Now showing items 1-20 of 305

    • Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

      Wang, Shuo; Yang, Bo; Ross, R. Paul; STANTON, CATHERINE; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; Jiangsu Province; 31771953; et al. (MDPI AG, 2020-01-08)
      Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.
    • Assessing the ability of Nisin A and derivatives thereof to inhibit Gram-negative bacteria from the genus Thermus

      Jonnala, Bhagya R. Yeluri; Feehily, Conor; O'Connor, Paula M.; Field, Des; Hill, Colin; Ross, R. Paul; McSweeney, P. L. H.; Sheehan, Diarmuid (JJ); Cotter, Paul D. (2020-12-09)
    • Diversity of Gut Microbiota and Bifidobacterial Community of Chinese Subjects of Different Ages and from Different Regions

      Yang, Bo; Yan, Shuang; Chen, Yang; Ross, R. Paul; STANTON, CATHERINE; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; National First-Class Discipline Program of Food Science and Technology; et al. (MDPI AG, 2020-07-24)
      Gut microbiota composition and functionality are closely linked to host health. In this study, the fecal microbiota and bifidobacterial communities of 111 healthy volunteers from four regions of China of varying age profiles (Child, 1–5 years; Young, 18–50 years; Elder, 60–80 years; Longevity, ≥90 years) were investigated via high-throughput sequencing. Canonical analysis revealed that the gut microbiota, as well as bifidobacteria profiles of the subjects, clustered according to their regions and age. Eight genera were shared among all subjects, however, certain genera distributed differently in subjects grouped by region and age. Faecalibacterium was enriched in samples from Zhongxiang, unclassified Ruminococcaceae and Christensenellaceae were enriched in the Longevity group, and Bifidobacterium was enriched in Child. Within Bifidobacterium, B. longum was the most abundant species in almost all samples except for Child, in which B. pseudocatenulatum was the most abundant. Additionally, the abundances of B. adolescentis and B. dentium were lower in Child. In conclusion, our results suggest that geography and age affect the structure of the gut microbiota, as well as Bifidobacterium composition, and this variation may greatly associate with the metabolic and immune changes that occur during the process of aging.
    • The Impact of Formulation on Lutein, Zeaxanthin, and meso-Zeaxanthin Bioavailability: A Randomised Double-Blind Placebo-Controlled Study

      Green-Gomez, Marina; Prado-Cabrero, Alfonso; Moran, Rachel; Power, Tommy; Gómez Gómez-Mascaraque, Laura; Stack, Jim; Nolan, John N.; Howard Foundation UK; Waterford Institute of Technology (WIT) President’s scholarship program (MDPI AG, 2020-08-18)
      Lutein (L), zeaxanthin (Z), and meso-zeaxanthin (MZ) have been the focus of research and commercial interest for their applications in human health. Research into formulations to enhance their bioavailability is merited. This 6 month randomised placebo-controlled trial involving 81 healthy volunteers compared the bioavailability of different formulations of free L, Z, and MZ in sunflower or omega-3 oil versus L, Z, and MZ diacetates (Ld, Zd, and MZd) in a micromicellar formulation. Fasting serum carotenoids, macular pigment, and skin carotenoid score were analysed at baseline and 6 months. Serum L, Z, and MZ concentrations increased in all active interventions compared to placebo (p < 0.001 to p = 0.008). The diacetate micromicelle formulation exhibited a significantly higher mean response in serum concentrations of Z and MZ compared to the other active interventions (p = 0.002 to 0.019). A micromicellar formulation with solubilised Z and MZ diacetates is a promising technology advancement that enhances the bioavailability of these carotenoids when compared to traditional carotenoid formulations (ISRCTN clinical trial registration number: ISRCTN18206561)
    • A Whey Fraction Rich in Immunoglobulin G Combined with Bifidobacterium longum subsp. infantis ATCC 15697 Exhibits Synergistic Effects against Campylobacter jejuni

