Now showing items 1-20 of 1201

    • Complete Genome Sequence of the Gamma-Aminobutyric Acid-Producing Strain Streptococcus thermophilus APC151

      Linares, Daniel M.; Arboleya, Silvia; Ross, R. Paul; Stanton, Catherine; Science Foundation Ireland (SFI); SFI/12/RC/2273 (American Society for Microbiology, 2017-04-27)
      Here is presented the whole-genome sequence of Streptococcus thermophilus APC151, isolated from a marine fish. This bacterium produces gamma-aminobutyric acid (GABA) in high yields and is biotechnologically suitable to produce naturally GABAenriched biofunctional yogurt. Its complete genome comprises 2,097 genes and 1,839,134 nucleotides, with an average GC content of 39.1%.
    • Application of Flow Cytometry to the Detection of Pathogenic Bacteria

      Kennedy, Deirdre; Wilkinson, Martin G. (Caister Academic Press, 2015)
      Outbreaks of infections have emphasized the necessity for rapid and economic detection methods for pathogens in samples ranging from those of clinical origin to food products during production and retail storage, and increasingly, in environmental samples. Flow cytometry (FCM) allows the rapid acquisition of multi-parametric data regarding cell populations within fluidised samples. However, the application of FCM to pathogen detection depends on the availability of specific fluorescent probes such as antibodies and RNA probes capable of detecting and isolating pathogens from these diverse samples. A particular issue for FCM methodology is the ability to recover and discriminate bacteria from the sample matrix which may pose a major technical hurdle towards accurate and sensitive analysis. This review article focuses on detection of pathogens using FCM in samples originating from food, water, environmental and clinical sources and outlines the current state of the art and potential future applications.
    • Separation of the effects of denaturation and aggregation on whey-casein protein interactions during the manufacture of a model infant formula

      Joyce, Aoife M.; Brodkorb, André; Kelly, Alan L.; O’Mahony, James A.; Irish Department of Agriculture, Food and the Marine; 10/RD/ProSurf/TMFRC/723 (Springer Science and Business Media LLC, 2016-10-10)
      Denaturation and aggregation of whey protein have been extensively studied but there is limited knowledge of their effects on processing properties of infant milk formulae (IMF) systems. In this study, the separate effects of denaturation and aggregation of whey protein on the physicochemical characteristics during processing of a model IMF were examined. Whey protein solutions (8%, w/w, protein) were pre-heated for 2 min at 72 or 85 °C, followed by addition of 2.2 mM calcium (Ca) (H-BCa), or at 85 °C after addition of the same level of Ca (H-ACa), to give pre-treated whey protein for inclusion in three model IMF systems, encoded as H-72-BCa, H-85-BCa and H-85-ACa, respectively. Unheated control samples without (UH-C) and with (UH-C-Ca) added Ca were also prepared. Model IMF systems (5.2%, w/w, protein, 60:40 whey protein:casein ratio, pH 6.8) were then prepared incorporating these pre-treated whey protein ingredients and subjected to lab-scale high-temperature short-time (HTST) heating at 85 °C for 2 min; whey protein denaturation was >81.2% in all samples after HTST. Aggregation of whey protein resulted in a significantly (P < 0.05) higher viscosity in sample H-85-ACa (8.3 mPa.s) compared to UH-C (4.0 mPa.s), and measurement of Ca ion concentration on heating showed that Ca ions enhanced whey protein aggregation, resulting in larger mean protein particle size. The results also suggest that pre-heating of whey protein had a preventative effect on aggregation of protein during HTST of IMF. This study clearly showed that aggregation is more influential than denaturation in determining viscosity development during HTST treatment of IMF, and that such viscosity development can be controlled by altering protein-protein interactions using, for example, pre-heat treatment of whey protein ingredients.
    • Forgotten fungi—the gut mycobiome in human health and disease

      Huseyin, Chloe E.; O’Toole, Paul W.; Cotter, Paul D.; Scanlan, Pauline D.; Science Foundation Ireland (SFI); Science Foundation Ireland-Royal Society University Research Fellowship; SFI/12/RC/2273 (Oxford University Press (OUP), 2017-04-18)
      The human body is home to a complex and diverse microbial ecosystem that plays a central role in host health. This includes a diversity of fungal species that is collectively referred to as our ‘mycobiome’. Although research into the mycobiome is still in its infancy, its potential role in human disease is increasingly recognised. Here we review the existing literature available on the human mycobiota with an emphasis on the gut mycobiome, including how fungi interact with the human host and other microbes. In doing so, we provide a comprehensive critique of the methodologies available to research the human mycobiota as well as highlighting the latest research findings from mycological surveys of different groups of interest including infants, obese and inflammatory bowel disease cohorts. This in turn provides new insights and directions for future studies in this burgeoning research area.
    • Characterisation of the Wetting Behaviour of Poor Wetting Food Powders and the Influence of Temperature and Film Formation

