Now showing items 1-20 of 2046

    • Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse

      van de Wouw, Marcel; Walsh, Aaron M; Crispie, Fiona; van Leuven, Lucas; Lyte, Joshua M; Boehme, Marcus; Clarke, Gerard; Dinan, Timothy G; Cotter, Paul D; Cryan, John F; et al. (Biomed Central, 2020-05-18)
      Background Mounting evidence suggests a role for the gut microbiota in modulating brain physiology and behaviour, through bi-directional communication, along the gut-brain axis. As such, the gut microbiota represents a potential therapeutic target for influencing centrally mediated events and host behaviour. It is thus notable that the fermented milk beverage kefir has recently been shown to modulate the composition of the gut microbiota in mice. It is unclear whether kefirs have differential effects on microbiota-gut-brain axis and whether they can modulate host behaviour per se. Methods To address this, two distinct kefirs (Fr1 and UK4), or unfermented milk control, were administered to mice that underwent a battery of tests to characterise their behavioural phenotype. In addition, shotgun metagenomic sequencing of ileal, caecal and faecal matter was performed, as was faecal metabolome analysis. Finally, systemic immunity measures and gut serotonin levels were assessed. Statistical analyses were performed by ANOVA followed by Dunnett's post hoc test or Kruskal-Wallis test followed by Mann-Whitney U test. Results Fr1 ameliorated the stress-induced decrease in serotonergic signalling in the colon and reward-seeking behaviour in the saccharin preference test. On the other hand, UK4 decreased repetitive behaviour and ameliorated stress-induced deficits in reward-seeking behaviour. Furthermore, UK4 increased fear-dependent contextual memory, yet decreased milk gavage-induced improvements in long-term spatial learning. In the peripheral immune system, UK4 increased the prevalence of Treg cells and interleukin 10 levels, whereas Fr1 ameliorated the milk gavage stress-induced elevation in neutrophil levels and CXCL1 levels. Analysis of the gut microbiota revealed that both kefirs significantly changed the composition and functional capacity of the host microbiota, where specific bacterial species were changed in a kefir-dependent manner. Furthermore, both kefirs increased the capacity of the gut microbiota to produce GABA, which was linked to an increased prevalence in Lactobacillus reuteri. Conclusions Altogether, these data show that kefir can signal through the microbiota-gut-immune-brain axis and modulate host behaviour. In addition, different kefirs may direct the microbiota toward distinct immunological and behavioural modulatory effects. These results indicate that kefir can positively modulate specific aspects of the microbiota-gut-brain axis and support the broadening of the definition of psychobiotic to include kefir fermented foods. Video abstract.
    • In vitro screening of different Pseudomonas fluorescens isolates to study lytic enzyme production and growth inhibition during antagonism of Fusarium oxysporum f. sp. cumini, wilt causing pathogen of cumin

      Rathore, Ridhdhi; Vakharia, Dinesh N; Rathore, Dheeraj S; Department of Biochemistry, College of Agriculture, Junagadh Agricultural University (Springer, 2020-05-12)
      Land plants exist in close association with bacterial and fungal microbes, where some associations can be pathogenic and others can be mutualistic/beneficial. One such relation exists between host plant, Cuminum cyminum L. (Cumin) and Fusarium oxysporum f. sp. cumini (Foc), the causal pathogen of cumin wilt and Pseudomonas fluorescens (Pf), where Pf acts as a bio-agent for inhibiting Foc and promoting plant growth of cumin. In this study, antagonism by 10 different Pf isolates against Foc was studied under laboratory conditions through percent growth inhibition and biochemical mechanisms. Among these Pf isolates, Pf-5 exhibited the highest in vitro growth inhibition (82.51%). A positive correlation was observed between percent growth inhibition and specific activities of hydrolytic enzymes, chitinase, β-1, 3 glucanase, and protease, where a negative correlation was observed with cell wall degrading enzymes, cellulase and polygalacturonase. To conclude, isolate Pf-5 could be a potential biocontrol agent for Fusarium wilt disease of cumin.
    • Investigating the impact of varying levels of inventory data detail on private sector harvest forecasting

