Now showing items 1-20 of 1537

    • Development of a benchmarking system for Irish beef farms using data envelopment analysis

      Finneran, Eoghan; Crosson, Paul (2013)
      Agricultural extension trends have involved greater use of collaborative “discussion group” dissemination approaches. These discussion groups involve regular participatory meetings between a consistent cohort of farmers and extension practitioners with occasional input from industry and research stakeholders. In Ireland, policy change, small farm scale and low incomes are some of the factors incentivising beef farmers and industry to seek increased whole-farm income efficiency. Whole-farm comparative analysis may provide a means of identifying and explaining efficiency drivers at farm level. This article describes the development of BEEFMARK, a benchmarking model with potential to act as a tool to facilitate farmer-farmer and farmer-adviser group learning within discussion groups. BEEFMARK utilised Data Envelopment Analysis (DEA) to measure beef farm income and scale efficiency and to identify and characterise efficient peer farms which act as benchmarks for similarly structured, but lower efficiency farms. Market derived gross output (€) per livestock unit was positively associated with farm efficiency while greater overhead and concentrate feed expenditure was negatively associated with income and scale efficiency.
    • Supports for Farmers

      Unknown author (Teagasc (Agriculture and Food Development Authority), Ireland, 2018)
      The objective of this publication is to provide up-to-date information to help improve the situation of farmers in rural Ireland. It is intended to provide up-to-date information to help improve the situation of farmers and people involved in providing services to the farming community and is based on our understanding of current regulation and practice. The information in this guide is intended as a general guide only and is not a legal interpretation.
    • Regulation of intestinal growth in response to variations in energy supply and demand

      Nilaweera, Kanishka N.; Speakman, J. R.; Science Foundation Ireland; Biotechnology and Biological Sciences Research Council (BBSRC); SFI/16/BBSRC/3389; BB/P009875/1 (Wiley, 2018-12-03)
      The growth of the intestine requires energy, which is known to be met by catabolism of ingested nutrients. Paradoxically, during whole body energy deficit including calorie restriction, the intestine grows in size. To understand how and why this happens, we reviewed data from several animal models of energetic challenge. These were bariatric surgery, cold exposure, lactation, dietary whey protein intake and calorie restriction. Notably, these challenges all reduced the adipose tissue mass, altered hypothalamic neuropeptide expression and increased intestinal size. Based on these data, we propose that the loss of energy in the adipose tissue promotes the growth of the intestine via a signalling mechanism involving the hypothalamus. We discuss possible candidates in this pathway including data showing a correlative change in intestinal (ileal) expression of the cyclin D1 gene with adipose tissue mass, adipose derived‐hormone leptin and hypothalamic expression of leptin receptor and the pro‐opiomelanocortin gene. The ability of the intestine to grow in size during depletion of energy stores provides a mechanism to maximize assimilation of ingested energy and in turn sustain critical functions of tissues important for survival.
    • Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods

      Linares, Daniel M.; Gómez, Carolina; Renes, Erica; Fresno, José M.; Tornadijo, María E.; Ross, R Paul; Stanton, Catherine; Science Foundation Ireland (Frontiers, 2017-05-18)
      Consumer interest in healthy lifestyle and health-promoting natural products is a major driving force for the increasing global demand of biofunctional dairy foods. A number of commercial sources sell synthetic formulations of bioactive substances for use as dietary supplements. However, the bioactive-enrichment of health-oriented foods by naturally occurring microorganisms during dairy fermentation is in increased demand. While participating in milk fermentation, lactic acid bacteria can be exploited in situ as microbial sources for naturally enriching dairy products with a broad range of bioactive components that may cover different health aspects. Several of these bioactive metabolites are industrially and economically important, as they are claimed to exert diverse health-promoting activities on the consumer, such as anti-hypertensive, anti-inflammatory, and anti-diabetic, anti-oxidative, immune-modulatory, anti-cholesterolemic, or microbiome modulation. This review aims at discussing the potential of these health-supporting bacteria as starter or adjunct cultures for the elaboration of dairy foods with a broad spectrum of new functional properties and added value.
    • An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping

      Velmurugan, Janaki; Milbourne, Dan; Connolly, Vincent; Heslop-Harrison, J. S.; Anhalt, Ulrike C. M.; Lynch, M. B.; Barth, Susanne; Teagasc Walsh Fellowship Programme (Frontiers, 2018-05-31)
      To address the lack of a truly portable, universal reference mapping population for perennial ryegrass, we have been developing a recombinant inbred line (RIL) mapping population of perennial ryegrass derived via single seed descent from a well-characterized F2 mapping population based on genetically distinct inbred parents in which the natural self-incompatibility (SI) system of perennial ryegrass has been overcome. We examined whether it is possible to create a genotyping by sequencing (GBS) based genetic linkage map in a small population of the F6 generation of this population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We successfully developed a genetic linkage map comprising 6074 SNP markers, placing a further 22080 presence and absence variation (PAV) markers on the map. We examined the resulting genetic map for general and RIL specific features. Overall segregation distortion levels were similar to those experienced in the F2 generation, but segregation distortion was reduced on linkage group 6 and increased on linkage group 7. Residual heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred parents of the F1 genotype from which the population is derived, pointing to a tendency for chromosomes to assort without recombining. This could affect the applicability of these lines and might make them more suitable for situations where repressed recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium (LD) analysis suggested that the map order was robust. We conclude that this RIL population, and subsequent F7 and F8 generations will be useful for genetic analysis and phenotyping of agronomic and biological important traits in perennial ryegrass.
    • The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate

      Popova, Milka; McGovern, Emily; McCabe, Matthew; Martin, Cécile; Doreau, Michel; Arbre, Marie; Meale, Sarah J.; Morgavi, Diego P.; Waters, Sinead M.; INRA; French ministry of Foreign Affairs and International Development; French ministry of National Education, Higher Education, and Research; FACCE-JPI (Frontiers, 2017-05-24)
      Microorganisms in the digestive tract of ruminants differ in their functionality and ability to use feed constituents. While cecal microbiota play an important role in post-rumen fermentation of residual substrates undigested in the rumen, limited knowledge exists regarding its structure and function. In this trial we investigated the effect of dietary supplementation with linseed oil and nitrate on methane emissions and on the structure of ruminal and cecal microbiota of growing bulls. Animals were allocated to either a CTL (control) or LINNIT (CTL supplemented with 1.9% linseed and 1.0% nitrates) diet. Methane emissions were measured using the GreenFeed system. Microbial diversity was assessed using amplicon sequencing of microbial genomic DNA. Additionally, total RNA was extracted from ruminal contents and functional mcrA and mtt genes were targeted in amplicon sequencing approach to explore the diversity of functional gene expression in methanogens. LINNIT had no effect on methane yield (g/kg DMI) even though it decreased methane production by 9% (g/day; P < 0.05). Methanobrevibacter- and Methanomassiliicoccaceae-related OTUs were more abundant in cecum (72 and 24%) compared to rumen (60 and 11%) irrespective of the diet (P < 0.05). Feeding LINNIT reduced the relative abundance of Methanomassiliicoccaceae mcrA cDNA reads in the rumen. Principal component analysis revealed significant differences in taxonomic composition and abundance of bacterial communities between rumen and cecum. Treatment decreased the relative abundance of a few Ruminococcaceae genera, without affecting global bacterial community structure. Our research confirms a high level of heterogeneity in species composition of microbial consortia in the main gastrointestinal compartments where feed is fermented in ruminants. There was a parallel between the lack of effect of LINNIT on ruminal and cecal microbial community structure and functions on one side and methane emission changes on the other. These results suggest that the sequencing strategy used here to study microbial diversity and function accurately reflected the absence of effect on methane phenotypes in bulls treated with linseed plus nitrate.
    • Grazing of dairy cows on pasture versus indoor feeding on total mixed ration: Effects on low-moisture part-skim Mozzarella cheese yield and quality characteristics in mid and late lactation

