Now showing items 1-20 of 2099

    • AGMEMOD Outlook for Agricultural and Food Markets in EU Member States 2018-2030

      Salomon, Petra; Banse, Martin; Donellan, Trevor; Hass, Marlen; Jongeneel, Roel; Laquai, Verena; van Leeuwen, Myrna; Reziti, Ioanna; Salputra, Guna; Zirngibl, Max-Emanuel; et al. (2020-07-31)
      Policy, administration and industry need medium-term projections of the expected developments in the agri-food markets for their decision-making processes. The EU Commission presents such projections for the EU as a whole in December of each year. Those projections and their assumptions regarding policy and macroeconomic developments are depicted to the level of individual EU Member States with the exception of Luxembourg, which is included in the figures of Belgium, by applying the partial equilibrium model AGMEMOD. The working paper briefly describes the approach to establish projections for the EU Member States. The projections cover the markets of main agricultural products, in particular for cereals and oilseeds (rapeseed and sunflower seed), livestock (cattle, pigs, goats and sheep), meat (beef, pork, and poultry), milk and dairy products (drinking milk, butter, cheese, skimmed milk powder, whole milk and semiskimmed milk powder). The outcomes comprise items like areas, livestock numbers, yields, production, trade and use, as well as prices. The individual projection results are displayed in tables.
    • Deltamethrin Residues in Milk and Cheese of Lactating Goats (Capra hircus)

      Marrone, Raffaele; Ramkumar, Abilasha; Smaldone, Giorgio; Rufrano, Domenico; Chirollo, Claudia; Veneziano, Vincenzo; Danaher, Martin; Anastasio, Aniello; University of Naples Federico II (MDPI AG, 2019-01-31)
      The distribution of pyrethroid insecticide deltamethrin (DLM) in goat milk and cheese (caciotta) following pour-on administration at the sheep dosage (DLMS-10 mL/60 kg body weight) and double dosage (DLMD-20 mL/60 kg body weight) was studied. DLM concentrations were measured in milk collected from study animals (No.14) before treatment and at 2, 4, 8, 12, 16, 24, 30, 36, 48, 56, until 168 h (7 days) post treatment and in caciotta cheese at 12 and 24 h post treatment. At both dosages, the maximum level of DLM residues in goat milk and cheese was below the maximum residue limit (MRL) of 20 μg kg−1 established for bovine milk (EU No 37/2010) at all time points. However, in terms of public health, higher DLM residues in cheese show that further specific studies should be performed on double dosage efficacy and pharmacokinetic and pharmacodynamics properties of ectoparasites in lactating goats.
    • Residual feed intake phenotype and gender affect the expression of key genes of the lipogenesis pathway in subcutaneous adipose tissue of beef cattle

