• Targeting the Microbiota to Address Diet-Induced Obesity: A Time Dependent Challenge

      Clarke, Siobhan F.; Murphy, Eileen F.; O'Sullivan, Orla; Ross, R Paul; O'Toole, Paul W.; Shanahan, Fergus; Cotter, Paul D.; Science Foundation Ireland; Alimentary Health Ltd (PLOS, 07/06/2013)
      Links between the gut microbiota and host metabolism have provided new perspectives on obesity. We previously showed that the link between the microbiota and fat deposition is age- and time-dependent subject to microbial adaptation to diet over time. We also demonstrated reduced weight gain in diet-induced obese (DIO) mice through manipulation of the gut microbiota with vancomycin or with the bacteriocin-producing probiotic Lactobacillus salivarius UCC118 (Bac+), with metabolic improvement achieved in DIO mice in receipt of vancomycin. However, two phases of weight gain were observed with effects most marked early in the intervention phase. Here, we compare the gut microbial populations at the early relative to the late stages of intervention using a high throughput sequencing-based analysis to understand the temporal relationship between the gut microbiota and obesity. This reveals several differences in microbiota composition over the intervening period. Vancomycin dramatically altered the gut microbiota composition, relative to controls, at the early stages of intervention after which time some recovery was evident. It was also revealed that Bac+ treatment initially resulted in the presence of significantly higher proportions of Peptococcaceae and significantly lower proportions of Rikenellaceae and Porphyromonadaceae relative to the gut microbiota of L. salivarius UCC118 bacteriocin negative (Bac-) administered controls. These differences were no longer evident at the later time. The results highlight the resilience of the gut microbiota and suggest that interventions may need to be monitored and continually adjusted to ensure sustained modification of the gut microbiota.
    • Technical note: Fourier transform infrared spectral analysis in tandem with 31P nuclear magnetic resonance spectroscopy elaborates detailed insights into phosphate partitioning during skimmed milk microfiltration and diafiltration

      Boiani, Mattia; Fitzgerald, Richard J.; Kelly, Philip M.; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme (Elsevier, 2018-09-27)
      Our previous study identified peaks in the 31P nuclear magnetic resonance (31P NMR) spectra of skim milk, denoting the interaction of different phosphate species such as inorganic and casein-associated phosphate during the separation of colloidal and serum phases of skim milk by microfiltration (MF) and diafiltration (DF). In the current study, we investigated the same samples generated by the aforementioned separation using attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy analysis. The results confirmed that the technique was not only capable of differentiating between the mineral equilibrium of the casein phosphate nanocluster (CPN) and milk serum, but also complemented the application of 31P NMR. An ATR-FTIR broad band in the region of 1,055 to 1,036 cm−1 and a specific band at 1,076 cm−1 were identified as sensitive to the repartitioning of different phosphate species in milk in accordance with the 31P NMR signals representing casein-associated phosphate and inorganic phosphate in the serum. A third ATR-FTIR signal at 1,034 cm−1 in milk, representing precipitated inorganic calcium phosphate, had not previously been detected by 31P NMR. Thus, the results indicate that a combination of ATR-FTIR and 31P NMR spectroscopies may be optimally used to follow mineral and protein phase changes in milk during membrane processing.
    • Technologies for detecting PSE in pork

      Mullen, Anne Maria; McDonagh, Ciara; Troy, Declan J. (Teagasc, 2003-02)
      The ability of a single, on-line measurement to predict the quality status of an entire muscle or even of a whole carcass was investigated. Variation between pork muscles for on-line measurements of pH, conductivity and colour was evaluated. Intermuscular variation was detected at 24h p ostmortem with higher pH and conductivity values in the topside (M. s emimembranosus) than the striploin (M . longissimus thoracis et lumborum). Correlations showed that a relationship exists between the muscles (r = 0.46-0.88, p<0.05) at 45min and 3h p ostmortem. The location within the topside or the striploin at which the measurements were taken did not influence the result. Shackling did not introduce a significant variation between sides for pH, conductivity and colour values up to 24h p ostmortem, showing measurements could be taken on either side of the carcass.
    • Technology transfer of research results (The 2xtra project)

