• Habitat Selection by Grazing Animals in Heterogeneous Environments: The Case of Hill Sheep In Western Ireland

      Williams, Bryony; Walls, Sean; Walsh, Michael; Gormally, Michael; Teagasc Walsh Fellowship Programme (Royal Irish Academy, 2012-10-19)
      Uplands and peatlands are of high conservation importance and, while grazing animals are a key management tool for conservation, grazing-related damage can easily occur. Damage to European uplands is most notable in Britain and Ireland, where Scottish Blackface is the dominant hill sheep breed. Therefore, if conservation strategies that address concerns of grazing-related damage are to be strengthened, the Scottish Blackface is a good subject and a better understanding of their resource use would be advantageous. While previous habitat selection studies of hill sheep have depended on direct observation, this particular study uses Global Positioning System tracking collars to determine ewe locations. The study site is on a mountainside in western Ireland that is dominated by blanket bog (52.8%) and wet heath (35.3%). Habitat mapping and ewe range and resource selection analyses indicated that habitat selection was significant (P < 0.05), typically acid grassland is selected most followed by wet heath, with blanket bog habitats selected least. Seasonal variation in habitat selection was also evident. These results (1) corroborate the findings of previous work elsewhere on plant community/habitat selection and (2) provide additional information that can be used to strengthen existing or new hill grazing management models that are used to aid decision-making. In particular, management plans should take into consideration the availability (both in terms of total area and connectivity) of the preferred sheep habitats and specifically consider grazing pressure in and between those habitats.
    • Heart to spine measurements to detect left atrial enlargement in dogs with mitral insufficiency

      Sánchez Salguero, Xavier; Prandi, David; Llabrés-Díaz, Francisco; Manzanilla, Edgar G; Badiella, Llorenç; Bussadori, Claudio (Biomed Central, 2019-11-20)
      Background Radiography is useful to determine left atrial (LA) size when echocardiography is not available. Recently, the authors have described Radiographic Left Atrial Dimension (RLAD) as a new radiographic measurement to assess LA size. The objective of this study was to assess the clinical usefulness of 2 new radiographic measurements to detect and quantify left atrial enlargement (LAE) compared to RLAD and using left atrium to aortic root (LA/Ao) ratio as gold standard. These new measurements, bronchus-to-spine (Br-Spine) and RLAD-to-spine (RLAD-Spine) may be more precise in cases were LA boundaries are not well defined. Fifty dogs, 25 with and 25 without LAE were recruited. Reference LA/Ao ratio was assessed by 2D echocardiography and LAE was considered if LA/Ao > 1.6. Br-spine was measured as a straight vertical line from the main stem bronchus to the ventral border of the vertebra situated immediately dorsal to the heart base. RLAD-Spine was measured from RLAD endpoint perpendicularly to spine. The correlation of RLAD, Br-Spine and RLAD-Spine methods with LA/Ao and their sensitivity and specificity for detecting LAE were calculated. Receiver Operating Characteristic (ROC) curves were used to estimate the optimal cut-off for each method. Results Correlations between Br-Spine, RLAD-Spine, RLAD and LA/Ao ratio were − 0.66, − 0.76 and 0.89 respectively (P < 0.001). Sensitivity at the optimal cut-off values for detecting LAE were 32.0, 64.0 and 96.0%, respectively. Specificity was 96.0% in all cases. Conclusion Br-Spine and RLAD-Spine were less sensitive radiographic measurements than RLAD in detecting LAE in dogs. Both Br-Spine and RLAD-Spine may not be good alternatives to RLAD.
    • Heart to spine measurements to detect left atrial enlargement in dogs with mitral insufficiency

