In December 2016, Teagasc restructured the Food Research Programme, creating a new department - Food Quality & Sensory Science. The articles in this collection include those authored by members of this department while they were in previous departments.

Recent Submissions

  • Optimization of protein recovery from bovine lung by pH shift process using response surface methodology

    Lynch, Sarah A.; Alvarez, Carlos; O'Neill, Eileen E.; Keenan, Derek F.; Mullen, Anne Maria; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; 11/F/043 (Wiley, 2017-09)
    BACKGROUND Response surface methodology (RSM) was used in a sequential manner to optimize solubilization and precipitation conditions in the recovery of protein from bovine lung using pH shift. RESULTS Separate D‐optimal designs were employed for protein solubilization and precipitation. Independent variables investigated for protein solubilization were time (10–120 min), temperature (4–20 °C), pH (8.0–11.0) and solvent/sample ratio (2.5–10). Variables for protein precipitation were time (0–60 min) and pH (4.25–6.00). Soluble protein yields ranged from 323 to 649 g kg−1 and the quadratic model for protein solubilization revealed a coefficient of determination R2 of 0.9958. Optimal conditions for maximum protein solubility were extraction time 140 min, temperature 19 °C, pH 10.8 and solvent/sample ratio 13.02. Protein precipitation yields varied from 407 to 667 g kg−1, giving a coefficient of determination R2 of 0.9335. Optimal conditions for maximum protein precipitation were pH 5.03 and 60 min. Based on the RSM model, solubilization conditions were manipulated to maximize protein solubilization under reduced water and alkaline usage. These conditions were also validated. CONCLUSION Models for solubilization and precipitation using bovine and porcine lung were validated; predicted and actual yields were in good agreement, showing cross‐species applicability of the results. © 2017 Society of Chemical Industry
  • The eating quality of beef from young dairy bulls derived from two breed types at three ages from two different production systems

    Nian, Yingqun; Kerry, J. P.; Prendiville, Robert; Allen, Paul; Teagasc Walsh Fellowship Programme (Teagasc (Agriculture and Food Development Authority), Ireland, 2017-07-08)
    Expansion of the Irish dairy herd has led to more dairy breed male calves being available for beef production. This study investigated the physico-chemical and sensory characteristics of beef from Holstein-Friesian (HF) and Jersey × HF (JEX) young bulls fed pasture grass only or pasture grass plus 2 kg concentrate during their first grazing season and slaughtered at 15, 19 or 22 mo of age. Longissimus thoracis (LT) muscles were collected from 67 carcasses. Postmortem pH, ultimate pH (pHu), meat colour, chemical composition, collagen content and solubility were evaluated. After ageing for 21 d, Warner-Bratzler shear force and cooking loss were determined, and assessments by a trained sensory panel were conducted. Meat from older animals was darker. The pHu, moisture and ash contents decreased, while residual roast beef flavour length increased with age. However, increasing age to slaughter did not negatively influence tenderness. JEX beef had lower cooking loss, was darker and redder, in addition to having higher sensory scores for initial tenderness and fattiness than HF beef. Warner-Bratzler variables were positively correlated with cooking loss and chewiness and were negatively correlated with intramuscular fat (IMF) content, soluble collagen and initial tenderness. In summary, most young dairy bull beef samples were acceptably tender after 21 d of ageing and half of them had acceptable IMF content. Slaughter age affected beef colour, pHu, chemical composition and flavour length. The eating quality of meat from the JEX breed type was considered to be superior to that of the HF breed type. Diet during the first season had no effect on meat quality traits.
  • Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs

    Horodyska, Justyna; Hamill, Ruth M.; Varley, Patrick F.; Wimmers, Klaus (PLOS, 2017-06-12)
    Feed conversion efficiency is a measure of how well an animal converts feed into live weight and it is typically expressed as feed conversion ratio (FCR). FCR and related traits like growth rate (e.g. days to 110 kg—D110) are of high interest for animal breeders, farmers and society due to implications on animal performance, feeding costs and environmental sustainability. The objective of this study was to identify genomic regions associated with FCR and D110 in pigs. A total of 952 terminal line boars, showing an individual variation in FCR, were genotyped using 60K SNP-Chips. Markers were tested for associations with estimated breeding values (EBV) for FCR and D110. For FCR, the largest number of associated SNPs was located on chromosomes 4 (30 SNPs), 1 (25 SNPs), X (15 SNPs) and 6 (12 SNPs). The most prominent genomic regions for D110 were identified on chromosomes 15 (10 SNPs), 1 and 4 (both 9 SNPs). The most significantly associated SNPs for FCR and D110 mapped 129.8 Kb from METTL11B (chromosome 4) and 32Kb from MBD5 (chromosome 15), respectively. A list of positional genes, closest to significantly associated SNPs, was used to identify enriched pathways and biological functions related to the QTL for both traits. A number of candidate genes were significantly overrepresented in pathways of immune cell trafficking, lymphoid tissue structure, organ morphology, endocrine system function, lipid metabolism, and energy production. After resequencing the coding region of selected positional and functional candidate genes, six SNPs were genotyped in a subset of boars. SNPs in PRKDC, SELL, NR2E1 and AKRIC3 showed significant associations with EBVs for FCR/D110. The study revealed a number of chromosomal regions and candidate genes affecting FCR/D110 and pointed to corresponding biological pathways related to lipid metabolism, olfactory reception, and also immunological status.
  • Future Protein Supply and Demand: Strategies and Factors Influencing a Sustainable Equilibrium

    Henchion, Maeve; Hayes, Maria; Mullen, Anne Maria; Fenelon, Mark; Tiwari, Brijesh; Department of Agriculture, Food and the Marine; 11/F/043 (MDPI, 2017-07-20)
    A growing global population, combined with factors such as changing socio-demographics, will place increased pressure on the world’s resources to provide not only more but also different types of food. Increased demand for animal-based protein in particular is expected to have a negative environmental impact, generating greenhouse gas emissions, requiring more water and more land. Addressing this “perfect storm” will necessitate more sustainable production of existing sources of protein as well as alternative sources for direct human consumption. This paper outlines some potential demand scenarios and provides an overview of selected existing and novel protein sources in terms of their potential to sustainably deliver protein for the future, considering drivers and challenges relating to nutritional, environmental, and technological and market/consumer domains. It concludes that different factors influence the potential of existing and novel sources. Existing protein sources are primarily hindered by their negative environmental impacts with some concerns around health. However, they offer social and economic benefits, and have a high level of consumer acceptance. Furthermore, recent research emphasizes the role of livestock as part of the solution to greenhouse gas emissions, and indicates that animal-based protein has an important role as part of a sustainable diet and as a contributor to food security. Novel proteins require the development of new value chains, and attention to issues such as production costs, food safety, scalability and consumer acceptance. Furthermore, positive environmental impacts cannot be assumed with novel protein sources and care must be taken to ensure that comparisons between novel and existing protein sources are valid. Greater alignment of political forces, and the involvement of wider stakeholders in a governance role, as well as development/commercialization role, is required to address both sources of protein and ensure food security.
  • Variation in the quality of meat from Irish steers at the time of slaughter.

    Moloney, Aidan P; Mullen, Anne Maria; Maher, S.C.; Buckley, D.J.; Kerry, J.P. (Teagasc, 2004-01-01)
    There is no information on the variation in quality, in particular tenderness, that exists in Irish Beef nor is there information on the variation that would remain if optimum practices were imposed at all stages of the beef production chain. Evaluation of the success of measures to improve beef consistency requires information on existing variation and the minimum variation achievable.The objectives of this project were (i) to establish the variation that exists in the quality of meat from Irish cattle, (ii) to quantify the minimum variation in meat quality that can be achieved in a practical beef production system, (iii) to determine the effects and mechanisms of additional sources of variation. The conclusions from this project are: • The M. longissimus dorsi (loin) was found to be more variable than the M. semimembranosus (topside) for most quality attributes examined (tenderness, sarcomere length and pH). The scale of variation within the loin was similar to that reported by the other research groups within the EU and US. Heifers were more variable than steers for most attributes, while there was no consistent classification effect on the variability of meat quality attributes. • Tenderness was equally variable in meat from genetically similar steers, managed similarly, compared to commercial steers randomly selected from a factory lairage but matched for weight and grade.This was likely a result of both groups being crossbred beef cattle of similar age, fat score, carcass weight and managed identically post-mortem. However, variation in tenderness of both groups was less than that observed in a survey of commercial throughput (experiment 1). This decrease is attributed to better pre-and-post-slaughter handling practices. • The data suggest that selection of sires (within a breed) with better than average conformation has no deleterious effect on the eating quality of beef of their progeny.A more comprehensive comparison of sires within a breed and between breeds is required to confirm the generality of this conclusion. • In a comparison of genotypes, gender and slaughter weights, there was no evidence that variation around the mean value for tenderness differed between breeds or liveweights after 14 days ageing. Bulls were more variable than steers for some quality traits but the variation in tenderness was similar for bulls and steers after 14 days ageing. • While optimising the management of animals during the pre and post-slaughter period reduced variation in tenderness, some residual variation remained. A large percentage of the residual variation in tenderness (Warner Bratzler shear force) after 2 and 7 days post-mortem was explained by proteolysis (breakdown of myofibrillar proteins).Variation in tenderness (Warner Bratzler shear force) after 2 days post-mortem was largely explained by phosphates (energy) and proteolysis, while sensory tenderness was largely explained by phosphates and glycolytic potential. • Further work is required to reduce residual variation in Irish beef and to determine the causes of this variation.
  • Future Protein Supply and Demand: Strategies and Factors Influencing a Sustainable Equilibrium

