The aim of the Teagasc Animal and Grassland Research & Innovation Programme is to increase the profitability, competitiveness and sustainability of Irish livestock production through research and innovation.

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  • Mid infrared spectroscopy and milk quality traits: a data analysis competition at the “International Workshop on Spectroscopy and Chemometrics 2021”

    Frizzarin, Maria; Bevilacqua, Antonio; Dhariyal, Bhaskar; Domijan, Katarina; Ferraccioli, Frederico; Hayes, Elena; Ifrim, Georgiana; Konkowleska, Agnieszka; Le Nguyễn, Thach; Mbaka, Uche; et al. (2021-09-06)
    chemometric data analysis challenge has been arranged during the first edition of the “International Workshop on Spectroscopy and Chemometrics”, organized by the Vistamilk SFI Research Centre and held online in April 2021. The aim of the competition was to build a calibration model in order to predict milk quality traits exploiting the information contained in mid-infrared spectra only. Three different traits have been provided, presenting heterogeneous degrees of prediction complexity thus possibly requiring trait-specific modelling choices. In this paper the different approaches adopted by the participants are outlined and the insights obtained from the analyses are critically discussed.
  • Disease screening profiles and colostrum management practices on 16 Irish suckler beef farms

    O’Shaughnessy, James; Earley, Bernadette; Barrett, Damien; Doherty, Michael L; Crosson, Paul; de Waal, Theo; Mee, John F; Teagasc Walsh Fellowship Programme (Springer Science and Business Media LLC, 2015)
    Background Calf output is a key element in determining the profitability of a suckler beef enterprise. Infectious agents such as Bovine Virus Diarrhoea (BVD) virus, colostrum management and parasitic challenge can all affect calf output. Prior to the national BVD eradication programme, there was little published information on either the prevalence or effect of BVD in Irish beef herds. There is little published information on colostrum management practices in Irish commercial beef herds and there have also been few studies published on the prevalence of liver fluke or rumen fluke infection in Irish beef herds. Sixteen farms participating in the Teagasc/Farmers Journal BETTER farm beef programme were used in this study. Fourteen herds were screened for the presence of BVD virus in 2010 using RT-PCR. In 13 herds, blood samples were collected from calves (2–14 days of age) in November 2011 - April 2012 to determine their passive immune status using the zinc sulphate turbidity (ZST) test, while in 12 herds, blood and faecal samples were taken in order to determine the level of exposure to gastrointestinal and hepatic helminths. Results The overall prevalence of BVD virus-positive cattle was 0.98% (range 0 - 3% per herd, range 0.6 - 3.0% per positive herd). Eighteen of the 82 calves (22%) sampled had ZST values less than 20 units (herd mean range 17.0 – 38.5 units) indicating a failure of passive transfer. The overall animal-level (herd-level) prevalence of liver fluke and rumen fluke infection in these herds was 40.5% (100%) and 20.8% (75%), respectively. Conclusions The potential costs associated with the presence of animals persistently infected with BVD virus through the increased use of antibiotics; the rate of failure of passive transfer of colostral immunoglobulins and the high prevalence of liver fluke infection in these herds highlight that some Irish suckler beef farms may not be realizing their economic potential due to a range of herd health issues. The use of farm-specific herd health plans should be further encouraged on Irish suckler beef farms.
  • Pasture allowance, duration, and stage of lactation—Effects on early and total lactation animal performance

    Claffey, A.; Delaby, L.; Lewis, E.; Boland, T.M.; Kennedy, Emer; Dairy Levy (American Dairy Science Association, 2019-10)
    Pasture availability in early spring can be limited due to climatic effects on grass production, increasing the likelihood of feed deficits in early lactation of spring-calving pasture-based systems. We hypothesized that restricting pasture allowance (PA) when animals are at peak milk production will have more negative implications on milk production compared with restricting animals before this period. A total of 105 cows were assigned to 1 of 7 grazing treatments from March 14 to October 31, 2016 (33 wk). The control treatment was offered a PA to achieve a postgrazing sward height > 3.5 cm and mean pasture allowance of 15.5 kg of dry matter per cow. The remaining treatments were offered a PA representing 60% of that offered to the control for a duration of 2 or 6 wk from March 14 (mid-March; MMx2 and MMx6), March 28 (end of March; EMx2 and EMx6), or April 11 (mid-April; MAx2 and MAx6). Within grazing treatment, animals were also assigned to 1 of 2 calving dates (early and late) based on days in milk (DIM) on March 14. Early calved (EC) cows were ≥36 DIM, while late calved (LC) were ≤35 DIM. Restricting PA for 2 and 6 wk reduced daily milk yield (−1.6 and −2.2 kg/cow, respectively), cumulative milk protein yield (−4.0 and −6.3 kg/cow, respectively), and cumulative milk solids yield (−5.8 and −9.5 kg/cow, respectively) in the first 10 wk of the experiment. Daily milk yield was similar across the treatments at the end of the 33-wk period (16.8 kg/cow, average of all treatments), as was daily milk solids yield (1.40 kg/cow). Cows in the EC group produced less milk over the first 10 wk of the experiment (20.0 kg/cow per day) compared with the LC animals (22.1 kg/cow per day). However, body weight was greater (+15 kg/cow) in the EC animals compared with the LC, while body condition score was similar (2.85). This outcome indicates that animals that are restricted later in early lactation (circa onset of peak milk production) partition a greater proportion of available energy to maintenance, resulting in greater losses in milk production. These data indicate that despite the immediate reduction in milk production, restricting intake of grazing cows to 80% of that required to achieve spring grazing targets for postgrazing sward height for up to 6 wk may be used as a method of managing short-term pasture deficits on farm with minimal effects on total lactation performance.
  • Purulent vaginal discharge diagnosed in pasture-based Holstein-Friesian cows at 21 days postpartum is influenced by previous lactation milk yield and results in diminished fertility