      Quinn, Erinn M.; Kilcoyne, Michelle; Walsh, Dan; Joshi, Lokesh; Hickey, Rita M.; Teagasc Walsh Fellowship Programme (MDPI AG, 2020-06-29)
      Evidence that whey proteins and peptides have health benefits beyond basic infant nutrition has increased dramatically in recent years. Previously, we demonstrated that a whey-derived immunoglobulin G-enriched powder (IGEP) enhanced adhesion of Bifidobacterium longum subsp. infantis ATCC 15697 (B. infantis) to HT-29 cells. In this study, we investigated the synergistic effect of IGEP-treated B. infantis on preventing the attachment of highly invasive Campylobacter jejuni 81–176 (C. jejuni) to intestinal HT-29 cells. The combination decreased the adherence of C. jejuni to the HT-29 cells by an average of 48% compared to the control (non-IGEP-treated B. infantis). We also confirmed that treatment of IGEP with sodium metaperiodate, which disables the biological recognition of the conjugated oligosaccharides, reduced adhesion of B. infantis to the intestinal cells. Thus, glycosylation of the IGEP components may be important in enhancing B. infantis adhesion. Interestingly, an increased adhesion phenotype was not observed when B. infantis was treated with bovine serum-derived IgG, suggesting that bioactivity was unique to milk-derived immunoglobulin-rich powders. Notably, IGEP did not induce growth of B. infantis within a 24 hours incubation period, as demonstrated by growth curves and metabolite analysis. The current study provides insight into the functionality of bovine whey components and highlights their potential in positively impacting the development of a healthy microbiota.
    • Effectiveness of current hygiene practices on minimization of Listeria monocytogenes in different mushroom production‐related environments

      Pennone, Vincenzo; Dygico, Kenneth Lyonel; Coffey, Aidan; Gahan, Cormac G.M.; Grogan, Helen; McAuliffe, Olivia; Burgess, Catherine M.; Jordan, Kieran; Department of Agriculture, Food and the Marine; 14/F/881 (Wiley, 2020-05-20)
      Background: The commercial production of Agaricus bisporus is a three stage process: 1) production of compost, also called “substrate”; 2) production of casing soil; and 3) production of the mushrooms. Hygiene practices are undertaken at each stage: pasteurization of the substrate, hygiene practices applied during the production of casing soil, postharvest steam cookout, and disinfection at the mushroom production facilities. However, despite these measures, foodborne pathogens, including Listeria monocytogenes, are reported in the mushroom production environment. In this work, the presence of L. monocytogenes was evaluated before and after the application of hygiene practices at each stage of mushroom production with swabs, samples of substrate, casing, and spent mushroom growing substrates. Results: L. monocytogenes was not detected in any casing or substrate sample by enumeration according to BS EN ISO 11290-2:1998. Analysis of the substrate showed that L. monocytogenes was absent in 10 Phase II samples following pasteurization, but was then present in 40% of 10 Phase III samples. At the casing production facility, 31% of 59 samples were positive. Hygiene improvements were applied, and after four sampling occasions, 22% of 37 samples were positive, but no statistically significant difference was observed (p > .05). At mushroom production facilities, the steam cookout process inactivated L. monocytogenes in the spent growth substrate, but 13% of 15 floor swabs at Company 1 and 19% of 16 floor swabs at Company 2, taken after disinfection, were positive. Conclusion: These results showed the possibility of L. monocytogenes recontamination of Phase III substrate, cross-contamination at the casing production stage and possible survival after postharvest hygiene practices at the mushroom growing facilities. This information will support the development of targeted measures to minimize L. monocytogenes in the mushroom industry.
    • Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals

      O’ Donnell, Michelle M.; Harris, Hugh M. B.; Ross, R. Paul; O'Toole, Paul W.; Science Foundation Ireland; 07/ IN.1/B1780 (Wiley, 2017-08-22)
      In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.
    • Food for thought: The role of nutrition in the microbiota-gut–brain axis

      Oriach, Clara Seira; Robertson, Ruairi C.; STANTON, CATHERINE; Cryan, John F.; Dinan, Timothy G.; Science Foundation Ireland; Health Research Board of Ireland; Sea Change Strategy; NutraMara programme; SMART FOOD project; et al. (Elsevier BV, 2016-04)
      Recent research has provided strong evidence for the role of the commensal gut microbiota in brain function and behaviour. Many potential pathways are involved in this bidirectional communication between the gut microbiota and the brain such as immune mechanisms, the vagus nerve and microbial neurometabolite production. Dysbiosis of gut microbial function has been associated with behavioural and neurophysical deficits, therefore research focused on developing novel therapeutic strategies to treat psychiatric disorders by targeting the gut microbiota is rapidly growing. Numerous factors can influence the gut microbiota composition such as health status, mode of birth delivery and genetics, but diet is considered among the most crucial factors impacting on the human gut microbiota from infancy to old age. Thus, dietary interventions may have the potential to modulate psychiatric symptoms associated with gut–brain axis dysfunction. Further clinical and in vivo studies are needed to better understand the mechanisms underlying the link between nutrition, gut microbiota and control of behaviour and mental health.
    • Oligosaccharides Isolated from MGO™ Manuka Honey Inhibit the Adhesion of Pseudomonas aeruginosa, Escherichia Coli O157:H7 and Staphylococcus Aureus to Human HT-29 cells