    Henchion, Maeve; Hayes, Maria; Mullen, Anne Maria; Fenelon, Mark A.; Tiwari, Brijesh (MDPI, 2017-07-20)
    A growing global population, combined with factors such as changing socio-demographics, will place increased pressure on the world’s resources to provide not only more but also different types of food. Increased demand for animal-based protein in particular is expected to have a negative environmental impact, generating greenhouse gas emissions, requiring more water and more land. Addressing this “perfect storm” will necessitate more sustainable production of existing sources of protein as well as alternative sources for direct human consumption. This paper outlines some potential demand scenarios and provides an overview of selected existing and novel protein sources in terms of their potential to sustainably deliver protein for the future, considering drivers and challenges relating to nutritional, environmental, and technological and market/consumer domains. It concludes that different factors influence the potential of existing and novel sources. Existing protein sources are primarily hindered by their negative environmental impacts with some concerns around health. However, they offer social and economic benefits, and have a high level of consumer acceptance. Furthermore, recent research emphasizes the role of livestock as part of the solution to greenhouse gas emissions, and indicates that animal-based protein has an important role as part of a sustainable diet and as a contributor to food security. Novel proteins require the development of new value chains, and attention to issues such as production costs, food safety, scalability and consumer acceptance. Furthermore, positive environmental impacts cannot be assumed with novel protein sources and care must be taken to ensure that comparisons between novel and existing protein sources are valid. Greater alignment of political forces, and the involvement of wider stakeholders in a governance role, as well as development/commercialization role, is required to address both sources of protein and ensure food security
  • Enzyme Modified Cheese Flavour Ingredients

    Wilkinson, M.; Kilcawley, Kieran; Mulholland, E. (Teagasc, 2000-09-01)
    Enzyme-modified cheeses (EMCs) are defined as concentrated cheese flavours produced enzymatically from cheeses of various ages and are principally used as an ingredient in processed foods, where they provide a cost-effective alternative to natural cheese. They can be used as the sole source of cheese flavour to intensify an existing cheese taste, or to impart a specific cheese character to a more bland product. Their main applications are in processed cheese, analogue cheese, cheese spreads, snack foods, soups, sauces, biscuits, dips and pet foods. Their main advantages over other cheese flavour ingredients are: low production costs, consistency, high flavour intensity, diverse flavour range, extended shelf- life, low storage costs and increased functionality. EMCs are generated utilising the same flavour pathways that occur in natural cheese ripening i.e. proteolysis, lipolysis and glycolysis. They are not as easy to differentiate as natural cheeses, as they are characterised by flavour and aroma alone as texture is not a factor in EMC production. The relationship of the flavour of EMCs to the flavour of the corresponding natural cheese remains unclear. This is especially true for Cheddar EMC which is commercially available in a range of Cheddar flavours . Despite the fact that a wide range of commercial EMCs are available, there is very little detailed information available regarding their properties or the specific production processes used. The main objective of this research was to build a knowledge base on EMC products and to utilise this to develop a biotechnological process for the production of improved enzyme modified cheeses for use as flavour ingredients. The strategy was to establish quantitative relationships between the compositional, proteolytic and lipolytic parameters and the sensory characteristics of EMCs. This data would then be used to develop a predictive model for flavour development in EMC production and the subsequent generation of an optimised EMC process enabling the generation of a range of cheese flavours from single or multiple substrates.
  • Model System for the Production of Enzyme Modified Cheese (EMC) Flavours.

