals from a Duroc-based sire line and 140 crossbred offspring from a commercial pig population. Some of the sires were closely related. There were 3 full sibs and 17 half sibs among the true fathers and 4 full sibs and 35 half sibs among all putative fathers. To define the number of SNP necessary, 5 SNP panels (40, 60, 80, 100, and 120 SNP) were assembled from the Illumina PorcineSNP60 Beadchip (Illumina, San Diego, CA) based on minor allele frequency (>0.3), high genotyping call rate (=90%), and equal spacing across the genome. For paternal identification considering only the 66 true sires in the data set, 60 SNP resulted in 100% correct assignment of the sire. By including additional putative sires (n = 304), 80 SNP were sufficient for 100% correct assignment of the sire. The following criteria were derived to identify the correct sire for the current data set: the logarithm of odds (LOD) score for assigning the correct sire was =5, the number of mismatches was =1, and the difference in the LOD score between the first and the second most likely sire was >5. If the correct sire was not present among all putative sires, the mean LOD for the most likely sire was close to zero or negative when using 100 SNP. More SNP would be needed for paternal identification if the number of putative sires increased and the degree of relatedness was greater than in the data set used here. The threshold for the number of mismatches can be adjusted according to the practical situation to account for the trade-off between false negatives and false positives. The latter can be avoided efficiently, ensuring that the correct father is being sampled. Nevertheless, a restriction on the number of putative sires is advisable to reduce the risk of assigning close relatives.

Records of cattle slaughtered at two Chilean slaughterhouses (SLH1 and SLH2) were used to determine prevalence and risk factors for carcasses with bruises. Bruise prevalence amounted to 12.3% but differed between slaughterhouses (20.8% for SLH1 and 8.6% for SLH2 respectively). Bruise severity grade 1 (mild) was most frequently recorded. The type of the animal, source of animal, the level of fat cover and lairage time were associated with the presence of bruises. Older categories of animals and animals that pass through a market before being moved to the slaughterhouse are more prone to show bruises. The results also indicate that under the reported Chilean circumstances animals that have longer lairage times (over 12 h) have a significantly reduced risk for bruises, except for oxen. Presence of bruises is also significantly associated with increased carcass pH values.

The importance of evaluating greenhouse gas (GHG) emissions from dairy cows within the whole farm setting is being realized as more important than evaluating these emissions in isolation. Current whole farm models aimed at evaluating GHG emissions make use of simple regression equations to predict enteric methane (CH4) production. The objective of the current paper is to evaluate the performance of nine CH4 prediction equations that are currently being used in whole farm GHG models. Data used to evaluate the prediction equations came from a collection of individual (IND) and treatment averaged (TRT) data. Equations were compared based on mean square prediction error (MSPE) and concordance correlation coefficient (CCC) analysis. In general, predictions were poor, with root MSPE (as a percentage of observed mean) values ranging from 20.2 to 52.5 for the IND database and from 24.0 to 38.2 for the TRT database and CCC values ranging from 0.009 to 0.493 for the IND database and from 0.000 to 0.271 for the TRT database. Overall, the equations of Moe & Tyrrell and IPCC Tier II performed best on the IND dataset, and the equations of Moe & Tyrrell and Kirchgeßner et al., performed best on the TRT dataset. Results show that the simple more generalized equations performed worse than those that attempted to represent important aspects of diet composition, but in general significant amounts of bias and deviation of the regression slope from unity existed for all equations. The low prediction accuracy of CH4 equations in whole farm models may introduce substantial error into inventories of GHG emissions and lead to incorrect mitigation recommendations.

SUMMARYMethane, in addition to being a significant source of energy loss to the animal that can range from 0·02 to 0·12 of gross energy intake, is one of the major greenhouse gases being targeted for reduction by the Kyoto protocol. Thus, one of the focuses of recent research in animal science has been to develop or improve existing methane prediction models in order to increase overall understanding of the system and to evaluate mitigation strategies for methane reduction. Several dynamic mechanistic models of rumen function have been developed which contain hydrogen gas balance sub-models from which methane production can be predicted. These models predict methane production with varying levels of success and in many cases could benefit from further development. Central to methane prediction is accurate volatile fatty acid prediction, representation of the competition for substrate usage within the rumen, as well as descriptions of protozoal dynamics and pH. Most methane models could also largely benefit from an expanded description of lipid metabolism and hindgut fermentation. The purpose of the current review is to identify key aspects of rumen microbiology that could be incorporated into, or have improved representation within, a model of ruminant digestion and environmental emissions.