    Ryan, Nicholas J.; Meade, Kieran G.; Williams, Erin J.; O'Farrelly, Cliona; Grant, Jim; Evans, Alexander C.O.; Beltman, Marijke E.; Department of Agriculture, Food and the Marine; 13/S/472 (American Dairy Science Association, 2020-01)
    In a subset of dairy cows, prolonged pathological uterine inflammation results in purulent vaginal discharge (PVD), which can have negative consequences for both fertility and milk production. However, unlike for intensive systems, analysis of the effects of PVD in predominantly pasture-based herds is limited. The objective of this study was to assess the effect of PVD in spring-calving, pasture-based dairy cows on production and reproduction indices, stratified according to previous full-lactation milk yield. We assessed clinical disease as defined by vaginal mucus score (VMS) in 440 Holstein-Friesian cows from 5 farms. Cows were categorized as healthy (VMS 0) or having PVD (VMS 1–3) at 21 d postpartum. We recorded 305-d milk, milk protein, and milk fat yields (kg) before and after disease diagnosis, as well as fertility data, such as services per conception and the calving–conception period (CCP). Using SAS 9.4 (SAS Institute Inc., Cary, NC), we analyzed data using PROC MIXED, PROC PHREG, and PROC LOGISTIC to determine the least squares means differences and hazard and odds ratios between the groups, respectively. Overall, a 60% prevalence of PVD was recorded at 21 d postpartum. Milk yield and milk constituents were similar between all VMS categories and between healthy cows and cows with PVD. Although cows in the 4 VMS categories had statistically similar CCP, cows with PVD had a significantly longer CCP than healthy cows on average (9 d). The hazard ratio for cows with PVD was 0.66, indicating a 34% higher risk of a prolonged CCP than healthy cows. Odds ratio analysis determined that cows with PVD were 3 times more likely not to conceive at all, twice as likely not to conceive at first service, twice as likely not to conceive by 100 d postpartum, and 3 times more likely to fail to conceive before 150 d postpartum compared with healthy cows. Cows were retrospectively categorized as having low or high milk yield, based on whether they were above or below the median 305-d milk yield of the study population (6,571 kg) in the lactation before vaginal mucus scoring. Based on a univariate odds ratio, high-yield cows were 1.6 times more likely to present with PVD in the subsequent lactation. The number of services per conception did not differ between healthy and PVD cows in the low- and high-yield groups. In the high-yield group, cows with PVD were 4.9 times more likely not to conceive, 2.7 times more likely to require multiple services to conceive, 2.1 times more likely to remain not pregnant by 100 d postpartum, and 4.4 times more likely to remain not pregnant by 150 d postpartum. The CCP was also significantly longer in cows with PVD than their healthy counterparts (115.9 ± 4.9 and 104 ± 7.4 d, respectively). In conclusion, PVD significantly increased the CCP in all cows, but to a greater extent in cows with a high milk yield in the lactation before disease diagnosis.
  • The gut microbiome influences the bioavailability of olanzapine in rats

    Cussotto, Sofia; Walsh, Jacinta; Golubeva, Anna V.; Zhdanov, Alexander V.; Strain, Conall R.; Fouhy, Fiona; Stanton, Catherine; Dinan, Timothy G.; Hyland, Niall P.; Clarke, Gerard; et al. (The Lancet, 2021-04-02)
    Background The role of the gut microbiome in the biotransformation of drugs has recently come under scrutiny. It remains unclear whether the gut microbiome directly influences the extent of drug absorbed after oral administration and thus potentially alters clinical pharmacokinetics. Methods In this study, we evaluated whether changes in the gut microbiota of male Sprague Dawley rats, as a result of either antibiotic or probiotic administration, influenced the oral bioavailability of two commonly prescribed antipsychotics, olanzapine and risperidone. Findings The bioavailability of olanzapine, was significantly increased (1.8-fold) in rats that had undergone antibiotic-induced depletion of gut microbiota, whereas the bioavailability of risperidone was unchanged. There was no direct effect of microbiota depletion on the expression of major CYP450 enzymes involved in the metabolism of either drug. However, the expression of UGT1A3 in the duodenum was significantly downregulated. The reduction in faecal enzymatic activity, observed during and after antibiotic administration, did not alter the ex vivo metabolism of olanzapine or risperidone. The relative abundance of Alistipes significantly correlated with the AUC of olanzapine but not risperidone. Interpretation Alistipes may play a role in the observed alterations in olanzapine pharmacokinetics. The gut microbiome might be an important variable determining the systemic bioavailability of orally administered olanzapine. Additional research exploring the potential implication of the gut microbiota on the clinical pharmacokinetics of olanzapine in humans is warranted. Funding This research is supported by APC Microbiome Ireland, a research centre funded by Science Foundation Ireland (SFI), through the Irish Government's National Development Plan (grant no. 12/RC/2273 P2) and by Nature Research-Yakult (The Global Grants for Gut Health; Ref No. 626891).
  • Quantification of cow milk yield and pre-weaning calf growth response in temperate pasture-based beef suckler systems: A meta-analysis