      Sánchez Salguero, Xavier; Prandi, David; Llabrés-Díaz, Francisco; Manzanilla, Edgar G.; Badiella, Llorenç; Bussadori, Claudio (Springer Science and Business Media LLC, 2019-11-20)
      Background: Radiography is useful to determine left atrial (LA) size when echocardiography is not available. Recently, the authors have described Radiographic Left Atrial Dimension (RLAD) as a new radiographic measurement to assess LA size. The objective of this study was to assess the clinical usefulness of 2 new radiographic measurements to detect and quantify left atrial enlargement (LAE) compared to RLAD and using left atrium to aortic root (LA/Ao) ratio as gold standard. These new measurements, bronchus-to-spine (Br-Spine) and RLAD-to-spine (RLAD-Spine) may be more precise in cases were LA boundaries are not well defined. Fifty dogs, 25 with and 25 without LAE were recruited. Reference LA/Ao ratio was assessed by 2D echocardiography and LAE was considered if LA/Ao > 1.6. Br-spine was measured as a straight vertical line from the main stem bronchus to the ventral border of the vertebra situated immediately dorsal to the heart base. RLAD-Spine was measured from RLAD endpoint perpendicularly to spine. The correlation of RLAD, Br-Spine and RLAD-Spine methods with LA/Ao and their sensitivity and specificity for detecting LAE were calculated. Receiver Operating Characteristic (ROC) curves were used to estimate the optimal cut-off for each method. Results: Correlations between Br-Spine, RLAD-Spine, RLAD and LA/Ao ratio were − 0.66, − 0.76 and 0.89 respectively (P < 0.001). Sensitivity at the optimal cut-off values for detecting LAE were 32.0, 64.0 and 96.0%, respectively. Specificity was 96.0% in all cases. Conclusion: Br-Spine and RLAD-Spine were less sensitive radiographic measurements than RLAD in detecting LAE in dogs. Both Br-Spine and RLAD-Spine may not be good alternatives to RLAD.
    • Herd health status and management practices on 16 Irish suckler beef farms

      O'Shaughnessy, James; Mee, John F; Doherty, Michael L.; Crosson, Paul; Barrett, Damien; Grady, Luke; Earley, Bernadette; Teagasc Walsh Fellowship Programme (Biomed Central, 2013-11-06)
      Background: There have been few studies published internationally which document herd health management practices in suckler beef herds and no published Irish studies. The study objective was to document herd health status and management practices on sixteen Irish suckler beef herds over a two year period (2009–2010). The farms used in the study were part of the Teagasc BETTER farm beef programme. The mean (s.d.) herd size, stocking rate and farm size was 68 cows (27.6), 2.0 LU/ha (0.3) and 64.3 (21.6) adjusted hectares, respectively. Two questionnaires were designed; 1) a farmer questionnaire to collect information on farm background and current herd health control practices and 2) a veterinary questionnaire to collect information on the extent of animal health advice given by veterinarians to their clients and identification of any on-farm herd health issues. Results: Dystocia, calf pneumonia, and calf diarrhoea, in that order, were identified as the primary herd health issues in these Irish suckler beef herds. In addition, substantial deficiencies in biosecurity practices were also identified on these farms. Conclusions: The findings of this study may serve as the focus for future research in animal health management practices in Irish suckler beef herds.
    • Heritability and impact of environmental effects during pregnancy on antral follicle count in cattle

      Walsh, S.W.; Mossa, F.; Butler, Stephen T.; Berry, Donagh; Scheetz, D.; Jimenez-Krassel, F.; Templeman, R.J.; Cater, F.; Lonergan, P.; Evans, A.C.O.; et al. (Elsevier for American Dairy Science Association, 2014-07)
      Previous studies have documented that ovarian antral follicle count (AFC) is positively correlated with number of healthy follicles and oocytes in ovaries (ovarian reserve), as well as ovarian function and fertility in cattle. However, environmental factors (e.g., nutrition, steroids) during pregnancy in cattle and sheep can reduce AFC in offspring. The role that genetic and environmental factors play in influencing the variability in AFC and, correspondingly, the size of the ovarian reserve, ovarian function, and fertility, are, however, poorly understood. The present study tests the hypothesis that variability in AFC in offspring is influenced not only by genetic merit but also by the dam age and lactation status (lactating cows vs. nonlactating heifers) and milk production during pregnancy. Antral follicle count was assessed by ultrasonography in 445 Irish Holstein-Friesian dairy cows and 522 US Holstein-Friesian dairy heifers. Heritability estimates for AFC (± standard error) were 0.31 ± 0.14 and 0.25 ± 0.13 in dairy cows and heifers, respectively. Association analysis between both genotypic sire data and phenotypic dam data with AFC in their daughters was performed using regression and generalized linear models. Antral follicle count was negatively associated with genetic merit for milk fat concentration. Also, AFC was greater in offspring of dams that were lactating (n = 255) compared with nonlactating dams (n = 89) during pregnancy and was positively associated with dam milk fat concentration and milk fat-to-protein ratio. In conclusion, AFC in dairy cattle is a moderately heritable genetic trait affected by age or lactation status and milk quality but not by level of dam’s milk production during pregnancy.
    • High level of treatment failure with commonly used anthelmintics on Irish sheep farms