      Gulati, Arunima; Galvin, Norann; Hennessy, Deirdre; McAuliffe, Stephen; O’Donovan, Michael; McManus, Jennifer J.; Fenelon, Mark; Guinee, Timothy P.; Department of Agriculture, Food and the Marine, Ireland; Dairy Levy Trust; 11/sf/309 (Elsevier for American Dairy Science Association, 2018-08-16)
      This study investigated the effects of 3 dairy cow feeding systems on the composition, yield, and biochemical and physical properties of low-moisture part-skim Mozzarella cheese in mid (ML; May–June) and late (LL; October–November) lactation. Sixty spring-calving cows were assigned to 3 herds, each consisting of 20 cows, and balanced on parity, calving date, and pre-experimental milk yield and milk solids yield. Each herd was allocated to 1 of the following feeding systems: grazing on perennial ryegrass (Lolium perenne L.) pasture (GRO), grazing on perennial ryegrass and white clover (Trifolium repens L.) pasture (GRC), or housed indoors and offered total mixed ration (TMR). Mozzarella cheese was manufactured on 3 separate occasions in ML and 4 in LL in 2016. Feeding system had significant effects on milk composition, cheese yield, the elemental composition of cheese, cheese color (green to red and blue to yellow color coordinates), the extent of flow on heating, and the fluidity of the melted cheese. Compared with TMR milk, GRO and GRC milks had higher concentrations of protein and casein and lower concentrations of I, Cu, and Se, higher cheese-yielding capacity, and produced cheese with lower concentrations of the trace elements I, Cu, and Se and higher yellowness value. Cheese from GRO milk had higher heat-induced flow and fluidity than cheese from TMR milk. These effects were observed over the entire lactation period (ML + LL), but varied somewhat in ML and LL. Feeding system had little, or no, effect on gross composition of the cheese, the proportions of milk protein or fat lost to cheese whey, the texture of the unheated cheese, or the energy required to extend the molten cheese. The differences in color and melt characteristics of cheeses obtained from milks with the different feeding systems may provide a basis for creating points of differentiation suited to different markets.
    • A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals

      Thapa, Ganesh; Gunupuru, Lokanadha R.; Hehir, James G.; Kahla, Amal; Mullins, Ewen; Doohan, Fiona M.; Department of Agriculture, Food and the Marine; Science Foundation Ireland; 11/S/103; 10/IN.1/B3028; 14IA2508 (Frontiers, 2018-06-26)
      Receptor-like kinases form the largest family of receptors in plants and play an important role in recognizing pathogen-associated molecular patterns and modulating the plant immune responses to invasive fungi, including cereal defenses against fungal diseases. But hitherto, none have been shown to modulate the wheat response to the economically important Fusarium head blight (FHB) disease of small-grain cereals. Homologous genes were identified on barley chromosome 6H (HvLRRK-6H) and wheat chromosome 6DL (TaLRRK-6D), which encode the characteristic domains of surface-localized receptor like kinases. Gene expression studies validated that the wheat TaLRRK-6D is highly induced in heads as an early response to both the causal pathogen of FHB disease, Fusarium graminearum, and its’ mycotoxic virulence factor deoxynivalenol. The transcription of other wheat homeologs of this gene, located on chromosomes 6A and 6B, was also up-regulated in response to F. graminearum. Virus-induced gene silencing (VIGS) of the barley HvLRRK-6H compromised leaf defense against F. graminearum. VIGS of TaLRRK-6D in two wheat cultivars, CM82036 (resistant to FHB disease) and cv. Remus (susceptible to FHB), confirmed that TaLRRK-6D contributes to basal resistance to FHB disease in both genotypes. Although the effect of VIGS did not generally reduce grain losses due to FHB, this experiment did reveal that TaLRRK-6D positively contributes to grain development. Further gene expression studies in wheat cv. Remus indicated that VIGS of TaLRRK-6D suppressed the expression of genes involved in salicylic acid signaling, which is a key hormonal pathway involved in defense. Thus, this study provides the first evidence of receptor like kinases as an important component of cereal defense against Fusarium and highlights this gene as a target for enhancing cereal resistance to FHB disease.
    • A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae) Population