    Sapkota, D.; Kelly, A.K.; Crosson, Paul; White, R.R.; McGee, Mark; Teagasc Walsh Fellowship Programme (Elsevier, 2020-11)
    The objectives of this study were to quantitatively summarize factors associated with cow milk yield (MY) and calf growth response in pasture-based beef cow-calf suckler systems and to discern how cow genotype and parity influenced these responses. A dataset of 344 treatment mean observations was compiled from 69 studies that reported data on cow MY, and calf pre-weaning average daily live weight gain (ADG) and/or weaning weight (WW). Data were analysed using linear mixed effects models with study and region included as random effects. Models were developed for cow MY, calf ADG and WW response and each model was evaluated based on different model fit statistics. The final cow MY model included cow origin (Dairybeef or Beef), cow maturity (early-maturing (EM) or late-maturing (LM) genotypes) and parity. Dairybeef produced 35.4% more milk (8.64 vs. 6.38 kg/day) than Beef cows, and LM produced 20.9% more milk (8.20 vs. 6.78 kg/day) than EM genotypes (P < 0.001). Multiparous cows had a 14.8% higher MY (8.11 vs. 7.06 kg/day) compared to primiparous cows (P < 0.001). Lactation curve persistency was better (P < 0.05) for Beef and EM compared to Dairybeef and LM genotype cows, respectively. The final models of calf ADG and WW included cow origin, cow maturity and parity. Calves from Dairybeef and LM cows were 14 and 20 kg heavier (P < 0.001) at weaning (210-day adjusted) compared to those from Beef and EM genotype cows, respectively. Calves from multiparous cows were 13 kg heavier at weaning than those from primiparous cows (P < 0.001). The response in calf ADG associated with a 1 kg increase in cow daily MY was 47 and 53 g for Dairybeef and Beef cows, respectively (P < 0.001). Corresponding responses for EM and LM cows were 51 and 55 g (P < 0.001). In conclusion, the relationships between cow MY and calf pre-weaning growth, as well as the quantitative impact of cow genotype and parity were determined for pasture-based beef suckler systems; the coefficients generated can be used for improving beef cow-calf management strategies, beef cattle breeding programmes and bio-economic modelling purposes.
  • Enduring Behavioral Effects Induced by Birth by Caesarean Section in the Mouse

    Morais, Livia H.; Golubeva, Anna V.; Moloney, Gerard M; Stanton, Catherine; Dinan, Timothy G.; Cryan, John F.; Science Foundation Ireland; European Union; Department of Agriculture, Food and the Marine; Science without Borders; et al. (2020-08-20)
    Birth by Caesarean (C)-section impacts early gut microbiota colonization and is associated with an increased risk of developing immune and metabolic disorders. Moreover, alterations of the microbiome have been shown to affect neurodevelopmental trajectories. However, the long-term effects of C-section on neurobehavioral processes remain unknown. Here, we demonstrated that birth by C-section results in marked but transient changes in microbiome composition in the mouse, in particular, the abundance of Bifidobacterium spp. was depleted in early life. Mice born by C-section had enduring social, cognitive, and anxiety deficits in early life and adulthood. Interestingly, we found that these specific behavioral alterations induced by the mode of birth were also partially corrected by co-housing with vaginally born mice. Finally, we showed that supplementation from birth with a Bifidobacterium breve strain, or with a dietary prebiotic mixture that stimulates the growth of bifidobacteria, reverses selective behavioral alterations in C-section mice. Taken together, our data link the gut microbiota to behavioral alterations in C-section-born mice and suggest the possibility of developing adjunctive microbiota-targeted therapies that may help to avert long-term negative consequences on behavior associated with C-section birth mode.
  • Milk production per cow and per hectare of spring-calving dairy cows grazing swards differing in Lolium perenne L. ploidy and Trifolium repens L. composition

