Now showing items 21-40 of 3547

    • 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.
    • A review of water quality policies in relation to public good benefits and community engagement in rural Ireland

      Daly, Karen; Breuil, Marion; Buckley, Cathal; O’ Donoghue, Cathal; Ryan, Mary; Seale, Catherine (Sciendo, 2017-04-06)
      This paper examines current recreational water use in the rural landscape in Ireland and reviews current EU policies and national regulations aimed at protecting water quality and the wider environment under agri-environmental schemes. Specifically, we review policy instruments that protect water for recreational use, their impacts and the challenges they pose for rural development against current requirements to increase public awareness and participation. In Ireland, there is limited experience in public participation in water quality protection and restoration and we highlight how this can be addressed by focussing on the specific contribution of water quality in rural areas in relation to the provision of recreational ecosystem services. These services provide the infrastructure for much of Ireland’s rural tourism sector. In this context, emerging participatory approaches to policy implementation are also assessed as national and local government prioritise community engagement for the second cycle under the EU Water Framework Directive (WFD).
    • 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 3.4.23.15) and the angiotensin-I-converting enzyme (ACE-I; EC 3.4.15.1). The enzyme dipeptidyl peptidase-IV (DPP-IV; EC 3.4.14.5) 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.
    • Rapid Communication: Large exploitable genetic variability exists to shorten age at slaughter in cattle

      Berry, D. P.; Cromie, A. R.; Judge, M. M. (Oxford University Press (OUP), 2017-10-01)
      Apprehension among consumers is mounting on the efficiency by which cattle convert feedstuffs into human edible protein and energy as well as the consequential effects on the environment. Most (genetic) studies that attempt to address these issues have generally focused on efficiency metrics defined over a certain time period of an animal’s life cycle, predominantly the period representing the linear phase of growth. The age at which an animal reaches the carcass specifications for slaughter, however, is also known to vary between breeds; less is known on the extent of the within-breed variability in age at slaughter. Therefore, the objective of the present study was to quantify the phenotypic and genetic variability in the age at which cattle reach a predefined carcass weight and subcutaneous fat cover. A novel trait, labeled here as the deviation in age at slaughter (DAGE), was represented by the unexplained variability from a statistical model, with age at slaughter as the dependent variable and with the fixed effects, among others, of carcass weight and fat score (scale 1 to 15 scored by video image analysis of the carcass at slaughter). Variance components for DAGE were estimated using either a 2-step approach (i.e., the DAGE phenotype derived first and then variance components estimated) or a 1-step approach (i.e., variance components for age at slaughter estimated directly in a mixed model that included the fixed effects of, among others, carcass weight and carcass fat score as well as a random direct additive genetic effect). The raw phenotypic SD in DAGE was 44.2 d. The genetic SD and heritability for DAGE estimated using the 1-step or 2-step models varied from 14.2 to 15.1 d and from 0.23 to 0.26 (SE 0.02), respectively. Assuming the (genetic) variability in the number of days from birth to reaching a desired carcass specifications can be exploited without any associated unfavorable repercussions, considerable potential exists to improve not only the (feed) efficiency of the animal and farm system but also the environmental footprint of the system. The beauty of the approach proposed, relative to strategies that select directly for the feed intake complex and enteric methane emissions, is that data on age at slaughter are generally readily available. Of course, faster gains may potentially be achieved if a dual objective of improving animal efficiency per day coupled with reduced days to slaughter was embarked on.
    • Mitigating Nutrition and Health Deficiencies in Older Adults: A Role for Food Innovation?

      Baugreet, Sephora; Hamill, Ruth M.; Kerry, Joseph P.; McCarthy, Sinéad N.; Teagasc; Department of Agriculture, Food and the Marine; 11F045 (Wiley, 2017-03-07)
      The aim of this review is to describe the factors contributing to diminished food intake, resulting in nutritional deficiencies and associated health conditions in older adults and proposes food innovation strategies to mitigate these. Research has provided convincing evidence of a link between healthy eating patterns and healthy aging. There is a need to target new food product development (NPD) with functional health benefits specifically designed to address the particular food-related needs of older consumers. When developing foods for older adults, consideration should be given to the increased requirements for specific macro- and micronutrients, especially protein, calcium, vitamin D, and vitamin B. Changes in chemosensory acuity, chewing difficulties, and reduced or poor swallowing ability should also be considered. To compensate for the diminished appetite and reduced intake, foods should be energy dense, nutritionally adequate, and, most importantly, palatable, when targeting this cohort. This paper describes the potential of new food product development to facilitate dietary modification and address health deficiencies in older adults.
    • Molecular characterization of Ralstonia solanacearum strains from Ethiopia and tracing potential source of bacterial wilt disease outbreak in seed potatoes