      McDonagh, Ciara; Byrne, Briege; Troy, Declan J.; Mullen, Anne Maria; Downey, Gerard; European Commission; European Union (Teagasc, 2008-02)
      The 2XTRA project (Technology Transfer Research Results Atlantic Area) was carried out with the aim of promoting economic activity based on research results and technologies developed within universities, research and technology institutes and companies in the European Atlantic Area. This collaborative work was carried out by a strong partnership of 13 entities across this region and included universities, research and technology institutes, private consultants and TBC (technology-based company) incubators. The specific goals of the project were: ● The exchange of information and experiences on technology transfer (TT) with a view to assisting project partners directly and feeding into their regional innovation systems. ● The promotion of new technology-based companies by drawing on collective experiences and developing methodologies relating to - identification and evaluation of business ideas - production of business plans, and - support of early stage companies internationalising. ● The creation of an Atlantic Area Network to support and promote technology-based companies (TBCs) and the technology transfer process. These objectives were achieved through defined activities carried out in three separate stages of this project.
    • Temporal and spatial differences in microbial composition during the manufacture of a Continental-type cheese

      O'Sullivan, Daniel; Cotter, Paul D.; O'Sullivan, Orla; Giblin, Linda; McSweeney, Paul L. H.; Sheehan, Jeremiah J.; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; 2012205 (American Society for Microbiology, 30/01/2015)
      We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine salted Continental-type cheese in cheeses produced early and late in the production day. Differences in microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that late production day cheeses had a more diverse microbial population than their early day equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were found to initially have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas and Bifidobacterium, not routinely associated with a Continental-type cheese produced from pasteurised milk were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.
    • A test bacterial decontamination system for meat products

      Ward, Oonagh C.; Logue, Catherine M.; Sheridan, James J.; European Union; FAIR CT 1027 (Teagasc, 2000-12)
      A pilot scale apparatus was designed to allow meat samples to be treated with steam at sub-atmospheric pressures and correspondingly reduced temperatures. Experiments were carried out to determine the effectiveness of sub-atmospheric steam decontamination in eliminating bacteria on the surface of fresh beef. This type of treatment can have special advantages in that steam can be produced at temperatures well below 100ºC. This means that the heat advantages of steam as a decontaminating agent can potentially be obtained at lower temperatures.
    • Texture of fruit and vegetable components of ready meals

      Downey, Gerard (Teagasc, 2000-12)
      Vegetable and fruit purées are important parts of prepared ready-meals. Further expansion of this food sector will depend among other things on improved and consistent product quality. Innovative organoleptic properties in ready-meal components will assist in product diversification and the growth of market share.
    • Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy

      Dalmasso, Marion; Strain, Ronan; Neve, Horst; Franz, C.M.A.P.; Cousin, Fabien J.; Ross, R Paul; Hill, Colin; Science Foundation Ireland; SFI/12/RC/2273 (PLOS, 09/06/2016)
      With the emergence of multi-drug resistant bacteria the use of bacteriophages (phages) is gaining renewed interest as promising anti-microbial agents. The aim of this study was to isolate and characterize phages from human fecal samples. Three new coliphages, ɸAPCEc01, ɸAPCEc02 and ɸAPCEc03, were isolated. Their phenotypic and genomic characteristics, and lytic activity against biofilm, and in combination with ciprofloxacin, were investigated. All three phages reduced the growth of E. coli strain DPC6051 at multiplicity of infection (MOI) between 10−3 and 105. A cocktail of all three phages completely inhibited the growth of E. coli. The phage cocktail also reduced biofilm formation and prevented the emergence of phage-resistant mutants which occurred with single phage. When combined with ciprofloxacin, phage alone or in cocktail inhibited the growth of E. coli and prevented the emergence of resistant mutants. These three new phages are promising biocontrol agents for E. coli infections.
    • Tn6188 - A Novel Transposon in Listeria monocytogenes Responsible for Tolerance to Benzalkonium Chloride