      Farrelly, Niall; O'Connor, Cian; Nieuwenhuis, Maarten; Phillips, Henry; Department of Agriculture, Food and the Marine; 14/C/824 (The Society of Irish Foresters, 2019-02-01)
      A comparison was made between four methods of generating roundwood production forecasts for private sector forests in Ireland which used varying levels of inventory data as inputs into the production Model. Two methods were based on stand variables: the Irish Dynamic Yield Model (IDYM) method and the General Yield Class (GYC) method. The other two methods were based on site variables used to derive predictions of productivity from climate and map-based data and include a local prediction (LPYC) and a national prediction of yield class (NPYC), the latter the same as that used in the All Ireland Roundwood Production Forecast 2016-2035 (Phillips et al. 2016). To determine the reliability of predictions for an individual stand, field measurements of yield class (GYC) were compared with the predictions of yield class derived using the NPYC and LPYC methods for 52 privately-owned stands of Sitka spruce in the north-west of Ireland. The prediction of yield class using the NPYC method had a low probability of agreement with GYC, with a large bias to under-predict yield class. The LPYC method had a higher probability of agreement and lower bias indicating a better assessment of local productivity. To assess the impact of the various productivity estimates on roundwood production forecasts, separate roundwood forecasts for the period 2016- 2035 were generated. The forecast produced using the NPYC method was used as a baseline for comparison purposes. As expected, the under-prediction of yield class using the NPYC method produced the lowest volume production estimate (318,454 m3) for the forecast period. Both the GYC and LPYC methods resulted in a significant increase in estimated volume production of between 25% and 29% over the baseline. The IDYM method provided the highest estimate of volume production (432,000 m3) for the forecast period, an increase of 35% over the baseline. The increased output predicted using the IDYM method is explained by the inclusion of stocking and basal area data, which more accurately reflected the increased growing stock of private forests than yield data derived using Forestry Commission yield models based on prescribed management. The increases in productivity associated with the use of LPYC, GYC and IDYM methods had the effect of producing shorter rotations and resulted in an increase in the area clearfelled and associated volume production. Perhaps more importantly, the timing of volume production was affected by using more accurate methods to assess productivity (i.e. LPYC, GYC, IDYM), owing to a higher yield-age profile of stands compared to those assessed using the NPYC predictions. The findings point to a possible under-estimation of the productivity for private stands in the All Ireland Roundwood Production Forecast and have implications for the timing of the forecasted volume which could be brought forward by 5 to 6 years. In the absence of field or aerial laser measurement of height and age, the use of the LPYC method is recommended for future private sector roundwood producion forecasts.
    • Self-association of bovine β-casein as influenced by calcium chloride, buffer type and temperature

      Li, Meng; Auty, Mark; Crowley, Shane V.; Kelly, Alan L.; O'Mahoney, James A.; Brodkorb, Andre; Irish Dairy Levy Research Trust; Teagasc Walsh Fellowship Programme; MDDT 6261 (Elsevier, 2018-09-25)
      The aim of this study was to investigate the aggregation behaviour of a pure β-casein (β-CNpure) and a β-casein concentrate (β-CNconc) as a function of temperature, buffer type (pH 6.8) and the presence of CaCl2. The particle size distribution and turbidity of β-casein (β-CN) dispersions were measured by dynamic light-scattering (DLS) and UV/vis spectroscopy between 4 and 55 °C. Upon heating (4–55 °C), the particle size of both β-CN samples increased, indicating self-association via hydrophobic interactions. It was shown that the self-association of β-CN increased with increasing β-CN concentration and that β-CNpure self-associated at significantly lower concentration than β-CNconc. Both turbidity and particle size measurements showed that the β-CN samples had similar aggregation behaviour in water and imidazole buffer (pH 6.8) but differed in sodium phosphate buffer (pH 6.8), especially at higher ionic calcium concentrations. Fourier Transform Infrared (FTIR) spectroscopy revealed very little change in the secondary structure of β-CN during heating (4–55 °C). The microstructure of β-CN aggregates was monitored during heating from 10 to 55 °C, followed by cooling to 10 °C, using polarised light microscopy. Spherical and heterogeneous aggregates were observed when heated at temperatures above 37 °C, which were reversible upon cooling. This study confirmed that β-CN undergoes self-association on heating that reverses upon cooling, with the aggregation process being highly dependent on the purity of β-CN, the solvent type and the presence of ionic calcium.
    • Structural mechanism and kinetics of in vitro gastric digestion are affected by process-induced changes in bovine milk

      Mulet-Cabero, Ana-Isabel; Mackie, Alan R.; Wilde, Peter J.; Fenelon, Mark A.; Brodkorb, Andre; Irish Dairy Levy Research Trust; Teagasc Walsh Fellowship Programme; BBSRC; MDDT6261; 2014029; et al. (Elsevier, 2018-03-27)
      Bovine milk is commonly exposed to processing, which can alter the structure, biochemical composition, physico-chemical properties and sensory quality. While many of these changes have been studied extensively, little is known about their effect on digestive behaviour. In this study, heat treatments of pasteurisation at 72 °C for 15 s or Ultra-High-Temperature (UHT) treatment at 140 °C for 3 s and homogenisation at pilot-plant scale were applied to whole milk. The gastric behaviour was investigated using a recently developed semi-dynamic adult in vitro model. The emptied digesta were analysed to assess the nutrient delivery kinetics, changes in microstructure and protein digestion. All samples showed protein aggregation and coagulum formation within the first 15 min of gastric digestion at which time the pH ranged from 5.5 to 6. Homogenised samples creamed regardless of heat treatment, whereas all non-homogenised samples exhibited sedimentation. The consistency of the coagulum of the heated samples was more fragmented compared to those of the non-heated samples. Rheological analysis showed that the higher the temperature of the heat treatment, the softer the obtained coagulum and the higher the protein hydrolysis at the end of digestion. The study also confirmed that gastric emptying of caseins from milk is delayed due to coagulation in the stomach, while β-lactoglobulin was emptied throughout the gastric phase, except for UHT-treated milk. The gastric behaviour also had an impact on the lipid and protein content of the emptied chyme. The homogenised samples seemed to release more nutrients at the end of gastric digestion
    • Using the Biocheck.UGent™ scoring tool in Irish farrow-to-finish pig farms: assessing biosecurity and its relation to productive performance