      Keane, Orla M; Keegan, Jason D; Good, Barbara; de Waal, Theo; Fanning, June; Gottstein, Michael; Casey, Micheal; Hurley, Christine; Sheehan, Maresa (Biomed Central, 2014-08-03)
      Background: In 2013 a Technology Adoption Program for sheep farmers was established to encourage the implementation of best management practices on sheep farms in Ireland. There were 4,500 participants in this programme in 2013. As part of this programme, farmers had the option to carry out a drench test to establish the efficacy of their anthelmintic treatment. Results: Flock faecal samples were collected before and after treatment administration and gastrointestinal nematode eggs enumerated. In total there were 1,893 participants in the task, however only 1,585 included both a pre- and post-treatment faecal sample. Of those, 1,308 provided information on the anthelmintic product that they used with 46%, 23% and 28% using a benzimidazole (BZ), levamisole (LEV) and macrocyclic lactone (ML) product respectively. The remaining farmers used a product inapplicable for inclusion in the task such as a flukicide or BZ/LEV combination product. Samples were included for analysis of drench efficacy if the pre-treatment flock egg count was ≥200 eggs per gram and the interval post-sampling was 10–14 days for BZ products, 4–7 days for LEV products and 14–18 days for ML products. These criteria reduced the number of valid tests to 369, 19.5% of all tests conducted. If the reduction post-treatment was ≥95% the treatment was considered effective. Only 51% of treatments were considered effective using this criterion. There was a significant difference in efficacy between the anthelmintic drug classes with BZ effective in only 30% of treatments, LEV effective in 52% of cases and ML effective in 76% of cases. Conclusions: Gastrointestinal nematode anthelmintic treatments, as practiced on Irish farms, have a high failure rate. There was a significant difference between the efficacies of the anthelmintic classes with BZ the least effective and ML the most effective.
    • Horizontal transmission of Escherichia coli O157:H7 during cattle housing, survival kinetics in feces and water of Escherichia coli O157:H7 and characterisation of E. coli O157:H7 isolates from cattle faeces and a feedlot environment

      Scott, Lourda; McGee, Philip; Sheridan, James J.; Earley, Bernadette; Leonard, Nola; European Union (Teagasc, 2005-12-01)
      Escherichia coli O157:H7 can cause severe illness and in some cases leading to death. Cattle are the main reservoir with transmission to humans occurring through contamination of food or the environment. Improved understanding of the survival and transmission and survival of E. coli O157:H7 on the farm is essential for developing future controls of this pathogen. This study showed that transmission of E. coli O157:H7 can occur rapidly in groups of housed cattle, with contamination of the pens and hides occurring in 24 hrs. The inoculation dose for cattle is lower than previously reported. Ingestion of bacteria from the hide through social grooming is important for pathogen transmission in housed cattle along with faecal contamination of the environment. Sampling hide will improve the estimation of prevalence of E. coli O157:H7 in pens.
    • Horizontal transmission of Escherichia coli O157:H7 during cattle housing, survival kinetics in feces and water of Escherichia coli O157:H7 and characterisation of E. coli O157:H7 isolates from cattle faeces and a feedlot environment.