      Muller, Anneliese; Rychli, Kathrin; Muhterem-Uyar, Meryem; Zaiser, Andreas; Stessl, Beatrix; Guinane, Caitriona M.; Cotter, Paul D.; Wagner, Martin; Schmitz-Esser, Stephan; Austrian Science Fund; et al. (PLOS, 02/10/2013)
      Controlling the food-borne pathogen Listeria (L.) monocytogenes is of great importance from a food safety perspective, and thus for human health. The consequences of failures in this regard have been exemplified by recent large listeriosis outbreaks in the USA and Europe. It is thus particularly notable that tolerance to quaternary ammonium compounds such as benzalkonium chloride (BC) has been observed in many L. monocytogenes strains. However, the molecular determinants and mechanisms of BC tolerance of L. monocytogenes are still largely unknown. Here we describe Tn6188, a novel transposon in L. monocytogenes conferring tolerance to BC. Tn6188 is related to Tn554 from Staphylococcus (S.) aureus and other Tn554-like transposons such as Tn558, Tn559 and Tn5406 found in various Firmicutes. Tn6188 comprises 5117 bp, is integrated chromosomally within the radC gene and consists of three transposase genes (tnpABC) as well as genes encoding a putative transcriptional regulator and QacH, a small multidrug resistance protein family (SMR) transporter putatively associated with export of BC that shows high amino acid identity to Smr/QacC from S. aureus and to EmrE from Escherichia coli. We screened 91 L. monocytogenes strains for the presence of Tn6188 by PCR and found Tn6188 in 10 of the analyzed strains. These isolates were from food and food processing environments and predominantly from serovar 1/2a. L. monocytogenes strains harboring Tn6188 had significantly higher BC minimum inhibitory concentrations (MICs) (28.5 ± 4.7 mg/l) than strains without Tn6188 (14 ± 3.2 mg/l). Using quantitative reverse transcriptase PCR we could show a significant increase in qacH expression in the presence of BC. QacH deletion mutants were generated in two L. monocytogenes strains and growth analysis revealed that ΔqacH strains had lower BC MICs than wildtype strains. In conclusion, our results provide evidence that Tn6188 is responsible for BC tolerance in various L. monocytogenes strains.
    • Tracking of Salmonella through the Pork Slaughter Process

      Prendergast, Deirdre M.; Duggan, Sharon J.; Duffy, Geraldine; Downey, Gerard; Safefood; National Development Plan 2007-2013 (Teagasc, 01/10/2009)
      To help address the problem of salmonellosis in the Republic of Ireland (RoI), a national Salmonella control programme was introduced in 1997 with a view to reducing the prevalence of Salmonella in pigs on the farm and on pig carcasses. The primary objective of this present study was to determine the correlation between the Salmonella serological and bacteriological status of pigs presented for slaughter and the Salmonella status of pork cuts following slaughter, dressing and chilling. Two additional studies investigated the prevalence and numbers of Salmonella spp. in the boning halls of four commercial pork abattoirs and at retail level in butcher shops and supermarkets in the RoI. The results indicated that categorisation of pig herds on the basis of a historical serological test for Salmonella was not a good predictor of the bacteriological Salmonella status of individual pigs at time of slaughter. However, it is acknowledged that serological testing does help in giving a rough estimate of the overall Salmonella status of a pig herd. There was a linear correlation between prevalence of Salmonella in caecal contents and on pork cuts at factory level; therefore, if the number of herds presented for slaughter with high levels of Salmonella (category 3) was reduced, there would be less potential for contamination of the lairage, equipment etc. and so less likelihood of Salmonella contamination on pork. The impact of crosscontamination during transport, lairage, processing and distribution cannot be ignored and measures to diminish this would significantly reduce the dissemination of Salmonella in the chain and the consequent risk posed. A key finding was the considerable variation in the incidence of Salmonella on different sampling days and in different slaughter plants.
    • Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility

      Casey, A.; Fox, Edward M.; Schmitz-Esser, Stephan; Coffey, Aidan; McAuliffe, Olivia; Jordan, Kieran; European Union; Teagasc Walsh Fellowship Programme; 265877; 266061 (Frontiers Media SA, 28/02/2014)
      Listeria monocytogenes is a virulent food-borne pathogen most often associated with the consumption of “ready-to-eat” foods. The organism is a common contaminant of food processing plants where it may persist for extended periods of time. A commonly used approach for the control of Listeria monocytogenes in the processing environment is the application of biocides such as quaternary ammonium compounds. In this study, the transcriptomic response of a persistent strain of L. monocytogenes (strain 6179) on exposure to a sub-lethal concentration of the quaternary ammonium compound benzethonium chloride (BZT) was assessed. Using RNA-Seq, gene expression levels were quantified by sequencing the transcriptome of L. monocytogenes 6179 in the presence (4 ppm) and absence of BZT, and mapping each data set to the sequenced genome of strain 6179. Hundreds of differentially expressed genes were identified, and subsequent analysis suggested that many biological processes such as peptidoglycan biosynthesis, bacterial chemotaxis and motility, and carbohydrate uptake, were involved in the response of L. monocyotogenes to the presence of BZT. The information generated in this study further contributes to our understanding of the response of bacteria to environmental stress. In addition, this study demonstrates the importance of using the bacterium's own genome as a reference when analysing RNA-Seq data.
    • Transcriptome analysis of porcine M. semimembranosus divergent in intramuscular fat as a consequence of dietary protein restriction

      Hamill, Ruth M; Aslan, Ozlem; Mullen, Anne Maria; O'Doherty, John V.; McBryan, Jean; Morris, Dermot G.; Sweeney, Torres; Department of Agriculture, Food and the Marine, Ireland (Biomed Central, 06/07/2013)
      Background: Intramuscular fat (IMF) content is positively correlated with aspects of pork palatability, including flavour, juiciness and overall acceptability. The ratio of energy to protein in the finishing diet of growing pigs can impact on IMF content with consequences for pork quality. The objective of this study was to compare gene expression profiles of Musculus semimembranosus (SM) of animals divergent for IMF as a consequence of protein dietary restriction in an isocaloric diet. The animal model was derived through the imposition of low or high protein diets during the finisher stage in Duroc gilts. RNA was extracted from post mortem SM tissue, processed and hybridised to Affymetrix porcine GeneChip® arrays. Results: IMF content of SM muscle was increased on the low protein diet (3.60 ± 0.38% versus 1.92 ± 0.35%). Backfat depth was also greater in animals on the low protein diet, and average daily gain and feed conversion ratio were lower, but muscle depth, protein content and moisture content were not affected. A total of 542 annotated genes were differentially expressed (DE) between animals on low and high protein diets, with 351 down-regulated and 191 up-regulated on the low protein diet. Transcript differences were validated for a subset of DE genes by qPCR. Alterations in functions related to cell cycle, muscle growth, extracellular matrix organisation, collagen development, lipogenesis and lipolysis, were observed. Expression of adipokines including LEP, TNFα and HIF1α were increased and the hypoxic stress response was induced. Many of the identified transcriptomic responses have also been observed in genetic and fetal programming models of differential IMF accumulation, indicating they may be robust biological indicators of IMF content. Conclusion: An extensive perturbation of overall energy metabolism in muscle occurs in response to protein restriction. A low protein diet can modulate IMF content of the SM by altering gene pathways involved in lipid biosynthesis and degradation; however this nutritional challenge negatively impacts protein synthesis pathways, with potential consequences for growth.
    • Tryptophan-Mediated Denaturation of β-Lactoglobulin A by UV Irradiation