    McClearn, B.; Gilliland, T.J.; Delaby, L.; Guy, C.; Dineen, M.; Coughlan, F.; McCarthy, B.; Dairy Research Ireland; Teagasc Walsh Fellowship Programme (American Dairy Science Association, 2019-09)
    Grazed grass is the cheapest feed available for dairy cows in temperate regions; thus, to maximize profits, dairy farmers must optimize the use of this high-quality feed. Previous research has defined the benefits of including white clover (Trifolium repens L.) in grass swards for milk production, usually at reduced nitrogen usage and stocking rate. The aim of this study was to quantify the responses in milk production of dairy cows grazing tetraploid or diploid perennial ryegrass (Lolium perenne L.; PRG) sown with and without white clover but without reducing stocking rate or nitrogen usage. We compared 4 grazing treatments in this study: tetraploid PRG-only swards, diploid PRG-only swards, tetraploid with white clover swards, and diploid with white clover swards. Thirty cows were assigned to each treatment, and swards were rotationally grazed at a farm-level stocking rate of 2.75 cows/ha and a nitrogen fertilizer rate of 250 kg/ha annually. Sward white clover content was 23.6 and 22.6% for tetraploid with white clover swards and diploid with white clover swards, respectively. Milk production did not differ between the 2 ploidies during this 4-yr study, but cows grazing the PRG-white clover treatments had significantly greater milk yields (+596 kg/cow per year) and milk solid yields (+48 kg/cow per year) compared with cows grazing the PRG-only treatments. The PRG-white clover swards also produced 1,205 kg of DM/ha per year more herbage, which was available for conserving and buffer feeding in spring when these swards were less productive than PRG-only swards. Although white clover is generally combined with reduced nitrogen fertilizer use, this study provides evidence that including white clover in either tetraploid or diploid PRG swards, combined with high levels of nitrogen fertilizer, can effectively increase milk production per cow and per hectare
  • Feed Restriction Reveals Distinct Serum Metabolome Profiles in Chickens Divergent in Feed Efficiency Traits

    Metzler-Zebeli, Barbara; Siegerstetter, Sina-Catherine; Magowan, Elizabeth; Lawlor, Peadar; O’Connell, Niamh; Zebeli, Qendrim; European Union; 311794 (MDPI AG, 2019-02-25)
    Restrictive feeding influences systemic metabolism of nutrients; however, this impact has not been evaluated in chickens of diverging feed efficiency. This study investigated the effect of ad libitum versus restrictive feeding (85% of ad libitum) on the serum metabolome and white blood cell composition in chickens of diverging residual feed intake (RFI; metric for feed efficiency). Blood samples were collected between days 33 and 37 post-hatch. While serum glucose was similar, serum uric acid and cholesterol were indicative of the nutritional status and chicken’s RFI, respectively. Feed restriction and RFI rank caused distinct serum metabolome profiles, whereby restrictive feeding also increased the blood lymphocyte proportion. Most importantly, 10 amino acids were associated with RFI rank in birds, whereas restrictive feeding affected almost all detected lysophosphatidylcholines, with 3 being higher and 6 being lower in restrictively compared to ad libitum fed chickens. As indicated by relevance networking, isoleucine, lysine, valine, histidine, and ornithine were the most discriminant for high RFI, whereas 3 biogenic amines (carnosine, putrescine, and spermidine) and 3 diacyl-glycerophospholipids (38:4, 38:5, and 40:5) positively correlated with feed intake and body weight gain, respectively. Only for taurine, feed intake mostly explained the RFI-associated variation, whereas for most metabolites, other host physiological factors played a greater role for the RFI-associated differences, and was potentially related to insulin-signaling, phospholipase A2, and arachidonic acid metabolism. Alterations in the hepatic synthesis of long-chain fatty acids and the need for precursors for gluconeogenesis due to varying energy demand may explain the marked differences in serum metabolite profiles in ad libitum and restrictively fed birds.
  • Pasture Feeding Changes the Bovine Rumen and Milk Metabolome

    O’Callaghan, Tom; Vázquez-Fresno, Rosa; Serra-Cayuela, Arnau; Dong, Edison; Mandal, Rupasri; Hennessy, Deirdre; McAuliffe, Stephen; Dillon, Pat; Wishart, David; Stanton, Catherine; et al. (MDPI AG, 2018-04-06)
    The purpose of this study was to examine the effects of two pasture feeding systems—perennial ryegrass (GRS) and perennial ryegrass and white clover (CLV)—and an indoor total mixed ration (TMR) system on the (a) rumen microbiome; (b) rumen fluid and milk metabolome; and (c) to assess the potential to distinguish milk from different feeding systems by their respective metabolomes. Rumen fluid was collected from nine rumen cannulated cows under the different feeding systems in early, mid and late lactation, and raw milk samples were collected from ten non-cannulated cows in mid-lactation from each of the feeding systems. The microbiota present in rumen liquid and solid portions were analysed using 16S rRNA gene sequencing, while 1H-NMR untargeted metabolomic analysis was performed on rumen fluid and raw milk samples. The rumen microbiota composition was not found to be significantly altered by any feeding system in this study, likely as a result of a shortened adaptation period (two weeks’ exposure time). In contrast, feeding system had a significant effect on both the rumen and milk metabolome. Increased concentrations of volatile fatty acids including acetic acid, an important source of energy for the cow, were detected in the rumen of TMR and CLV-fed cows. Pasture feeding resulted in significantly higher concentrations of isoacids in the rumen. The ruminal fluids of both CLV and GRS-fed cows were found to have increased concentrations of p-cresol, a product of microbiome metabolism. CLV feeding resulted in increased rumen concentrations of formate, a substrate compound for methanogenesis. The TMR feeding resulted in significantly higher rumen choline content, which contributes to animal health and milk production, and succinate, a product of carbohydrate metabolism. Milk and rumen-fluids were shown to have varying levels of dimethyl sulfone in each feeding system, which was found to be an important compound for distinguishing between the diets. CLV feeding resulted in increased concentrations of milk urea. Milk from pasture-based feeding systems was shown to have significantly higher concentrations of hippuric acid, a potential biomarker of pasture-derived milk. This study has demonstrated that 1H-NMR metabolomics coupled with multivariate analysis is capable of distinguishing both rumen-fluid and milk derived from cows on different feeding systems, specifically between indoor TMR and pasture-based diets used in this study.
  • Calf disbudding and castration