      Fitzpatrick, John J.; Salmon, Justine; Ji, Junfu; Miao, Song (Hosokawa Powder Technology Foundation, 2017)
      Characterisation of the wettability of five poor wetting food powders was performed using static immersion and contact angle measurements. The effect of temperature (20, 50 and 70 °C) on wettability showed varying effects on the powders. Higher temperatures majorly improved the wettability of chocolate and high fat powders but worsened the wettability of sodium caseinate and milk protein isolate. Rate-limiting regime testing was performed by pouring a fixed mass of powder on to the surface of water in an agitated beaker and visually assessing what was rate-limiting rehydration after 1 minute. The rate limiting regime tended to be floating at lower agitation speeds and dispersed clumps of varying sizes at higher speeds. However, there were major differences observed between the powders. Some of the powders formed strong films at powder/water interfaces, that could act as a barrier to water penetration and wettability. Consequently, force displacement testing was performed on a layer of powder on the water surface to assess the strength of any powder film formed. Some of the powders formed strong films that may in-part explain their poor wetting behaviour and their propensity to form strong clumps that were difficult to disrupt.
    • Glycomacropeptide Reduces Intestinal Epithelial Cell Barrier Dysfunction and Adhesion of Entero-Hemorrhagic and Entero-Pathogenic Escherichia coli in Vitro

      Feeney, Shane; Ryan, Joseph; Kilcoyne, Michelle; Joshi, Lokesh; Hickey, Rita; Teagasc Walsh Fellowship; Department of Agriculture and Food, Ireland; 10/RD/NUIG/707 (Multidisciplinary Digital Publishing Institute, 2017-10-27)
      In recent years, the potential of glycosylated food components to positively influence health has received considerable attention. Milk is a rich source of biologically active glycoconjugates which are associated with antimicrobial, immunomodulatory, anti-adhesion, anti-inflammatory and prebiotic properties. Glycomacropeptide (GMP) is the C-terminal portion of kappa-casein that is released from whey during cheese-making by the action of chymosin. Many of the biological properties associated with GMP, such as anti-adhesion, have been linked with the carbohydrate portion of the protein. In this study, we investigated the ability of GMP to inhibit the adhesion of a variety of pathogenic Escherichia coli strains to HT-29 and Caco-2 intestinal cell lines, given the importance of E. coli in causing bacterial gastroenteritis. GMP significantly reduced pathogen adhesion, albeit with a high degree of species specificity toward enteropathogenic E. coli (EPEC) strains O125:H32 and O111:H2 and enterohemorrhagic E. coli (EHEC) strain 12900 O157:H7. The anti-adhesive effect resulted from the interaction of GMP with the E. coli cells and was also dependent on GMP concentration. Pre-incubation of intestinal Caco-2 cells with GMP reduced pathogen translocation as represented by a decrease in transepithelial electrical resistance (TEER). Thus, GMP is an effective in-vitro inhibitor of adhesion and epithelial injury caused by E. coli and may have potential as a biofunctional ingredient in foods to improve gastrointestinal health.
    • Boarfish (Capros aper): review of a new capture fishery and its valorization potential

      Egerton, Sian; Culloty, Sarah; Whooley, Jason; STANTON, CATHERINE; Ross, R. Paul; Irish Research Council (IRC); Biomarine Ingredients Ireland Ltd. via the IRC Enterprise Partnership Scheme (Oxford University Press (OUP), 2017-04-18)
      The world’s fish stocks, although renewable, are a finite resource. European capture fisheries have remained stagnant in terms of volume for many years. To remain profitable, fishers are looking for new opportunities to diversify, reduce costs, and maximize profits. The targeted fishing of boarfish (Capros aper) in Europe is an excellent example of such adaptation. Using this fishery as a case study, we highlight how established fisheries are adapting to changes faced by the industry. We begin by compiling the knowledge to date on the taxonomy, biology, and ecology of the understudied boarfish and go on to provide a comprehensive overview of its expansion as a targeted fishery in Europe, examining the range of valorization options currently being investigated.
    • Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments

      Doyle, Conor J.; O'Toole, Paul W.; Cotter, Paul D.; Teagasc Walsh Fellowship; internal Teagasc funding; 2013030; RMIS6364 (Wiley, 2017-09-14)
      Metagenomic-based analyses have the potential to revolutionize our understanding of the microbiology of food production and processing environments. By adopting such approaches, it will be possible to more accurately determine sources of microbial contamination, identify critical control points for such contaminants, and select practices that optimize quality and safety. This mini-review will discuss the merits of adopting metagenostic-based approaches, highlight novel insights that they have provided to date and consider how they could be further implemented.
    • Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

      Doyle, Conor J.; Gleeson, David; O'Toole, Paul W.; Cotter, Paul D.; Teagasc Walsh Fellowship; internal Teagasc funding; 2013030; RMIS6364 (American Society for Microbiology, 2017-01-15)
      In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota.
    • Economic Assessment of Waterborne Outbreak of Cryptosporidiosis

      Chyzheuskaya, Aksana; Cormican, Martin; Srivinas, Raghavendra; O’Donovan, Diarmuid; Prendergast, Martina; O’Donoghue, Cathal; Morris, Dearbháile (Centers for Disease Control and Prevention (CDC), 2017-10)
      In 2007, a waterborne outbreak of Cryptosporidium hominis infection occurred in western Ireland, resulting in 242 laboratory-confirmed cases and an uncertain number of unconfirmed cases. A boil water notice was in place for 158 days that affected 120,432 persons residing in the area, businesses, visitors, and commuters. This outbreak represented the largest outbreak of cryptosporidiosis in Ireland. The purpose of this study was to evaluate the cost of this outbreak. We adopted a societal perspective in estimating costs associated with the outbreak. Economic cost estimated was based on totaling direct and indirect costs incurred by public and private agencies. The cost of the outbreak was estimated based on 2007 figures. We estimate that the cost of the outbreak was >€19 million (≈€120,000/day of the outbreak). The US dollar equivalent based on today’s exchange rates would be $22.44 million (≈$142,000/day of the outbreak). This study highlights the economic need for a safe drinking water supply.
    • Preparation and Characterization of Nanoparticles Made from Co-Incubation of SOD and Glucose

      Cai, Liping; Lin, Chuntong; Yang, Nannan; Huang, Zhijie; Miao, Song; Chen, Xiaochao; Pan, Jianru; Rao, Pingfan; Liu, Shutao; National key research and development projects; et al. (Multidisciplinary Digital Publishing Institute, 2017-12-19)
      The attractive potential of natural superoxide dismutase (SOD) in the fields of medicine and functional food is limited by its short half-life in circulation and poor permeability across the cell membrane. The nanoparticle form of SOD might overcome these limitations. However, most preparative methods have disadvantages, such as complicated operation, a variety of reagents-some of them even highly toxic-and low encapsulation efficiency or low release rate. The aim of this study is to present a simple and green approach for the preparation of SOD nanoparticles (NPs) by means of co-incubation of Cu/Zn SOD with glucose. This method was designed to prepare nanoscale aggregates based on the possible inhibitory effect of Maillard reaction on heating-induced aggregation during the co-incubation. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) results indicated that the Maillard reaction occurred during the co-incubation process. It was found that enzymatically active NPs of Cu/Zn SOD were simultaneously generated during the reaction, with an average particle size of 175.86 ± 0.71 nm, and a Zeta potential of -17.27 ± 0.59 mV, as established by the measurement of enzymatic activity, observations using field emission scanning electron microscope, and analysis of dynamic light scattering, respectively. The preparative conditions for the SOD NPs were optimized by response surface design to increase SOD activity 20.43 fold. These SOD NPs showed storage stability for 25 days and better cell uptake efficacy than natural SOD. Therefore, these NPs of SOD are expected to be a potential drug candidate or functional food factor. To our knowledge, this is the first report on the preparation of nanoparticles possessing the bioactivity of the graft component protein, using the simple and green approach of co-incubation with glucose, which occurs frequently in the food industry during thermal processing.
    • Bacteriophages and Bacterial Plant Diseases