      Lane, Johnathan A.; Calonne, Julie; Slattery, Helen; Hickey, Rita M. (MDPI AG, 2019-10-01)
      Historically, honey is known for its anti-bacterial and anti-fungal activities and its use for treatment of wound infections. Although this practice has been in place for millennia, little information exists regarding which manuka honey components contribute to the protective nature of this product. Given that sugar accounts for over 80% of honey and up to 25% of this sugar is composed of oligosaccharides, we have investigated the anti-infective activity of manuka honey oligosaccharides against a range of pathogens. Initially, oligosaccharides were extracted from a commercially-available New Zealand manuka honey—MGO™ Manuka Honey (Manuka Health New Zealand Ltd.)—and characterized by High pH anion exchange chromatography coupled with pulsed amperiometric detection. The adhesion of specific pathogens to the human colonic adenocarcinoma cell line, HT-29, was then assessed in the presence and absence of these oligosaccharides. Manuka honey oligosaccharides significantly reduced the adhesion of Escherichia coli O157:H7 (by 40%), Staphylococcus aureus (by 30%), and Pseudomonas aeruginosa (by 52%) to HT-29 cells. This activity was then proven to be concentration dependent and independent of bacterial killing. This study identifies MGO™ Manuka Honey as a source of anti-infective oligosaccharides for applications in functional foods aimed at lowering the incidence of infectious diseases.
    • The Effect of High Pressure Processing on Polyphenol Oxidase Activity, Phytochemicals and Proximate Composition of Irish Potato Cultivars

      Tsikrika, Konstantina; O’Brien, Nora; Rai, Dilip K.; Department of Agriculture, Food and Marine; 17/F/299 (MDPI AG, 2019-10-19)
      Polyphenol oxidase (PPO) activity, proximate composition, and phytochemicals were determined in four common Irish potato cultivars following a high pressure processing (HPP) at 600 MPa for 3 min. PPO activity was significantly (p < 0.05) lower in all HPP treated samples, while the overall proximate composition was not affected. The total phenolic content was significantly higher in the HPP treated samples. Chlorogenic acid levels significantly decreased with simultaneous increase of caffeic acid and p-coumaric acid levels upon HPP treatment. No significant changes were observed in rutin and ferulic acid levels, although their levels varied, depending on the potato cultivars, while the levels of cytotoxic glycoalkaloids (α-solanine and α-chaconine) remained unaltered.
    • Draft Genome Sequences of the Type Strains of Six Macrococcus Species

      Mazhar, Shahneela; Altermann, Eric; Hill, Colin; McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; 2015055 (American Society for Microbiology, 2019-05-09)
      We report here the draft genome sequences of Macrococcus bovicus ATCC 51825T, Macrococcus carouselicus ATCC 51828T, Macrococcus equipercicus ATCC 51831T, Macrococcus brunensis CCM4811T, Macrococcus hajekii CCM4809T, and Macrococcus lamae CCM4815T. The availability of the genome sequences of these species will enable cross-species comparison, which could lead to a more comprehensive understanding of organisms of the Macrococcus genus.
    • Vangl2 disruption alters the biomechanics of late spinal neurulation leading to spina bifida in mouse embryos