      McKenna, Clare; Porter, Richard K.; Keogh, Kate A.; Waters, Sinead M.; McGee, Mark; Kenny, David A.; Teagasc Walsh Fellowship Programme; RMIS: 6092 (Springer Science and Business Media LLC, 2018-09-20)
      Background Feed accounts for up to 75% of costs in beef production systems, thus any improvement in feed efficiency (FE) will benefit the profitability of this enterprise. Residual feed intake (RFI) is a measure of FE that is independent of level of production. Adipose tissue (AT) is a major endocrine organ and the primary metabolic energy reservoir. It modulates a variety of processes related to FE such as lipid metabolism and glucose homeostasis and thus measures of inter-animal variation in adiposity are frequently included in the calculation of the RFI index. The aim of this study was to determine the effect of phenotypic RFI status and gender on the expression of key candidate genes related to processes involved in energy metabolism within AT. Dry matter intake (DMI) and average daily gain (ADG) were measured over a period of 70 d for 52 purebred Simmental heifers (n = 24) and bulls (n = 28) with an initial BW±SD of 372±39.6 kg and 387±50.6 kg, respectively. Residual feed intake was calculated and animals were ranked within gender by RFI into high (inefficient; n = 9 heifers and n = 8 bulls) and low (efficient; n = 9 heifers and n = 8 bulls) groups. Results Average daily gain ±SD and daily DMI ±SD for heifers and bulls were 1.2±0.4 kg and 9.1±0.5 kg, and 1.8±0.3 kg and 9.5±1 kg respectively. High RFI heifers and bulls consumed 10% and 15% more (P < 0.05) than their low RFI counterparts, respectively. Heifers had a higher expression of all genes measured than bulls (P < 0.05). A gender × RFI interaction was detected for HMGCS2(P < 0.05) in which high RFI bulls tended to have lower expression of HMGCS2 than low RFI bulls (P < 0.1), whereas high RFI heifers had higher expression than low RFI heifers (P < 0.05) and high RFI bulls (P < 0.05). SLC2A4 expression was consistently higher in subcutaneous AT of low RFI animals across gender. Conclusion The findings of this study indicate that low RFI cattle exhibit upregulation of the molecular mechanisms governing glucose metabolism in adipose tissue, in particular, glucose clearance. The decreased expression of SLC2A4 in the inefficient cattle may result in less efficient glucose metabolism in these animals. We conclude that SLC2A4 may be a potential biomarker for RFI in cattle.
    • Human skin microbiota is a rich source of bacteriocin-producing staphylococci that kill human pathogens

      O'Sullivan, Julie N; Rea, Mary C; O'Connor, Paula M; Hill, Colin; Ross, R Paul; Science Foundation Ireland; SFI/12/RC/2273 (Oxford University Press (OUP), 2018-12-24)
      The demand for novel antimicrobial therapies due to the threat posed by antimicrobial resistance has resulted in a growing interest in the protective role of our skin bacteria and the importance of competition among bacteria on the skin. A survey of the cultivable bacteria on human skin was undertaken to identify the capacity of the skin microbiota to produce bacteriocins with activity against skin pathogens. Twenty-one bacteriocins produced by bacteria isolated from seven sites on the human body of each subject exhibited inhibition spectra ranging from broad to narrow range, inhibiting many Gram-positive bacteria, including opportunistic skin pathogens such as Propionibacterium acnes (recently renamed Cutibacterium acnes), Staphylococcus epidermidis and methicillin-resistant Staphylococcus aureus (MRSA). Sequencing indicated that the antimicrobial-producing isolates were predominately species/strains of the Staphylococcus genus. Colony mass spectrometry revealed peptide masses that do not correspond to known bacteriocins. In an era where antibiotic resistance is of major concern, the inhibitory effect of novel bacteriocins from the bacteria of skin origin demonstrates the antimicrobial potential that could be harnessed from within the human skin microbiota.
    • Equivalence analysis to support environmental safety assessment: Using nontarget organism count data from field trials with cisgenically modified potato

      van der Voet, Hilko; Goedhart, Paul W.; Lazebnik, Jenny; Kessel, Geert J. T.; Mullins, Ewen; van Loon, Joop J. A.; Arpaia, Salvatore; European Union; 289706 (Wiley, 2019-02-14)
      This paper considers the statistical analysis of entomological count data from field experiments with genetically modified (GM) plants. Such trials are carried out to assess environmental safety. Potential effects on nontarget organisms (NTOs), as indicators of biodiversity, are investigated. The European Food Safety Authority (EFSA) gives broad guidance on the environmental risk assessment (ERA) of GM plants. Field experiments must contain suitable comparator crops as a benchmark for the assessment of designated endpoints. In this paper, a detailed protocol is proposed to perform data analysis for the purpose of assessing environmental safety. The protocol includes the specification of a list of endpoints and their hierarchical relations, the specification of intended levels of data analysis, and the specification of provisional limits of concern to decide on the need for further investigation. The protocol emphasizes a graphical representation of estimates and confidence intervals for the ratio of mean abundances for the GM plant and its comparator crop. Interpretation relies mainly on equivalence testing in which confidence intervals are compared with the limits of concern. The proposed methodology is illustrated with entomological count data resulting from multiyear, multilocation field trials. A cisgenically modified potato line (with enhanced resistance to late blight disease) was compared to the original conventional potato variety in the Netherlands and Ireland in two successive years (2013, 2014). It is shown that the protocol encompasses alternative schemes for safety assessment resulting from different research questions and/or expert choices. Graphical displays of equivalence testing at several hierarchical levels and their interpretation are presented for one of these schemes. The proposed approaches should be of help in the ERA of GM or other novel plants.
    • Variance components for bovine tuberculosis infection and multi-breed genome-wide association analysis using imputed whole genome sequence data