      Kehoe, Joseph James; Remondetto, Gabriel E; Subirade, Muriel; Morris, Edwin R; Brodkorb, Andre (American Chemical Society, 04/06/2008)
      β-Lactoglobulin A, a genetic variant of one of the main whey proteins, was irradiated at 295 nm for 24 h. After irradiation, 18% of the protein was denatured (determined by reverse-phase chromatography). The fluorescence spectrum of the irradiated protein was red-shifted compared to that of the native protein, indicating a change in protein folding. Sulfhydryl groups, which are buried in native β-lactoglobulin, were exposed following irradiation and became available for quantification using the Ellman assay. The quantity of exposed sulfhydryls increased, but the number of total sulfhydryl groups decreased. Gel permeation chromatography showed that some protein aggregation occurred during irradiation. Fourier transform infrared (FTIR) spectroscopy of irradiated β-lactoglobulin revealed changes in the secondary structure, comparable to that of early events during heat-induced denaturation. There was evidence for some photo-oxidation of tryptophan.
    • The two peptide lantibiotic lacticin 3147 acts synergistically with polymyxin to inhibit Gram negative bacteria

      Draper, Lorraine A.; Cotter, Paul D.; Hill, Colin; Ross, R Paul; Science Foundation Ireland; 10/IN.1/B3027 (Biomed Central, 26/09/2013)
      Background: The emergence of bacterial drug resistance encourages the re-evaluation of the potential of existing antimicrobials. Lantibiotics are post-translationally modified, ribosomally synthesised antimicrobial peptides with a broad spectrum antimicrobial activity. Here, we focussed on expanding the potential of lacticin 3147, one of the most studied lantibiotics and one which possesses potent activity against a wide range of Gram positive species including many nosocomial pathogens. More specifically, our aim was to investigate if lacticin 3147 activity could be enhanced when combined with a range of different clinical antibiotics. Results: Initial screening revealed that polymyxin B and polymyxin E (colistin) exhibited synergistic activity with lacticin 3147. Checkerboard assays were performed against a number of strains, including both Gram positive and Gram negative species. The resultant fractional inhibitory concentration (FIC) index values established that, while partial synergy was detected against Gram positive targets, synergy was obvious against Gram negative species, including Cronobacter and E. coli. Conclusions: Combining lacticin 3147 with low levels of a polymyxin could provide a means of broadening target specificity of the lantibiotic, while also reducing polymyxin use due to the lower concentrations required as a result of synergy.
    • The ultra-rapid chilling of lamb carcasses

      McGeehin, Brian; Sheridan, James J.; Department of Agriculture, Food and the Marine (Teagasc, 1999-01)
      The practice in Irish commercial abattoirs is to chill lamb carcasses for a period of approximately 16 hours at 2 - 4°C, at which stage the core temperature of the carcass has reached 7°C. Chilling in this manner is considered necessary because it is generally held that faster chilling leads to toughening of the meat. The objective of this work was to develop a continuous ultra-rapid chilling system for lambs which would reduce carcass chilling time without adversely affecting the quality of the meat.
    • Ultrasound-assisted extraction of polyphenols from potato peels: profiling and kinetic modelling

      Kumari, Bibha; Tiwari, Brijesh; Hossain, Mohammad B; Rai, Dilip K.; Brunton, Nigel; Department of Agriculture, Food and Marine; FIRM/11/F/050 (Wiley, 2017-02-14)
      Ultrasound‐assisted extraction (UAE) at 33 and 42 kHz has been investigated in the extraction of polyphenols from peels of two potato varieties, cream‐skinned Lady Claire (LC) and pink‐skinned Lady Rosetta (LR), commonly used in snack food production. Extraction efficacy between the UAE‐untreated (control) and the UAE‐treated extracts was assessed on the total phenolic content and antioxidant capacities (DPPH and FRAP). Application of UAE showed significantly higher recovery of phenolic compounds compared to solid–liquid extraction process alone. Lower ultrasonic frequency (33 kHz) was more effective in recovering polyphenols compared to 42 kHz ultrasonic treatment. The liquid chromatography‐tandem mass spectrometry revealed that chlorogenic acid and caffeic acid were the most prevalent phenolics in LR peels, whereas caffeic acid was dominant in LC peels. Peleg's equation showed a good correlation (R2 > 0.92) between the experimental values and the predicted values on the kinetics of UAE of phenolic compounds.
    • Understanding and Exploiting Phage–Host Interactions

