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

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

      Bolton, Declan J.; Sheridan, James J. (Teagasc, 2002-02)
      It is generally accepted that HACCP principles should be incorporated into the food safety control systems in meat processing plants to better assure food safety. The objective of this project was to publish detailed HACCP slaughter documents for the Irish beef, pork and lamb processing industries. These would provide the necessary information and detail to facilitate the implementation of HACCP on the slaughter floor (from lairage to chilling) in Irish meat plants. To this end `HACCP for Irish Beef Slaughter' was published in October 2000, `HACCP for Irish Pork Slaughter' in December 2001 and `HACCP for Irish Lamb Slaughter' will be available early in 2002. These are non-generic, detailed documents which provide the scientific basis for establishing critical control points (CCP), critical limits, monitoring and corrective action procedures.
    • Hazard analysis and critical control point (HACCP) and hygiene control auditing in Irish beef abattoirs

      Bolton, Declan J.; Pearce, Rachel; Tergney, Anabel; Howlett, Brendan (Teagasc, 2007-06)
      This project validated two innovative technologies for use in improving the safety of Irish beef. Online monitoring was developed and successfully tested as a tool for controlling faecal contamination on beef carcasses with the resultant reduction in microbial counts. A novel anti-microbial, LactiSAL®, was also tested and validated for use in the beef industry. Sponge swabbing using a polyurethane sponge was developed and validated for use in carcass testing as required in European Commission Decision 2001/471/EC. The costs of developing and implementing a HACCP system in Irish beef slaughter plants were assessed. Furthermore, a guide to relevant food safety legislation, including the development and auditing of HACCP and prerequisites for beef slaughter (in compliance with 2001/471/EC and the European Commission Hygiene Regulations), was developed and published.
    • The health status of Irish honeybee colonies in 2006

      Coffey, M. F.; Barth, Susanne; Hayes, K.; Breen, James (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      This study assessed the health status of Irish honeybee colonies and provides a snapshot of the incidence of a number of important colony parasites/pathogens including: the mite Varroa destructor; three associated viruses (deformed wing virus (DWV), acute bee paralysis virus (ABPV) and Kashmir virus (KBV)); the tracheal mite Acarapis woodi; the microsporidian Nosema spp., and the insect Braula coeca. During June/July 2006, 135 samples of adult bees were collected from productive colonies throughout Ireland and standard techniques were used to determine the presence and absence of the parasites and pathogens. Varroa destructor was positively identified in 72.6% of the samples and was widely distributed. Although the samples were analysed for three viruses, DWV, ABPV and KBV, only DWV was detected (frequency = 12.5%). Acarapis woodi and Nosema spp. occurred in approximately 11% and 22% of the samples, respectively, while B. coeca, a wingless dipteran that was once common in Irish honeybee colonies, was very rare (3.7%). Samples where all the pathogens/parasites were jointly absent were statistically under-represented in Leinster and DWV was statistically over-represented in Munster. In Ulster, there was over-representation of the categories where all parasites/pathogens were jointly absent and for A. woodi, and underrepresentation of V. destructor.
    • Heat-induced Maillard reaction of the tripeptide IPP and ribose: Structural characterization and implication on bioactivity

      Jiang, Zhanmei; Rai, Dilip K; O'Connor, Paula M.; Brodkorb, Andre (Elsevier, 2012-09-28)
      Maillard reaction products (MRPs) were prepared from aqueous model mixtures containing 60 g L− 1 ribose and 30 g L− 1 of the bioactive tripeptide IPP (Ile-Pro-Pro), heated at 98 °C. MRP and associated reactions with changes in IPP were observed within one hour of heat-treatment. The pH of MRPs decreased significantly during the heat treatment of IPP–ribose mixtures from 9.0 to 7.6 after one hour. The amino group content, IPP and ribose concentration decreased significantly during heat treatment. The fluorescence intensity of the IPP–ribose MRPs reached the maximum within 2 h. Modification of the UV/vis spectra for IPP–ribose MRPs was mainly due to a condensation reaction of IPP with ribose. Compounds with molecular weight between 300 and 650 Da were dominant while compounds smaller than 250 Da were also produced during the reactions, as characterized by size exclusion chromatography. Mass spectrometry revealed that IPP was conjugated to ribose at the N-terminal (m/z of 458.3) upon heat-treatment. The presence of ribose also promoted peptide degradation to dehydrated IP (m/z of 211.1). IPP–ribose MRPs lost the known angiotensin-I-converting enzyme (ACE) inhibitory activity of IPP; however, strong antioxidant properties were detected.
    • Herbicide Efficacy Evaluation