      Thorogood, Daniel; Yates, Steven; Manzanares, Chloé; Skot, Leif; Hegarty, Matthew; Blackmore, Tina; Barth, Susanne; Studer, Bruno; Biotechnology and Biological Sciences Research Council; Swiss National Science Foundation; Teagasc Walsh Fellowship Programme; BB/J004405/1; PP00P2 138988 (Frontiers, 2017-08-02)
      Self-incompatibility (SI) is a mechanism that many flowering plants employ to prevent fertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour. Although a number of single locus mechanisms have been characterised in detail, no multi-locus systems have been fully elucidated. Historically, examples of the genetic analysis of multi-locus SI, to make analysis tractable, are either made on the progeny of bi-parental crosses, where the number of alleles at each locus is restricted, or on crosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass (Lolium perenne L.) possesses a well-documented two locus (S and Z) gametophytic incompatibility system. A more universal, realistic proof of principle study was conducted in a perennial ryegrass population in which allelic and non-allelic diversity was not artificially restricted. A complex pattern of pollinations from a diallel cross was revealed which could not possibly be interpreted easily per se, even with an already established genetic model. Instead, pollination scores were distilled into principal component scores described as Compatibility Components (CC1-CC3). These were then subjected to a conventional genome-wide association analysis. CC1 associated with markers on linkage groups (LGs) 1, 2, 3, and 6, CC2 exclusively with markers in a genomic region on LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodium physical map revealed highly significantly associated markers with peak associations with genes adjacent and four genes away from the chromosomal locations of candidate SI genes, S- and Z-DUF247, respectively. Further significant associations were found in a Brachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG 1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genome between B. distachyon and L. perenne. Significant associations with gene sequences aligning with marker sequences on Lolium LGs 3 and 6 were also identified. We therefore demonstrate the power of a novel association genetics approach to identify the genes controlling multi-locus gametophytic SI systems and to identify novel loci potentially involved in already established SI systems.
    • Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice

      Kaliannan, Kanakaraju; Robertson, Ruairi C; Murphy, Kiera; Stanton, Catherine; Kang, Chao; Wang, Bin; Hao, Lei; Bhan, Atul K; Kang, Jing X; Sansun Life Sciences; Fortune Education Foundation (Biomed Central, 2018-11-13)
      Background Understanding the mechanism of the sexual dimorphism in susceptibility to obesity and metabolic syndrome (MS) is important for the development of effective interventions for MS. Results Here we show that gut microbiome mediates the preventive effect of estrogen (17β-estradiol) on metabolic endotoxemia (ME) and low-grade chronic inflammation (LGCI), the underlying causes of MS and chronic diseases. The characteristic profiles of gut microbiome observed in female and 17β-estradiol-treated male and ovariectomized mice, such as decreased Proteobacteria and lipopolysaccharide biosynthesis, were associated with a lower susceptibility to ME, LGCI, and MS in these animals. Interestingly, fecal microbiota-transplant from male mice transferred the MS phenotype to female mice, while antibiotic treatment eliminated the sexual dimorphism in MS, suggesting a causative role of the gut microbiome in this condition. Moreover, estrogenic compounds such as isoflavones exerted microbiome-modulating effects similar to those of 17β-estradiol and reversed symptoms of MS in the male mice. Finally, both expression and activity of intestinal alkaline phosphatase (IAP), a gut microbiota-modifying non-classical anti-microbial peptide, were upregulated by 17β-estradiol and isoflavones, whereas inhibition of IAP induced ME and LGCI in female mice, indicating a critical role of IAP in mediating the effects of estrogen on these parameters. Conclusions In summary, we have identified a previously uncharacterized microbiome-based mechanism that sheds light upon sexual dimorphism in the incidence of MS and that suggests novel therapeutic targets and strategies for the management of obesity and MS in males and postmenopausal women.
    • Blood parameters as biomarkers in a Salmonella spp. disease model of weaning piglets