      Rodrigues da Costa, Maria; Gasa, Josep; Calderón Díaz, Julia A; Postma, Merel; Dewulf, Jeroen; McCutcheon, Gerard; Manzanilla, Edgar G; Department of Agriculture Food and the Marine; 14/S/832 (Biomed Central, 2019-03-01)
      Background Biosecurity is one of the main factors affecting disease occurrence and antimicrobial use, and it is associated with performance in pig production. However, the importance of specific measures could vary depending on the (national) context. The aim of this study was to describe the biosecurity status in a cohort of Irish pig farms, to investigate which of those biosecurity aspects are more relevant by using the Biocheck.UGent™ scoring system, and to study the impact of such aspects on farm performance. Results External biosecurity score was high compared to most countries due to the characteristics of the Irish pig sector (i.e. purchasing only semen and breeding gilts on farm). The internal biosecurity score was lower and had greater variability among farms than other EU countries. Using multivariable linear regression, the biosecurity practices explained 8, 23, and 16% of variability in piglet mortality, finisher mortality, and average daily gain, respectively. Three clusters of farms were defined based on their biosecurity scores (0 to 100) using principal components and hierarchical clustering analysis. Scores for clusters 1, 2 and 3 were (mean ± SD) 38 ± 7.6, 61 ± 7.0 and 66 ± 9.8 for internal and 73 ± 5.1, 74 ± 5.3 and 86 ± 4.5 for external biosecurity. Cluster 3 had lower piglet mortality (P = 0.022) and higher average daily gain (P = 0.037) when compared to cluster 2. Conclusions Irish farms follow European tendencies with internal biosecurity posing as the biggest liability. Our results suggest that practices related to the environment and region, feed, water and equipment supply, and the management of the different stages, need to be addressed in lower performing farms to improve productive performance. Further studies on the economic impact of these biosecurity practices including complementary data on herd health, gilt rearing, piglet management, vaccination and feeding strategies are needed.
    • Genome-wide association study of endo-parasite phenotypes using imputed whole-genome sequence data in dairy and beef cattle

      Twomey, Alan J; Berry, Donagh P; Evans, Ross D; Doherty, Michael L; Graham, David A; Purfield, Deirdre C; Department of Agriculture, Food and the Marine; Science Foundation Ireland; 16/RC/3835 (Biomed Central, 2019-04-18)
      Background Quantitative genetic studies suggest the existence of variation at the genome level that affects the ability of cattle to resist to parasitic diseases. The objective of the current study was to identify regions of the bovine genome that are associated with resistance to endo-parasites. Methods Individual cattle records were available for Fasciola hepatica-damaged liver from 18 abattoirs. Deregressed estimated breeding values (EBV) for F. hepatica-damaged liver were generated for genotyped animals with a record for F. hepatica-damaged liver and for genotyped sires with a least one progeny record for F. hepatica-damaged liver; 3702 animals were available. In addition, individual cow records for antibody response to F. hepatica on 6388 genotyped dairy cows, antibody response to Ostertagia ostertagi on 8334 genotyped dairy cows and antibody response to Neospora caninum on 4597 genotyped dairy cows were adjusted for non-genetic effects. Genotypes were imputed to whole-sequence; after edits, 14,190,141 single nucleotide polymorphisms (SNPs) and 16,603,644 SNPs were available for cattle with deregressed EBV for F. hepatica-damaged liver and cows with an antibody response to a parasitic disease, respectively. Association analyses were undertaken using linear regression on one SNP at a time, in which a genomic relationship matrix accounted for the relationships between animals. Results Genomic regions for F. hepatica-damaged liver were located on Bos taurus autosomes (BTA) 1, 8, 11, 16, 17 and 18; each region included at least one SNP with a p value lower than 10−6. Five SNPs were identified as significant (q value < 0.05) for antibody response to N. caninum and were located on BTA21 or 25. For antibody response to F. hepatica and O. ostertagi, six and nine quantitative trait loci (QTL) regions that included at least one SNP with a p value lower than 10−6 were identified, respectively. Gene set enrichment analysis revealed a significant association between functional annotations related to the olfactory system and QTL that were suggestively associated with endo-parasite phenotypes. Conclusions A number of novel genomic regions were suggestively associated with endo-parasite phenotypes across the bovine genome and two genomic regions on BTA21 and 25 were associated with antibody response to N. caninum.
    • Are some teat disinfectant formulations more effective against specific bacteria isolated on teat skin than others?