      Ring, S. C.; Purfield, D. C.; Good, M.; Breslin, P.; Ryan, E.; Blom, A.; Evans, R. D.; Doherty, M. L.; Bradley, D. G.; Berry, D. P.; et al. (Public Library of Science (PLoS), 2019-02-14)
      Bovine tuberculosis (bTB) is an infectious disease of cattle generally caused by Mycobacterium bovis, a bacterium that can elicit disease humans. Since the 1950s, the objective of the national bTB eradication program in Republic of Ireland was the biological extinction of bTB; that purpose has yet to be achieved. Objectives of the present study were to develop the statistical methodology and variance components to undertake routine genetic evaluations for resistance to bTB; also of interest was the detection of regions of the bovine genome putatively associated with bTB infection in dairy and beef breeds. The novelty of the present study, in terms of research on bTB infection, was the use of beef breeds in the genome-wide association and the utilization of imputed whole genome sequence data. Phenotypic bTB data on 781,270 animals together with imputed whole genome sequence data on 7,346 of these animals’ sires were available. Linear mixed models were used to quantify variance components for bTB and EBVs were validated. Within-breed and multi-breed genome-wide associations were undertaken using a single-SNP regression approach. The estimated genetic standard deviation (0.09), heritability (0.12), and repeatability (0.30) substantiate that genetic selection help to eradicate bTB. The multi-breed genome-wide association analysis identified 38 SNPs and 64 QTL regions associated with bTB infection; two QTL regions (both on BTA23) identified in the multi-breed analysis overlapped with the within-breed analyses of Charolais, Limousin, and Holstein-Friesian. Results from the association analysis, coupled with previous studies, suggest bTB is controlled by an infinitely large number of loci, each having a small effect. The methodology and results from the present study will be used to develop national genetic evaluations for bTB in the Republic of Ireland. In addition, results can also be used to help uncover the biological architecture underlying resistance to bTB infection in cattle.
    • Complete Genome Sequence of Mannheimia varigena Isolated from Bovine Milk

      McCabe, Matthew S.; Esnault, Gaelle; Murray, Gerard; Earley, Bernadette; Cormican, Paul; Department of Agriculture, Food and the Marine; 11/S/131 (American Society for Microbiology, 2019-02-21)
      Mannheimia varigena is a pathogen of cattle that has been isolated from diseased lung and udder. There are currently complete genome sequences for 4 M. varigena isolates, all from lungs of cattle in the United States. We report a complete genome sequence of M. varigena isolated from bovine milk in Ireland.
    • Enrichment and Assessment of the Contributions of the Major Polyphenols to the Total Antioxidant Activity of Onion Extracts: A Fractionation by Flash Chromatography Approach

      Hossain, Mohammad; Lebelle, Justine; Birsan, Rares; Rai, Dilip; Department of Agriculture, Food and the Marine; FIRM 06/NITAFRC/6 (MDPI AG, 2018-11-27)
      The present study extensively fractionated crude red onion extract in order to identify the polyphenols which contributed most in the total antioxidant capacity of the onion extract using a flash chromatography system. The flash separations produced 70 fractions which were tested for their total phenol content, total flavonoid content, and antioxidant capacities as measured by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP) assays. Out of these 70 fractions, four fractions which were representatives of the four major peaks of the flash chromatograms, were further analysed for their constituent polyphenols using liquid chromatography tandem mass spectrometry (LC-MS/MS). The main contributor of onion antioxidant capacity is quercetin glycoside followed by quercetin aglycone although quercetin aglycone had higher antioxidant capacity than its glycosidic counterparts. High abundance of quercetin glycosides such as quercetin-3,4′-diglucoside and quercetin-4′-glucoside had compensated for their relatively low antioxidant capacities. A Higher degree of glycosylation resulted in lower antioxidant capacity. The fractionation approach also contributed in enrichment of the onion antioxidant polyphenols. A >9 folds enrichment was possible by discarding the early fractions (fractions 1–15) which contained the main bulk of the extracts, predominantly sugars.
    • Factors Influencing Farmer Willingness to Reduce Aggression between Pigs