Accuracy and bias of estimated breeding values are important measures of the quality of genetic evaluations. A sampling method that accounts for the uncertainty in the estimation of genetic group effects was used to calculate accuracy and bias of estimated effects. The method works by repeatedly simulating phenotypes for multiple traits for a defined data and pedigree structure. These simulated values are analysed using BLUP with genetic groups in the relationship matrix. Accuracies and biases are then calculated as correlations among and differences between true and estimated values across all replicates, respectively. The method was applied to the Irish beef production data set for 15 traits and with 15 genetic groups to account for differences in breed means. Accuracy and bias of estimated genetic groups effects, estimated comparisons between genetic groups effects, estimated breeding values within genetic group, and estimated breeding values across genetic group were calculated. Small biases were detected for most estimated genetic group effects and most estimated comparisons between genetic group effects. Most of these were not of importance relative to the phenotypic standard deviation of the traits involved. For example, a bias of 0.78% of the phenotypic standard deviation was detected for carcass conformation in Aberdeen Angus. However, one trait, calf quality, which has very few performance records in the data set, displayed larger bias ranging from -10.31% to 5.85% of the phenotypic standard deviation across the different estimated genetic group effects. Large differences were observed in the accuracies of genetic group effects, ranging from 0.02 for feed intake in Holstein, which had no data recorded, to >0.97 for carcass conformation, a trait with large amounts of data recorded in the different genetic groups. Large differences were also observed in the accuracies of the comparisons among genetic group effects. The accuracies of the estimated breeding values within genetic group and estimated breeding values across genetic group were sometimes different; for example, carcass conformation in Belgian Blue had an average accuracy within genetic group of 0.69 compared to an average accuracy across genetic group of 0.89. This suggests that the accuracy of genetic groups should be taken into account when publishing estimated breeding values across genetic groups.

Genetic parameters for eating quality assessed by trained taste panellists were estimated on longissimus thoracis et lumborum (LTL) muscle in Scottish Blackface lambs, comprising lines previously divergently selected for carcass lean content (FAT and LEAN lines) as well as crosses between these lines. Also, relationships between eating quality assessments and fatty acid composition were investigated. Eating quality and fatty acid phenotypic measurements were made on 350 male lambs at ca. 8 months of age. Eating quality measurements included 18 descriptive terms and fatty acid composition measurements included in total 17 fatty acids of three types: saturated, monounsaturated and polyunsaturated. The FAT line had juicier meat and more vegetable flavour than the LEAN line. Most of the eating quality traits were moderately to highly heritable, with heritabilities ranging from 0.21 (lamb flavour) to 0.92 (sweet flavour). Lamb flavour, juiciness and overall liking were strongly negatively correlated with individual polyunsaturated fatty acids, with the correlations being significantly different from zero. Overall liking was strongly positively correlated with the proportion of total monounsaturated fatty acids. This study provides new information on genetic parameters for eating quality traits in sheep, which may lead to novel opportunities for genetically improving these traits.

The endogenous occurrence of natural hormones obstructs the application of classical targeted methods as confirmatory options. In the case of estradiol, the ultimate confirmation of its exogenous administration relies on gas chromatography coupled to combustion/isotope ratio mass spectrometry (GC-C/IRMS). A serum dipeptide composed of pyroglutamic acid and phenylalanine was identified as a potential biomarker of estradiol treatments in adult cows. To evaluate its potential to pinpoint suspicious samples, samples from prepubertal females under different estrogenic treatments have been analyzed. The results confirmed the up-regulation of the dipeptide in adult bovines. The 2-week-old females exhibited short-lasting responses only in a few animals. The 6-month-old female showed a delayed but clear increase on the biomarker level. The composition of the anabolic preparations, the dose, and/or the administration route are possible additional reasons for the reduced response in young animals. A comparison to previous results reported by various researchers is included.

The main pathogenic enterohemorrhagic Escherichia coli (EHEC) strains are defined as Shiga toxin (Stx)-producing E. coli (STEC) belonging to one of the following serotypes: O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28. Each of these five serotypes is known to be associated with a specific subtype of the intimin-encoding gene ( eae ). The objective of this study was to evaluate the prevalence of bovine carriers of these “top five” STEC in the four adult cattle categories slaughtered in France. Fecal samples were collected from 1,318 cattle, including 291 young dairy bulls, 296 young beef bulls, 337 dairy cows, and 394 beef cows. A total of 96 E. coli isolates, including 33 top five STEC and 63 atypical enteropathogenic E. coli (aEPEC) isolates, with the same genetic characteristics as the top five STEC strains except that they lacked an stx gene, were recovered from these samples. O157:H7 was the most frequently isolated STEC serotype. The prevalence of top five STEC (all serotypes included) was 4.5% in young dairy bulls, 2.4% in young beef bulls, 1.8% in dairy cows, and 1.0% in beef cows. It was significantly higher in young dairy bulls ( P < 0.05) than in the other 3 categories. The basis for these differences between categories remains to be elucidated. Moreover, simultaneous carriage of STEC O26:H11 and STEC O103:H2 was detected in one young dairy bull. Lastly, the prevalence of bovine carriers of the top five STEC, evaluated through a weighted arithmetic mean of the prevalence by categories, was estimated to 1.8% in slaughtered adult cattle in France.