      Buttimer, Colin; McAuliffe, Olivia; Ross, R. P.; Hill, Colin; O’Mahony, Jim; Coffey, Aidan; CIT Rísam Ph.D. Scholarship (Frontiers Media SA, 2017-01-20)
      Losses in crop yields due to disease need to be reduced in order to meet increasing global food demands associated with growth in the human population. There is a well-recognized need to develop new environmentally friendly control strategies to combat bacterial crop disease. Current control measures involving the use of traditional chemicals or antibiotics are losing their efficacy due to the natural development of bacterial resistance to these agents. In addition, there is an increasing awareness that their use is environmentally unfriendly. Bacteriophages, the viruses of bacteria, have received increased research interest in recent years as a realistic environmentally friendly means of controlling bacterial diseases. Their use presents a viable control measure for a number of destructive bacterial crop diseases, with some phage-based products already becoming available on the market. Phage biocontrol possesses advantages over chemical controls in that tailor-made phage cocktails can be adapted to target specific disease-causing bacteria. Unlike chemical control measures, phage mixtures can be easily adapted for bacterial resistance which may develop over time. In this review, we will examine the progress and challenges for phage-based disease biocontrol in food crops.
    • Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB

      Buttimer, Colin; Hendrix, Hanne; Oliveira, Hugo; Casey, Aidan; Neve, Horst; McAuliffe, Olivia; Ross, R. Paul; Hill, Colin; Noben, Jean-Paul; O'Mahony, Jim; et al. (Frontiers Media SA, 2017-01-24)
      Enterobacteria phage vB_PcaM_CBB is a “jumbo” phage belonging to the family Myoviridae. It possesses highly atypical whisker-like structures along the length of its contractile tail. It has a broad host range with the capability of infecting species of the genera Erwinia, Pectobacterium, and Cronobacter. With a genome of 355,922 bp, excluding a predicted terminal repeat of 22,456 bp, phage CBB is the third largest phage sequenced to date. Its genome was predicted to encode 554 ORFs with 33 tRNAs. Based on prediction and proteome analysis of the virions, 29% of its predicted ORFs could be functionally assigned. Protein comparison shows that CBB shares between 33–38% of its proteins with Cronobacter phage GAP32, coliphages PBECO4 and 121Q as well as Klebsiella phage vB_KleM_Rak2. This work presents a detailed and comparative analysis of vB_PcaM_CBB of a highly atypical jumbo myoviridae phage, contributing to a better understanding of phage diversity and biology.
    • Predicted Release and Analysis of Novel ACE-I, Renin, and DPP-IV Inhibitory Peptides from Common Oat (Avena sativa) Protein Hydrolysates Using in Silico Analysis

      Bleakley, Stephen; Hayes, Maria; O’ Shea, Nora; Gallagher, Eimear; Lafarga, Tomas; Teagasc Walsh Fellowship; Irish Department of Agriculture, Food and Marine (DAFM); Spanish Ministry of Economy, Industry, and Competitiveness; 2016073; FIRM 11/SF/317; et al. (Multidisciplinary Digital Publishing Institute, 2017-12-04)
      The renin-angiotensin-aldosterone system (RAAS) plays an important role in regulating hypertension by controlling vasoconstriction and intravascular fluid volume. RAAS itself is largely regulated by the actions of renin (EC and the angiotensin-I-converting enzyme (ACE-I; EC The enzyme dipeptidyl peptidase-IV (DPP-IV; EC also plays a role in the development of type-2 diabetes. The inhibition of the renin, ACE-I, and DPP-IV enzymes has therefore become a key therapeutic target for the treatment of hypertension and diabetes. The aim of this study was to assess the bioactivity of different oat (Avena sativa) protein isolates and their ability to inhibit the renin, ACE-I, and DPP-IV enzymes. In silico analysis was carried out to predictthe likelihood of bioactive inhibitory peptides occurring from oat protein hydrolysates following in silico hydrolysis with the proteases papain and ficin. Nine peptides, including FFG, IFFFL, PFL, WWK, WCY, FPIL, CPA, FLLA, and FEPL were subsequently chemically synthesised, and their bioactivities were confirmed using in vitro bioassays. The isolated oat proteins derived from seven different oat varieties were found to inhibit the ACE-I enzyme by between 86.5 ± 10.7% and 96.5 ± 25.8%, renin by between 40.5 ± 21.5% and 70.9 ± 7.6%, and DPP-IV by between 3.7 ± 3.9% and 46.2 ± 28.8%. The activity of the synthesised peptides was also determined.
    • Preliminary characterization of a novel β-agarase from Thalassospira profundimonas