      Fitzpatrick, Sarah R; Garvey, Mary; Flynn, Jim; Jordan, Kieran; Gleeson, David; Dairy Research Ireland; Teagasc Walsh Fellowship Programme; 2016054 (Biomed Central, 2019-04-25)
      The use of pre- and post-milking teat disinfectants can reduce teat bacterial load and aid in the collection of high-quality milk. The objective of this study was to compare the reduction in bacteria populations on teat skin after the application of different commercial teat disinfectant products. Ten teat disinfectant products were applied to the teats of 10 Holstein–Friesian cows. One cow received one teat disinfectant product at each sampling point before cluster application for milking. A composite swab sample was taken of the 4 teats of each cow before and after teat disinfectant application. Swab samples were placed on three different selective agars to enumerate bacterial counts of staphylococcal, streptococcal and coliforms isolates on teat skin. Staphylococcal isolates were the most prominent bacterial group recovered on teat swabs (49%), followed by streptococcal (36%) and coliform (15%) isolates before the application of disinfectant. The average bacterial reductions on teat skin were shown to be 76%, 73% and 60% for staphylococcal, streptococcal and coliform isolates, respectively. All of the teat disinfectant products tested reduced teat bacterial load for all three bacterial groups. Product 4 containing 0.6% w/w diamine was the most effective against bacterial populations of staphylococcal and streptococcal isolates on teat skin with a reduction of 90% and 94%, respectively. Whereas product 10, which contained 0.5% w/w iodine, resulted in the highest reduction in coliforms on teat skin with a reduction of 91%. Results from this study suggest that specific bacterial population loads on teats can be reduced using different teat disinfectant formulations.
    • Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle

      Johnston, Dayle; Malo Estepa, Irene; Ebhardt, H. Alexander; Crowe, Mark; Diskin, Michael G.; Science Foundation Ireland; 13/IA/2025 (Elsevier, 2018-04-12)
      Current bovine pregnancy detection methods are not reliable until at least day 28 post artificial insemination (AI). The bovine estrous cycle is approximately 21 days; consequently, producers miss an opportunity to rebreed at the next estrous event. Therefore, commercial interest exists for the discovery of novel biomarkers of pregnancy which could reliably detect pregnancy status at or before day 21 of pregnancy. The objective of the present study was to use liquid chromatography tandem mass spectrometry (LC-MS/MS) to perform a global, label-free, proteomics study on (i) milk whey and (ii) extracellular vesicle (EV) enriched milk whey samples, from day 21 of pregnancy, compared with day 21 of the estrous cycle, in order to identify potential protein biomarkers of early pregnancy. The estrous cycles of 10 dairy cows were synchronized, they went through one (control) estrous cycle and these cows were artificially inseminated during the following estrus. These cows were confirmed pregnant by ultrasound scanning. Milk whey samples were collected on day 21 of the estrous cycle and on day 21 post AI. Milk whey samples and EV enriched milk whey samples were analyzed by LC-MS/MS and subsequent analyzes of the label-free quantitative data was performed in MaxQuant and Perseus. Four proteins (APOB, SPADH1, PLIN2 and LPO) were differentially expressed between the proteomes of milk whey from day 21 of pregnancy and day 21 of the estrous cycle (P < 0.05). Ten proteins (PIGR, PGD, QSOX1, MUC1, SRPRA, MD2, GAPDH, FOLR1, GPRC5B and HHIPL2) were differentially expressed between the proteomes of EV enriched milk whey from day 21 of pregnancy and day 21 of the estrous cycle (P < 0.05). These proteins are potential milk whey biomarkers of early pregnancy.
    • Infection exposure, detection and causes of death in perinatal mortalities in Polish dairy herds

      Jawor, Paulina; Król, Dawid; Mee, John F.; Sołtysiak, Zenon; Dzimira, Stanisław; Larska, Magdalena; Stefaniak, Tadeusz; The National Centre for Research and Development; PBS2/A8/20/2013; PBS2/A8/24/2013 (Elsevier, 2017-07-29)
      The objective of this study was to determine the prevalence and types of infections in perinatal mortality (PM) cases from Polish dairy farms and the relevance of the presence of infection to the cause of death. This prospective longitudinal study was carried out on 121 PM and 21 control calves with a gestation of ≥260 days. Six control calves were euthanized and examined using the same protocol as for PM calves. Material was collected over a 20-month period between November 2013 and June 2015. The PM and control calves were collected from 29 to 5 herds, respectively. Blood samples from calves were tested for antibodies to Neospora caninum, glycoprotein B of BoHV-1, BVDV and SBV using ELISAs and Leptospira hardjo and Leptospira pomona with the microscopic agglutination test. Brain and kidney samples from all PM and six euthanized control calves were tested using real time PCR to detect Neospora caninum, pathogenic Leptospira spp., BoHV-1 and SBV; brain was examined histopathologically for detection of N. caninum cysts. Samples from eight inner organs from all PM and six control calves were cultured aerobically, anaerobically and microaerobically. Ear samples from all PM and control calves were tested for BVDV using an antigen ELISA. In total, 21.5% of PM calves were infected (antigen and/or antibody-positive) in utero; none of the control calves were infected. Direct evidence of infection (culture, Ag-ELISA, PCR, histopathology) was detected in 9.1% of PM calves. Gestation length in infected singletons was shorter than in uninfected singletons (274 ± 8 vs. 279 ± 7 days; P < 0.01). The odds ratio for diagnosis of infection in single pregnancies ≤275 days was 3.75 (95% CI:1.2–12.1), (P < 0.05). Infection was the cause of death in 10% of calves. The most common infections detected in these Polish PM calves were parasitic (11.6% of PM cases), viral (7.4%) and bacterial (5%). This study demonstrated that indirect evidence of infection is detected more frequently than direct, coinfection is rare, infection is rarely accompanied by gross lesions and is rarely a cause of death in cases of PM.
    • Removing prophylactic antibiotics from pig feed: how does it affect their performance and health?