    Earley, Bernadette; McGee, Mark; O’Riordan, Edward G; Marquette, Gabriela (Veterinary Ireland Journal, 2019-05)
    The degree of tissue damage associated with disbudding is determined by the stage of development of the horn bud, eg. in younger calves, the burning of the vessels surrounding the horn bud is su icient, whereas the whole bud needs to be removed (by levering it out from the side) when the horn is further developed. Setting definitive ages for disbudding or dehorning is di icult since horn bud development occurs later in beef breeds than in the dairy breeds. Castration of bull calves induces a stress response (increase in the stress hormone, cortisol), which is influenced by the age of the calf. Castration-induced pain may be greater among younger calves compared with older calves because their nervous system and coping mechanisms (stress response) are not fully developed.
  • Effect of split marketing on the welfare, performance, and carcass traits of finishing pigs

    Conte, S.; Lawlor, Peadar; O'Connell, N.; Boyle, Laura A; Teagasc Walsh Fellowship Programme (Oxford University Press (OUP), 2012-01-01)
    The aim of this study was to compare a split marketing (SM) strategy, in which the heaviest pigs in a group are removed and slaughtered earlier than the others, with an all-out (AO) marketing strategy, in which all pigs are removed from the pen simultaneously and slaughtered on the same day, in terms of welfare, performance, and carcass traits of noncastrated (i.e., intact) male and female pigs. The experimental treatments were arranged in a 2 × 2 factorial array with 1) marketing strategy (SM vs. AO) and 2) sex (males vs. females), which yielded 4 treatment groups of 14 pigs (73.1 ± 4.8 kg): male SM, male AO, female SM, and female AO (7 replicates/group). Pigs in AO groups were all slaughtered after 6 wk on trial, whereas in SM groups the 3 heaviest pigs were removed and slaughtered 2 wk before the remainder of the group, which were slaughtered at the same time as the AO pigs. Pigs were fed a liquid diet from a long trough 3 times daily. Behavioral observations were conducted before and after SM, the day of SM, and 1 and 2 wk later. Behavior was recorded both during and between feed events, and skin lesions were scored on all, except the 3 pigs removed from SM groups before and 2 wk after SM. Growth performance, feed efficiency, and carcass traits were recorded. The number of aggressive interactions during feed events decreased after the 3 pigs were removed from SM groups. This reduction in aggressive interactions was observed on the day of SM in male groups (before SM: 24.3 vs. the day of SM: 14.7, SED = 3.31, P < 0.05 for interaction) and in subsequent observations in female groups (before SM: 21.4 vs. days after SM: 13.4, SED = 3.31, P < 0.05 for interaction). However, SM had no effect on behaviors recorded between feed events or on the number and severity of skin lesions (P > 0.10). There were no differences between the 11 remaining pigs in SM groups and the 14 pigs in AO groups in terms of growth performance, feed efficiency, and carcass traits of female or intact male pigs (P > 0.10). However, reduced within-pen CV in carcass weight was detected in pigs from SM groups compared with pigs from AO groups (8.6 vs. 10.9, SEM = 0.72, P < 0.05). Therefore, in restrictively fed pigs, a SM strategy improved the welfare of both female and intact male pigs by reducing aggressive interactions during feeding but had no effect on performance or carcass traits.
  • Longitudinal study of the effect of rubber slat mats on locomotory ability, body, limb and claw lesions, and dirtiness of group housed sows