      Barba-Vidal, Emili; Buttow Roll, Victor Fernando; Garcia Manzanilla, Edgar; Torrente, Carlos; Moreno Muñoz, Jose Antonio; PeÂrez, Jose Francisco; Martin-Orue, Susana Maria; Spanish Ministry of Education and Science; Laboratorios Ordesa S.L.; CNPQ Brazil; AGL 2012-31924 (PLOS, 2017-10-26)
      Background The weaning pig is used as an experimental model to assess the impact of diet on intestinal health. Blood parameters (BP) are considered a useful tool in humans, but there is very scarce information of such indicators in the weaning pig. The objective of the present study is to evaluate the use of different BP as indicators in an experimental model of salmonellosis. Methodology Seventy-two 28-day-old piglets were divided into four groups in a 2x2 factorial arrangement, with animals receiving or not a probiotic combination based on B. infantis IM1® and B. lactis BPL6 (109 colony forming units (cfu)/d) and orally challenged or not a week later with Salmonella Typhimurium (5x108 cfu). Blood samples of one animal per pen (N = 24) were taken four days post-inoculation for the evaluation of different BP using an I-stat® System and of plasmatic concentrations of zinc, iron and copper. Principal findings Results reported marginal deficiencies of zinc in piglets at weaning. Moreover, plasmatic zinc, copper and iron presented good correlations with weight gain (r 0.57, r -0.67, r 0.54 respectively; P < 0.01). Blood electrolytes (Na+, Cl- and K+) decreased (P < 0.01) only when the performance of the animals was seriously compromised and clinical symptoms were more apparent. Acid-base balance parameters such as HCO3-, TCO2 and BEecf significantly correlated with weight gain, but only in the challenged animals (r -0.54, r -0.55, and r -0.51, respectively; P < 0.05), suggesting metabolic acidosis depending on Salmonella infection. Glucose was affected by the challenge (P = 0.040), while Htc and Hgb increased with the challenge and decreased with the probiotic (P < 0.05). Furthermore, correlations of Glu, Htc and Hgb with weight gain were observed (P < 0.05). Overall, BP could be regarded as simple, useful indexes to assess performance and health of weaning piglets.
    • Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape (Brassica napus)

      Rathore, Ridhdhi; Dowling, David N.; Forristal, Patrick D.; Spink, John; Cotter, Paul D.; Bulgarelli, Davide; Germaine, Kieran J.; Teagasc Walsh Fellowship Programme; Royal Society of Edinburgh/Scottish Government Personal Research Fellowship (Frontiers, 2017-08-09)
      Gaining a greater understanding of the plant microbiota and its interactions with its host plant heralds a new era of scientific discovery in agriculture. Different agricultural management practices influence soil microbial populations by changing a soil’s physical, chemical and biological properties. However, the impact of these practices on the microbiota associated with economically important crops such as oilseed rape, are still understudied. In this work we investigated the impact of two contrasting crop establishment practices, conventional (plow based) and conservation (strip–tillage) systems, on the microbiota inhabiting different plant microhabitats, namely rhizosphere, root and shoot, of winter oilseed rape under Irish agronomic conditions. Illumina 16S rRNA gene sequence profiling showed that the plant associated microhabitats (root and shoot), are dominated by members of the bacterial phyla Proteobacteria, Actinobacteria and Bacteroidetes. The root and shoot associated bacterial communities displayed markedly distinct profiles as a result of tillage practices. We observed a very limited ‘rhizosphere effect’ in the root zone of WOSR, i.e., there was little or no increase in bacterial community richness and abundance in the WOSR rhizosphere compared to the bulk soil. The two tillage systems investigated did not appear to lead to any major long term differences on the bulk soil or rhizosphere bacterial communities. Our data suggests that the WOSR root and shoot microbiota can be impacted by management practices and is an important mechanism that could allow us to understand how plants respond to different management practices and environments.
    • Genetic variability in the humoral immune response to bovine herpesvirus-1 infection in dairy cattle and genetic correlations with performance traits