      Diana, Alessia; Boyle, Laura A; Leonard, Finola C; Carroll, Ciaran; Sheehan, Eugene; Murphy, Declan; Manzanilla, Edgar G; Teagasc Walsh Fellowship Programme (Biomed Central, 2019-02-26)
      Background Antibiotics (AB) are an important tool to tackle infectious disease in pig farms; however some research indicates that their frequent mis/over-use may contribute to the development of antibiotic resistance and the WHO has declared that this issue should be addressed. Little is known about the long term consequences of withdrawing prophylactic AB from pig feed; hence we aimed to assess its effects on performance and health of pigs from weaning to slaughter. Six batches of 140 pigs each were monitored on a commercial farm through the weaner and finisher stages to slaughter. In-feed antibiotics were not added to the feed for half of the pigs (NOI) and were added in the other half (ABI) within each batch for the whole weaner stage. Individual pigs in both treatments were treated with parenteral administrations if and when detected as ill or lame. Productive performance, parenteral treatments and mortality were recorded on farm and the presence of respiratory disease was recorded at slaughter. Pen was considered the experimental unit. Results ABI pigs showed higher growth (P = 0.018) and feed intake (P = 0.048) than NOI pigs in the first weaner stage but feed efficiency was not affected (NOI = 1.48 vs. ABI = 1.52). Despite an initial reduction in performance, NOI pigs had similar performance in finisher stage (ADG: NOI = 865.4 vs. ABI = 882.2) and minimal effects on health compared to ABI pigs. No difference between treatments was found at the abattoir for the percentage of pigs affected by pneumonia, pleurisy, pleuropneumonia and abscesses (P > 0.05). Mortality rate was not affected by treatment during the weaner stage (P = 0.806) although it tended to be slightly higher in NOI than ABI pigs during the finisher stage (P = 0.099). Parenteral treatments were more frequent in NOI pigs during the weaner stage (P <  0.001) while no difference was recorded during the finisher stage (P = 0.406). Conclusions These data suggest that the removal of prophylactic in-feed antibiotics is possible with only minor reductions in productive performance and health which can be addressed by improved husbandry and use of parenteral antibiotics.
    • Moderate-intensity aerobic and resistance exercise is safe and favorably influences body composition in patients with quiescent Inflammatory Bowel Disease: a randomized controlled cross-over trial

      Cronin, Owen; Barton, Wiley; Moran, Carthage; Sheehan, Donal; Whiston, Ronan; Nugent, Helena; McCarthy, Yvonne; Molloy, Catherine B; O’Sullivan, Orla; Cotter, Paul D; et al. (2019-02-12)
      Background Overweight and metabolic problems now add to the burden of illness in patients with Inflammatory Bowel Disease. We aimed to determine if a program of aerobic and resistance exercise could safely achieve body composition changes in patients with Inflammatory Bowel Disease. Methods A randomized, cross-over trial of eight weeks combined aerobic and resistance training on body composition assessed by Dual Energy X-ray Absorptiometry was performed. Patients in clinical remission and physically inactive with a mean age of 25 ± 6.5 years and Body Mass Index of 28.9 ± 3.8 were recruited from a dedicated Inflammatory Bowel Disease clinic. Serum cytokines were quantified, and microbiota assessed using metagenomic sequencing. Results Improved physical fitness was demonstrated in the exercise group by increases in median estimated VO2max (Baseline: 43.41mls/kg/min; post-intervention: 46.01mls/kg/min; p = 0.03). Improvement in body composition was achieved by the intervention group (n = 13) with a median decrease of 2.1% body fat compared with a non-exercising group (n = 7) (0.1% increase; p = 0.022). Lean tissue mass increased by a median of 1.59 kg and fat mass decreased by a median of 1.52 kg in the exercising group. No patients experienced a deterioration in disease activity scores during the exercise intervention. No clinically significant alterations in the α- and β-diversity of gut microbiota and associated metabolic pathways were evident. Conclusions Moderate-intensity combined aerobic and resistance training is safe in physically unfit patients with quiescent Inflammatory Bowel Disease and can quickly achieve favourable body compositional changes without adverse effects. Trial registration The study was registered at; Trial number: NCT02463916 .
    • Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