      Peden, Rachel; Akaichi, Faical; Camerlink, Irene; Boyle, Laura; Turner, Simon; Scotland’s Rural College (SRUC) (MDPI AG, 2018-12-22)
      Aggression between pigs remains an important animal welfare issue despite several solutions existing. Uptake of livestock welfare research relies on various stakeholders being willing to recommend or adopt changes to farm structure or management (e.g., veterinarians, researchers, farmers). This survey provides insight into the attitudes and practices of 122 UK and Irish pig farmers regarding aggression between growing pigs. Our aim was to understand why mitigation strategies are not adequately implemented. The majority of farmers mixed pigs at least once during production and had tried at least one mitigation strategy in the past. Farmers expressed limited willingness to implement strategies in the future, and a structural equation model revealed that this was directly influenced by their beliefs about the outcome of controlling aggression, and their perception of their ability to implement the necessary changes. Willingness was indirectly influenced by their perceptions of aggression as a problem and views of relevant stakeholder groups. Veterinarians had the greatest impact on farmer behavior. We recommend that researchers test research findings in practice, calculate cost-benefits of implementation, and transfer knowledge through various sources. This study showed that structural equation modeling is a valuable tool to understand farmer behavior regarding specific and entrenched animal welfare issues.
    • Multi-Stakeholder Focus Groups on Potential for Meat Inspection Data to Inform Management of Pig Health and Welfare on Farm

      van Staaveren, Nienke; Doyle, Bernadette; Hanlon, Alison; Boyle, Laura; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; 11/S/107 (MDPI AG, 2019-02-19)
      Meat inspection (MI) findings can act as a valuable source of information on pig health and welfare. The PIG WELFare INDicators (PIGWELFIND) project (Research Stimulus Fund 11/S/107) was developed to progress the development of ante and post mortem MI as a pig health and welfare diagnostic tool in Ireland. Three multi-stakeholder focus groups were organized to explore areas of conflict and agreement between stakeholders’ vision for including pig health and welfare indicators in MI and on how to achieve this vision. Each focus group consisted of eight stakeholders: pig producers, Teagasc pig advisors, pig processors, veterinarians involved in MI, private veterinary practitioners, and personnel with backgrounds in general animal health and welfare and food safety policy. In general, stakeholders expressed positive attitudes towards the use of MI data to inform pig health and welfare when standardization of recording and feedback is improved, and the MI system provides real-time benchmarking possibilities. Most emphasis was placed on health indicators as a first priority, while it was felt that welfare-related indicators could be included after practical barriers had been addressed (i.e., line speed/feasibility, standardization and training of meat inspectors, data ownership). Recommendations are made to further progress the development of MI as a pig health and welfare diagnostic tool and address some of these barriers.
    • Relating growth potential and biofilm formation of Shigatoxigenic Escherichia coli to in planta colonisation and the metabolome of ready- to-eat crops

