• 16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

      Fouhy, Fiona; Clooney, Adam G; Stanton, Catherine; Claesson, Marcus J; Cotter, Paul D (Biomed Central, 2016-06-24)
      Background Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data differed depending on the primers and sequencing platform that were used. The results demonstrate the risks in comparing data generated using different sequencing approaches and highlight the merits of choosing a standardised approach for sequencing in situations where a comparison across multiple sequencing runs is required.
    • Acrylamide formation in potato products

      Brunton, Nigel; Gormley, Ronan T.; Butler, Francis; Cummins, Enda; Danaher, Martin; O'Keeffe, Michael (Teagasc, 2006-08)
      Acrylamide, a substance classified as a potential carcinogen, occurs in heated starchy foods at concentrations many times in excess of levels permitted in drinking water. Early surveys indicated that levels of acrylamide in potato products such as French fries and potato crisps were the highest of the foodstuffs investigated. The present project addressed this issue by determining levels of acrylamide precursors (asparagine and reducing sugars) in raw potatoes and levels of acrylamide in (i) potato products from different storage regimes, (ii) spot-sampled potatoes purchased from a local supermarket, (iii) samples that received pre-treatments and were fried at different temperatures and (iv) French fries reheated in different ovens.A risk assessment of the estimated acrylamide intake from potato products for various cohorts of the Irish population was also conducted.
    • Adding value to beef forequarter muscles

      Kenny, Tony; Lennon, Ann; Ward, Patrick; Sullivan, Paul; McDonald, Karl; Downey, Gerard; O'Neill, Eileen (Teagasc, 2008-11)
      The forequarter constitutes 50% of the weight of a beef carcase but only about 25% of its value. To fulfill the objectives of this project, the work was organised into 4 parts as follows: 1.Characterisation of the available raw material, in terms of properties of individual muscles seamed out from carcasses of representative types of animals produced in Ireland. 2.Comparison of yields and operator time for seaming and conventional boning. 3.Utilisation of separated muscles in added-value products using appropriate tenderising, bonding and forming technology. 4.Transfer of the knowledge and technology to the industry.
    • Adding value to Beef Forequarter Muscles

      Kenny, Tony; Lennon, Ann; Ward, Patrick; Sullivan, Paul; McDonald, Karl; O’Neill, Eileen; Downey, Gerard (Teagasc, 2008-11-01)
      The forequarter constitutes 50% of the weight of a beef carcase but only about 25% of its value.To fulfill the objectives of this project, the work was organised into 4 parts as follows: 1.Characterisation of the available raw material, in terms of properties of individual muscles seamed out from carcasses of representative types of animals produced in Ireland. 2.Comparison of yields and operator time for seaming and conventional boning. 3.Utilisation of separated muscles in added-value products using appropriate tenderising, bonding and forming technology. 4.Transfer of the knowledge and technology to the industry.
    • Adding value to cull cow beef

      O'Donovan, Michael; Minchin, William; Buckley, Frank; Kenny, David; Shalloo, Laurence (Teagasc, 2009-08-01)
      This project addressed the prospects of increasing the value of cull cow beef and examined the potential of a number of different management and dietary strategies. In Ireland, the national cow herd contributes 350,000 animals to total beef production annually, which represents 22% of all cattle slaughtered (DAF, 2007). A dominant feature of beef production in Ireland is the disposal of cows from the dairy and beef industries, the time of year at which culling occurs influences the number of cows available for slaughter. Suitability of a cow for slaughter is generally not a consideration for dairy or beef farmers.
    • Adding value to milk by increasing its protein and CLA contents