      Scott, Lourda; McGee, Philip; Sheridan, James J.; Earley, Bernadette; Leonard, Nola (Teagasc, 2005-12-01)
      Ruminant livestock, particularly cattle, are considered the primary reservoir of E. coli O157:H7. This study examined the transmission of E. coli O157:H7 within groups of cattle during winter housing. Holstein Friesian steers were grouped in 6 pens of 5 animals. An animal inoculated with, and proven to be shedding a marked strain of E. coli O157:H7 was introduced into each pen. Fecal (rectal swabs) and hide samples (900cm2 right rump) were taken from the thirty six animals throughout the study. Water, feed and gate/partition samples from each pen were also examined. Within 24h of introducing the inoculated animals into the pens, samples collected from the drinking water, pen barriers and animal hides were positive for the pathogen. Within 48h, the hides of 20 of 30 (66%) cohort animals from the 6 pens were contaminated with E. coli O157:H7. The first positive fecal samples from the non-inoculated cohort animals were detected three days after the introduction of the inoculated steers. Over the 23 days of the study 15 of 30 cohort animals shed the marked E. coli O157:H7 strain in their feces on at least one occasion. Animal behavior in the pens was monitored over a 12h period using CCTV cameras. The camera footage showed an average of 13 instances of animal grooming in each pen per hour. The study suggests that transmission of E. coli O157:H7 between animals may occur following ingestion of the pathogen at low levels, and that animal hide may be an important source of transmission.
    • The host immune response to gastrointestinal nematode infection in sheep

      McRae, Kathryn M.; Stear, Michael J.; Good, Barbara; Keane, Orla M; Teagasc Walsh Fellowship Programme; Allan and Grace Kay Overseas Scholarship; European Union; BBSRC Animal Health Research Club; BB/l004070/1 (Wiley, 2015-10-20)
      Gastrointestinal nematode infection represents a major threat to the health, welfare and productivity of sheep populations worldwide. Infected lambs have a reduced ability to absorb nutrients from the gastrointestinal tract, resulting in morbidity and occasional mortality. The current chemo-dominant approach to nematode control is considered unsustainable due to the increasing incidence of anthelmintic resistance. In addition there is growing consumer demand for food products from animals not subjected to chemical treatment. Future mechanisms of nematode control must rely on alternative, sustainable strategies such as vaccination or selective breeding of resistant animals. Such strategies take advantage of the host's natural immune response to nematodes. The ability to resist gastrointestinal nematode infection is considered to be dependent on the development of a protective acquired immune response; although the precise immune mechanisms involved in initiating this process remain to be fully elucidated. In this paper current knowledge on the innate and acquired host immune response to gastrointestinal nematode infection in sheep and the development of immunity is reviewed.
    • Host-Microbiota Interactions in Ileum and Caecum of Pigs Divergent in Feed Efficiency Contribute to Nutrient Utilization

      Reyer, Henry; Oster, Michael; McCormack, Ursula M.; Muráni, Eduard; Gardiner, Gillian E.; Ponsuksili, Siriluck; Lawlor, Peadar G.; Wimmers, Klaus; European Union; 311794 (MDPI AG, 2020-04-14)
      The composition of the intestinal microbiota plays an important role in the digestion and utilization of nutrients and for gut health. Low-fiber diets stimulate digestion and absorption processes, predominantly in the upper region of the gastrointestinal tract, thereby increasing the conversion of feed into body weight. As a consequence, the chemical composition of digesta after duodenal and jejunal absorption processes and passage has a limited complexity affecting colonization and molecular profiles of enterocytes in the hind gut. To decipher ileal and caecal microbial ecosystems and host transcriptional profiles that are beneficial for effective use of the remaining nutrients, pigs differing in feeding efficiency were studied. Biological functions that were consistently enriched at both the gene and microbiota levels comprise immunity-related processes, which ensure the integrity of the gastrointestinal tract. In addition, the differential abundance of certain genera, including Rothia, Subdoligranulu, Leeia and Cellulosilyticum, reflects the establishment of a microbial profile that supports the digestion of endogenously indigestible dietary components in highly feed-efficient pigs. Overall, the results indicate the potential to promote these beneficial functions and further improve feed efficiency through manipulation of dietary and probiotic strategies.
    • How herd best linear unbiased estimates affect the progress achievable from gains in additive and nonadditive genetic merit