    Calderon Diaz, Julia; Fahey, A. G.; KilBride, A. L.; Green, L. E.; Boyle, Laura A; Teagasc Walsh Fellowship Programme (Oxford University Press (OUP), 2013-08-01)
    This study evaluated the influence of floor type on sow welfare with particular focus on lameness, claw lesions (CL), and injuries. The study used 164 gilts housed in groups of 8 from AI to 110 d of pregnancy in pens with concrete (n = 84) slatted floor left uncovered or covered by 10-mm rubber slat mats (n = 80) through 2 parities. Lameness (0 = normal to 5 = severe), limb (0 = normal to 6 = severe) and body (0 = normal to 5 = severe) lesions, and manure on the body (MOB; score 0 to 2) were recorded at AI, 24 to 72 h postmixing, between 50 and 70 d of pregnancy, and 2 wk before farrowing. Claw lesions (score 0 = normal to 3 = severe) were recorded at AI and between 50 and 70 d of pregnancy. The dirtiness and wetness of the floors was scored weekly (score 0 = clean to 4 = >75% of the pen soiled/wet). Data from the first and second parities were analyzed separately. Sows were categorized as nonlame (score ≤ 1) or lame (score ≥ 2). Median (Me) scores were calculated for CL and body and limb lesions and were classified as less than or equal to the median or greater than the median lesion scores. Sows on rubber slat mats had a reduced risk of lameness during both parities (P < 0.01) compared with sows on concrete. They also had an increased risk of scores greater than the median for toe overgrowth (Me = 2 and Me = 3 in the first and second parity, respectively) and heel sole crack (HSC; Me = 3) during both parities (P < 0.01) and for cracks in the wall (CW; Me = 4) and white line damage (WL; Me = 4; P < 0.01) in the first and second parity, respectively. There was a reduced risk of lameness in sows with scores greater than the median for HSC (P = 0.05) in the first parity and WL (Me = 3; P < 0.01) and CW (Me = 3; P < 0.05) in the second parity. Wounds (Me = 3) and severe lesions (Me = 0) on the limbs with scores greater than the median were associated with an increased risk of lameness (P < 0.01) in the first and second parity, respectively. Sows on rubber slat mats had a reduced risk of scores greater than the median for swellings (Me = 4) and wounds (P < 0.01) during both parities. Pens with rubber slat mats were dirtier than uncovered pens (P < 0.01); however, there was no association between MOB and flooring type. There was also no association between body lesion score and flooring type. In this study, CL were not associated with an increased risk of lameness. Therefore, even though rubber slat mats were associated with an increased risk of CL, they improved the welfare of group housed sows by reducing the risk of lameness and limb lesions.
  • Effects of gestation housing system and floor type during lactation on locomotory ability; body, limb, and claw lesions; and lying-down behavior of lactating sows

    Calderon Diaz, Julia; Fahey, A. G.; Boyle, Laura A; Teagasc Walsh Fellowship Programme (Oxford University Press (OUP), 2014-04-01)
    This study evaluated the influence of housing system during gestation and floor type during lactation on the welfare and lying-down behavior of lactating sows. Multiparous sows (n = 85) were housed either in individual gestation stalls (n = 42) or loose (n = 43) in a single dynamic group with 2 electronic sow feeders moved to farrowing crates on either slatted steel (n = 48) or cast iron (n = 37) flooring. Lameness (0 = normal to 5 = severely lame) was scored on transfer to the farrowing crate (-5 d). Limb and body lesions were recorded on -5 d, 24 h after entering the farrowing crate (-4 d), 10-d postpartum, and before weaning. Claw lesions were recorded on -5 d and before weaning, whereas all behavioral observations were made on -5, -4, and 10 d. Median (Me) scores were calculated for claw, body, and limb lesions and classified as either less than or equal to the Me or greater than the Me lesion scores. Sows were classified as nonlame (£ 1) or lame (³ 2). Loose-housed sows had an increased (P < 0.01) risk of lameness; a reduced (P < 0.05) risk for claw lesions, particularly white line damage, horizontal wall cracks, and dewclaw injuries; and a reduced (P < 0.05) risk for calluses and bursitis on the limbs compared to stall-housed sows. Sows housed on cast iron floors during lactation had a reduced (P < 0.01) risk for heel overgrowth and erosion and heel-sole cracks compared with sows on slatted steel floors. There was no (P > 0.05) association between flooring type during lactation and body lesion score. On -4 d, loose-housed sows had a shorter latency to lie down (P < 0.01), spent more time inactive (P < 0.05), and shifted weight between the limbs more often (P = 0.05) while standing compared with stall-housed sows. Lame sows had a shorter (P < 0.01) latency to lie down compared to nonlame sows on -5 and -4 d. In conclusion, there was an increased risk of lameness in sows housed loose compared to those housed in gestation stalls on transfer to the farrowing crate. Claw health deteriorated in the farrowing crate regardless of gestation housing or floor type but the deterioration in claw health was increased on slatted steel compared to on cast iron
  • Quantification of cow milk yield and pre-weaning calf growth response in temperate pasture-based beef suckler systems: A meta-analysis

    Sapkota, D.; Kelly, A.K.; Crosson, P.; White, R.R.; McGee, M.; Teagasc Walsh Fellowship Programme (Elsevier BV, 2020-11)
    The objectives of this study were to quantitatively summarize factors associated with cow milk yield (MY) and calf growth response in pasture-based beef cow-calf suckler systems and to discern how cow genotype and parity influenced these responses. A dataset of 344 treatment mean observations was compiled from 69 studies that reported data on cow MY, and calf pre-weaning average daily live weight gain (ADG) and/or weaning weight (WW). Data were analysed using linear mixed effects models with study and region included as random effects. Models were developed for cow MY, calf ADG and WW response and each model was evaluated based on different model fit statistics. The final cow MY model included cow origin (Dairybeef or Beef), cow maturity (early-maturing (EM) or late-maturing (LM) genotypes) and parity. Dairybeef produced 35.4% more milk (8.64 vs. 6.38 kg/day) than Beef cows, and LM produced 20.9% more milk (8.20 vs. 6.78 kg/day) than EM genotypes (P < 0.001). Multiparous cows had a 14.8% higher MY (8.11 vs. 7.06 kg/day) compared to primiparous cows (P < 0.001). Lactation curve persistency was better (P < 0.05) for Beef and EM compared to Dairybeef and LM genotype cows, respectively. The final models of calf ADG and WW included cow origin, cow maturity and parity. Calves from Dairybeef and LM cows were 14 and 20 kg heavier (P < 0.001) at weaning (210-day adjusted) compared to those from Beef and EM genotype cows, respectively. Calves from multiparous cows were 13 kg heavier at weaning than those from primiparous cows (P < 0.001). The response in calf ADG associated with a 1 kg increase in cow daily MY was 47 and 53 g for Dairybeef and Beef cows, respectively (P < 0.001). Corresponding responses for EM and LM cows were 51 and 55 g (P < 0.001). In conclusion, the relationships between cow MY and calf pre-weaning growth, as well as the quantitative impact of cow genotype and parity were determined for pasture-based beef suckler systems; the coefficients generated can be used for improving beef cow-calf management strategies, beef cattle breeding programmes and bio-economic modelling purposes.
  • Block Chain and Internet of Nano-Things for Optimizing Chemical Sensing in Smart Farming