      Galea, Gabriel L.; Nychyk, Oleksandr; Mole, Matteo A.; Moulding, Dale; Savery, Dawn; Nikolopoulou, Evanthia; Henderson, Deborah J.; Greene, Nicholas D. E.; Copp, Andrew J. (The Company of Biologists, 2018-03-12)
      Human mutations in the planar cell polarity component VANGL2 are associated with the neural tube defect spina bifida. Homozygous Vangl2 mutation in mice prevents initiation of neural tube closure, precluding analysis of its subsequent roles in neurulation. Spinal neurulation involves rostral-to-caudal ‘zippering’ until completion of closure is imminent, when a caudal-to-rostral closure point, ‘Closure 5’, arises at the caudal-most extremity of the posterior neuropore (PNP). Here, we used Grhl3Cre to delete Vangl2 in the surface ectoderm (SE) throughout neurulation and in an increasing proportion of PNP neuroepithelial cells at late neurulation stages. This deletion impaired PNP closure after the ∼25-somite stage and resulted in caudal spina bifida in 67% of Grhl3Cre/+Vangl2Fl/Fl embryos. In the dorsal SE, Vangl2 deletion diminished rostrocaudal cell body orientation, but not directional polarisation of cell divisions. In the PNP, Vangl2 disruption diminished mediolateral polarisation of apical neuroepithelial F-actin profiles and resulted in eversion of the caudal PNP. This eversion prevented elevation of the caudal PNP neural folds, which in control embryos is associated with formation of Closure 5 around the 25-somite stage. Closure 5 formation in control embryos is associated with a reduction in mechanical stress withstood at the main zippering point, as inferred from the magnitude of neural fold separation following zippering point laser ablation. This stress accommodation did not happen in Vangl2-disrupted embryos. Thus, disruption of Vangl2-dependent planar-polarised processes in the PNP neuroepithelium and SE preclude zippering point biomechanical accommodation associated with Closure 5 formation at the completion of PNP closure.
    • Draft Genome Sequences of Macrococcus caseolyticus, Macrococcus canis, Macrococcus bohemicus, and Macrococcus goetzii

      Mazhar, Shahneela; Altermann, Eric; Hill, Colin; McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; 2015055 (American Society for Microbiology, 2019-05-09)
      Here, we present the draft genome sequences of 14 strains of 4 species of the genus Macrococcus. These strains were isolated from bovine milk and tongue samples obtained during a screening program.
    • Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory

      Egan, Kevin; Kelleher, Philip; Field, Des; Rea, Mary; Ross, R Paul; Cotter, Paul D.; Hill, Colin; Department of Agriculture, Food and the Marine; Science Foundation Ireland; DAFM 13/F/462; et al. (American Society for Microbiology, 2017-10-26)
      This paper reports the full genome sequence of the antimicrobial-producing bacterium Geobacillus stearothermophilus DSM 458, isolated in a sugar beet factory in Austria. In silico analysis reveals the presence of a number of novel bacteriocin biosynthetic genes.
    • Identification and characterisation of capidermicin, a novel bacteriocin produced by Staphylococcus capitis

      Lynch, David; O’Connor, Paula M.; Cotter, Paul D.; Hill, Colin; Field, Des; Begley, Máire; Cork Institute of Technology RISAM PhD scholarship (Public Library of Science (PLoS), 2019-10-16)
      One hundred human-derived coagulase negative staphylococci (CoNS) were screened for antimicrobial activity using agar-based deferred antagonism assays with a range of indicator bacteria. Based on the findings of the screen and subsequent well assays with cell free supernatants and whole cell extracts, one strain, designated CIT060, was selected for further investigation. It was identified as Staphylococcus capitis and herein we describe the purification and characterisation of the novel bacteriocin that the strain produces. This bacteriocin which we have named capidermicin was extracted from the cell-free supernatant of S. capitis CIT060 and purified to homogeneity using reversed-phase high performance liquid chromatography (RP-HPLC). Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric (MS) analysis revealed that the capidermicin peptide has a mass of 5,464 Da. Minimal inhibitory concentration (MIC) experiments showed that capidermicin was active in the micro-molar range against all the Gram-positive bacteria that were tested. Antimicrobial activity was retained over a range of pHs (2–11) and temperatures (10–121°C x 15 mins). The draft genome sequence of S. capitis CIT060 was determined and the genes predicted to be involved in the biosynthesis of capidermicin were identified. These genes included the predicted capidermicin precursor gene, and genes that are predicted to encode a membrane transporter, an immunity protein and a transcriptional regulator. Homology searches suggest that capidermicin is a novel member of the family of class II leaderless bacteriocins.
    • The gut microbiota and the liver. Pathophysiological and clinical implications