      Merget, Bernhard; Forbes, Ken J; Brennan, Fiona; McAteer, Sean P; Shepherd, Tom; Strachan, Norval J; Holden, Nicola; FSA; Scottish Rural & Environment Science & Analytical Services Division; FS101056 (Cold Spring Harbor Laboratory, 2019-01-17)
      Contamination of fresh produce with pathogenic Escherichia coli, including Shigatoxigenic E. coli (STEC), represents a serious risk to human health. Colonisation is governed by multiple bacterial and plant factors that can impact on the probability and suitability of bacterial growth. Thus, we aimed to determine whether the growth potential of STEC for plants associated with foodborne outbreaks (two leafy vegetables and two sprouted seed species), is predictive for colonisation of living plants as assessed from growth kinetics and biofilm formation in plant extracts. Fitness of STEC was compared to environmental E. coli, at temperatures relevant to plant growth. Growth kinetics in plant extracts varied in a plant-dependent and isolate-dependent manner for all isolates, with spinach leaf lysates supporting the fastest rates of growth. Spinach extracts also supported the highest levels of biofilm formation. Saccharides were identified as the major driver of bacterial growth, although no single metabolite could be correlated with growth kinetics. The highest level of in planta colonisation occurred on alfalfa sprouts, though internalisation was 10-times more prevalent in the leafy vegetables than in sprouted seeds. Marked differences in in planta growth meant that growth potential could only be inferred for STEC for sprouted seeds. In contrast, biofilm formation in extracts related to spinach colonisation. Overall, the capacity of E. coli to colonise, grow and internalise within plants or plant-derived matrices were influenced by the isolate type, plant species, plant tissue type and temperature, complicating any straight-forward relationship between in vitro and in planta behaviours. Importance Fresh produce is an important vehicle for STEC transmission and experimental evidence shows that STEC can colonise plants as secondary hosts, but differences in the capacity to colonise occur between different plant species and tissues. Therefore, an understanding of the impact of these plant factors have on the ability of STEC to grow and establish is required for food safety considerations and risk assessment. Here, we determined whether growth and the ability of STEC to form biofilms in plants extracts could be related to specific plant metabolites or could predict the ability of the bacteria to colonise living plants. Growth rates for sprouted seeds (alfalfa and fenugreek) exhibited a positive relationship between plant extracts and living plants, but not for leafy vegetables (lettuce and spinach). Therefore, the detailed variations at the level of the bacterial isolate, plant species and tissue type all need to be considered in risk assessment.
    • The impact of cattle dung pats on earthworm distribution in grazed pastures

      Bacher, M. G.; Fenton, O.; Bondi, G.; Creamer, R. E.; Karmarkar, M.; Schmidt, O.; Department of Agriculture, Food and the Marine; 13/S/468 (Springer Science and Business Media LLC, 2018-12-19)
      Background Grazed grassland management regimes can have various effects on soil fauna. For example, effects on earthworms can be negative through compaction induced by grazing animals, or positive mediated by increases in sward productivity and cattle dung pats providing a food source. Knowledge gaps exist in relation to the behaviour of different earthworm species i.e. their movement towards and aggregation under dung pats, the legacy effects of pats and the spatial area of recruitment. The present study addressed these knowledge gaps in field experiments, over 2 years, using natural and simulated dung pats on two permanent, intensively grazed pastures in Ireland. Results Dung pats strongly affected spatial earthworm distribution, with up to four times more earthworms aggregating beneath pats, than in the control locations away from pats. In these earthworm communities comprising 11 species, temporally different aggregation and dispersal patterns were observed, including absence of individual species from control locations, but no clear successional responses. Epigeic species in general, but also certain species of the anecic and endogeic groups were aggregating under dung. Sampling after complete dung pat disappearance (27 weeks after application) suggested an absence of a dung pat legacy effect on earthworm communities. Based on species distributions, the maximum size of the recruitment area from which earthworms moved to pats was estimated to be 3.8 m2 per dung pat. Since actual grazing over 6 weeks would result in the deposition of about 300 dung pats per ha, it is estimated that a surface area of 1140 m2 or about 11% of the total grazing area can be influenced by dung pats in a given grazing period. Conclusions This study showed that the presence of dung pats in pastures creates temporary hot spots in spatial earthworm species distribution, which changes over time. The findings highlight the importance of considering dung pats, temporally and spatially, when sampling earthworms in grazed pastures. Published comparisons of grazed and cut grasslands probably reached incorrect conclusions by ignoring or deliberately avoiding dung pats. Furthermore, the observed intense aggregation of earthworms beneath dung pats suggests that earthworm functions need to be assessed separately at these hot spots.
    • Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.)