      Rafter, Pierce; Gormley, Isobel C; Parnell, Andrew C; Kearney, John F; Berry, Donagh P; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 14/IA/2576; 16/RC/3835 (Biomed Central, 2020-03-04)
      Background The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. The main aim here was to determine if it is possible to impute copy number variants (CNVs) using the flanking single nucleotide polymorphism (SNP) haplotype structure in cattle. While this objective was achieved using high-density genotype panels (i.e., 713,162 SNPs), a secondary objective investigated the concordance of CNVs called with this high-density genotype panel compared to CNVs called from a medium-density panel (i.e., 45,677 SNPs in the present study). This is the first study to compare CNVs called from high-density and medium-density SNP genotypes from the same animals. High (and medium-density) genotypes were available on 991 Holstein-Friesian, 1015 Charolais, and 1394 Limousin bulls. The concordance between CNVs called from the medium-density and high-density genotypes were calculated separately for each animal. A subset of CNVs which were called from the high-density genotypes was selected for imputation. Imputation was carried out separately for each breed using a set of high-density SNPs flanking the midpoint of each CNV. A CNV was deemed to be imputed correctly when the called copy number matched the imputed copy number. Results For 97.0% of CNVs called from the high-density genotypes, the corresponding genomic position on the medium-density of the animal did not contain a called CNV. The average accuracy of imputation for CNV deletions was 0.281, with a standard deviation of 0.286. The average accuracy of imputation of the CNV normal state, i.e. the absence of a CNV, was 0.982 with a standard deviation of 0.022. Two CNV duplications were imputed in the Charolais, a single CNV duplication in the Limousins, and a single CNV duplication in the Holstein-Friesians; in all cases the CNV duplications were incorrectly imputed. Conclusion The vast majority of CNVs called from the high-density genotypes were not detected using the medium-density genotypes. Furthermore, CNVs cannot be accurately predicted from flanking SNP haplotypes, at least based on the imputation algorithms routinely used in cattle, and using the SNPs currently available on the high-density genotype panel.
    • Lactobacillus mucosae DPC 6426 as a bile-modifying and immunomodulatory microbe

      Ryan, Paul M; Stolte, Ellen H; London, Lis E E; Wells, Jerry M; Long, Sarah L; Joyce, Susan A; Gahan, Cormac G M; Fitzgerald, Gerald F; Ross, R. P; Caplice, Noel M; et al. (Biomed Central, 2019-02-08)
      Background Lactobacillus mucosae DPC 6426 has previously demonstrated potentially cardio-protective properties, in the form of dyslipidaemia and hypercholesterolemia correction in an apolipoprotein-E deficient mouse model. This study aims to characterise the manner in which this microbe may modulate host bile pool composition and immune response, in the context of cardiovascular disease. Lactobacillus mucosae DPC 6426 was assessed for bile salt hydrolase activity and specificity. The microbe was compared against several other enteric strains of the same species, as well as a confirmed bile salt hydrolase-active strain, Lactobacillus reuteri APC 2587. Results Quantitative bile salt hydrolase assays revealed that enzymatic extracts from Lactobacillus reuteri APC 2587 and Lactobacillus mucosae DPC 6426 demonstrate the greatest activity in vitro. Bile acid profiling of porcine and murine bile following incubation with Lactobacillus mucosae DPC 6426 confirmed a preference for hydrolysis of glyco-conjugated bile acids. In addition, the purified exopolysaccharide and secretome of Lactobacillus mucosae DPC 6426 were investigated for immunomodulatory capabilities using RAW264.7 macrophages. Gene expression data revealed that both fractions stimulated increases in interleukin-6 and interleukin-10 gene transcription in the murine macrophages, while the entire secretome was necessary to increase CD206 transcription. Moreover, the exopolysaccharide elicited a dose-dependent increase in nitric oxide and interleukin-10 production from RAW264.7 macrophages, concurrent with increased tumour necrosis factor-α secretion at all doses. Conclusions This study indicates that Lactobacillus mucosae DPC 6426 modulates both bile pool composition and immune system tone in a manner which may contribute significantly to the previously identified cardio-protective phenotype.
    • Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa

      Zhou, Xingya; Yang, Bo; Stanton, Catherine; Ross, R. Paul; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; Fundamental Research Funds for the Central Universities; National Firs-Class Discipline Program of Food Science and Technology; et al. (Springer Science and Business Media LLC, 2020-02-03)
      Background Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis. Results In this study, to explore the genomic diversity and mine potential probiotic characteristics of L. gasseri, 92 strains of L. gasseri were isolated from Chinese human feces and identified based on 16 s rDNA sequencing, after draft genomes sequencing, further average nucleotide identity (ANI) value and phylogenetic analysis reclassified them as L. paragasseri (n = 79) and L. gasseri (n = 13), respectively. Their pan/core-genomes were determined, revealing that L. paragasseri had an open pan-genome. Comparative analysis was carried out to identify genetic features, and the results indicated that 39 strains of L. paragasseri harboured Type II-A CRISPR-Cas system while 12 strains of L. gasseri contained Type I-E and II-A CRISPR-Cas systems. Bacteriocin operons and the number of carbohydrate-active enzymes were significantly different between the two species. Conclusions This is the first time to study pan/core-genome of L. gasseri and L. paragasseri, and compare their genetic diversity, and all the results provided better understating on genetics of the two species.
    • Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