      Abdurahman, A.; Griffin, D.; Elphinstone, J.; Struik, P. C.; Schulz, S.; Schulte‐Geldermann, E.; Sharma, K.; Walsh Fellowship of Teagasc -Ireland; US Agency for International Development (USAID); Centre for Crop Systems Analysis of Wageningen University; et al. (Wiley, 2017-02-06)
      Bacterial wilt, caused by Ralstonia solanacearum, is emerging as a major threat to potato production in Ethiopia, reaching epidemic proportions in the Chencha district recently, with a prevalence of 97% of potato fields in 2015. The recent disease outbreak in the district coincided with a significant introduction of seed potatoes. This research was therefore initiated to genetically characterize the pathogen so as to trace its source, identify its relationship with outbreaks in the rest of the country, and make intervention recommendations. Ralstonia solanacearum isolates were sampled both from seed and ware potato fields in Chencha and from seed potato fields in production regions suspected of being potential sources of the pathogen. Multiplex PCR and phylogenetic analysis of partial endoglucanase gene sequences identified all of the isolates as phylotype IIB sequevar 1. VNTR sequence analysis distinguished 11 different haplotypes, nine of which were unique to the Chencha district. However, one of the haplotypes was common to all seed potato producer regions of Ethiopia except for the Shashemene area. The unique and diverse VNTR haplotypes of the pathogen in Chencha indicates that it is well established in the district. When a geographical map of the VNTR haplotypes was superimposed with the main cross-regional seed potato distribution pattern of the country, it became evident that the pathogen was being disseminated via latently infected seed from the Holeta-Jeldu area in the Central Highlands of Ethiopia. Identification of largely uninfected highland districts and multiplication of high-grade seed potato exclusively in those districts should be given priority.
    • 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.
    • Limitation of Grassland Productivity by Low Temperature and Seasonality of Growth

      Wingler, Astrid; Hennessy, Deirdre (Frontiers Media SA, 2016-07-27)
      The productivity of temperate grassland is limited by the response of plants to low temperature, affecting winter persistence and seasonal growth rates. During the winter, the growth of perennial grasses is restricted by a combination of low temperature and the lack of available light, but during early spring low ground temperature is the main limiting factor. Once temperature increases, growth is stimulated, resulting in a peak in growth in spring before growth rates decline later in the season. Growth is not primarily limited by the ability to photosynthesize, but controlled by active regulatory processes that, e.g., enable plants to restrict growth and conserve resources for cold acclimation and winter survival. An insufficient ability to cold acclimate can affect winter persistence, thereby also reducing grassland productivity. While some mechanistic knowledge is available that explains how low temperature limits plant growth, the seasonal mechanisms that promote growth in response to increasing spring temperatures but restrict growth later in the season are only partially understood. Here, we assess the available knowledge of the physiological and signaling processes that determine growth, including hormonal effects, on cellular growth and on carbohydrate metabolism. Using data for grass growth in Ireland, we identify environmental factors that limit growth at different times of the year. Ideas are proposed how developmental factors, e.g., epigenetic changes, can lead to seasonality of the growth response to temperature. We also discuss perspectives for modeling grass growth and breeding to improve grassland productivity in a changing climate.
    • An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly

      Velmurugan, Janaki; Mollison, Ewan; Barth, Susanne; Marshall, David; Milne, Linda; Creevey, Christopher J.; Lynch, Bridget; Meally, Helena; McCabe, Matthew; Milbourne, Dan; et al. (Oxford University Press (OUP), 2016-06-06)
      Background and aims: High density genetic linkage maps that are extensively anchored to assembled genome sequences of the organism in question are extremely useful in gene discovery. To facilitate this process in perennial ryegrass (Lolium perenne L.), a high density single nucleotide polymorphism (SNP)- and presence/absence variant (PAV)-based genetic linkage map has been developed in an F2 mapping population that has been used as a reference population in numerous studies. To provide a reference sequence to which to align genotyping by sequencing (GBS) reads, a shotgun assembly of one of the grandparents of the population, a tenth-generation inbred line, was created using Illumina-based sequencing. Methods: The assembly was based on paired-end Illumina reads, scaffolded by mate pair and long jumping distance reads in the range of 3-40 kb, with >200-fold initial genome coverage. A total of 169 individuals from an F2 mapping population were used to construct PstI-based GBS libraries tagged with unique 4-9 nucleotide barcodes, resulting in 284 million reads, with approx. 1·6 million reads per individual. A bioinformatics pipeline was employed to identify both SNPs and PAVs. A core genetic map was generated using high confidence SNPs, to which lower confidence SNPs and PAVs were subsequently fitted in a straightforward binning approach. Key results: The assembly comprises 424 750 scaffolds, covering 1·11 Gbp of the 2·5 Gbp perennial ryegrass genome, with a scaffold N50 of 25 212 bp and a contig N50 of 3790 bp. It is available for download, and access to a genome browser has been provided. Comparison of the assembly with available transcript and gene model data sets for perennial ryegrass indicates that approx. 570 Mbp of the gene-rich portion of the genome has been captured. An ultra-high density genetic linkage map with 3092 SNPs and 7260 PAVs was developed, anchoring just over 200 Mb of the reference assembly. Conclusions: The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community.
    • 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.
    • Study on the Association between Tail Lesion Score, Cold Carcass Weight, and Viscera Condemnations in Slaughter Pigs