      Murphy, J.J.; Stanton, Catherine; O'Donovan, Michael; Kavanagh, S.; Maher, J.; Patton, Joe; Mohammed, Riaz (Teagasc, 2008-08-01)
      The mid-summer milk protein study was undertaken on 34 commercial dairy farms in 2005 to evaluate the influence of dietary and management variables on milk protein content in mid-season. Data on grass composition, genetic merit of the herds and milk protein content were collected and analysed by multiple regression. Both calving date and genetic merit for milk protein content were significantly associated with milk protein content and were used as adjustment factors when evaluating the association between measures of grass quality and milk protein content. Milk protein content was associated with grass OMD (P = 0.04) and NDF content (P = 0.02) but not with CP content (P = 0.80). It is concluded that herds calving earlier, with a greater genetic merit for milk protein content and consuming better quality pasture would have greater milk protein contents in mid-season.
    • Adding Value To Under utilised Fish Species

      Fagan, John; Gormley, Ronan T.; Mitchell, Michelle; Downey, Gerard (Teagasc, 2006-02-01)
      Tightening fish quotas and supply shortages for conventional species are causing major difficulties for both fishermen and seafood processors. There is a need, therefore, to explore the potential of underutilised fish species both as fillets or portions and as added-value products. The current project at Ashtown Food Research Centre (AFRC) addressed this issue for a number of underutilised species via (a) sous vide processing (with savoury sauces),(b)marinating (salt- and sugar-based marinades) and (c) via a combination of freeze-chilling and modified atmosphere packaging (MAP).A range of physico-chemical and sensory tests was conducted on the products and their shelf-life status was also determined.
    • Adding value to under-utilised fish species

      Fagan, John; Gormley, Ronan T.; Mitchell, Michelle; Downey, Gerard (Teagasc, 2006-02)
      Tightening fish quotas and supply shortages for conventional species are causing major difficulties for both fishermen and seafood processors. There is a need, therefore, to explore the potential of underutilised fish species both as fillets or portions and as added-value products. The current project at Ashtown Food Research Centre (AFRC) addressed this issue for a number of underutilised species via (a) sous vide processing (with savoury sauces),(b)marinating (salt- and sugar-based marinades) and (c) via a combination of freeze-chilling and modified atmosphere packaging (MAP).A range of physico-chemical and sensory tests was conducted on the products and their shelf-life status was also determined.
    • Administration of a live culture of Lactococcus lactis DPC 3147 into the bovine mammary gland stimulates the local host immune response, particularly IL-1β and IL-8 gene expression

      Beecher, Christine; Daly, Mairead; Berry, Donagh P.; Klostermann, Katja; Flynn, James; Meaney, William J; Hill, Colin; McCarthy, Tommie V.; Ross, R Paul; Giblin, Linda (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 2009-05-18)
      Mastitis is one of the most costly diseases to the dairy farming industry. Conventional antibiotic therapy is often unsatisfactory for successful treatment of mastitis and alternative treatments are continually under investigation. We have previously demonstrated, in two separate field trials, that a probiotic culture, Lactococcus lactis DPC 3147, was comparable to antibiotic therapy to treat bovine mastitis. To understand the mode of action of this therapeutic, we looked at the detailed immune response of the host to delivery of this live strain directly into the mammary gland of six healthy dairy cows. All animals elicited signs of udder inflammation 7 h post infusion. At this time, clots were visible in the milk of all animals in the investigation. The most pronounced increase in immune gene expression was observed in Interleukin (IL)-1b and IL-8, with highest expression corresponding to peaks in somatic cell count. Infusion with a live culture of a Lc. lactis leads to a rapid and considerable innate immune response.
    • Algal Proteins: Extraction, Application, and Challenges Concerning Production

      Bleakley, Stephen; Hayes, Maria (MDPI, 2017-04-26)
      Population growth combined with increasingly limited resources of arable land and fresh water has resulted in a need for alternative protein sources. Macroalgae (seaweed) and microalgae are examples of under-exploited “crops”. Algae do not compete with traditional food crops for space and resources. This review details the characteristics of commonly consumed algae, as well as their potential for use as a protein source based on their protein quality, amino acid composition, and digestibility. Protein extraction methods applied to algae to date, including enzymatic hydrolysis, physical processes, and chemical extraction and novel methods such as ultrasound-assisted extraction, pulsed electric field, and microwave-assisted extraction are discussed. Moreover, existing protein enrichment methods used in the dairy industry and the potential of these methods to generate high value ingredients from algae, such as bioactive peptides and functional ingredients are discussed. Applications of algae in human nutrition, animal feed, and aquaculture are examined
    • The altered gut microbiota in adults with cystic fibrosis