      Dunne, F. L.; McParland, Sinead; Kelleher, Margaret M.; Walsh, S.W.; Berry, Donagh; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 16/RC/3835 (Elsevier, 2019-04-10)
      Sustainable dairy cow performance relies on coevolution in the development of breeding and management strategies. Tailoring breeding programs to herd performance metrics facilitates improved responses to breeding decisions. Although herd-level raw metrics on performance are useful, implicitly included within such statistics is the mean herd genetic merit. The objective of the present study was to quantify the expected response from selection decisions on additive and nonadditive merit by herd performance metrics independent of herd mean genetic merit. Performance traits considered in the present study were age at first calving, milk yield, calving to first service, number of services, calving interval, and survival. Herd-level best linear unbiased estimates (BLUE) for each performance trait were available on a maximum of 1,059 herds, stratified as best, average, and worst for each performance trait separately. The analyses performed included (1) the estimation of (co)variance for each trait in the 3 BLUE environments and (2) the regression of cow-level phenotypic performance on either the respective estimated breeding value (EBV) or the heterosis coefficient of the cow. A fundamental assumption of genetic evaluations is that 1 unit change in EBV equates to a 1 unit change in the respective phenotype; results from the present study, however, suggest that the realization of the change in phenotypic performance is largely dependent on the herd BLUE for that trait. Herds achieving more yield, on average, than expected from their mean genetic merit, had a 20% greater response to changes in EBV as well as 43% greater genetic standard deviation relative to herds within the worst BLUE for milk yield. Conversely, phenotypic performance in fertility traits (with the exception of calving to first service) tended to have a greater response to selection as well as a greater additive genetic standard deviation within the respective worst herd BLUE environments; this is suggested to be due to animals performing under more challenging environments leading to larger achievable gains. The attempts to exploit nonadditive genetic effects such as heterosis are often the basis of promoting cross-breeding, yet the results from the present study suggest that improvements in phenotypic performance is largely dependent on the environment. The largest gains due to heterotic effects tended to be within the most stressful (i.e., worst) BLUE environment for all traits, thus suggesting the heterosis effects can be beneficial in mitigating against poorer environments.
    • How much grassland biomass is available in Ireland in excess of livestock requirements?

      McEniry, Joseph; Crosson, Paul; Finneran, Eoghan; McGee, Mark; Keady, Tim; O'Kiely, Padraig; Department of Agriculture, Food and the Marine; RSF 07 557 (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Grassland is a dominant biomass resource in Ireland and underpins most animal production systems. However, other commercial uses for grassland biomass exist, including, for example, the production of biogas through anaerobic digestion for the generation of heat, electricity and transport fuel. The objective of this study was to estimate the annual grassland resource available in Ireland in excess of livestock requirements under six contrasting scenarios. Under current grassland management and production practices there is an estimated average annual grassland resource of ca. 1.7 million tonnes of dry matter (DM) available in excess of livestock requirements. Only a small proportion of this resource (0.39 million tonnes of DM per annum) would be available if the targets set out in ‘Food Harvest 2020’ were achieved. However, increasing nitrogen (N) fertiliser input (to the limit permitted by the E.U. Nitrates Directive) combined with increasing the grazed grass utilisation rate of cattle (from 0.60 to 0.80 kg DM ingested by livestock per kg DM grown) has the potential to significantly increase this average resource to 12.2 million t DM/annum, even when allowing for achievement of ‘Food Harvest 2020’ targets. Under these scenarios, alternative uses for grassland biomass such as anaerobic digestion and green biorefining would not compete with traditional dairy, beef and lamb production systems, but could provide an alternative enterprise and income to farmers.
    • Identification of functional candidate variants and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing

      Lam, S.; Miglior, F.; Fonseca, P.A.S.; Gómez-Redondo, I.; Zeidan, J.; Suárez-Vega, A.; Schenkel, F.; Guan, L.L.; Waters, Sinéad M; Stothard, P.; et al. (Elsevier, 2021-02-28)
      The identification of functional genetic variants and associated candidate genes linked to feed efficiency may help improve selection for feed efficiency in dairy cattle, providing economic and environmental benefits for the dairy industry. This study used RNA-sequencing data obtained from liver tissue from 9 Holstein cows [n = 5 low residual feed intake (RFI), n = 4 high RFI] and 10 Jersey cows (n = 5 low RFI, n = 5 high RFI), which were selected from a single population of 200 animals. Using RNA-sequencing, 3 analyses were performed to identify: (1) variants within low or high RFI Holstein cattle; (2) variants within low or high RFI Jersey cattle; and (3) variants within low or high RFI groups, which are common across both Holstein and Jersey cattle breeds. From each analysis, all variants were filtered for moderate, modifier, or high functional effect, and co-localized quantitative trait loci (QTL) classes, enriched biological processes, and co-localized genes related to these variants, were identified. The overlapping of the resulting genes co-localized with functional SNP from each analysis in both breeds for low or high RFI groups were compared. For the first two analyses, the total number of candidate genes associated with moderate, modifier, or high functional effect variants fixed within low or high RFI groups were 2,810 and 3,390 for Holstein and Jersey breeds, respectively. The major QTL classes co-localized with these variants included milk and reproduction QTL for the Holstein breed, and milk, production, and reproduction QTL for the Jersey breed. For the third analysis, the common variants across both Holstein and Jersey breeds, uniquely fixed within low or high RFI groups were identified, revealing a total of 86,209 and 111,126 functional variants in low and high RFI groups, respectively. Across all 3 analyses for low and high RFI cattle, 12 and 31 co-localized genes were overlapping, respectively. Among the overlapping genes across breeds, 9 were commonly detected in both the low and high RFI groups (INSRR, CSK, DYNC1H1, GAB1, KAT2B, RXRA, SHC1, TRRAP, PIK3CB), which are known to play a key role in the regulation of biological processes that have high metabolic demand and are related to cell growth and regeneration, metabolism, and immune function. The genes identified and their associated functional variants may serve as candidate genetic markers and can be implemented into breeding programs to help improve the selection for feed efficiency in dairy cattle.
    • Identification of possible cow grazing behaviour indicators for restricted grass availability in a pasture-based spring calving dairy system

      Werner, Jessica; Umstatter, Christina; Kennedy, Emer; Grant, Jim; Leso, Lorenzo; Geoghegan, Anne; Shalloo, Laurence; Schick, Matthias; O'Brien, Bernadette; Science Foundation Ireland; et al. (Elsevier, 2018-12-05)
      Precision livestock farming uses biosensors to measure different parameters of individual animals to support farmers in the decision making process. Although sensor development is advanced, there is still little implementation of sensor-based solutions on commercial farms. Especially on pasture-based dairy systems, the grazing management of cows is largely not supported by technology. A key factor in pasture-based milk production is the correct grass allocation to maximize the grass utilization per cow, while optimizing cow performance. Currently, grass allocation is mostly based on subjective eye measurements or calculations per herd. The aim of this study was to identify possible indicators of insufficient or sufficient grass allocation in the cow grazing behaviour measures. A total number of 30 cows were allocated a restricted pasture allowance of 60% of their intake capacity. Their behavioural characteristics were compared to those of 10 cows (control group) with pasture allowance of 100% of their intake capacity. Grazing behaviour and activity of cows were measured using the RumiWatchSystem for a complete experimental period of 10 weeks. The results demonstrated that the parameter of bite frequency was significantly different between the restricted and the control groups. There were also consistent differences observed between the groups for rumination time per day, rumination chews per bolus and frequency of cows standing or lying.
    • Identification of the blue light intensity administered to one eye required to suppress bovine plasma melatonin and investigation into effects on milk production in grazing dairy cows