      Stone, Edel; Campbell, Katrina; Grant, Irene; McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; Teagasc; 2016034; 0027 (MDPI, 2019-06-18)
      Initially described a century ago by William Twort and Felix d’Herelle, bacteriophages are bacterial viruses found ubiquitously in nature, located wherever their host cells are present. Translated literally, bacteriophage (phage) means ‘bacteria eater’. Phages interact and infect specific bacteria while not affecting other bacteria or cell lines of other organisms. Due to the specificity of these phage–host interactions, the relationship between phages and their host cells has been the topic of much research. The advances in phage biology research have led to the exploitation of these phage–host interactions and the application of phages in the agricultural and food industry. Phages may provide an alternative to the use of antibiotics, as it is well known that the emergence of antibiotic-resistant bacterial infections has become an epidemic in clinical settings. In agriculture, pre-harvest and/or post-harvest application of phages to crops may prevent the colonisation of bacteria that are detrimental to plant or human health. In addition, the abundance of data generated from genome sequencing has allowed the development of phage-derived bacterial detection systems of foodborne pathogens. This review aims to outline the specific interactions between phages and their host and how these interactions may be exploited and applied in the food industry.
    • Unravelling the metabolic impact of SBS-associated microbial dysbiosis: Insights from the piglet short bowel syndrome model

      Pereira-Fantini, Prue; Byars, Sean G; Pitt, James; Lapthorne, Susan; Fouhy, Fiona; Cotter, Paul D.; Bines, Julie E.; Science Foundation Ireland; SFI/12/RC/2273 (Springer Nature, 2017-02-23)
      Liver disease is a major source of morbidity and mortality in children with short bowel syndrome (SBS). SBS-associated microbial dysbiosis has recently been implicated in the development of SBS-associated liver disease (SBS-ALD), however the pathological implications of this association have not been explored. In this study high-throughput sequencing of colonic content from the well-validated piglet SBS-ALD model was examined to determine alterations in microbial communities, and concurrent metabolic alterations identified in urine samples via targeted mass spectrometry approaches (GC-MS, LC-MS, FIA-MS) further uncovered impacts of microbial disturbance on metabolic outcomes in SBS-ALD. Multi-variate analyses were performed to elucidate contributing SBS-ALD microbe and metabolite panels and to identify microbe-metabolite interactions. A unique SBS-ALD microbe panel was clearest at the genus level, with discriminating bacteria predominantly from the Firmicutes and Bacteroidetes phyla. The SBS-ALD metabolome included important alterations in the microbial metabolism of amino acids and the mitochondrial metabolism of branched chain amino acids. Correlation analysis defined microbe-metabolite clustering patterns unique to SBS-ALD and identified a metabolite panel that correlates with dysbiosis of the gut microbiome in SBS.
    • Up-grading of low value meats and by-products for use in consumer foods

      Kenny, Tony; Desmond, Eoin; Ward, Patrick (Teagasc, 1999-02)
      Animal offals can be divided into (1) edible offals and by-products including fats, blood, and low-grade trimmings such as poultry skin and pork hock meat; (2) extracts from edible offals for use as ingredients in food products; (3) inedible offals; (4) hides and skins; (5) raw materials for extraction of pharmaceuticals or chemicals; (6) raw materials for sundry by-products.
    • Upgrading the cold chain for consumer food products

      Gormley, Ronan T.; Brennan, Martine H.; Butler, Francis (Teagasc, 2000-12)
      The prepared consumer foods sector in Ireland is undergoing sustained dynamic growth. Products that are distributed chilled or frozen require a cold chain and there is potential to increase product quality by optimising the cold chain. This potential prompted the current study.