      Ring, S. C.; Graham, D. A.; Sayers, Riona; Byrne, N.; Kelleher, M. M.; Doherty, M. L.; Berry, Donagh P.; Department of Agriculture, Food and the Marine (Elsevier for American Dairy Science Association, 2018-04-26)
      Bovine herpesvirus-1 (BoHV-1) is a viral pathogen of global significance that is known to instigate several diseases in cattle, the most notable of which include infectious bovine rhinotracheitis and bovine respiratory disease. The genetic variability in the humoral immune response to BoHV-1 has, to our knowledge, not ever been quantified. Therefore, the objectives of the present study were to estimate the genetic parameters for the humoral immune response to BoHV-1 in Irish female dairy cattle, as well as to investigate the genetic relationship between the humoral immune response to BoHV-1 with milk production performance, fertility performance, and animal mortality. Information on antibody response to BoHV-1 was available to the present study from 2 BoHV-1 sero-prevalence research studies conducted between the years 2010 to 2015, inclusive; after edits, BoHV-1 antibody test results were available on a total of 7,501 female cattle from 58 dairy herds. National records of milk production (i.e., 305-d milk yield, fat yield, protein yield, and somatic cell score; n = 1,211,905 milk-recorded cows), fertility performance (i.e., calving performance, pregnancy diagnosis, and insemination data; n = 2,365,657 cows) together with animal mortality data (i.e., birth, farm movement, death, slaughter, and export events; n = 12,853,257 animals) were also available. Animal linear mixed models were used to quantify variance components for BoHV-1 as well as to estimate genetic correlations among traits. The estimated genetic parameters for the humoral immune response to BoHV-1 in the present study (i.e., heritability range: 0.09 to 0.16) were similar to estimates previously reported for clinical signs of bovine respiratory disease in dairy and beef cattle (i.e., heritability range: 0.05 to 0.11). Results from the present study suggest that breeding for resistance to BoHV-1 infection could reduce the incidence of respiratory disease in cattle while having little or no effect on genetic selection for milk yield or milk constituents (i.e., genetic correlations ranged from −0.13 to 0.17). Moreover, even though standard errors were large, results also suggest that breeding for resistance to BoHV-1 infection may indirectly improve fertility performance while also reducing the incidence of mortality in older animals (i.e., animals >182 d of age). Results can be used to inform breeding programs of potential genetic gains achievable for resistance to BoHV-1 infection in cattle.
    • A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

      Cao, Yu; Fanning, Séamus; Proos, Sinéad; Jordan, Kieran; Srikumar, Shabarinath; Department of Agriculture, Food and Marine; Enterprise Ireland; 13/F/423; IP 2015 0380 (Frontiers, 2017-09-21)
      The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.
    • Editorial: Microbial Food Safety along the Dairy Chain

      Fox, Edward M.; Fanning, Seamus; Corsetti, Aldo; Jordan, Kieran (Frontiers, 2017-08-23)
      Milk is susceptible to contamination with pathogenic and spoilage organisms and, therefore, Microbial food safety along the dairy chain is an important topic, from public health and industry perspectives. The dairy chain is an integral part of global food supply, with dairy food products a staple component of recommended healthy diets. The dairy food chain from production through to the consumer is complex, with various opportunities for microbial contamination of ingredients or food products, and as such interventions are key to preventing or controlling such contamination. Dairy foods often include a microbial control step in their production such as pasteurization, but in some cases may not, as with raw milk products. Microbial contamination may lead to a deterioration in food quality due to spoilage organisms, or may become a health risk to consumers should the contaminant be a pathogenic microorganism. As such food safety and food production are intrinsically linked.
    • Novel “gel demineralizing” method for protein recovery from fat rendering waste stream based on its gelling properties