      Murphy, Barbara A.; Herlihy, Mary M.; Nolan, Margaret B.; O'Brien, Christiane; Furlong, John G.; Butler, Stephen T.; Equiliume Ltd.; Teagasc (American Dairy Science Association, 2021-08)
      Long-day photoperiod is known to positively affect milk production in confinement dairy systems, and it has been hypothesized that pineal melatonin (MT) secretion plays a substantial role in this process. Specialized mammalian photoreceptors that regulate MT secretion are optimally stimulated by short wavelength blue light. We investigated the blue light intensity administered to one eye required to suppress MT secretion in nonlactating dairy cows, and subsequently examined effects on milk production in grazing dairy cows. Following a 14-d light-dark 8:16 h environmental conditioning period, 5 nonlactating Holstein-Friesian cows were exposed to treatments of <1, 70, 125, 175, and 225 lx for 8 additional hours using a 5 × 5 Latin square design. Light was administered via headpieces fitted with light-emitting diodes emitting blue light (465 nm) to the right eye. All cows were then exposed to a light-dark 16:8 h cycle for one night via the indoor lighting system (>200 lx white light). Plasma samples collected at regular intervals were assayed for MT. A dose-dependent effect of light treatment on mean circulating MT concentrations (and 95% CI) was observed [9.4 (7.2, 12.3), 5.0 (3.8, 6.6), 4.4 (3.3, 5.7), 3.3 (2.5, 4.3) and 1.7 (1.3, 2.3) ng/mL for treatments of 0, 70, 125, 175, and 225 lx, respectively. Only the 225 lx treatment acutely suppressed plasma melatonin concentration to levels similar to the light-dark 16:8 h treatment [1.9 (1.4, 2.5) ng/mL]. Forty spring-calving cows were blocked on parity, calving date and Economic Breeding Index for milk production and assigned to the control treatment or blue light to a single eye (LT) treatment from calving through 32 wk of lactation. The cows assigned to LT treatment were fitted with headpieces providing 225 lx of blue light to the right eye from 1700 until 0000 h. Mean milk production (and 95% CI) during 32 wk of lactation was not affected by treatment [20.3 (19.3, 21.3) vs. 20.9 (19.8, 22.0) kg/d, control and LT, respectively]. Within multiparous cows, a treatment by week interaction was detected, whereby LT treatment increased milk production during the first 12 wk of lactation [25.8 (24.3, 27.3) vs. 28.0 (26.5, 29.5) kg/d; +8.5%], but had no effect thereafter. Treatment did not affect plasma insulin-like growth factor 1. We identified the blue light intensity to one eye required to acutely suppress MT concentrations. Transient favorable effects on milk production were observed in multiparous cows. It remains unclear how single-eye blue light treatment affects galactopoiesis in grazing dairy cows, and further research is needed to explore whether this modality of light delivery represents a useful means to aid productivity in pasture-based dairy systems. Key words: melatonin, photoperiod, blue light, milk production, insulin-like growth factor
    • Identifying challenges to manage body weight variation in pig farms implementing all-in-all-out management practices and their possible implications for animal health: a case study

      Rodrigues da Costa, Maria; García Manzanilla, Edgar; Diana, Alessia; van Staaveren, Nienke; Torres-Pitarch, Alberto; Boyle, Laura A; Calderón Díaz, Julia A; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; 14/S/832; et al. (Biomed Central, 2021-01-11)
      Background Managing body weight (BW) variation is a challenge in farrow-to-finish farms implementing all-in/all-out (AIAO) production systems due to the lack of “off-site” facilities to segregate slow growing pigs (SGP). This case study investigated different approaches to managing BW variation in a farrow-to-finish commercial pig farm with a self-declared AIAO management and the possible implications for animal health. Case presentation A total of 1096 pigs (1047 pigs born within 1 week plus 49 pigs born 1 week later) were tracked until slaughter as they moved through the production stages. Piglets were individually tagged at birth and their location on the farm was recorded on a weekly basis. In total, 10.3% of pigs died during lactation. Four main cohorts of pigs were created at weaning and retrospectively identified: cohort 1 = pigs weaned at 21 days (4.5%); cohort 2 = pigs weaned at 28 days (81.0%), which was sub-divided at the end of the first nursery stage into sub-cohort 2a = pigs split at 3 weeks post-weaning (29.7%); sub-cohort 2b = pigs split at 3 weeks post-weaning from cohort 2a and split again 5 weeks post-weaning (35.5%) and sub-cohort 2c = remaining smaller size pigs from cohort 2b (10.9%); cohort 3 = pigs weaned at 35 days (2.7%) and cohort 4 = pigs weaned at 49 days (1.5%) that were later mixed with SPG, delayed pigs from other cohorts and sick/injured pigs that recovered. Four strategies to manage BW variation were identified: i) earlier weaning (cohort 1); ii) delayed weaning of SGP (cohort 3 and 4); iii) re-grading pens by BW (sub-cohorts 2a, 2b and 2c) and, iv) delayed movement of SGP to the next production stage (several pigs from all cohorts). A higher percentage of delayed pigs presented pericarditis, pleurisy and enzootic pneumonia like lesions at slaughter compared with pigs under other strategies. Conclusion A variety of management practices were implemented to minimise BW variation during the production cycle. However, several cohorts of pigs were created disrupting AIAO management. Earlier weaning should only be practiced under specific circumstances where optimal animal health and welfare are guaranteed. Delayed weaning of SGP and delaying pigs to move to the next production stage could negatively affect animal health and should be avoided.
    • Identifying Single Copy Orthologs in Metazoa