      Doyle, Jennifer L; Berry, Donagh P; Veerkamp, Roel F; Carthy, Tara R; Evans, Ross D; Walsh, Siobhán W; Purfield, Deirdre C; Science Foundation Ireland; SF 14/IA/2576; 16/RC/3835 (2020-01-30)
      Background Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variability may contribute to differences in the overall value of the carcass since primal cuts vary greatly in price; such variability may also hinder successful genome-based association studies. Therefore, the objective of our study was to identify genomic regions that are associated with five muscularity linear type traits and to determine if these significant regions are common across five different breeds. Analyses were carried out using linear mixed models on imputed whole-genome sequence data in each of the five breeds, separately. Then, the results of the within-breed analyses were used to conduct an across-breed meta-analysis per trait. Results We identified many quantitative trait loci (QTL) that are located across the whole genome and associated with each trait in each breed. The only commonality among the breeds and traits was a large-effect pleiotropic QTL on BTA2 that contained the MSTN gene, which was associated with all traits in the Charolais and Limousin breeds. Other plausible candidate genes were identified for muscularity traits including PDE1A, PPP1R1C and multiple collagen and HOXD genes. In addition, associated (gene ontology) GO terms and KEGG pathways tended to differ between breeds and between traits especially in the numerically smaller populations of Angus, Hereford, and Simmental breeds. Most of the SNPs that were associated with any of the traits were intergenic or intronic SNPs located within regulatory regions of the genome. Conclusions The commonality between the Charolais and Limousin breeds indicates that the genetic architecture of the muscularity traits may be similar in these breeds due to their similar origins. Conversely, there were vast differences in the QTL associated with muscularity in Angus, Hereford, and Simmental. Knowledge of these differences in genetic architecture between breeds is useful to develop accurate genomic prediction equations that can operate effectively across breeds. Overall, the associated QTL differed according to trait, which suggests that breeding for a morphologically different (e.g. longer and wider versus shorter and smaller) more efficient animal may become possible in the future.
    • Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism

      Golubeva, Anna V.; Joyce, Susan A.; Moloney, Gerard; Burokas, Aurelijus; Sherwin, Eoin; Arboleya, Silvia; Flynn, Ian; Khochanskiy, Dmitry; Moya-Pérez, Angela; Peterson, Veronica; et al. (Elsevier, 2017-09-21)
      Autism spectrum disorder (ASD) is one of the most prevalent neurodevelopmental conditions worldwide. There is growing awareness that ASD is highly comorbid with gastrointestinal distress and altered intestinal microbiome, and that host-microbiome interactions may contribute to the disease symptoms. However, the paucity of knowledge on gut-brain axis signaling in autism constitutes an obstacle to the development of precision microbiota-based therapeutics in ASD. To this end, we explored the interactions between intestinal microbiota, gut physiology and social behavior in a BTBR T+ Itpr3tf/J mouse model of ASD. Here we show that a reduction in the relative abundance of very particular bacterial taxa in the BTBR gut – namely, bile-metabolizing Bifidobacterium and Blautia species, - is associated with deficient bile acid and tryptophan metabolism in the intestine, marked gastrointestinal dysfunction, as well as impaired social interactions in BTBR mice. Together these data support the concept of targeted manipulation of the gut microbiota for reversing gastrointestinal and behavioral symptomatology in ASD, and offer specific plausible targets in this endeavor.
    • Effect of phytase, carbohydrase, and protease addition to a wheat distillers dried grains with solubles and rapeseed based diet on in vitro ileal digestibility, growth, and bone mineral density of grower-finisher pigs