      Burke, D.G.; Fouhy, Fiona; Harrison, M. J; Rea, Mary C; Cotter, Paul D; O’Sullivan, O.; Stanton, Catherine; Hill, C.; Shanahan, F.; Plant, B. J; Ross, R. Paul (Biomed Central, 2017-03-09)
      Background Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction in the gastrointestinal tract, as well as frequent antibiotic exposure, undoubtedly disrupts the gut microbiota. To analyse the effects of CF and its management on the microbiome, we compared the gut microbiota of 43 individuals with CF during a period of stability, to that of 69 non-CF controls using 454-pyrosequencing of the 16S rRNA gene. The impact of clinical parameters, including antibiotic therapy, on the results was also assessed. Results The CF-associated microbiome had reduced microbial diversity, an increase in Firmicutes and a reduction in Bacteroidetes compared to the non-CF controls. While the greatest number of differences in taxonomic abundances of the intestinal microbiota was observed between individuals with CF and the healthy controls, gut microbiota differences were also reported between people with CF when grouped by clinical parameters including % predicted FEV1 (measure of lung dysfunction) and the number of intravenous (IV) antibiotic courses in the previous 12 months. Notably, CF individuals presenting with severe lung dysfunction (% predicted FEV1 ≤ 40%) had significantly (p < 0.05) reduced gut microbiota diversity relative to those presenting with mild or moderate dysfunction. A significant negative correlation (−0.383, Simpson’s Diversity Index) was also observed between the number of IV antibiotic courses and gut microbiota diversity. Conclusions This is one of the largest single-centre studies on gut microbiota in stable adults with CF and demonstrates the significantly altered gut microbiota, including reduced microbial diversity seen in CF patients compared to healthy controls. The data show the impact that CF and it's management have on gut microbiota, presenting the opportunity to develop CF specific probiotics to minimise microbiota alterations.
    • The altered gut microbiota in adults with cystic fibrosis

      Burke, D.G.; Fouhy, Fiona; Harrison, M. J; Rea, Mary C; Cotter, Paul D; O’Sullivan, Orla; Stanton, Catherine; Hill, C.; Shanahan, F.; Plant, B. J; Ross, R. Paul (Biomed Central, 2017-03-09)
      Background Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction in the gastrointestinal tract, as well as frequent antibiotic exposure, undoubtedly disrupts the gut microbiota. To analyse the effects of CF and its management on the microbiome, we compared the gut microbiota of 43 individuals with CF during a period of stability, to that of 69 non-CF controls using 454-pyrosequencing of the 16S rRNA gene. The impact of clinical parameters, including antibiotic therapy, on the results was also assessed. Results The CF-associated microbiome had reduced microbial diversity, an increase in Firmicutes and a reduction in Bacteroidetes compared to the non-CF controls. While the greatest number of differences in taxonomic abundances of the intestinal microbiota was observed between individuals with CF and the healthy controls, gut microbiota differences were also reported between people with CF when grouped by clinical parameters including % predicted FEV1 (measure of lung dysfunction) and the number of intravenous (IV) antibiotic courses in the previous 12 months. Notably, CF individuals presenting with severe lung dysfunction (% predicted FEV1 ≤ 40%) had significantly (p < 0.05) reduced gut microbiota diversity relative to those presenting with mild or moderate dysfunction. A significant negative correlation (−0.383, Simpson’s Diversity Index) was also observed between the number of IV antibiotic courses and gut microbiota diversity. Conclusions This is one of the largest single-centre studies on gut microbiota in stable adults with CF and demonstrates the significantly altered gut microbiota, including reduced microbial diversity seen in CF patients compared to healthy controls. The data show the impact that CF and it's management have on gut microbiota, presenting the opportunity to develop CF specific probiotics to minimise microbiota alterations.
    • Alternative uses for co-products: Harnessing the potential of valuable compounds from meat processing chains