The aim of the present study was to determine the degree of consistency of individual differences in behavioural responses of heifer calves over time and across different situations. Twenty-five Holstein Friesian heifer calves were individually subjected to the same set of four behavioural tests at 3, 16 and 29 weeks of age. The tests involved measuring the calves' responses to a stationary human, a novel object, an open field (novel environment), and to tethering restraint. Principal component analysis (PCA) of measures recorded at each age was used to identify independent dimensions underlying the calves' reactivity to these situations. The consistency of individual differences was established by ranking the behavioural scores and the scores of factors extracted by PCA and then estimating the correlations between the ranks of each individual calf at each of the test ages. At each age, PCA revealed four factors that could be labelled: "locomotion", "vocalisation", "interaction with a novel object", and "interaction with a human". Individual differences in 7 of 13 behavioural measures and in scores of all factors except "interaction with a human" were consistent between 16 and 29 weeks of age. Rank orders for scores of the factor labelled "interaction with a novel object" were significantly correlated across all three ages. Our results support the existence in calves of stable characteristics mediating reactivity to challenge. Multiple behavioural dimensions obtained with PCA suggest that behavioural responsiveness of calves to challenge is governed by a number of underlying factors rather than univariate phenomena, such as fearfulness or coping style. (C) 2003 Elsevier B.V. All rights reserved.

This study was conducted to investigate the performance, carcass characteristics, and meat quality of lambs fed barley/triticale silage treated with/without inoculant and enzyme mixture-based diets with similar barley supplementation. Thirty Tahirova x Sakiz crossbred weaned ram lambs (mean body weight: 34 +/- 0.5 kg) were used in this study. Lambs were randomly divided into groups of 3 and fed the respective diets. These 3 diets were: 1) hay grass + barley, 2) triticale/barley silage + barley, and 3) triticale/barley silage with inoculants and enzyme mixture + barley. There were significant differences among groups in daily live weight gain (P < 0.001). Cold carcass weight and dressing percentage based on empty body weight and carcass conformation scores were not significantly different among groups, but fatness scores and proportion of omental and mesenteric fat were significantly affected by diet (P < 0.05). No differences were found in terms of meat lightness (L*), redness (a*), and yellowness (b*) values for M. longissimus thoracis muscle. However, silage-fed lambs in both groups had higher shear force values than hay-fed lambs in the current study (P < 0.05). It can be concluded that barley/triticale silages offered with concentrate had no unfavorable effect on lamb performance, carcass characteristics, and meat quality. İstanbul Üniversitesi (574- 14082006)

Escherichia coli O157:H7 is a major foodborne human pathogen causing disease worldwide. Cattle are a major reservoir for this pathogen and those that shed E. coli O157: H7 at >10(4) CFU/g feces have been termed "super-shedders". A rich microbial community inhabits the mammalian intestinal tract, but it is not known if the structure of this community differs between super-shedder cattle and their non-shedding pen mates. We hypothesized that the super-shedder state is a result of an intestinal dysbiosis of the microbial community and that a "normal" microbiota prevents E. coli O157: H7 from reaching super-shedding levels. To address this question, we applied 454 pyrosequencing of bacterial 16S rRNA genes to characterize fecal bacterial communities from 11 super-shedders and 11 contemporary pen mates negative for E. coli O157: H7. The dataset was analyzed by using five independent clustering methods to minimize potential biases and to increase confidence in the results. Our analyses collectively indicated significant variations in microbiome composition between super-shedding and non-shedding cattle. Super-shedders exhibited higher bacterial richness and diversity than non-shedders. Furthermore, seventy-two operational taxonomic units, mostly belonging to Firmicutes and Bacteroidetes phyla, were identified showing differential abundance between these two groups of cattle. The operational taxonomic unit affiliation provides new insight into bacterial populations that are present in feces arising from super-shedders of E. coli O157:H7.