    Kilcawley, Kieran N; Beresford, Tom; Lee, B.; Wilkinson, M.G. (Teagasc, 2002-04-01)
    Natural cheese flavour ingredients, in the form of enzyme modified cheeses (EMCs), are widely used in the convenience food industry and can provide high volume added opportunities for the cheese industry. Many EMCs are produced using commercial enzyme preparations and previous studies have indicated that they contain side activities in addition to their stated main activity (see DPRC Report No.10). Therefore, it is critical that the exact enzyme complement of these preparations are known before they can be used to produce EMC of specific requirements on a consistent basis. The scientific basis of rapid enzyme mediated flavour formation in the production of EMCs is not fully understood. Consequently this knowledge gap is a major obstacle in the development of high value cheese flavour ingredients. Hence, a major objective of this project was to deepen the scientific understanding of flavour formation with a view to the production of natural enzyme-mediated dairy flavour ingredients with commercial potential. The ultimate aim was to develop the technology to produce customised high value dairy flavour ingredients in an optimised process.
  • Effect of pulse flours on the physiochemical characteristics and sensory acceptance of baked crackers

    Millar, Kim A.; Barry-Ryan, Catherine; Burke, Roisin; Hussey, Karen; McCarthy, Sinead; Gallagher, Eimear (Wiley, 2017-03-29)
    Pulse flours offer nutritional alternatives to wheat flour in the production of baked snacks due to their high protein and fibre levels and low glycaemic index. In this study, broad-bean (Vicia faba), yellow-pea and green-pea (Pisum sativum) flours were each blended with wheat flour at 40% in the formulation of chemically leavened crackers. The effects of flour type and baking time on the physiochemical properties, sensory acceptability, nutritional composition and antioxidant activity of the crackers were observed in comparison with 100% wheat crackers. Broad-bean crackers had the highest protein content and antioxidant activity (13 g per 100 g DM and 38.8 mgAAE per 100 g DM, respectively). Yellow-pea crackers had the highest fibre content (12 g per 100 g DM). Physical dimensions and colour attributes were significantly affected by pulse-flour substitution. Yellow-pea and broad-bean crackers were significantly preferred by consumers compared to the control, demonstrating the potential application of these flours to improve the eating quality and nutritional profile of crackers.
  • 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.
  • Enhancement of pigmeat quality by altering pre-slaughter management.

    Lawlor, Peadar G; Lynch, P.B.; Mullane, J.; Kerry, Joseph; Hogan, S.A.; Allen, Paul (Teagasc, 2005-10-25)
    The studies presented in this report were conducted to investigate the effect of breed, slaughter weight, castration of male pigs and strategic feeding strategies on the performance of pigs to slaughter and on their carcass quality.
  • Evaluation of beef eating quality by Irish consumers

    McCarthy, Sinead; Henchion, Maeve; White, A.; Brandon, K.; Allen, Paul; Department of Agriculture, Food and the Marine; 04/R&D/TN/256 (Elsevier, 2017-05-08)
    A consumer's decision to purchase beef is strongly linked to its sensory properties and consistent eating quality is one of the most important attributes. Consumer taste panels were held according to the Meat Standards Australia guidelines and consumers scored beef according to its palatability attributes and completed a socio-demographic questionnaire. Consumers were able to distinguish between beef quality on a scale from unsatisfactory to premium with high accuracy. Premium cuts of beef scored significantly higher on all of the scales compared to poorer quality cuts. Men rated grilled beef higher on juiciness and flavour scales compared to women. Being the main purchaser of beef had no impact on rating scores. Overall the results show that consumers can judge eating quality with high accuracy. Further research is needed to determine how best to communicate inherent benefits that are not visible into extrinsic eating quality indicators, to provide the consumer with consistent indications of quality at the point of purchase.
  • Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach

    Prieto-Calvo, M.A.; Omer, M.K.; Alveseike, O.; Lopez, M.; Alvarez-Ordonez, A.; Prieto, M. (Teagasc (Agriculture and Food Development Authority), Ireland, 2016-12-30)
    Phenotypic, chemotaxonomic and genotypic data from 12 strains of Escherichia coli were collected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS) and Fourier transform-infrared (FT-IR) spectroscopic profiles. The objectives were to compare several identification systems for E. coli and to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157 E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR), sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST) . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing of E. coli to species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy) for a more precise characterisation and identification of E. coli. The results showed that identification of E. coli strains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns.
  • 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.
  • Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation

    Kelleher, Philip; Bottacini, Francesca; Mahony, Jennifer; Kilcawley, Kieran N; van Sinderen, Douwe (Biomed Central, 2017-03-29)
    Background Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production. Results In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon. Conclusions Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted.
  • New Weapons to Fight Old Enemies: Novel Strategies for the (Bio)control of Bacterial Biofilms in the Food Industry

    Coughlan, Laura M.; Cotter, Paul D.; Hill, Colin; Alvarez-Ordonez, Avelino (Frontiers, 2016-10-18)
    Biofilms are microbial communities characterized by their adhesion to solid surfaces and the production of a matrix of exopolymeric substances, consisting of polysaccharides, proteins, DNA and lipids, which surround the microorganisms lending structural integrity and a unique biochemical profile to the biofilm. Biofilm formation enhances the ability of the producer/s to persist in a given environment. Pathogenic and spoilage bacterial species capable of forming biofilms are a significant problem for the healthcare and food industries, as their biofilm-forming ability protects them from common cleaning processes and allows them to remain in the environment post-sanitation. In the food industry, persistent bacteria colonize the inside of mixing tanks, vats and tubing, compromising food safety and quality. Strategies to overcome bacterial persistence through inhibition of biofilm formation or removal of mature biofilms are therefore necessary. Current biofilm control strategies employed in the food industry (cleaning and disinfection, material selection and surface preconditioning, plasma treatment, ultrasonication, etc.), although effective to a certain point, fall short of biofilm control. Efforts have been explored, mainly with a view to their application in pharmaceutical and healthcare settings, which focus on targeting molecular determinants regulating biofilm formation. Their application to the food industry would greatly aid efforts to eradicate undesirable bacteria from food processing environments and, ultimately, from food products. These approaches, in contrast to bactericidal approaches, exert less selective pressure which in turn would reduce the likelihood of resistance development. A particularly interesting strategy targets quorum sensing systems, which regulate gene expression in response to fluctuations in cell-population density governing essential cellular processes including biofilm formation. This review article discusses the problems associated with bacterial biofilms in the food industry and summarizes the recent strategies explored to inhibit biofilm formation, with special focus on those targeting quorum sensing.
  • Biotechnological applications of functional metagenomics in the food and pharmaceutical industries

    Coughlan, Laura M.; Cotter, Paul D.; Hill, Colin; Alvarez-Ordonez, Avelino (Frontiers Media S. A., 2015-06-30)
    Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.
  • A note on challenge trials to determine the growth of Listeria monocytogenes on mushrooms (Agaricus bisporus)

    Leong, Dara; Alvarez-Ordonez, Avelino; Jordan, Kieran (Teagasc (Agriculture and Food Development Authority), Ireland, 2015-12-30)
    In the EU, food is considered safe with regard to Listeria monocytogenes if the number of micro-organisms does not exceed 100 colony forming units (cfu)/g throughout its shelf-life. Therefore, it is important to determine if a food supports growth of L. monocytogenes. Guidelines for conducting challenge tests for growth assessment of L. monocytogenes on foods were published by the European Union Reference Laboratory (EURL) in 2014. The aim of this study was to use these guidelines to determine if refrigerated, fresh, whole, closed-cap, prepackaged mushrooms (Agaricus bisporus) support the growth of L. monocytogenes. Three batches of mushrooms were artificially inoculated at approximately 100 cfu/g with a three-strain mix of L. monocytogenes and incubated for 2 days at 8°C followed by 4 days at 12°C. L. monocytogenes numbers were determined (in triplicate for each batch) on days 0, 2 and 6. Water activity, pH and total bacterial counts were also determined. There was no increase in the number of L. monocytogenes above the threshold of 0.5 log cfu/g in any of the replicates. In 8 of 9 replicates, the numbers decreased indicating that A. bisporus do not support the growth of L. monocytogenes. As the EU regulations allow < 100 cfu/g if the food cannot support growth of L. monocytogenes, the significance of this study is that mushrooms with < 100 cfu/g may be within the regulations and therefore, quantitative rather than qualitative determination may be required.
  • Enhancement of pigmeat quality by altering pre-slaughter management