      Quigley, Eamonn M.M.; STANTON, CATHERINE; Murphy, Eileen F. (Elsevier BV, 2012-11-06)
      The term microbiota is used to describe the complete population of microorganisms that populate a certain location, such as the gut, and is preferred to the term flora as the former incorporates not just bacteria but also archaea, viruses, and other microorganisms, such as protozoa. Though the potential role of the microbiota (through such concepts as ‘‘the putrefactive principle associated with faeces’’ and ‘‘intestinal toxins’’) in the pathogenesis of systemic disorders has been recognized since antiquity, a firm scientific basis for a role for the gut microbiome in liver disease did not emerge until the middle of the last century with the recognition of the relationship between hepatic coma and the absorption of nitrogenous substances from the intestine [1]. This was followed by the description of abundant coliforms in the small intestine of cirrhotics [2] and the role of bacteria was clinched by trials demonstrating that antibiotics led to clinical improvement in hepatic encephalopathy (HE) [3]. Subsequently, these same gut-derived bacteria were implicated in another complication of chronic liver disease and portal hypertension, spontaneous bacterial peritonitis. Most recently, more credence has been given to a suggestion that has lingered in the background for decades, namely, that the gut microbiota might play a role in the pathogenesis or progression of certain liver diseases, including alcoholic liver disease [4], non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steato-hepatitis (NASH) [5], total parenteral nutrition (TPN)/intestinal failure-related liver disease (IFALD) [6], and primary sclerosing cholangitis (PSC) [7], either through the direct effects of bacteria or their products, via inflammatory mediators such as tumor necrosis factor a (TNF), whose release had been triggered by constituents of the microbiota, or, as in the case of primary sclerosing cholangitis (PSC), through cross-reactivity between microbial antigens and human tissue components (e.g., atypical anti-nuclear cytoplasmic antibodies (p-ANCA), in PSC, recognize both tubulin beta isoform 5 in human neutrophils, and the bacterial cell division protein FtsZ) [8]. Indeed, inflammatory mediators have also been implicated in the development and maintenance of the hyperdynamic circulation that is a feature of portal hypertension [9], in impairing liver function and contributing to haemostatic failure [10]. It is in these contexts that modulation of the microbiota has emerged as a potential therapeutic strategy in the management of liver disease
    • Low numbers of ovarian follicles ≥3 mm in diameter are associated with low fertility in dairy cows

      Mossa, F.; Walsh, S.W.; Butler, Stephen T.; Berry, Donagh; Carter, F.; Lonergan, P.; Smith, G.W.; Ireland, J.J.; Evans, A.C.O. (American Dairy Science Association, 2012-05-01)
      The total number of ovarian follicles ≥3 mm in diameter (antral follicle count, AFC) during follicular waves varies among cattle of similar age, but AFC is highly repeatable within individuals. We hypothesized that lower AFC could be associated with reduced fertility in cattle. The AFC was assessed by ultrasonography for 2 d consecutively during the first wave of follicular growth of the estrous cycle, 4.6 ± 1.43 d (mean ± SD) after estrus, in 306 Holstein-Friesian dairy cows approximately 70 d postpartum. Cows were classified into 3 groups based on AFC: low (AFC ≤15), intermediate (AFC = 16 to 24), and high (AFC ≥25). During the cycle in which AFC was assessed and in subsequent cycles, cows were artificially inseminated (AI) following detection of estrus, and pregnancy status was assessed using ultrasonography. Cows with high AFC had 3.34 times greater odds of being pregnant at the end of the breeding season compared with cows with low AFC; the odds of a successful pregnancy at first service were 1.75 times greater in the intermediate compared with the low group. The predicted probability of a successful pregnancy by the end of the breeding period (length of breeding season was 86 ± 16.3 d) was 94, 88, and 84% for the high, intermediate, and low AFC groups, respectively. No difference was evident among groups in 21-d submission rate (proportion of all cows detected in estrus and submitted for AI in the first 21 d of the breeding season), but the interval from calving to conception was shorter in the high (109.5 ± 5.1 d) versus low (117.1 ± 4 d) group, and animals with intermediate AFC received fewer services during the breeding season (2.3 ± 0.1) compared with animals with low AFC (2.7 ± 0.1). Lactating cows with ≤15 ovarian follicles have lower reproductive performance compared with cows with higher numbers of follicles, but the existence of a positive association between high numbers of ovarian follicles and fertility is yet to be established.
    • Impact of direct and indirect heating systems in broiler units on environmental conditions and flock performance

