• Surface decontamination of meat using thermal processes

      McCann, Máiréad; Sheridan, James J.; Downey, Gerard (Teagasc, 2007-02)
      This study investigated the effectiveness of a novel heat apparatus for decontamination of meat surfaces inoculated with important foodborne pathogens using either steam or dry air.
    • Survival characteristics of monophasic Salmonella Typhimurium 4,[5],12:i:- strains derived from pig feed ingredients and compound feed

      Burns, Ann Marie; Duffy, Geraldine; Walsh, Des; Tiwari, Brijesh; Grant, Jim; Lawlor, Peadar G; Gardiner, Gillian E.; Teagasc Walsh Fellowship Programme; 2011010 (Elsevier, 2015-12-09)
      The presence of Salmonella in animal feed or feed ingredients at the feed mill or on-farm is a cause for concern, as it can be transmitted to food-producing animals and subsequently to humans. The objective of this study was to determine the survival characteristics of five feed ingredient- and feed-derived monophasic Salmonella Typhimurium 4,[5],12:i:- strains. The first part of the study investigated thermal inactivation using an immersed heating coil apparatus. A Weibull model provided a good fit, with low RMSE values (0.04–0.43) and high R2 values (0.93–0.99) obtained. There was considerable inter-strain variation in heat resistance, with D-values ranging from 397.83 to 689 s at 55 °C, 11.35–260.95 s at 60 °C and 1.12 to 6.81 at 65 °C. Likewise, z-values ranged from 2.95 to 5.44 °C. One strain demonstrated a significantly higher thermal tolerance, even though it had been isolated from a meal feed. However, overall the strains investigated do not appear to be that much more heat resistant than Salmonella previously studied. The second part of this study involved assessing the ability of the five Salmonella strains to survive during storage over a 28-day period in pelleted weaner pig feed treated with 0.3% sodium butyrate. While a mean reduction in the Salmonella count of 0.79 log10 CFU was seen in the treated feed during the storage period, a reduction (albeit only 0.49 log10 CFU) was also observed in the control feed. Although there was no overall effect of treatment, sodium butyrate resulted in reductions in Salmonella counts of 0.75 and 0.22 log10 CFU at days 14 and 24 of feed storage, respectively but at the end of the 28-day storage period counts were 0.25 log10 CFU higher in the treated feed. Therefore, the sodium butyrate used appears unsuitable as an agent for feed treatment perhaps due to the protective coating on the particular feed additive used. Overall, the results of this study enhance knowledge about the behaviour and survival characteristics of monophasic S. Typhimurium 4,[5],12:i:- strains in animal feed and may assist the feed industry and pig producers in implementing effective intervention strategies for their control.
    • The survival of added escherichia coli O157:H7 in natural mineral water and its products and the development of a rapid method for enumeration of the heterotrophic bacteria in natural mineral water

      Kerr, Marie; Fitzgerald, Margaret; Sheridan, James J. (Teagasc, 2000-12)
      The consumption of natural mineral water is rapidly growing and outpacing all other beverages on a global scale. In Europe, bottled water already has a bigger market share than carbonated soft drinks. Yet there is only a limited availability of information on the microbiological safety and quality of bottled natural mineral waters sold within the European Community. As natural mineral water does not receive any bacteriocidal treatment prior to bottling, the risk of pathogen contamination is a public health concern. Pathogen contamination may occur as a result of over exploitation of natural mineral water resources i.e. over abstraction by commercial bottling companies may lead to disturbance of the water table causing contaminated surface water to be drawn down into ground water supplies (Green and Green 1994). Such contamination was implicated in an outbreak of cholera associated with the consumption of bottled natural mineral water in Portugal in 1974 (Blake et al. 1977). The transport and dissemination of E. coli and enterococci in a limestone aquifer had been demonstrated by Personné et al. (1998), confirmation that E. coli can survive the transitory period from the surface to underground water supplies, thus raising the question of E. coli O157:H7 with its low infective dose < 10 cells (Willshaw et al. 1994 and Tilden et al. 1996) surviving the transitory period from surface to a natural mineral water aquifer.
    • Symposium review: Genomic investigations of flavor formation by dairy microbiota

      McAuliffe, Olivia; Kilcawley, Kieran N; Stefanovic, Ewelina; Teagasc Walsh Fellowship programme; Dairy Research Ireland; IRCSET; EU Marie Curie Actions Clarin Co-Fund (Elsevier, 2018-10-19)
      Flavor is one of the most important attributes of any fermented dairy product. Dairy consumers are known to be willing to experiment with different flavors; thus, many companies producing fermented dairy products have looked at culture manipulation as a tool for flavor diversification. The development of flavor is a complex process, originating from a combination of microbiological, biochemical, and technological aspects. A key driver of flavor is the enzymatic activities of the deliberately inoculated starter cultures, in addition to the environmental or “nonstarter” microbiota. The contribution of microbial metabolism to flavor development in fermented dairy products has been exploited for thousands of years, but the availability of the whole genome sequences of the bacteria and yeasts involved in the fermentation process and the possibilities now offered by next-generation sequencing and downstream “omics” technologies is stimulating a more knowledge-based approach to the selection of desirable cultures for flavor development. By linking genomic traits to phenotypic outputs, it is now possible to mine the metabolic diversity of starter cultures, analyze the metabolic routes to flavor compound formation, identify those strains with flavor-forming potential, and select them for possible commercial application. This approach also allows for the identification of species and strains not previously considered as potential flavor-formers, the blending of strains with complementary metabolic pathways, and the potential improvement of key technological characteristics in existing strains, strains that are at the core of the dairy industry. An in-depth knowledge of the metabolic pathways of individual strains and their interactions in mixed culture fermentations can allow starter blends to be custom-made to suit industry needs. Applying this knowledge to starter culture research programs is enabling research and development scientists to develop superior starters, expand flavor profiles, and potentially develop new products for future market expansion.
    • Symposium review: Lactococcus lactis from nondairy sources: Their genetic and metabolic diversity and potential applications in cheese

      McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; Dairy Research Ireland; EU Marie Curie Actions Clarin Co-Fund; Irish Research Council for Science, Engineering and Technology; European Union (Elsevier, 2018-02-13)
      The widespread dissemination of species of the lactic acid bacteria (LAB) group in different environments testifies to their extraordinary niche adaptability. Members of the LAB are present on grass and other plant material, in dairy products, on human skin, and in the gastrointestinal and reproductive tracts. The selective pressure imparted by these specific environments is a key driver in the genomic diversity observed between strains of the same species deriving from distinct habitats. Strains that are exploited in the dairy industry for the production of fermented dairy products are often referred to as “domesticated” strains. These strains, which initially may have occupied a nondairy niche, have become specialized for growth in the milk environment. In fact, comparative genome analysis of multiple LAB species and strains has revealed a central trend in LAB evolution: the loss of ancestral genes and metabolic simplification toward adaptation to nutritionally rich environments. In contrast, “environmental” strains, or those from raw milk, plants, and animals, exhibit diverse metabolic capabilities and lifestyle characteristics compared with their domesticated counterparts. Because of the limited number of established dairy strains used in fermented food production today, demand is increasing for novel strains, with concerted efforts to mine the microbiota of natural environments for strains of technological interest. Many studies have concentrated on uncovering the genomic and metabolic potential of these organisms, facilitating comparative genome analysis of strains from diverse environments and providing insight into the natural diversity of the LAB, a group of organisms that is at the core of the dairy industry. The natural biodiversity that exists in these environments may be exploited in dairy fermentations to expand flavor profiles, to produce natural “clean label” ingredients, or to develop safer products.
    • Symposium review: Structure-function relationships in cheese

      Lamichhane, Prabin; Kelly, Alan L.; Sheehan, Jeremiah J.; Dairy Levy Trust; Teagasc Walsh Fellowship Programme; Ornua; RMIS6259 (Elsevier, 2017-10-18)
      The quality and commercial value of cheese are primarily determined by its physico-chemical properties (e.g., melt, stretch, flow, and color), specific sensory attributes (e.g., flavor, texture, and mouthfeel), usage characteristics (e.g., convenience), and nutritional properties (e.g., nutrient profile, bioavailability, and digestibility). Many of these functionalities are determined by cheese structure, requiring an appropriate understanding of the relationships between structure and functionality to design bespoke functionalities. This review provides an overview of a broad range of functional properties of cheese and how they are influenced by the structural organization of cheese components and their interactions, as well as how they are influenced by environmental factors (e.g., pH and temperature).
    • Synergistic Nisin-Polymyxin Combinations for the Control of Pseudomonas Biofilm Formation

      Field, Des; Seisling, Nynke; Cotter, Paul D.; Ross, R Paul; Hill, Colin; Science Foundation Ireland; TIDA14/TIDA/2286; 10/IN.1/B3027; 11/PI/1137; SFI/12/RC/2273 (Frontiers, 26/10/2016)
      The emergence and dissemination of multi-drug resistant pathogens is a global concern. Moreover, even greater levels of resistance are conferred on bacteria when in the form of biofilms (i.e., complex, sessile communities of bacteria embedded in an organic polymer matrix). For decades, antimicrobial peptides have been hailed as a potential solution to the paucity of novel antibiotics, either as natural inhibitors that can be used alone or in formulations with synergistically acting antibiotics. Here, we evaluate the potential of the antimicrobial peptide nisin to increase the efficacy of the antibiotics polymyxin and colistin, with a particular focus on their application to prevent biofilm formation of Pseudomonas aeruginosa. The results reveal that the concentrations of polymyxins that are required to effectively inhibit biofilm formation can be dramatically reduced when combined with nisin, thereby enhancing efficacy, and ultimately, restoring sensitivity. Such combination therapy may yield added benefits by virtue of reducing polymyxin toxicity through the administration of significantly lower levels of polymyxin antibiotics.
    • Synthesis of trypsin-resistant variants of the Listeria-active bacteriocin salivaricin P

      O'Shea, Eileen F.; O'Connor, Paula M.; Cotter, Paul D.; Ross, R Paul; Hill, Colin; Department of Agriculture, Food and the Marine, Ireland; Science Foundation Ireland; Teagasc Walsh Fellowship Programme (American Society for Microbiology, 25/06/2010)
      Two-component Salivaricin P-like bacteriocins have demonstrated potential as antimicrobials capable of controlling infections in the gastrointestinal tract (GIT). The anti-Listeria activity of salivaricin P is optimal when the individual peptides, Sln1 and Sln2, are added in succession in a 1:1 ratio. However, as degradation by digestive proteases may compromise the functionality of these peptides within the GIT we investigated the potential to create salivaricin variants with enhanced resistance to the intestinal protease, trypsin. A total of 11 variants of the salivaricin P components were generated in which conservative modifications at the trypsin-specific cleavage sites were explored in order to protect the peptides from trypsin degradation while maintaining their potent antimicrobial activity. Analysis of these variants revealed that eight were resistant to trypsin digestion while retaining antimicrobial activity. Combining the complementary trypsin resistant variants Sln1-5 and Sln2-3 resulted in a MIC50 of 300 nM against Listeria monocytogenes, a 3.75-fold reduction in activity compared to wild-type salivaricin P. This study demonstrates the potential of engineering bacteriocins variants which are resistant to specific protease action but which retain significant antimicrobial activity.
    • 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.