    Vimalajeewa, Dixon; Thakur, Subhasis; Breslin, John; Berry, Donagh P.; Balasubramaniam, Sasitharan; Science Foundation Ireland; European Union; 13/1A/1977; 16/RC/3835 (2020)
    The use of Internet of Things (IoT) with the Internet of Nano Things (IoNT) can further expand decision making systems (DMS) to improve reliability as it provides a new spectrum of more granular level data to make decisions. However, growing concerns such as data security, transparency and processing capability challenge their use in real-world applications. DMS integrated with Block Chain (BC) technology can contribute immensely to overcome such challenges. The use of IoNT and IoT along with BC for making DMS has not yet been investigated. This study proposes a BC-powered IoNT (BC-IoNT) system for sensing chemicals level in the context of farm management. This is a critical application for smart farming, which aims to improve sustainable farm practices through controlled delivery of chemicals. BC-IoNT system includes a novel machine learning model formed by using the Langmuir molecular binding model and the Bayesian theory, and is used as a smart contract for sensing the level of the chemicals. A credit model is used to quantify the traceability and credibility of farms to determine if they are compliant with the chemical standards. The accuracy of detecting the chemicals of the distributed BC-IoNT approach was ≥ 90% and the centralized approach was ≤ 80%. Also, the efficiency of sensing the level of chemicals depends on the sampling frequency and variability in chemical level among farms.
  • Qualitative and quantitative differences in endometrial inflammatory gene expression precede the development of bovine uterine disease

    Brewer, Amy; Cormican, Paul; Lim, Joseph J.; Chapwanya, Aspinas; O’Farrelly, Cliona; Meade, Kieran G.; Department of Agriculture, Food and the Marine; 13/S/472 (Springer Science and Business Media LLC, 2020-10-26)
    The transcriptome of the endometrium early postpartum was profled to determine if infammatory gene expression was elevated in cows which subsequently developed uterine disease. Endometrial cytobrush samples were collected at 7 days postpartum (DPP) from 112 Holstein–Friesian dairy cows, from which 27 were retrospectively chosen for RNA-seq on the basis of disease classifcation [ten healthy and an additional 17 diagnosed with cytological endometritis (CYTO), or purulent vaginal discharge (PVD)] at 21 DPP. 297 genes were signifcantly diferentially expressed between cows that remained healthy versus those that subsequently developed PVD, including IL1A and IL1B (adjusted p < 0.05). In contrast, only 3 genes were signifcantly diferentially expressed in cows which subsequently developed CYTO. Accounting for the early physiological infammatory status present in cows which do not develop disease enhanced the detection of diferentially expressed genes associated with CYTO and further expression profling in 51 additional cows showed upregulation of multiple immune genes, including IL1A, IL1B and TNFA. Despite the expected heterogeneity associated with natural infection, enhanced activation of the infammatory response is likely a key contributory feature of both PVD and CYTO development. Prognostic biomarkers of uterine disease would be particularly valuable for seasonal-based dairy systems where any delay to conception undermines sustainability.
  • Can increased dietary fibre level and a single enrichment device reduce the risk of tail biting in undocked growing-finishing pigs in fully slatted systems?

    Chou, Jen-Yun; O'Driscoll, Keelin; Sandercock, Dale A.; D’Eath, Rick B.; Teagasc Walsh Fellowship Programme; Scotland’s Rural College; Department of Agriculture, Food and the Marine (Public Library of Science (PLoS), 2020-10-30)
    This study evaluated the effectiveness of combined dietary and enrichment strategies to manage tail biting in pigs with intact tails in a conventional fully-slatted floor housing system. A 2 × 2 × 2 factorial design was used. Pigs had either a high fibre (weaner 5.3% and finisher 11.6% of crude fibre) or standard fibre diet (weaner 3.7% and finisher 5.9% of crude fibre). In the weaner stage, pigs had either a spruce wooden post (supplied in a wall-mounted dispenser) or a rubber floor toy as a enrichment device, and in the finisher stage, they had either the same or alternate enrichment item. Six hundred and seventy-two pigs were assigned to 48 pens of 14 pigs and followed from weaning until slaughter. Individual tail lesion scores and pen level behaviours were directly recorded every 2 weeks. Twenty-six pens had tail biting outbreaks and 161 injured pigs needed removal for treatment. Pigs fed with the high fibre diet performed more tail biting (p < 0.05) and tended to have a worse tail damage scores than those fed the standard fibre diet (p = 0.08). Pigs which had the floor toy as weaners and wood as finishers tended to have fewer tail lesions in the finisher stage than their counterparts (p = 0.06). Pigs receiving the floor toy as enrichment interacted with the enrichment more frequently overall (p < 0.001) and performed fewer harmful behaviours in the weaner stage (p < 0.05). Overall, higher fibre in the diet in a relatively barren environment did not help reduce tail biting or tail lesions. Altering the fibre level in the pigs’ diet and providing a single enrichment device to undocked pigs on fully slatted floors resulted in a high level of tail biting and a large proportion of pigs with partial tail amputation.
  • Does Diversity Matter? Behavioural Differences between Piglets Given Diverse or Similar Forms of Enrichment Pre-Weaning