      Zeng, Cheng; Zhang, Longtao; Miao, Song; Zhang, Yi; Zeng, Shaoxiao; Zheng, Baodong; Regional Demonstration of Marine Economy Innovative Development Project; the Science and Technology Plan of Fujian Province; China Scholarship for Visiting Scholar; 12PYY001SF08; et al. (Springer Science and Business Media LLC, 2016-07-15)
      Background The objective of this study was to characterize the agarase from a newly isolated agarolytic bacterium Thalassospira profundimaris fst-13007. Results Agarase-fst was purified to homogeneity which apparent molecular weight was 66.2 kDa. Its activity was optimal at 45 °C and pH 8 and was stable at pH 5–9 or 30–50 °C. Agarase-fst required Mn2+ for agarase activity and inhibition by Cu2+, Fe3+ and EDTA. Tests of hydrolysis pattern and substrate specificity, TLC analysis and mass spectrometry of the hydrolysis products revealed that it is an endo-type β-agarase hydrolyzing agarose into neoagarobiose, neoagarotetraose and neoagarohexaose. Results of MALDI-TOF-TOF/MS indicate that it lack of homology to previously identified proteins and present conserved domain of β-agarase. Conclusion Agarase-fst from T. profundimaris fst-13007 was confirmed to be a novel endo-type β-agarase.
    • A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

      Vartia, Salla; Villanueva-Cañas, José L.; Finarelli, John; Farrell, Edward D.; Collins, Patrick C.; Hughes, Graham M.; Carlsson, Jeanette E. L.; Gauthier, David T.; McGinnity, Philip; Cross, Thomas F.; et al. (The Royal Society, 2016-01)
      This study examines the potential of next-generation sequencing based ‘genotyping-by-sequencing’ (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.
    • Draft Genome Sequence of Lactobacillus casei DPC6800, an Isolate with the Potential to Diversify Flavor in Cheese

      Stefanovic, Ewelina; Casey, Aidan; Cotter, Paul; Cavanagh, Daniel; Fitzgerald, Gerald; McAuliffe, Olivia; Dairy Research Ireland; Teagasc; 6156; 6224 (American Society for Microbiology, 2016-04-28)
      Lactobacillus casei is a nonstarter lactic acid bacterium commonly present in various types of cheeses. It is believed that strains of this species have a significant impact on the development of cheese flavor. The draft genome sequence of L. casei DPC6800, isolated from a semi-hard Dutch cheese, is reported.
    • The impact of environmental conditions on Campylobacter jejuni survival in broiler faeces and litter

      Smith, Shaun; Meade, Joseph; Gibbons, James; McGill, Kevina; Bolton, Declan; Whyte, Paul; Irish Department of Agriculture, Food and Marine; 11SF328 (PubMed Central, 2016-06-28)
      Introduction Campylobacter jejuni is the leading bacterial food-borne pathogen within the European Union, and poultry meat is an important vehicle for its transmission to humans. However, there is limited knowledge about how this organism persists in broiler litter and faeces. The aim of this study was to assess the impact of a number of environmental parameters, such as temperature, humidity, and oxygen, on Campylobacter survival in both broiler litter and faeces. Materials and methods Used litter was collected from a Campylobacter-negative broiler house after final depopulation and fresh faeces were collected from transport crates. Samples were confirmed as Campylobacter negative according to modified ISO methods for veterinary samples. Both sample matrices were inoculated with 9 log10 CFU/ml C. jejuni and incubated under high (≥85%) and low (≤70%) relative humidity conditions at three different temperatures (20°C, 25°C, and 30°C) under both aerobic and microaerophilic atmospheres. Inoculated litter samples were then tested for Campylobacter concentrations at time zero and every 2 hours for 12 hours, while faecal samples were examined at time zero and every 24 hours for 120 hours. A two-tailed t-test assuming unequal variance was used to compare mean Campylobacter concentrations in samples under the various temperature, humidity, and atmospheric conditions. Results and discussion C. jejuni survived significantly longer (P≤0.01) in faeces, with a minimum survival time of 48 hours, compared with 4 hours in used broiler litter. C. jejuni survival was significantly enhanced at 20°C in all environmental conditions in both sample matrices tested compared with survival at 25°C and 30°C. In general, survival was greater in microaerophilic compared with aerobic conditions in both sample matrices. Humidity, at the levels examined, did not appear to significantly impact C. jejuni survival in any sample matrix. The persistence of Campylobacter in broiler litter and faeces under various environmental conditions has implications for farm litter management, hygiene, and disinfection practices.
    • The impact of biosecurity and partial depopulation on Campylobacter prevalence in Irish broiler flocks with differing levels of hygiene and economic performance