      Teixeira, Dayane Lemos; Harley, Sarah; Hanlon, Alison; O’Connell, Niamh Elizabeth; More, Simon John; Manzanilla, Edgar Garcia; Boyle, Laura Ann; Department of Agriculture, Food and the Marine; RSF 11/S/107 (Frontiers Media SA, 2016-03-14)
      The aim of this study was to assess the relationship between tail lesions, cold carcass weight, and viscera condemnations in an Irish abattoir. The following data were collected at the evisceration point from every third pig slaughtered over 7 days: farm identification, sex, tail lesion score, viscera inspection outcome, and cold carcass weight. Tail lesions were scored according to a 5-point scale. Disease lesions responsible for lung (pleurisy, pneumonia, and abscess), heart (pericarditis), and liver (ascariasis) condemnation were recorded based on the decision of the veterinary inspector (VI). Data on 3,143 pigs from 61 batches were available. The relationship between disease lesions, tail lesion score, and cold carcass weight was studied at individual carcass level, while the relationship between disease lesions and tail lesion score was studied at both carcass and batch level. Tail lesions (score ≥1) were found in 72% of the study population, with 2.3% affected by severe tail lesions (scores ≥3). Pleurisy (13.7%) followed by pneumonia (10.4%) showed the highest prevalence, whereas the prevalence of ascariasis showed the greatest variation between batches (0–75%). Tail lesion score, pleurisy, pleuropneumonia, and pericarditis were associated with reductions in carcass cold weight (P ≤ 0.05) ranging from 3 to 6.6 kg. Tail lesion score was associated with condemnations for pleurisy, pneumonia, and pleuropneumonia (P ≤ 0.05) at a batch level. VI shift was associated with condemnations for pneumonia, pleuropneumonia, and pericarditis (P ≤ 0.05) at a carcass level and with pneumonia at a batch level. Sex was not associated with viscera condemnations but males were more likely to be affected by tail lesions. The relationship between overall tail lesion score and the lung diseases at batch level supports the relationship between poor health and poor welfare of pigs on farms. The inclusion of tail lesion scores at post-mortem meat inspection should be considered as a health and welfare diagnostic tool.
    • 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.
    • Responses in lactose yield, lactose percentage and protein-to-protein-plus-lactose ratio from index selection in New Zealand dairy cattle

      Sneddon, NW; Lopez-Villalobos, N; Davis, SR; Hickson, RE; Shalloo, L; Garrick, DJ; Geary, U; Livestock Improvement Corporation Pat Shannon scholarship (Informa UK Limited, 2016-03-16)
      The breeding goal of the New Zealand dairy industry is to improve the genetic capability of cows to convert pasture-based feed into farmer profit. The New Zealand dairy industry exports over 95% of milk produced and the most significant product by export volume is whole milk powder (WMP). The current selection objective, breeding worth (BW), will increase yields of protein and fat, potentially shifting milk composition further from the ideal composition for making WMP. This study aimed to investigate the correlated responses in lactose yield (LY), lactose percentage (LP) and protein-to-protein-plus-lactose ratio (P:P + L) from selection for BW, BW plus LY, BW plus LP and BW plus P:P + L. Selection for BW is predicted to have per-cow responses of 54.92 kg milk/year, 2.22 kg fat/year, 1.78 kg protein/year and 2.84 kg lactose/year. When lactose was included in the selection objective in the form of LY, LP or P:P + L, genetic responses ranged from −59.98 kg to 61.08 kg milk/year and from −2.67 kg to 3.70 kg lactose/year. The industry could reduce imported lactose requirements per tonne of WMP by 6%–11% by including lactose into the selection objective, compared with selection on BW alone.
    • 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.