      Álvarez, Carlos; Drummond, Liana; Mullen, Anne Maria (Elsevier, 2018-11)
      Fat rendering is a common process in the meat industry, whereby fatty or oily materials are melted away or cooked from the solid portion of the animal tissue. Once the fat, and more solid protein in the form of greaves, has been removed a co-product called glue water or stick water is produced which in generally considered a waste product. This study was established to investigate ways to revalorise this product and reduce the economic and environmental impact of this waste material. Proximate characterisation shows it contains 1.1–1.3% w/w of protein along with similar concentration of ashes (1.3% w/w). While low in protein this is a key pollutant if the product is disposed of, and could also represent an interesting protein source for downstream applications. In order to recover these proteins the salt has to be removed. Therefore, after the techno-functional properties of the raw material and of the recovered proteins were evaluated, especially those related to gelling formation, a new demineralizing method based on the excellent gelling properties of these proteins was developed and results compared with those obtained from three different ultrafiltration membranes (10, 3 and 1 kDa MWCO). Protein recovery was greater for the new method (79–90%) (50–77%); however, the amount of salt removed was higher when ultrafiltration was employed (90% compared to 81%).
    • Effect of human chorionic gonadotrophin administration 2 days after insemination on progesterone concentration and pregnancy per artificial insemination in lactating dairy cows

      Sánchez, J. M.; Randi, F.; Passaro, C.; Mathew, D. J.; Butler, S. T.; Lonergan, P.; Department of Agriculture, Food and the Marine; 13S528 (Elsevier for American Dairy Science Association, 2018-03-28)
      The aim of this study was to examine the effect of a single administration of human chorionic gonadotrophin (hCG) during the establishment of the corpus luteum (CL) on progesterone (P4) concentration and pregnancy per artificial insemination (P/AI) in lactating dairy cows. Postpartum spring-calving lactating dairy cows (n = 800; mean ± SD days in milk and parity were 78.5 ± 16.7 and 2.3 ± 0.8, respectively) on 3 farms were enrolled on the study. All cows underwent the same fixed-time AI (FTAI) protocol involving a 7-d progesterone-releasing intravaginal device with gonadotrophin-releasing hormone (GnRH) administration at device insertion, prostaglandin at device removal followed by GnRH 56 h later, and AI 16 h after the second GnRH injection. Cows were blocked on days postpartum, body condition score, and parity and randomly assigned to receive either 3,000 IU of hCG 2 d after FTAI or no further treatment (control). Blood samples were collected on d 7 and 14 postestrus by coccygeal venipuncture on a subset of 204 cows to measure serum P4 concentration, and pregnancy was diagnosed by ultrasonography approximately 30 and 70 d after FTAI. Administration of hCG caused an increase in circulating P4 concentrations compared with the control treatment on d 7 (+22.2%) and d 14 (+25.7%). The P/AI at 30 d after FTAI was affected by treatment, farm, body condition score, and calving to service interval. Overall, administration of hCG decreased P/AI (46.3% vs. 55.1% for the control). Among cows that did not become pregnant following AI, a greater proportion of control cows exhibited a short repeat interval (≤17 d) compared with cows treated with hCG (8.6% vs. 2.8%, respectively). In addition, the percentages of cows pregnant at d 21 (59.6% vs. 52.0%) and d 42 (78.3% vs. 71.9%) were greater in control than in hCG-treated cows. The overall incidence of embryo loss was 10.7% and was not affected by treatment. There was a tendency for an interaction between treatment and CL status at synchronization protocol initiation for both P4 concentration and P/AI. In conclusion, administration of hCG 2 d after FTAI increased circulating P4 concentrations. Unexpectedly, cows treated with hCG had lower fertility; however, this negative effect on fertility was manifested primarily in cows lacking a CL at the onset of the synchronization protocol.
    • Sustainability indicators for improved assessment of the effects of agricultural policy across the EU: Is FADN the answer?