      Smith, Shaun; Messam, Locksley L. McV.; Meade, Joseph; Gibbons, James; McGill, Kevina; Bolton, Declan; Whyte, Paul; Irish Department of Agriculture, Food and Marine; 11SF328 (PubMed, 2016-05-10)
      Background: Campylobacter jejuni is the leading bacterial food-borne pathogen within the European Union (EU), and poultry meat is the primary route for transmission to humans. Material and methods: This study examined the impact of partial depopulation (thinning), season, and farm performance (economic, hygiene, and biosecurity) on Campylobacter prevalence in Irish broilers over a 13-month period. Ten caecal samples were taken per flock, for a total of 211 flocks from 23 farms during the duration of the study. Campylobacter was isolated and enumerated according to modified published ISO methods for veterinary samples. Biosecurity was evaluated through a questionnaire based on risk factors for Campylobacter identified in previous studies. Hygiene compliance was assessed from audit records taken over the course of 1 year. All information relating to biosecurity and hygiene was obtained directly from the processing company. This was done to ensure farmers were unaware they were being monitored for Campylobacter prevalence and prevent changes to their behaviour. Results and discussion: Farms with high performance were found to have significantly lower Campylobacter prevalence at first depopulation compared with low-performance farms across all seasons (P≤0.01). Peak Campylobacter levels were observed during the summer season at first thin in both the high- and low-performance groups. Campylobacter prevalence was found to increase to ≥85% in both high- and low-performance farms across all seasons at final depopulation, suggesting that Campylobacter was introduced during the first depopulation. On low-performance farms, four biosecurity interventions were found to significantly reduce the odds of a flock being Campylobacter positive (physical step-over barrier OR=0.17, house-specific footwear OR=0.13, absence of water body within 0.5 km OR=0.13, two or more broiler houses on a farm OR=0.16), compared with farms without these interventions. For high-performance farms, no single biosecurity intervention was identified as significant as this group had full compliance with multiple factors. High-performance farms had significantly better feed conversion ratios compared with low-performance farms (1.61 v 1.67 (P≤0.01)). No differences in flock mortality rates were observed (P≥0.05). This highlights the impact of season, biosecurity, partial depopulation, and farm performance on Campylobacter prevalence in Irish broilers.
    • Thermus and the Pink Discoloration Defect in Cheese

      Quigley, Lisa; O’Sullivan, Daniel J.; Daly, David; O’Sullivan, Orla; Burdikova, Zuzana; Vana, Rostislav; Beresford, Tom P.; Ross, R. Paul; Fitzgerald, Gerald F.; McSweeney, Paul L. H.; et al. (American Society for Microbiology, 2016-06-28)
      A DNA sequencing-based strategy was applied to study the microbiology of Continental-type cheeses with a pink discoloration defect. The basis for this phenomenon has remained elusive, despite decades of research. The bacterial composition of cheese containing the defect was compared to that of control cheese using 16S rRNA gene and shotgun metagenomic sequencing as well as quantitative PCR (qPCR). Throughout, it was apparent that Thermus, a carotenoid-producing genus, was present at higher levels in defect-associated cheeses than in control cheeses. Prompted by this finding and data confirming the pink discoloration to be associated with the presence of a carotenoid, a culture-based approach was employed, and Thermus thermophilus was successfully cultured from defect-containing cheeses. The link between Thermus and the pinking phenomenon was then established through the cheese defect equivalent of Koch’s postulates when the defect was recreated by the reintroduction of a T. thermophilus isolate to a test cheese during the manufacturing process. IMPORTANCE Pink discoloration in cheese is a defect affecting many cheeses throughout the world, leading to significant financial loss for the dairy industry. Despite decades of research, the cause of this defect has remained elusive. The advent of high-throughput, next-generation sequencing has revolutionized the field of food microbiology and, with respect to this study, provided a means of testing a possible microbial basis for this defect. In this study, a combined 16S rRNA, whole-genome sequencing, and quantitative PCR approach was taken. This resulted in the identification of Thermus, a carotenoid-producing thermophile, in defect-associated cheeses and the recreation of the problem in cheeses to which Thermus was added. This finding has the potential to lead to new strategies to eliminate this defect, and our method represents an approach that can be employed to investigate the role of microbes in other food defects of unknown origin.