      Mullen, Anne Maria; Alvarez Garcia, Carlos; Zeugolis, Dimitrios; Henchion, Maeve; O'Neill, Eileen; Drummond, Liana (Elsevier, 2017-05-03)
      Opportunities for exploiting the inherent value of protein-rich meat processing co-products, in the context of increased global demand for protein and for sustainable processing systems, are discussed. While direct consumption maybe the most profitable route for some, this approach is influenced greatly by local and cultural traditions. A more profitable and sustainable approach may be found in recognizing this readily available and under-utilised resource can provide high value components, such as proteins, with targeted high value functionality of relevance to a variety of sectors. Applications in food & beverages, petfood biomedical and nutrition arenas are discussed. Utilization of the raw material in its entirety is a necessary underlying principle in this approach to help maintain minimum waste generation. Understanding consumer attitudes to these products, in particular when used in food or beverage systems, is critical in optimizing commercialization strategies.
    • Antibiotic resistance in foodborne pathogens

      Duffy, Geraldine; Walsh, Ciara (Teagasc, 2005-02)
      Wide-spread antibiotic resistance among bacterial pathogens is now a serious public health issue and multi-antibiotic resistance has been reported in many foodborne pathogens including Salmonella and E. coli.
    • Antibiotic Resistance in the Gut Microbiota

      Fouhy, Fiona (2014)
      Antibiotic resistance is an increasing threat to our ability to treat infectious diseases. Thus, understanding the effects of antibiotics on the gut microbiota, as well as the potential for such populations to act as a reservoir for resistance genes, is imperative. This thesis set out to investigate the gut microbiota of antibiotic treated infants compared to untreated controls using high-throughput DNA sequencing. The results demonstrated the significant effects of antibiotic treatment, resulting in increased proportions of Proteobacteria and decreased proportions of Bifidobacterium. The species diversity of bifidobacteria was also reduced. This thesis also highlights the ability of the human gut microbiota to act as an antibiotic resistance reservoir. Using metagenomic DNA extracted from faecal samples from adult males, PCR was employed to demonstrate the prevalence and diversity of aminoglycoside and β-lactam resistance genes in the adult gut microbiota and highlighted the merits of the approach adopted. Using infant faecal samples, we constructed and screened a second fosmid metagenomic bank for the same families of resistance genes and demonstrated that the infant gut microbiota is also a reservoir for resistance genes. Using in silico analysis we highlighted the existence of putative aminoglycoside and β-lactam resistance determinants within the genomes of Bifidobacterium species. In the case of the β- lactamases, these appear to be mis-annotated. However, through homologous recombination-mediated insertional inactivation, we have demonstrated that the putative aminoglycoside resistance proteins do contribute to resistance. In additional studies, we investigated the effects of short bowel syndrome on infant gut microbiota, the immune system and bile acid metabolism. We also sequenced the microbiota of the human vermiform appendix, highlighting its complexity. Finally, this thesis demonstrated the strain specific nature of 2 different probiotic CLA-producing Bifidobacterium breve on the murine gut microbiota.
    • Antimicrobial antagonists against food pathogens; a bacteriocin perspective

      O'Connor, Paula M.; Ross, R Paul; Hill, Colin; Cotter, Paul D. (Elsevier, 2015-02-03)
      Efforts are continuing to find novel bacteriocins with enhanced specificity and potency. Traditional plating techniques are still being used for bacteriocin screening studies, however, the availability of ever more bacterial genome sequences and the use of in silico gene mining tools have revealed novel bacteriocin gene clusters that would otherwise have been overlooked. Furthermore, synthetic biology and bioengineering-based approaches are allowing scientists to harness existing and novel bacteriocin gene clusters through expression in different hosts and by enhancing functionalities. The same principles apply to bacteriocin producing probiotic cultures and their application to control pathogens in the gut. We can expect that the recent developments on bacteriocins from Lactic Acid Bacteria (LAB) described here will contribute greatly to increased commercialisation of bacteriocins in food systems.
    • Application of class-modelling techniques to near infrared data for food authentication purposes