      Torres-Pitarch, Alberto; McCormack, Ursula M.; Beattie, Violet; Magowan, Elizabeth; Gardiner, Gillian; Pérez-Vendrell, Anna; Torrallardona, David; O'Doherty, John; Lawlor, Peadar G; European Union; et al. (Elsevier, 2018-07-07)
      The use of rapeseed meal (RSM) and wheat distillers dried grains with solubles (wDDGS) in pig diets is increasing and dietary supplementation with exogenous enzymes has been suggested as means of improving feed efficiency in pigs. The objective of this experiment was to examine the effect of phytase (Phy), a xylanase and β-glucanase complex (XB), protease (Prot) and their various combinations when included in a wDDGS- and RSM-based diet fed to grower-finisher pigs. As the P- and Ca- sparing effect of Phy is well proven, the objective was to examine the additional effects of Phy beyond its P- and Ca-sparing effects. A total of 144 pigs with an initial live weight of 40.1 ± 2.0 kg were assigned to 8 treatments with 9 pens (4 female and 5 male pens) per treatment and 2 females or 2 males per pen. The basal diet was formulated to contain 96 and 200 g/kg of RSM and wDDGS, respectively. The basal diet was supplemented with Phy (0 or 100 mg/kg), XB (0 or 100 mg/kg), and Prot (0 or 200 mg/kg) in a 2 × 2 × 2 factorial arrangement of treatments. Experimental diets were fed for 76 d. Average daily gain (ADG) and average daily feed intake (ADFI) were recorded, and gain to feed (G:F) was calculated. Carcass quality variables were measured at slaughter and the left forelimb of pigs fed the unsupplemented, the Phy supplemented and the Phy + Prot supplemented diets were removed to determine bone mineral density in the third metacarpal. The inclusion of Phy, XB and Prot in the diets increased in vitro ileal digestibility of dry matter and organic matter (P < 0.05). A tendency towards a 3-way interaction among Phy, XB and Prot was observed for ADG (P = 0.06) and G:F (P = 0.06). The 2-way interactions and main effects did not reveal any improvement for any variable measured in vivo in response to dietary enzyme supplementation. Bone mineral density was not different for pigs fed the unsupplemented, the Phy supplemented and the Phy + Prot supplemented diets. In conclusion, the in vitro ileal digestibility improvements observed were not always reflected in improvements in pig growth, feed efficiency or both. The efficacy of Phy was not reduced when supplemented in combination with Prot, as ADG, G:F, carcass quality and bone mineralization were unchanged.
    • Effect of floor type on performance, lying time and dirt scores of finishing beef cattle: A meta-analysis

      Keane, Michael P.; McGee, Mark; O'Riordan, Edward G.; Kelly, Alan K.; Earley, Bernadette; Teagasc Walsh Fellowship Programme; WF2013073 (Elsevier BV, 2018-03-29)
      Data from individual studies evaluating the effect of housing systems on performance, lying time and dirt scores of finishing beef cattle are conflicting. The objective of this study was to collate the data from previous animal housing studies and quantify, through meta-analysis, the effect of floor type on animal performance, lying time and dirt scores. From 38 peer-reviewed articles, published between 1969 and 2017, 18 were determined to be eligible for meta-analysis. Papers were included in the study if they contained information on the effect of floor surface on animal performance (average daily liveweight gain (ADG), feed conversion ratio (FCR) and carcass weight), lying behaviour or animal cleanliness. There was no difference (P > 0.10) in ADG, FCR or carcass weight between concrete slatted floors (CSF) and CSF overlaid with rubber mats (RM). Using RM had no effect (P > 0.10) on lying duration or dirt scores of cattle. There was no difference (P > 0.10) in the ADG, FCR, carcass weight, lying duration or cleanliness of cattle housed on CSF or straw bedding. It was concluded that using RM or straw instead of CSF had no effect on performance, lying time or dirt scores.
    • Investigating the role of stocking rate and prolificacy potential on profitability of grass based sheep production systems

      Bohan, A.; Creighton, P.; Boland, T.M.; Shalloo, Laurence; Earle, Elizabeth; McHugh, Noirin; Department of Agriculture, Food and the Marine; 15/S/696 (Elsevier BV, 2018-02-21)
      The objective of this study was to simulate and compare the profitability of a grass based sheep production system under three stocking rates and two prolificacy rates. Analysis was conducted using the Teagasc Lamb Production Model (TLPM), a stochastic budgetary simulation model of a sheep farm. Experimental data from the Teagasc Athenry Research Demonstration Flock was used to parameterise the model at three stocking rates (10, 12 and 14 ewes/ha) and two prolificacy potentials (1.5 and 1.8 lambs weaned per ewe joined to the ram). The TLPM assessed the performance of the key factors affecting profitability and was also used to evaluate the spread in profitability associated with some stochastic variables included in the analysis. The number of lambs weaned per hectare increased with stocking rate and prolificacy potential from 16 lambs/ha to 27 lambs/ha resulting in carcass weight produced per hectare ranging from 272 kg/ha to 474 kg/ha. Increasing stocking rates resulted in lower individual lamb performance from grass and milk, thereby increasing the proportion of lambs which required concentrate for finishing, which resulted in higher input costs on a per animal basis. As the number of lambs weaned per hectare increased, net profit increased from €361/ha to €802/ha. Across all stocking rates, increasing weaning rate from 1.5 to 1.8 lambs weaned per ewe joined increased net profit, on average, by €336/ha. Increasing stocking rate, at 1.5 lambs weaned per ewe joined, increased net profit on average by €15/ha while increasing stocking rate, at 1.8 lambs weaned per ewe joined increased net profit on average by €87/ha. Risk analysis showed that across all stocking rates the high prolificacy scenarios achieved greater profits across the variation in input variables. Results from this study indicate that lambs weaned per hectare linked with grass growth and utilisations are the key drivers of profitability on Irish grass based sheep production systems.