    Lawlor, Peadar G; Lynch, P.B.; Mullane, J.; Kerry, J. P.; Hogan, S. A.; Allen, Paul (Teagasc, 2005-10-25)
    The studies presented in this report were conducted to investigate the effect of breed, slaughter weight, castration of male pigs and strategic feeding strategies on the performance of pigs to slaughter and on their carcass quality. The effect of breed, gender and feeding regimen on the performance of pigs and their carcass quality was examined in the first study (Section 3). From weaning to slaughter Landrace-sired pigs grew at a similar rate but had a better feed conversion efficiency compared with Duroc-sired pigs. Landrace-sired pigs also had a higher carcass lean and greater muscle depth than Duroc-sired pigs. Entire male pigs grew more efficiently, had lower lean content in their carcasses and had a reduced kill out yield when compared with gilts. The eye muscle depth was greater for gilts than entire males. Diluting the diet with grass-meal (GM) reduced growth rate, caused a deterioration in feed conversion efficiency, reduced back fat thickness, reduced eye muscle thickness and reduced kill out yield compared to the control feeding regimen of a cereal based diet. Compensatory growth was observed during a re-alimentation period following a period of diet dilution with grass-meal. However, where it did occur, in most cases it was only partial. Adding 5% rapeseed oil instead of lard to the finisher diet increased nitrogen utilization efficiency and phosphorous utilization efficiency. The effect of gender (boar, castrate, gilt) and slaughter weight (80 to 120kg) on pig performance, carcass quality, meat quality, and nitrogen excretion was investigated in the second study (Section 4). Boars grew faster than gilts and more efficiently than castrates or gilts. Castrates had a higher kill out yield than boars. Nitrogen excretion from castrates was similar to gilts which were both higher than that from boars. The processing value of carcasses from castrates may be higher than that of boars and gilts. In particular castrates had heavier loins and bellies than either boars or gilts. Carcasses from castrates and gilts had a higher temperature (recorded 24 hours post slaughter) than boars. However, pH24 was not affected by gender. The intramuscular fat content of the l. dorsi in castrates was higher than that of boars or gilts, however at 1.65% this was well below the level (2.0%) above which any noticeable sensory attributes might be detected. Feed intake increased with increasing slaughter weight and feed conversion efficiency deteriorated. N excretion also increased with each increment in weight. Carcass lean content increased up to 90kg live EOP 4939.doc 4 25/10/2005 weight then reached a plateau and declined after 110kg live weight. Heavier carcasses yielded more product for approximately the same slaughtering cost and the associated larger muscles could make it easier to use seam butchery techniques that result in lean, well-trimmed, attractive cuts and joints. The pH45 and pH24 were reduced with increasing slaughter weight and drip loss increased. Heavier pigs may be more prone to the development of PSE than lighter pigs as their carcass temperature remains higher for longer than that of lighter pigs.
  • Comparative Proteomic Profiling of Divergent Phenotypes for Water Holding Capacity across the Post Mortem Ageing Period in Porcine Muscle Exudate

    Di Luca, Alessio; Hamill, Ruth M; Mullen, Anne Maria; Slavov, Nikolai; Giuliano, Elia (PLOS, 2016-03-07)
    Two dimensional Difference Gel Electrophoresis (2-D DIGE) and mass spectrometry were applied to investigate the changes in metabolic proteins that occur over a seven day (day 1, 3 and 7) post mortem ageing period in porcine centrifugal exudate from divergent meat quality phenotypes. The objectives of the research were to enhance our understanding of the phenotype (water holding capacity) and search for biomarkers of this economically significant pork quality attribute. Major changes in protein abundance across nine phenotype-by-time conditions were observed. Proteomic patterns were dominated by post mortem ageing timepoint. Using a machine learning algorithm (l1-regularized logistic regression), a model was derived with the ability to discriminate between high drip and low drip phenotypes using a subset of 25 proteins with an accuracy of 63%. Models discriminating between divergent phenotypes with accuracy of 72% and 73% were also derived comparing respectively, high drip plus intermediate phenotype (considered as one phenotype) versus low drip and comparing low drip plus intermediate phenotype (considered as one phenotype) versus high drip. In all comparisons, the general classes of discriminatory proteins identified include metabolic enzymes, stress response, transport and structural proteins. In this research we have enhanced our understanding of the protein related processes underpinning this phenotype and provided strong data to work toward development of protein biomarkers for water holding capacity.

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