      Oliveri, P.; Di Egidio, V.; Woodcock, T.; Downey, Gerard (Elsevier, 2011)
      Following the introduction of legal identifiers of geographic origin within Europe, methods for confirming any such claims are required. Spectroscopic techniques provide a method for rapid and non-destructive data collection and a variety of chemometric approaches have been deployed for their interrogation. In this present study, class-modelling techniques (SIMCA, UNEQ and POTFUN) have been deployed after data compression by principal component analysis for the development of class-models for a set of olive oil and honey. The number of principal components, the confidence level and spectral pre-treatments (1st and 2nd derivative, standard normal variate) were varied, and a strategy for variable selection was tried. Models were evaluated on a separate validation sample set. The outcomes are reported and criteria for selection of the most appropriate models for any given application are discussed.
    • The Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality Defects

      O'Sullivan, Daniel (2015)
      High throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencingbased approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbeassociated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses.
    • Aroma compound diacetyl suppresses glucagon-like peptide-1 production and secretion in STC-1 cells

      McCarthy, Triona; Bruen, Christine; O'Halloren, Fiona; Schellekens, Harriet; Kilcawley, Kieran N; Cryan, John F.; Giblin, Linda (Elsevier, 2017-01-21)
      Diacetyl is a volatile flavour compound that has a characteristic buttery aroma and is widely used in the flavour industry. The aroma of a food plays an important role in food palatability and thus intake. This study investigates the effect of diacetyl on the satiety hormone, glucagon-like peptide (GLP-1), using the enteroendocrine cell line, STC-1. Diacetyl decreased proglucagon mRNA and total GLP-1 from glucose stimulated STC-1 cells. This dampening effect on GLP-1 appears to be mediated by increasing intracellular cAMP levels, increasing synthesis of the G protein coupled receptor, GPR120, and its recruitment to the cell surface. Voltage gated Ca2+ channels, K+ATP channels and the α-gustducin taste pathway do not appear to be involved. These findings demonstrate that components contributing to food palatability suppress GLP-1. This ability of diacetyl to reduce satiety signals may contribute to overconsumption of some palatable foods.
    • Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires

      Giblin, Linda; Butler, Stephen T.; Kearney, Breda M.; Waters, Sinead M.; Callanan, Michael J.; Berry, Donagh P. (Biomed Central, 2010-07-29)
      Background: Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire. Results: All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P < 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P < 0.1). The G allele of LEP-1238 was associated (P < 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer gestation length and tended to associate (P < 0.1) with an increase in calving difficulty, calf perinatal mortality and somatic cells in the milk. LEP-963 exhibited an association (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and gestation length. It also tended to associate with milk yield (P < 0.1). The R25C SNP associated (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and length of gestation. The T allele of the Y7F SNP significantly associated with reduced angularity (P < 0.01) and reduced milk protein yield (P < 0.05). There was also a tendency (P < 0.1) for Y7F to associate with increased body condition score, reduced milk yield and shorter gestation (P < 0.1). A80V associated with reduced survival in the herd (P < 0.05). Conclusions Several leptin polymorphisms (LEP-2470, LEP-1238, LEP-963, Y7F and R25C) associated with the energetically expensive process of lactogenesis. Only SNP Y7F associated with energy storage. Associations were also observed between leptin polymorphisms and calving difficulty, gestation length and calf perinatal mortality. The lack of an association between the leptin variants investigated with calving interval in this large data set would question the potential importance of these leptin variants, or indeed leptin, in selection for improved fertility in the Holstein-Friesian dairy cow.