      Smith, Shaun; Meade, Joseph; Gibbons, James; McGill, Kevina; Bolton, Declan; Whyte, Paul; Department of Agriculture, Food and the Marine; 11SF328 (Elsevier BV, 2016-11-11)
      This study compared the impact of three indirect heating systems to direct gas flame heaters on a selection of flock performance and environmental indicators in commercial broiler units. No statistically significant differences (P≥0.05) were found in flock mortality rates, bird weight, water consumption, stress response, carbon dioxide, ammonia, temperature, relative humidity, litter quality, within-flock Campylobacter levels or mean Campylobacter counts when flock data from any of the three indirect heating systems were compared to flocks reared in houses with direct heating systems. Differences in litter quality were observed between upper and lower litter layers in all houses, regardless of heating type, which may have implications for bird health and welfare. Carbon dioxide concentrations in houses with direct heating systems were significantly higher than those in houses with indirect heating systems during the first 10 days of bird life (P≤0.05). This was due to the increased use of heating systems during this period of the flock cycle. Differences in CO2 concentrations had no effect on flock performance, possibly due to the fact that concentrations did not exceed known safe levels. A statistically significant increase in stress response was observed in birds as a result of partial depopulation (thinning) within houses, irrespective of heating system type used (P≤0.05). Stress associated with thinning may have consequences for bird welfare and food safety. In conclusion, the results of our study suggest that indirect heating systems do not appear to negatively impact on flock performance, stress response, within-flock Campylobacter levels or mean Campylobacter counts and do not appear to significantly alter environmental conditions within broiler houses when compared to houses equipped with direct heating systems. Indirect systems are a viable alternative for heating broiler houses in terms of flock performance, bird welfare and food safety.
    • Defining optimal DEM resolutions and point densities for modelling hydrologically sensitive areas in agricultural catchments dominated by microtopography

      Thomas, I.A.; Jordan, P.; Shine, O.; Fenton, Owen; Mellander, Per-Erik; Dunlop, P.; Murphy, P.N.C.; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine (Elsevier BV, 2017-02)
      Defining critical source areas (CSAs) of diffuse pollution in agricultural catchments depends upon the accurate delineation of hydrologically sensitive areas (HSAs) at highest risk of generating surface runoff pathways. In topographically complex landscapes, this delineation is constrained by digital elevation model (DEM) resolution and the influence of microtopographic features. To address this, optimal DEM resolutions and point densities for spatially modelling HSAs were investigated, for onward use in delineating CSAs. The surface runoff framework was modelled using the Topographic Wetness Index (TWI) and maps were derived from 0.25 m LiDAR DEMs (40 bare-earth points m−2), resampled 1 m and 2 m LiDAR DEMs, and a radar generated 5 m DEM. Furthermore, the resampled 1 m and 2 m LiDAR DEMs were regenerated with reduced bare-earth point densities (5, 2, 1, 0.5, 0.25 and 0.125 points m−2) to analyse effects on elevation accuracy and important microtopographic features. Results were compared to surface runoff field observations in two 10 km2 agricultural catchments for evaluation. Analysis showed that the accuracy of modelled HSAs using different thresholds (5%, 10% and 15% of the catchment area with the highest TWI values) was much higher using LiDAR data compared to the 5 m DEM (70–100% and 10–84%, respectively). This was attributed to the DEM capturing microtopographic features such as hedgerow banks, roads, tramlines and open agricultural drains, which acted as topographic barriers or channels that diverted runoff away from the hillslope scale flow direction. Furthermore, the identification of ‘breakthrough’ and ‘delivery’ points along runoff pathways where runoff and mobilised pollutants could be potentially transported between fields or delivered to the drainage channel network was much higher using LiDAR data compared to the 5 m DEM (75–100% and 0–100%, respectively). Optimal DEM resolutions of 1–2 m were identified for modelling HSAs, which balanced the need for microtopographic detail as well as surface generalisations required to model the natural hillslope scale movement of flow. Little loss of vertical accuracy was observed in 1–2 m LiDAR DEMs with reduced bare-earth point densities of 2–5 points m−2, even at hedgerows. Further improvements in HSA models could be achieved if soil hydrological properties and the effects of flow sinks (filtered out in TWI models) on hydrological connectivity are also considered.
    • Collective unconscious: How gut microbes shape human behavior

      Dinan, Timothy G.; Stilling, Roman M.; STANTON, CATHERINE; Cryan, John F.; Science Foundation Ireland; Health Research Board of Ireland; European Union; SFI/12/RC/2273; HRA_POR/2011/23; HRA_POR/2012/32 (Elsevier BV, 2015-04)
      The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.