      Mitchell, B.J. (Teagasc, 2201-03-01)
      The objective of this series of trials was to determine if recently introduced herbicide formulations give better weed control in cereals and grassland than those presently in use. Effect on crop yield and quality was also examined where appropriate. In 1995, field trials were carried out with a new diflufenican/flurtamone formulation, Bacara, in winter wheat and barley. In both cases, the results showed that this new formulation gave commercially acceptable weed control of a wide range of annual weeds and grasses, when applied at doses between 260 and 350 g a.i. per hectare. None of the products tested had any adverse effects on crop yield or quality. Between 1996 and 1998 a number of new sulfonylurea herbicides, based on carfentrazone and flupyrsulfuron methyl (Lexus series), were tested at trial sites in Carlow and Clonmel. Most of the formulations gave weed control similar to Cougar, which was included in all these trials as standard comparison treatment, without affecting crop yield or quality. New herbicide trials for the control of broad and curled leaf dock (Rumex spp.) in pasture were carried out. Most of the herbicides investigated gave better overall control of both species than the standard dicamba/mecoprop based products. One of the sulfonylyurea-based herbicides controlled broad leaf dock only, and occasionally retarded grass development, but had no effect on clover. Fluroxypyr-based products gave long term control of both dock species without any effect on the grass, but eliminated clover present in the sward. In all trials some dock regrowth was evident one year after treatment.
    • Herd health status and management practices on 16 Irish suckler beef farms

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

      Chinnadurai, Kathirvelan; Kanwal, Harpreet K; Tyagi, Amrish K; Stanton, Catherine; Ross, Paul (Biomed Central, 2013-08-07)
      Background Hypercholesterolemia and oxidative stress are the main stimulating factors responsible for coronary artery disease and progression of atherosclerosis. Dairy food products are rich in conjugated linoleic acid (CLA) which is considered as an important component due to its potential health benefits such as anticarcinogenic, antiatherogenic, antidiabetic and antiadipogenic properties. In the present study, the effect of CLA enriched ghee on the antioxidant enzyme system and antiatherogenic properties in Wistar rats has been studied. Methods Female Wistar rats of 21 days were taken for the study and fed with soybean diet (Control diet), low CLA diet and high CLA ghee diet (treatments) for thirty five days for studying antioxidative enzymes and sixteen weeks in case of antiatherogenic studies. Results Feeding of high CLA enhanced ghee during pubescent period in rats lead to an increase in catalase (CAT) and superoxide dismutase (SOD) enzyme activities in blood and increased CAT, SOD and glutathione transferase (GST) enzymes activities in liver by 27, 130 and 168 percent, respectively. Plasma nitrate concentration and Haemoglobin levels remained the same in all the treatments. Feeding of high CLA ghee resulted in lower (P < 0.01) plasma cholesterol & triglyceride level (52.17 and 30.27%), and higher high density lipoproteins (33.26%) than feeding of soybean oil (control group) and thus manifested in decreased (P < 0.05) atherogenic index (from 0.472 to 0.244). Lesser cholesterol and triglyceride levels were observed in the liver and aorta of high CLA fed rats than in those of the other groups. Histopathological studies of liver showed normal hepatic cords with portal triad in the high CLA ghee fed rats whereas fatty degeneration of hepatocytes containing fat vacuoles was observed in the liver of the other groups. Conclusion This paper is the first report of the antioxidant and antiatherogenic properties of the high CLA enriched ghee suggesting that high CLA ghee can be used as a potential food for decreasing the risk of cardiovascular diseases, particularly in India, where, ghee is widely used for culinary and medicinal purposes.
    • High conjugated linoleic acid enriched ghee (clarified butter) increases the antioxidant and antiatherogenic potency in female Wistar rats

      Chinnadurai, Kathirvelan; Kanwal, Harpreet K; Tyagi, Amrish K; Stanton, Catherine; Ross, R Paul (Biomed Central, 2013-08-07)
      Background: Hypercholesterolemia and oxidative stress are the main stimulating factors responsible for coronary artery disease and progression of atherosclerosis. Dairy food products are rich in conjugated linoleic acid (CLA) which is considered as an important component due to its potential health benefits such as anticarcinogenic, antiatherogenic, antidiabetic and antiadipogenic properties. In the present study, the effect of CLA enriched ghee on the antioxidant enzyme system and antiatherogenic properties in Wistar rats has been studied. Methods: Female Wistar rats of 21 days were taken for the study and fed with soybean diet (Control diet), low CLA diet and high CLA ghee diet (treatments) for thirty five days for studying antioxidative enzymes and sixteen weeks in case of antiatherogenic studies. Results: Feeding of high CLA enhanced ghee during pubescent period in rats lead to an increase in catalase (CAT) and superoxide dismutase (SOD) enzyme activities in blood and increased CAT, SOD and glutathione transferase (GST) enzymes activities in liver by 27, 130 and 168 percent, respectively. Plasma nitrate concentration and Haemoglobin levels remained the same in all the treatments. Feeding of high CLA ghee resulted in lower (P < 0.01) plasma cholesterol & triglyceride level (52.17 and 30.27%), and higher high density lipoproteins (33.26%) than feeding of soybean oil (control group) and thus manifested in decreased (P < 0.05) atherogenic index (from 0.472 to 0.244). Lesser cholesterol and triglyceride levels were observed in the liver and aorta of high CLA fed rats than in those of the other groups. Histopathological studies of liver showed normal hepatic cords with portal triad in the high CLA ghee fed rats whereas fatty degeneration of hepatocytes containing fat vacuoles was observed in the liver of the other groups. Conclusion: This paper is the first report of the antioxidant and antiatherogenic properties of the high CLA enriched ghee suggesting that high CLA ghee can be used as a potential food for decreasing the risk of cardiovascular diseases, particularly in India, where, ghee is widely used for culinary and medicinal purposes.
    • High level of treatment failure with commonly used anthelmintics on Irish sheep farms

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

      Perdereau, Aude C; Kelleher, Colin T; Douglas, Gerry C.; Hodkinson, Trevor R (Biomed Central, 2014-08-07)
      Background Salix caprea is a cold-tolerant pioneer species that is ecologically important in Europe and western and central Asia. However, little data is available on its population genetic structure and molecular ecology. We describe the levels of geographic population genetic structure in natural Irish populations of S. caprea and determine the extent of gene flow and sexual reproduction using both chloroplast and nuclear simple sequence repeats (SSRs). Results A total of 183 individuals from 21 semi-natural woodlands were collected and genotyped. Gene diversity across populations was high for the chloroplast SSRs (H T  = 0.21-0.58) and 79 different haplotypes were discovered, among them 48% were unique to a single individual. Genetic differentiation of populations was found to be between moderate and high (mean G ST  = 0.38). For the nuclear SSRs, G ST was low at 0.07 and observed heterozygosity across populations was high (H O  = 0.32-0.51); only 9.8% of the genotypes discovered were present in two or more individuals. For both types of markers, AMOVA showed that most of the variation was within populations. Minor geographic pattern was confirmed by a Bayesian clustering analysis. Gene flow via pollen was found to be approximately 7 times more important than via seeds. Conclusions The data are consistent with outbreeding and indicate that there are no significant barriers for gene flow within Ireland over large geographic distances. Both pollen-mediated and seed-mediated gene flow were found to be high, with some of the populations being more than 200 km apart from each other. These findings could simply be due to human intervention through seed trade or accidental transportation of both seeds and pollen. These results are of value to breeders wishing to exploit natural genetic variation and foresters having to choose planting material.
    • High levels of gene flow and genetic diversity in Irish populations of Salix caprea L. inferred from chloroplast and nuclear SSR markers

      Perdereau, Aude C; Kelleher, Colin T; Douglas, Gerry C.; Hodkinson, Trevor R (Biomed Central, 2014-08-07)
      Background: Salix caprea is a cold-tolerant pioneer species that is ecologically important in Europe and western and central Asia. However, little data is available on its population genetic structure and molecular ecology. We describe the levels of geographic population genetic structure in natural Irish populations of S. caprea and determine the extent of gene flow and sexual reproduction using both chloroplast and nuclear simple sequence repeats (SSRs). Results: A total of 183 individuals from 21 semi-natural woodlands were collected and genotyped. Gene diversity across populations was high for the chloroplast SSRs (HT = 0.21-0.58) and 79 different haplotypes were discovered, among them 48% were unique to a single individual. Genetic differentiation of populations was found to be between moderate and high (mean GST = 0.38). For the nuclear SSRs, GST was low at 0.07 and observed heterozygosity across populations was high (HO = 0.32-0.51); only 9.8% of the genotypes discovered were present in two or more individuals. For both types of markers, AMOVA showed that most of the variation was within populations. Minor geographic pattern was confirmed by a Bayesian clustering analysis. Gene flow via pollen was found to be approximately 7 times more important than via seeds. Conclusions: The data are consistent with outbreeding and indicate that there are no significant barriers for gene flow within Ireland over large geographic distances. Both pollen-mediated and seed-mediated gene flow were found to be high, with some of the populations being more than 200 km apart from each other. These findings could simply be due to human intervention through seed trade or accidental transportation of both seeds and pollen. These results are of value to breeders wishing to exploit natural genetic variation and foresters having to choose planting material.
    • High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources

      Perdereau, Aude C.; Douglas, Gerry C.; Hodkinson, Trevor R.; Kelleher, Colin T.; Teagasc Walsh Fellowship Programme (Biomed Central, 2013-08-07)
      Background: Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation. Results: Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix. Conclusions: The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes.
    • High Pressure Processing of Dairy Foods

      Donnelly, W.J.; Beresford, Tom; Lane, C.N.; Walsh-O'Grady, D.; O'Connor, P.; Fitzgerald, R.J.; Murphy, P.M.; O'Reilly, C.; Morgan, S.M.; Ross, R.Paul; Kelly, A. (Teagasc, 2000-09-01)
      The term High Pressure Processing (HPP) is used to describe the technology whereby products are exposed to very high pressures in the region of 50 - 800 MPa (500 - 8000 Atmospheres). The potential application of HPP in the food industry has gained popularity in recent years, due to developments in the construction of HPP equipment which makes the technology more affordable. Applying HPP to food products results in modifications to interactions between individual components, rates of enzymatic reactions and inactivation of micro-organisms. The first commercial HPP products appeared on the market in 1991 in Japan, where HPP is now being used commercially for products such as jams, sauces, fruit juices, rice cakes and desserts. The pioneering research into the application of HPP to milk dates back to the end of the 19th century. Application of HPP to milk has been shown to modify its gel forming characteristics as well as reducing its microbial load. HPP offers the potential to induce similar effects to those generated by heat on milk protein. Recent reports have also indicated that HPP could accelerate the ripening of cheese. Much of the Irish cheese industry is based on the production of Cheddar cheese, the ripening time for which can vary from 4 - 12 months or more, depending on grade. A substantial portion of the cost associated with Cheddar manufacture is therefore attributed to storage under controlled conditions during ripening. Thus, any technology which may accelerate the ripening of Cheddar cheese while maintaining a balanced flavour and texture is of major economic significance. While food safety is a dominant concern, consumers are increasingly demanding foods that maintain their natural appearance and flavour, while free of chemical preservatives. HPP offers the food industry the possibility of achieving these twin goals as this technology can lead to reduced microbial loads without detrimentally effecting the nutritional or sensory qualities of the product. The development of food ingredients with novel functional properties offers the dairy industry an opportunity to revitalise existing markets and develop new ones. HPP can lead to modifications in the structure of milk components, in particular protein, which may provide interesting possibilities for the development of high value nutritional and functional ingredients. Hence these projects set out to investigate the potential of HPP in the dairy industry and to identify products and processes to which it could be applied.
    • High pressure technology in the manufacture of minimally-processed meat products

      Troy, Declan J.; Crehan, Clodagh; Mullen, Anne Maria; Desmond, Eoin (Teagasc, 2001-07)
      High hydrostatic pressure processing was applied to raw minced meat prior to product formulation and the results indicate that with 50 MPa pressure it was possible to reduce the salt in frankfurters from 2.5% to 1.5% without compromising the safety and overall quality. Similarly the phosphate content of frankfurters could be reduced from 0.5% to 0.25% after pressure treatment. Cook loss from the treated frankfurters was significantly reduced indicating a higher yield of product due to the high pressure.
    • High-Resolution Denitrification Kinetics in Pasture Soils Link N2O Emissions to pH, and Denitrification to C Mineralization

      Samad, Md Sainur; Bakken, Lars R.; Nadeem, Shahid; Clough, Timothy J.; de Klein, Cecile A. M.; Richards, Karl G.; Lanigan, Gary; Morales, Sergio E. (PLOS, 2016-03-18)
      Denitrification in pasture soils is mediated by microbial and physicochemical processes leading to nitrogen loss through the emission of N2O and N2. It is known that N2O reduction to N2 is impaired by low soil pH yet controversy remains as inconsistent use of soil pH measurement methods by researchers, and differences in analytical methods between studies, undermine direct comparison of results. In addition, the link between denitrification and N2O emissions in response to carbon (C) mineralization and pH in different pasture soils is still not well described. We hypothesized that potential denitrification rate and aerobic respiration rate would be positively associated with soils. This relationship was predicted to be more robust when a high resolution analysis is performed as opposed to a single time point comparison. We tested this by characterizing 13 different temperate pasture soils from northern and southern hemispheres sites (Ireland and New Zealand) using a fully automated-high-resolution GC detection system that allowed us to detect a wide range of gas emissions simultaneously. We also compared the impact of using different extractants for determining pH on our conclusions. In all pH measurements, soil pH was strongly and negatively associated with both N2O production index (IN2O) and N2O/(N2O+N2) product ratio. Furthermore, emission kinetics across all soils revealed that the denitrification rates under anoxic conditions (NO+N2O+N2 μmol N/h/vial) were significantly associated with C mineralization (CO2 μmol/h/vial) measured both under oxic (r2 = 0.62, p = 0.0015) and anoxic (r2 = 0.89, p<0.0001) conditions.
    • High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses

      O'Sullivan, Daniel J.; Fallico, Vincenzo; O’Sullivan, Orla; McSweeney, Paul L H; Sheehan, Jeremiah J; Cotter, Paul D.; Giblin, Linda (Biomed Central, 2015-11-17)
      Background The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts. Results Amplicons were initially cloned to facilitate Sanger sequencing of individual gene fragments to ensure that a variety of hdc and tdc genes were present. Once this was established, high throughput DNA sequencing of these amplicons was performed to provide a more in-depth analysis of the histamine- and tyramine-producing bacteria present in the cheeses. High-throughput sequencing resulted in generation of a total of 1,563,764 sequencing reads and revealed that Lactobacillus curvatus, Enterococcus faecium and E. faecalis were the dominant species with tyramine producing potential, while Lb. buchneri was found to be the dominant species harbouring histaminogenic potential. Commonly used cheese starter bacteria, including Streptococcus thermophilus and Lb. delbreueckii, were also identified as having biogenic amine producing potential in the cheese studied. Molecular analysis of bacterial communities was then further complemented with HPLC quantification of histamine and tyramine in the sampled cheeses. Conclusions In this study, high-throughput DNA sequencing successfully identified populations capable of amine production in a variety of cheeses. This approach also gave an insight into the broader hdc and tdc complement within the various cheeses. This approach can be used to detect amine producing communities not only in food matrices but also in the production environment itself.
    • High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses

      O'Sullivan, Daniel J.; Fallico, Vincenzo; O’Sullivan, Orla; McSweeney, Paul L H; Sheehan, Jeremiah J; Cotter, Paul D.; Giblin, Linda (Biomed Central, 2015-11-17)
      Background: The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts. Results: Amplicons were initially cloned to facilitate Sanger sequencing of individual gene fragments to ensure that a variety of hdc and tdc genes were present. Once this was established, high throughput DNA sequencing of these amplicons was performed to provide a more in-depth analysis of the histamine- and tyramine-producing bacteria present in the cheeses. High-throughput sequencing resulted in generation of a total of 1,563,764 sequencing reads and revealed that Lactobacillus curvatus, Enterococcus faecium and E. faecalis were the dominant species with tyramine producing potential, while Lb. buchneri was found to be the dominant species harbouring histaminogenic potential. Commonly used cheese starter bacteria, including Streptococcus thermophilus and Lb. delbreueckii, were also identified as having biogenic amine producing potential in the cheese studied. Molecular analysis of bacterial communities was then further complemented with HPLC quantification of histamine and tyramine in the sampled cheeses. Conclusions: In this study, high-throughput DNA sequencing successfully identified populations capable of amine production in a variety of cheeses. This approach also gave an insight into the broader hdc and tdc complement within the various cheeses. This approach can be used to detect amine producing communities not only in food matrices but also in the production environment itself.
    • High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

      Fouhy, Fiona; Guinane, Caitriona M.; Hussey, Seamus; Wall, Rebecca; Ryan, C. Anthony; Dempsey, Eugene M.; Murphy, Brendan; Ross, R Paul; Fitzgerald, Gerald F; Stanton, Catherine; Cotter, Paul D. (American Society for Microbiology, 2012-09-04)
      The infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA and rpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions of Proteobacteria (P = 0.0049) and significantly lower proportions of Actinobacteria (P = 0.00001) (and the associated genus Bifidobacterium [P = 0.0132]) as well as the genus Lactobacillus (P = 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, the Proteobacteria levels remained significantly higher in the treated infants (P = 0.0049), but the Actinobacteria, Bifidobacterium, and Lactobacillus levels had recovered and were similar to those in the control samples. Despite this recovery of total Bifidobacterium numbers, rpoB-targeted pyrosequencing revealed that the number of different Bifidobacterium species present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.
    • Historical Grassland Turboveg Database Project. 2067 Relevés recorded by Dr Austin O’ Sullivan 1962 – 1982

      Bourke, David; Hochstrasser, Tamara; Nolan, Stephen; Schulte, Rogier P.; National Parks and Wildlife Service (Teagasc, 2007-09-01)
      The more common grassland types occupy about 70% of the Irish landscape (O’Sullivan, 1982), but information on these vegetation types is rare. Generally, Irish grasslands are distinguished based on the intensity of their management (improved or semi-natural grasslands), and the drainage conditions and acidity of the soil (dry or wet, calcareous or acidic grassland types) (Fossitt, 2000). However, little is known about their floristic composition and the changes in floristic composition over time. The current knowledge on grassland vegetation is mostly based on a survey of Irish grasslands by Dr. Austin O’Sullivan completed in the 1960’s and 1970’s (O’Sullivan, 1982). In this survey O’Sullivan identified Irish grassland types in accordance with the classification of continental European grasslands based on the principles of the School of Phytosociology. O’Sullivan distinguished five main grassland types introducing agricultural criteria as well as floristic criteria into grassland classification (O’Sullivan, 1982). In 1978, O’Sullivan made an attempt at mapping Ireland’s vegetation types including the five grassland types distinguished in his later publication as well as two types of peatland vegetation (Figures 1 and 2). This map was completed using 1960’s soils maps (National Soil Survey, Teagasc, Johnstown Castle) and a subsample of the dataset on the composition of Irish grasslands. Phytosociological classification of vegetation is based on the full floristic composition of the vegetation as determined by assessing the abundance and spatial structure of the plant species in a given area. The actual area of the survey (or relevé) is determined according to strict criteria, which include how representative the sample area is for the wider vegetation (i.e. how many of the species found in the wider area are also present in the survey area).