      Creevey, Christopher J.; Muller, Jean; Doerks, Tobias; Thompson, Julie D.; Arendt, Detlev; Bork, Peer; European Union; Science Foundation Ireland; LSH-2004-1.1.5-3; 07/SK/B1236A (PLOS, 2011-12-01)
      The identification of single copy (1-to-1) orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene. Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence. To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis) to 99.8% (human) with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.
    • Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue

      Johnston, Dayle; Earley, Bernadette; Cormican, Paul; Murray, Gerard; Kenny, David A.; Waters, Sinead M.; McGee, Mark; Kelly, Alan K; McCabe, Matthew; Department of Agriculture, Food and the Marine; et al. (Biomed Central, 2017-05-02)
      Background Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Results Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences. Conclusions The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD.
    • Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

      McCabe, Matthew; Cormican, Paul; Keogh, Kate; O'Connor, Aaron; O'Hara, Eoin; Palladino, Rafael Alejandro; Kenny, David A.; Waters, Sinead M.; Science Foundation Ireland; Teagasc Walsh Fellowship Programme; et al. (PLOS, 2015-07-30)
      Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.
    • Impact of agronomic practices of an intensive dairy farm on nitrogen concentrations in a karst aquifer in Ireland

      Huebsch, Manuela; Horan, Brendan; Blum, P.; Richards, Karl G.; Grant, Jim; Fenton, Owen; Teagasc Walsh Fellowship Programme (Elsevier, 24/09/2013)
      Exploring the relationship between agricultural nitrogen loading on a dairy farm and groundwater reactive nitrogen concentration such as nitrate is particularly challenging in areas underlain by thin soils and karstified limestone aquifers. The objective of this study is to relate changes in detailed agronomic N-loading, local weather conditions, hydrogeological and geological site characteristics with groundwater N occurrence over an 11-year period on an intensive dairy farm with free draining soils and a vulnerable limestone aquifer. In addition, the concept of vertical time lag from source to receptor is considered. Statistical analysis used regression with automatic variable selection. Four scenarios were proposed to describe the relationships between paddock and groundwater wells using topographic and hydrogeological assumptions. Monitored nitrate concentrations in the studied limestone aquifer showed a general decrease in the observed time period (2002–2011). Statistical results showed that a combination of improved agronomic practices and site specific characteristics such as thicknesses of the soil and unsaturated zone together with hydrogeological connections of wells and local weather conditions such as rainfall, sunshine and soil moisture deficit were important explanatory variables for nitrate concentrations. Statistical results suggested that the following agronomic changes improved groundwater quality over the 11-year period: reductions in inorganic fertiliser usage, improvements in timing of slurry application, the movement of a dairy soiled water irrigator to less karstified areas of the farm and the usage of minimum cultivation reseeding on the farm. In many cases the explanatory variables of farm management practices tended to become more important after a 1- or 2-year time lag. Results indicated that the present approach can be used to elucidate the effect of farm management changes to groundwater quality and therefore the assessment of present and future legislation implementations.