      Kelly, Edel; Latruffe, Laure; Desjeux, Yann; Ryan, Mary; Uthes, Sandra; Diazabakanab, Ambre; Dillon, Emma; Finn, John; European Union; 613800 (Elsevier, 2018-06)
      Policy reform of the CAP and society’s expectations of agriculture have resulted in a growing need for improved information on the effectiveness of policy in achieving high-level objectives for more sustainable practice in agriculture. This is a high priority given its importance for consumers, public policy and private industry. Data collection programmes will need to adapt their scope if their information is to adequately address new information needs about high-level objectives. Assessment of sustainability at the farm level is hindered by the lack of data with which to derive appropriate, meaningful, and relevant indicators. This is particularly problematic for assessment of agricultural sustainability across the European Union (EU). Various databases exist at the EU scale regarding agricultural data sources and we identify one of these, the EU Farm Accountancy Data Network (FADN), as having considerable potential to assess farm-level sustainability at EU level. We critique several examples of published work that has attempted to assess agricultural sustainability using: FADN data alone; FADN data in combination with data from supplementary surveys, and; FADN data in combination with data from other EU databases. We conclude that the FADN would need to broaden its scope of data collection if it is to address the new information needs of policy, and we discuss the challenges in expanding FADN with a view towards wider farm-level assessment of sustainability. These include careful selection of indicators based on various criteria, the representativeness of the FADN, and the need to include new themes to address environmental, social, and animal welfare effects of policy.
    • Perinatal immuno/inflammatory responses in the presence or absence of bovine fetal infection

      Jawor, Paulina; Mee, John F; Stefaniak, Tadeusz; The National Centre for Research and Development; PBS2/A8/20/2013 (Biomed Central, 2018-11-01)
      Background It is known that the bovine fetus can mount an immune and inflammatory reaction to infection, but it is not known whether there is a contemporaneous maternal response. Nor is it known whether the response of calves which die perinatally, with or without infection, differs from that of live perinates. Hence, the objective of this study was to determine if acute phase reactant and immunoglobulin concentrations differed between calves (and their dams) in three groups: live calves (CC; n = 21) and dead calves with (PM INF+; n = 22) or without (PM INF-; n = 89) in utero infection. In calf plasma, serum amyloid A, haptoglobin, immunoglobulins M, G1 and G2 and interleukin-6 were measured. In dam serum, SAA and Hp was measured and in amniotic and abomasal fluid, IL-6 was measured. Results Live calves had higher plasma concentrations of SAA and IL-6 than dead calves with (PM INF+) or without (PM INF-) in utero infection. Calves in the PM INF-, but not PM INF+ group, had higher Hp concentrations than calves in the CC group. Calves in the PM INF+ group had higher IgG1 concentrations than calves in the PM INF- and CC groups. Except for higher IgG1 and IgG2 concentrations, biomarker values did not differ significantly between dead calves with or without in utero infection. Live calves had higher IL-6 concentrations in abomasal fluid compared to PM INF- calves. There were no significant differences in blood biomarker concentrations between dams of the three groups of calves. Amniotic fluid IL-6 concentrations were higher from the dams of control calves than the dams of uninfected calves. Conclusions Differences in biomarkers (higher Hp and IgG1; lower SAA and IL-6) between perinatal mortalities and live perinates probably reflect differences between these two groups in age at sampling (SAA and IL-6) and in utero infection (IgG1). Out of the six analytes measured in calves, only IgG1 and IgG2 were biomarkers of (chronic) in utero infection.
    • Correction to: 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 (Biomed Central, 2018-11-07)
      In the original publication of this article [1], some errors in Table 4 need to be corrected as below: