Recent Submissions

  • Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome.

    Pasolli, Edoardo; De Filippis, Francesca; Mauriello, Italia E; Cumbo, Fabio; Walsh, Aaron M; Leech, John; Cotter, Paul D; Segata, Nicola; Ercolini, Danilo (2020-05-25)
  • Vancomycin and nisin A are effective against biofilms of multi-drug resistant Staphylococcus aureus isolates from human milk.

    Angelopoulou, Angeliki; Field, Des; Pérez-Ibarreche, Mariana; Warda, Alicja K; Hill, Colin; Ross, R Paul (2020-05-29)
  • Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics.

    Alexa Oniciuc, Elena A; Walsh, Calum J; Coughlan, Laura M; Awad, Amal; Simon, Cezara A; Ruiz, Lorena; Crispie, Fiona; Cotter, Paul D; Alvarez-Ordóñez, Avelino (2020-02-18)
    Here, the role of the dairy-processing chain as a reservoir of antimicrobial resistance (AR) determinants and a source of novel biocontrol quorum-sensing inhibitors is assessed through a functional metagenomics approach. A metagenomic library comprising ∼22,000 recombinant clones was built from DNA isolated from raw milk, raw milk cheeses, and cheese-processing environment swab samples. The high-throughput sequencing of 9,216 recombinant clones showed that lactic acid bacteria (LAB) dominated the microbial communities of raw milk cheese, while Gram-negative microorganisms of animal or soil origin dominated the microbiota of raw milk and cheese-processing environments. Although functional screening of the metagenomic library did not recover potential quorum-sensing inhibitors, in silico analysis using an in-house database built specifically for this study identified homologues to several genes encoding proteins with predicted quorum-quenching activity, among which, the QsdH hydrolase was the most abundant. In silico screening of the library identified LAB, and especially Lactococcus lactis, as a relevant reservoir of AR determinants in cheese. Functional screening of the library allowed the isolation of 13 recombinant clones showing an increased resistance toward ampicillin, which in all cases was accompanied by a reduced susceptibility to a wide range of β-lactam antibiotics. This study shows that the dairy-processing environment is a rich reservoir of AR determinants, which vary by sample source, and suggests that combining next-generation sequencing with functional metagenomics can be of use in overcoming the limitations of both approaches.IMPORTANCE The study shows the potential of functional metagenomics analyses to uncover the diversity of functions in microbial communities prevailing in dairy products and their processing environments, evidencing that lactic acid bacteria (LAB) dominate the cheese microbiota, whereas Gram-negative microorganisms of animal or soil origin dominate the microbiota of milk and cheese-processing environments. The functional and in silico screening of the library allowed the identification of LAB, and especially Lactococcus lactis, as a relevant reservoir of antimicrobial resistance (AR) determinants in cheese. Quorum-quenching (QQ) determinants were not recovered through the execution of wet-lab function-based screenings but were detected through in silico sequencing-based analyses.
  • Pitfalls in Single Clone CRISPR-Cas9 Mutagenesis to Fine-map Regulatory Intervals.

    Tian, Ruoyu; Pan, Yidan; Etheridge, Thomas H A; Deshmukh, Harshavardhan; Gulick, Dalia; Gibson, Greg; Bao, Gang; Lee, Ciaran M (2020-05-04)
  • Dietary Patterns Are Associated with Serum Metabolite Patterns and Their Association Is Influenced by Gut Bacteria among Older German Adults.

    Oluwagbemigun, Kolade; Foerster, Jana; Watkins, Claire; Fouhy, Fiona; Stanton, Catherine; Bergmann, Manuela M; Boeing, Heiner; Nöthlings, Ute (2020-01)
  • MHealth and perceived quality of care delivery: a conceptual model and validation.

    O'Connor, Yvonne; Andreev, Pavel; O'Reilly, Philip (2020-02-27)
  • Comparison of Faba Bean Protein Ingredients Produced Using Dry Fractionation and Isoelectric Precipitation: Techno-Functional, Nutritional and Environmental Performance.

    Vogelsang-O'Dwyer, Martin; Petersen, Iben Lykke; Joehnke, Marcel Skejovic; Sørensen, Jens Christian; Bez, Juergen; Detzel, Andreas; Busch, Mirjam; Krueger, Martina; O'Mahony, James A; Arendt, Elke K; et al. (2020-03-11)
  • Simulation in Neonatal Resuscitation.

    Garvey, Aisling A; Dempsey, Eugene M (2020-02-25)
  • Editorial: Factors Underpinning and Influencing Drivers' Aberrant Behaviors Across the Life Course.

    Lucidi, Fabio; Bosco, Andrea; Mallia, Luca; Setti, Annalisa (2020-01-22)
  • The potential of bone morphogenetic protein 2 as a neurotrophic factor for Parkinson's disease.

    Goulding, Susan R; Sullivan, Aideen M; O'Keeffe, Gerard W; Collins, Louise M
  • Comparative Genomics Analysis of from Different Niches.

    Wang, Shuo; Yang, Bo; Ross, R Paul; Stanton, Catherine; Zhao, Jianxin; Zhang, Hao; Chen, Wei (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.
  • Powder and Reconstituted Properties of Commercial Infant and Follow-On Formulas.

    Murphy, Eoin G; Regost, Nicolas E; Roos, Yrjö H; Fenelon, Mark A (2020-01-13)
    The physical properties of 15 commercially available infant formulas (IF) and follow-on (FO) formulas were analysed. Powders made with intact milk proteins were classified into two groups; Type I-homogenous mixtures of milk powder particles (n = 6); and Type II-heterogeneous mixtures of milk powder particles and tomahawk-shaped α-lactose monohydrate crystals (n = 6). Powders made using hydrolysed proteins were classified as Type III powders (n = 3). Type II powders exhibited similar flow characteristics to Type I powders despite having significantly (p < 0.05) smaller particle size, lower circularity, and greater elongation. Type III powders exhibited lowest particles size, highest surface free fat, and poorest flow properties (p < 0.05 for all). Upon reconstitution of powders (12.5% w/w), no significant difference (p < 0.05) in apparent viscosity was observed between Type I and II powders. Reconstituted Type III powders had relatively poor stability to separation compared to Type I and II powders, caused by large starch granules and/or poor emulsification by hydrolysed proteins. Overall, this study illustrated the range of physical behaviour and structures present in commercial IF powders. In particular, the effect of dry addition of lactose and the hydrolysis of protein were found to have major effects on physical properties.
  • Bifidobacterium breve UCC2003 Induces a Distinct Global Transcriptomic Program in Neonatal Murine Intestinal Epithelial Cells.

    Kiu, Raymond; Treveil, Agatha; Harnisch, Lukas C; Caim, Shabhonam; Leclaire, Charlotte; van Sinderen, Douwe; Korcsmaros, Tamas; Hall, Lindsay J (2020-07-02)
  • Inhibition of UBE2L6 attenuates ISGylation and impedes ATRA-induced differentiation of leukemic cells.

    Orfali, Nina; Shan-Krauer, Deborah; O'Donovan, Tracey R; Mongan, Nigel P; Gudas, Lorraine J; Cahill, Mary R; Tschan, Mario P; McKenna, Sharon L (2020-05-01)
  • Rescuer Exertion and Fatigue Using Two-Thumb vs. Two-Finger Method During Simulated Neonatal Cardiopulmonary Resuscitation.

    Reynolds, Claire; Cox, Jennifer; Livingstone, Vicki; Dempsey, Eugene Michael (2020-04-02)
    Background: Rescuer fatigue during neonatal CPR can affect CPR quality leading to reduced cerebral and myocardial perfusion. Aim: To investigate rescuer fatigue during simulated neonatal CPR using both objective (heart rate and cardiac output) and subjective measures. Methods: A randomized crossover manikin study performed. Nineteen doctors working in neonatology were randomized to (a) two-thumb term, (b) two-finger term, (c) two-thumb preterm, or (d) two-finger preterm group. Cardiac output and heart rate were measured with a non-invasive cardiac output monitor. A Likert scale assessed participants' level of perceived exertion. Results: In the preterm group, the mean change in HR from rest to 5 min in the TT group was 11.58 bpm (SD 6.22) vs. 9.94 bpm (SD 8.48), (p-value 0.36). There was no difference in change in CO, 2.10 (SD 1.15) in the TT group vs. 1.39 (SD 1.63) in TF group (p value 0.23). There was no difference in BORG RPE rating. In the term group, the mean change in HR from rest to 5 min was 15 bpm (SD 8.40) in TT group and 13 bpm (SD 7.86) in TF group, (p-value 0.416). The median change in CO from rest to 5 min was 1.50 (0.78 to 2.42 IQR) in TT group vs. 1.60 (0.65 to 3.0 IQR) in TF group. Conclusion: Providing chest compressions is associated with an increase in both heart rate and cardiac output. We did not identify difference between objective and subjective measures of fatigue between either technique in a preterm or term model.
  • Association of distinct type 1 bone morphogenetic protein receptors with different molecular pathways and survival outcomes in neuroblastoma.

    Alshangiti, Amnah M; Wyatt, Sean L; McCarthy, Erin; Collins, Louise M; Hegarty, Shane V; Sullivan, Aideen M; O'Keeffe, Gerard W (2020-04-23)
    Neuroblastoma (NB) is a paediatric cancer that arises in the sympathetic nervous system. Patients with stage 4 tumours have poor outcomes and 20% of high-risk cases have MYCN amplification. The bone morphogenetic proteins (BMPs) play roles in sympathetic neuritogenesis, by signalling through bone morphogenetic protein receptor (BMPR)2 and either BMPR1A or BMPR1B. Alterations in BMPR2 expression have been reported in NB; it is unknown if the expression of BMPR1A or BMPR1B is altered. We report lower BMPR2 and BMPR1B, and higher BMPR1A, expression in stage 4 and in MYCN-amplified NB. Kaplan-Meier plots showed that high BMPR2 or BMPR1B expression was linked to better survival, while high BMPR1A was linked to worse survival. Gene ontology enrichment and pathway analyses revealed that BMPR2 and BMPR1B co-expressed genes were enriched in those associated with NB differentiation. BMPR1A co-expressed genes were enriched in those associated with cell proliferation. Moreover, the correlation between BMPR2 and BMPR1A was strengthened, while the correlation between BMPR2 and BMPR1B was lost, in MYCN-amplified NB. This suggested that differentiation should decrease BMPR1A and increase BMPR1B expression. In agreement, nerve growth factor treatment of cultured sympathetic neurons decreased Bmpr1a expression and increased Bmpr1b expression. Overexpression of dominant negative BMPR1B, treatment with a BMPR1B inhibitor and treatment with GDF5, which signals via BMPR1B, showed that BMPR1B signalling is required for optimal neuritogenesis in NB cells, suggesting that loss of BMPR1B may alter neuritogenesis. The present study shows that expression of distinct BMPRs is associated with different survival outcomes in NB.
  • The Impact of Primer Design on Amplicon-Based Metagenomic Profiling Accuracy: Detailed Insights into Bifidobacterial Community Structure.

    Mancabelli, Leonardo; Milani, Christian; Lugli, Gabriele Andrea; Fontana, Federico; Turroni, Francesca; van Sinderen, Douwe; Ventura, Marco (2020-01-17)
    Next Generation Sequencing (NGS) technologies have overcome the limitations of cultivation-dependent approaches and allowed detailed study of bacterial populations that inhabit the human body. The consortium of bacteria residing in the human intestinal tract, also known as the gut microbiota, impacts several physiological processes important for preservation of the health status of the host. The most widespread microbiota profiling method is based on amplification and sequencing of a variable portion of the 16S rRNA gene as a universal taxonomic marker among members of the Bacteria domain. Despite its popularity and obvious advantages, this 16S rRNA gene-based approach comes with some important limitations. In particular, the choice of the primer pair for amplification plays a major role in defining the accuracy of the reconstructed bacterial profiles. In the current study, we performed an in silico PCR using all currently described 16S rRNA gene-targeting primer pairs (PP) in order to assess their efficiency. Our results show that V3, V4, V5, and V6 were the optimal regions on which to design 16S rRNA metagenomic primers. In detail, PP39 (Probio_Uni/Probio_Rev), PP41 (341F/534R), and PP72 (970F/1050R) were the most suitable primer pairs with an amplification efficiency of >98.5%. Furthermore, the Bifidobacterium genus was examined as a test case for accurate evaluation of intra-genus performances at subspecies level. Intriguingly, the in silico analysis revealed that primer pair PP55 (527f/1406r) was unable to amplify the targeted region of any member of this bacterial genus, while several other primer pairs seem to rather inefficiently amplify the target region of the main bifidobacterial taxa. These results highlight that selection of a 16S rRNA gene-based PP should be done with utmost care in order to avoid biases in microbiota profiling results.
  • Cumulative financial stress as a potential risk factor for cancer-related fatigue among prostate cancer survivors.

    Lu, Liya; Gavin, Anna; Drummond, Frances J; Sharp, Linda; CancerResearch@UCC, University College Cork, Cork, Ireland. (2020-08-01)
  • Intervention protocol: OPtimising thERapy to prevent avoidable hospital Admission in the Multi-morbid elderly (OPERAM): a structured medication review with support of a computerised decision support system.

    Crowley, Erin K; Sallevelt, Bastiaan T G M; Huibers, Corlina J A; Murphy, Kevin D; Spruit, Marco; Shen, Zhengru; Boland, Benoît; Spinewine, Anne; Dalleur, Olivia; Moutzouri, Elisavet; et al. (2020-03-17)
  • Protocol for the development and validation procedure of the managing the link and strengthening transition from child to adult mental health care (MILESTONE) suite of measures.

    Santosh, P; Adams, L; Fiori, F; Davidović, N; de Girolamo, G; Dieleman, G C; Franić, T; Heaney, N; Lievesley, K; Madan, J; et al. (2020-04-16)

View more