      Knorst, Verena; Byrne, Stephen; Yates, Steven; Asp, Torben; Widmer, Franco; Studer, Bruno; Kölliker, Roland; Swiss National Science Foundation; 31003A_138358 (Springer Science and Business Media LLC, 2018-11-30)
      Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grass species in temperate regions. Its yield, quality and persistency can significantly be reduced by bacterial wilt, a serious disease caused by Xanthomonas translucens pv. graminis. Although a major QTL for bacterial wilt resistance has previously been reported, detailed knowledge on underlying genes and DNA markers to allow for efficient resistance breeding strategies is currently not available. We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F1 individuals was pooled and sequenced using the Illumina HiSeq 2000 platform. Allele frequencies of 18 × 106 single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP™ markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance. This study highlights the power of pooled DNA sequencing to efficiently target binary traits in biparental mapping populations. It delivers genome sequence data, SNP markers and potential candidate genes which will allow to implement marker-assisted strategies to fix bacterial wilt resistance in outcrossing breeding populations of Italian ryegrass.
    • Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses

      Della Bartola, Michele; Byrne, Stephen; Mullins, Ewen; Department of Agriculture, Food and the Marine; 15/S/618 SCOPE (MDPI AG, 2020-04-23)
      Potato virus Y (PVY) is the most economically important virus infecting cultivated potato (Solanum tuberosum L.). Accurate diagnosis is crucial to regulate the trade of tubers and for the sanitary selection of plant material for propagation. However, high genetic diversity of PVY represents a challenge for the detection and classification of isolates. Here, the diversity of Irish PVY isolates from a germplasm collection and commercial sites was investigated using conventional molecular and serological techniques. Recombinant PVY isolates were prevalent, with PVYNTNa being the predominant genotype. In addition, we evaluated Nanopore sequencing to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, PLRV) and five PVY genotypes in a subset of eight potato plants. De novo assembly of Nanopore sequencing reads produced single contigs covering greater than 90% of the viral genome and sharing greater than 99.5% identity to the consensus sequences obtained with Illumina sequencing. Interestingly, single near full genome contigs were obtained for different isolates of PVY co-infecting the same plant. Mapping reads to available reference viral genomes enabled us to generate near complete genome sequences sharing greater than 99.90% identity to the Illumina-derived consensus. This is the first report describing the use of Oxford Nanopore’s MinION to detect and genotype potato viruses. We reconstructed the genome of PVY and other RNA viruses; indicating the technologies potential for virus detection in potato production systems, and for the study of genetic diversity of highly heterogeneous viruses such as PVY.
    • Effect of water-to-feed ratio on feed disappearance, growth rate, feed efficiency, and carcass traits in growing-finishing pigs

      O’Meara, Fiona M; Gardiner, Gillian E; O’Doherty, John V; Lawlor, Peadar G; Teagasc Walsh Scholarship Programme (Oxford University Press (OUP), 2020-04-03)
      The optimum proportion of water for preparing liquid feed to maximize growth and optimize feed efficiency (FE) in growing-finishing pigs is not known. The aim of the current study was, using an automatic short-trough sensor liquid feeding system, to identify the water-to-feed ratio at which growth was maximized and feed was most efficiently converted to live-weight. Two experiments were conducted in which four commercially used water-to-feed ratios were fed: 2.4:1, 3.0:1, 3.5:1, and 4.1:1 on a dry matter (DM) basis (the equivalent of 2:1, 2.5:1, 3.0:1, and 3.5:1 on a fresh matter basis). Each experiment comprised 216 pigs, penned in groups of 6 same sex (entire male and female) pigs/pen with a total of 9 pen replicates per treatment. The first experiment lasted 62 days (from 40.6 to 102.2 kg at slaughter) and the second experiment was for 76 days (from 31.8 to 119.6 kg at slaughter). Overall, in Exp. 1, FE was 0.421, 0.420, 0.453, and 0.448 (s.e. 0.0081 g/g; P < 0.01) for pigs fed at 2.4:1, 3.0:1, 3.5:1, and 4.1:1, respectively. Overall, in Exp. 2, average daily gain was 1,233, 1,206, 1,211, and 1,177 (s.e. 12.7 g/day; P < 0.05) for pigs fed at 2.4:1, 3.0:1, 3.5:1, and 4.1:1, respectively. At slaughter, in Exp. 1, dressing percentage was 76.7, 76.6, 76.7, and 75.8 (s.e. 0.17%; P < 0.01) for 2.4:1, 3.0:1, 3.5:1, and 4.1:1, respectively. There were no differences between treatment groups for DM, organic matter, nitrogen, gross energy, or ash digestibilities. These findings indicate that liquid feeding a diet prepared at a water-to-feed ratio of 3.5:1 maximizes FE of growing-finishing pigs without negatively affecting dressing percentage. Therefore, preparing liquid feed for growing-finishing pigs at a water-to-feed ratio of 3.5:1 DM is our recommendation for a short-trough liquid feeding system.
    • Bifidobacterium longum subsp. infantis ATCC 15697 and Goat Milk Oligosaccharides Show Synergism In Vitro as Anti-Infectives against Campylobacter jejuni

      Quinn, Erinn M.; Slattery, Helen; Walsh, Dan; Joshi, Lokesh; Hickey, Rita M.; Teagasc Walsh Fellowship Programme (MDPI AG, 2020-03-17)
      Bifidobacteria are known to inhibit, compete with and displace the adhesion of pathogens to human intestinal cells. Previously, we demonstrated that goat milk oligosaccharides (GMO) increased the attachment of Bifidobacterium longum subsp. infantis ATCC 15697 to intestinal cells in vitro. In this study, we aimed to exploit this effect as a mechanism for inhibiting pathogen association with intestinal cells. We examined the synergistic effect of GMO-treated B. infantis on preventing the attachment of a highly invasive strain of Campylobacter jejuni to intestinal HT-29 cells. The combination decreased the adherence of C. jejuni to the HT-29 cells by an average of 42% compared to the control (non-GMO treated B. infantis). Increasing the incubation time of the GMO with the Bifidobacterium strain resulted in the strain metabolizing the GMO, correlating with a subsequent 104% increase in growth over a 24 h period when compared to the control. Metabolite analysis in the 24 h period also revealed increased production of acetate, lactate, formate and ethanol by GMO-treated B. infantis. Statistically significant changes in the GMO profile were also demonstrated over the 24 h period, indicating that the strain was digesting certain structures within the pool such as lactose, lacto-N-neotetraose, lacto-N-neohexaose 3′-sialyllactose, 6′-sialyllactose, sialyllacto-N-neotetraose c and disialyllactose. It may be that early exposure to GMO modulates the adhesion of B. infantis while carbohydrate utilisation becomes more important after the bacteria have transiently colonised the host cells in adequate numbers. This study builds a strong case for the use of synbiotics that incorporate oligosaccharides sourced from goat′s milk and probiotic bifidobacteria in functional foods, particularly considering the growing popularity of formulas based on goat milk.
    • Effects of oligosaccharides on particle structure, pasting and thermal properties of wheat starch granules under different freezing temperatures

      Su, Han; Tu, Jinjin; Zheng, Mingging; Deng, Kaibo; Miao, Song; Zeng, Shaoxiao; Zheng, Baodong; Lu, Xu; National Natural Science Foundation of China; Science and Technology Major Project of Fujian Province of China; et al. (Elsevier, 2020-06-15)
      The effects of fructooligosaccharides (FOS), galactooligosaccharides (GOS), and xylooligosaccharides (XOS) on gelatinization, retrogradation, thermal properties and particle size of wheat starch at different freezing temperatures were studied. The results showed that the wheat starch porosity, particle size, peak viscosity increased with increasing freezing temperature. With the addition of 16% oligosaccharides to starch, the porosity, particle size, crystallinity, initial gelatinization temperature, peak value, breakdown and retrogradation viscosity of the starch granules significantly decreased in the order of XOS > GOS > FOS. However, the pasting temperature of the granules increased. The addition of oligosaccharides (especially XOS, which has the most significant effect in inhibiting starch retrogradation) can inhibit the formation of starch crystal structures to a certain extent, reduce the damage from ice crystals to starch granules and delay starch retrogradation. Therefore, functional oligosaccharides can be used as a potentially effective additive to increase freezing stability in frozen starch-based foods.
    • Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder.

      McHugh, Aoife J; Feehily, Conor; Fenelon, Mark A; Gleeson, David; Hill, Colin; Cotter, Paul D; Department of Agriculture, Food and the Marine; Science Foundation Ireland; European Union; 14/F/883; et al. (American Society for Microbiology, 2020-04-07)
      Microorganisms from the environment can enter the dairy supply chain at multiple stages, including production, milk collection, and processing, with potential implications for quality and safety. The ability to track these microorganisms can be greatly enhanced by the use of high-throughput DNA sequencing (HTS). Here HTS, both 16S rRNA gene amplicon and shotgun metagenomic sequencing were applied to investigate the microbiomes of fresh mid- and late-lactation milk collected from farm bulk tanks, collection tankers, milk silos, skimmed milk silos, a cream silo, and powder samples to investigate the microbial changes throughout a skim milk powder manufacturing process. 16S rRNA gene analysis established that the microbiota of raw milks from farm bulk tanks and in collection tankers were very diverse but that psychrotrophic genera associated with spoilage, Pseudomonas and Acinetobacter, were present in all samples. Upon storage within the whole-milk silo at the processing facility, the species Pseudomonas fluorescens and Acinetobacter baumannii became dominant. The skimmed milk powder generated during the mid-lactation period had a microbial composition that was very different from that of raw milk; specifically, two thermophilic genera, Thermus and Geobacillus, were enriched. In contrast, the microbiota of skimmed milk powder generated from late-lactation milk more closely resembled that of the raw milk and was dominated by spoilage-associated psychrotrophic bacteria. This study demonstrates that the dairy microbiota can differ significantly across different sampling days. More specifically, HTS can be used to trace microbial species from raw milks through processing to final powdered products.IMPORTANCE Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from raw milk to the end product. Routine implementation of high-throughput sequencing would elucidate the factors that influence population dynamics. This will enable a manufacturer to adopt control measures specific to each stage of processing and respond in an effective manner, which would ultimately lead to increased food safety and quality.
    • Transforming Sitka Spruce Plantations

      Wilson, Edward R.; Ní Dhubháin, Aine; Short, Ian; Teagasc Walsh Fellowship Programme (Teagasc, 2020)
      The TranSSFor project is comparing conventional thinning in Sitka spruce plantations with two alternative thinning regimes.
    • Farming for Nature. The Role of Results-Based Payments

      O'Rourke, Eileen; Finn, John A. (Teagasc and National Parks and Wildlife Service (NPWS), 2020)
      Agricultural habitats cover approximately half the European Union (EU) and an estimated 50% of all species and several habitats of conservation concern in the EU depend on agricultural management. Reversing the loss of European biodiversity is clearly dependent on the conservation of farmland biodiversity. Results-based approaches are the focus of a growing discussion about improved biodiversity conservation and environmental performance of EU agri-environmental policies. This book outlines lessons learned from a collection of Irish case studies that have implemented results-based approaches and payments for the conservation of farmland habitats and species. The case studies include prominent projects and programmes: the Burren Programme, AranLIFE, KerryLIFE, the NPWS Farm Plan Scheme and Result-Based Agri-environmental Payment Schemes (RBAPS) project. This work is intended for an international audience of practitioners, policymakers and academics interested in results-based approaches for the conservation of biodiversity and the provision of ecosystem services.