    Schmitt, Océane; Poidevin, Aurélie; O'Driscoll, Keelin; Department of Agriculture, Food and the Marine; 13S428 (MDPI AG, 2020-10-09)
    This study investigated the behavioural effects of providing different enrichment materials to suckling piglets from 7 days-old until weaning. One object was attached to the pen wall (WALL), and the other was suspended in the middle of the pen (MID). Control group had the hessian fabric in both locations, and the two diverse groups had hessian and bamboo stick in alternate locations (i.e., BMID-HWALL and HMID-BWALL). Piglets behaviour was recorded on D0 (object introduction), D1, D5, D8, D12, and D14; at weaning and 1, 3, 5 and 15 days after. Groups did not differ in approaching or interacting with objects on D0. MID objects attracted more attention than WALL objects (p < 0.01). Piglets interacted more with hessian than bamboo (p < 0.001). They performed more oral manipulation and shaking with hessian (p < 0.001), but more pushing of bamboo (p < 0.001). Interactions with objects increased with time (p < 0.001), especially with hessian (p < 0.01), while interest in bamboo remained unchanged. Control piglets performed more biting than piglets with diverse enrichment (pooled data), both pre- and post-weaning (p < 0.05). Therefore, providing different types of enrichment material can reduce biting behaviour pre- and post-weaning. Hessian was favoured, possibly because this was easier to bite and shake, which were the behaviours most often observed.
  • Growth performance and hematological changes of weaned beef calves diagnosed with respiratory disease using respiratory scoring and thoracic ultrasonography

    Cuevas-Gómez, Inmaculada; McGee, Mark; McCabe, Matthew; Cormican, Paul; O’Riordan, Edward; McDaneld, Tara; Earley, Bernadette; US-Ireland Tripartite Grant; 2018US-IRL200 (Oxford University Press (OUP), 2020-10-23)
    This study investigated (i) the effect of clinical bovine respiratory disease (BRD) and associated lung consolidations on growth performance and hematological profiles of recently weaned beef calves and (ii) the relationship between clinical respiratory signs and lung consolidation detected by thoracic ultrasonography (TUS). One hundred and fifty-three weaned beef calves (209 (SD; 35.8) days old and 306 (SD; 26.3) kg, at arrival) purchased and transported from auction markets were accommodated indoors in concrete slatted floor pens. Calves were weighed weekly from arrival until d 28 and on d 65 post-arrival. Assessment of BRD and blood sample collection for hematological profiles were performed on scheduled days (at arrival, on d 7, 14 and 28) and on other days upon BRD diagnosis. Animals were assessed for BRD using a total clinical respiratory score (CRS) of five clinical signs (rectal temperature, ear position, cough, nasal secretion and eye secretion with each ranging from normal (0) to abnormal (3)), and TUS scores (normal (0) to lung consolidation ≥ 1 cm2 (2)). Based on CRS, 35% of calves were CRS+ (CRS ≥5) and 65% were CRS- (CRS <5). Although no lung consolidations (TUS-) were detected at arrival, 34% of calves developed lung consolidation (≥ 1 cm2 ) (TUS+) during the first 28 d post-arrival. Only fever (>39.6o C) and nasal discharge were weakly associated (r 0.19, P <0.05) with lung consolidation. On the day of BRD detection, neutrophil number and neutrophil:lymphocyte ratio was 58% and 73% greater, respectively, in BRD calves with lung consolidation compared to healthy calves. From d 0 to 65, calf ADG did not differ (P >0.05) between CRS+ and CRS- calves, but was 0.09 kg/d lower (P <0.05) for TUS+ compared to TUS- calves. Calves classified as BRD (CRS+TUS ≥5) with lung consolidation had lower (P <0.05) ADG from arrival until d 28 than healthy calves and BRD calves without lung consolidation (0.11 ± 0.10 vs. 0.53 ± 0.07 vs. 0.57 ± 0.10 kg/d, respectively); however, no differences in ADG were observed from d 0 to 65. Conventional methods to diagnose BRD failed to detect calves with lung lesions. Thoracic ultrasonography is a useful tool to detect lung lesions and its implementation in combination with CRS should provide a more accurate and early diagnosis of BRD, which is fundamental to successful treatment, animal welfare and growth performance.

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