Microbiology (Scholarly Articles)

Permanent URI for this collection

Browse

Recent Submissions

  • Publication
    Stochastic modelling of pesticide transport to drinking water sources via runoff and resulting human health risk assessment
    (Elsevier, 2024-02-09) Harmon O'Driscoll, J.; McGinley, J.; Healy, M.G.; Siggins, Alma; Mellander, P.-E.; Morrison, L.; Gunnigle, E.; Ryan, P.C.; Environmental Protection Agency
    A modelling framework was developed to facilitate a probabilistic assessment of health risks posed by pesticide exposure via drinking water due to runoff, with the inclusion of influential site conditions and in-stream processes. A Monte-Carlo based approach was utilised to account for the inherent variability in pesticide and population properties, as well as site and climatic conditions. The framework presented in this study was developed with an ability to integrate different data sources and adapt the model for various scenarios and locations to meet the users¿ needs. The results from this model can be used by farm advisors and catchment managers to identify lower risk pesticides for use for given soil and site conditions and implement risk mitigation measures to protect water resources. Pesticide concentrations in surface water, and their risk of regulatory threshold exceedances, were simulated for fifteen pesticides in an Irish case study. The predicted concentrations in surface water were then used to quantify the level of health risk posed to Irish adults and children. The analysis indicated that herbicides triclopyr and MCPA occur in the greatest concentrations in surface water, while mecoprop was associated with the highest potential for health risks. The study found that the modelled pesticides posed little risk to human health under current application patterns and climatic conditions in Ireland using international acceptable intake values. A sensitivity study conducted examined the impact seasonal conditions, timing of application, and instream processes, have on the transport of pesticides to drinking water.
  • Publication
    Lectin microarray profiling demonstrates equivalent global glycosylation for whey protein ingredients enriched with α-lactalbumin and milk fat globule membrane
    (Elsevier, 2022-12-22) Le Berre, Marie; Joubran, Yousef; Joshi, Lokesh; O'Regan, Jonathan; Kilcoyne, Michelle
    Human milk fat globule membrane (MFGM) and whey proteins are nutritionally and functionally valuable, with many beneficial bioactivities associated with their glycosylation. However glycosylation of milk components other than free milk oligosaccharides are underinvestigated. Whey protein concentrate (WPC) ingredients with various enrichments or depletions are used in infant formula (IF) formulations to contribute to human milk equivalence and bioactivity benefits, but their overall or global glycosylation has not been compared. We compared the global glycosylation of commercial WPC ingredients for use in various IF formulations; two MFGM-enriched WPC ingredients (high fat HF1 and lower fat HF2), an α-lactalbumin-enriched WPC (WPC Lac) which has α-lactalbumin concentration closer to human milk and significantly less β-lactoglobulin which is not present in human milk, and two base WPC ingredients (WPC 80 and WPC 35) using lectin microarray profiling. WPC Lac and WPC HF1 glycosylation were highly similar to each other and both somewhat similar to WPC 35, while WPC HF2 was more similar to the base WPC 80 ingredient. N-linked glycosylation analysis demonstrated that WPC HF1 and WPC Lac were qualitatively most similar to one another, with WPC 80 and WPC 35 having similar structures, confirming lectin microarray profiling as a valuable method to compare global glycosylation. Thus WPC Lac may be a valuable ingredient for providing equivalent glycosylation to MFGM supplementation.
  • Publication
    Examination of oestrus-dependent alterations of bovine cervico-vaginal mucus glycosylation for potential as optimum fertilisation indicators
    (Royal Society of Chemistry, 2021-03-09) Le Berre, Marie; Gerlach, Jared Q.; Loughrey, Catherine; Creavin, Aileen; Pluta, Katarzyna; Gallagher, Mary; Carrington, Stephen D.; Joshi, Lokesh; Kilcoyne, Michelle; Science Foundation Ireland; Royal Society of Chemistry Analytical Chemistry Trust Fund; Health Research Board
    Oestrus is the period in the sexual cycle of female mammals during which ovulation occurs, where they become most receptive to mating and are most fertile. Efficient detection of oestrus is a key component in successful reproductive livestock management programmes and a major factor in the efficiency and profitability of dairy farms. Oestrus detection in cattle is most often performed by visual observation of the primary signs of oestrus, such as mounting behaviour and standing heat, to facilitate more successful prediction of optimal time points for artificial insemination. This is a time-consuming method and requires a skilled, diligent observer. Biological measurements using easily accessible biomolecules in the cervico-vaginal mucus could provide an alternative strategy to physical methods of oestrus detection, which would provide an inexpensive means of rapidly and accurately assessing the onset of oestrus. In this study, glycosylation changes in cervico-vaginal mucus from three heifers following oestrus induction were investigated as a proof of concept to assess whether potential glycosylation-based trends could be useful for oestrus stage indication. Mucus collected at different time points following oestrus induction was immobilised in a microarray format and their glycosylation interrogated with a panel of fluorescently labelled lectins, carbohydrate-binding proteins with different specificities. Individual animal-specific glycosylation patterns were observed, however each pattern followed a similar trend around oestrus. This unique oestrus-associated glycosylation was identified by a combination of relative binding of the lectins SNA-I and WFA for each animal. This alteration in cervico-vaginal mucus glycosylation could potentially be exploited in future to more accurately identify optimal fertilisation intervention points compared to visual signs. More effective oestrus biomarkers will lead to more successful livestock reproductive programmes, decreasing costs and animal stress.
  • Publication
    OpenTCC: An open source low-cost temperature-control chamber
    (Elsevier, 2020-02-24) Sánchez, Carlos; Dessì, Paolo; Duffy, Maeve; Lens, Piet N.L.; Science Foundation Ireland
    Microbial electrochemical technologies (MET) are emerging systems for environmental applications such as renewable energy production or pollution remediation. MET research often requires stable temperatures and low levels of electromagnetic interference. Due to the presence of electrical wires and sensors, heating MET using water jacket recirculation can raise safety issues, whereas heating coils may affect the results of electrochemical analyses. The proposed open-source temperature-control chamber (OpenTCC) aims to provide a low-cost solution for controlling temperature (in the range 20–55 °C) while simultaneously reducing the electromagnetic interferences caused by switching mode power supplies. OpenTCC consists of a light and cheap structure, incorporating eight heating pads and two Peltier-cooling modules powered by open-source electronic circuits. Its hardware is controlled by an Arduino microcontroller and a Python interface which provides data-logging and serve as a basis for programable temperature cycles. The system has a modular design to allow stacking several independent modules. OpenTCC provides a reliable and tunable temperature control at lower costs than currently available commercial temperature controllers and provides a platform for field-specific upgrades. Though optimized for MET, Open-TCC can be adapted to other laboratory applications due to its flexible design.
  • Publication
    The dairy biorefinery: Integrating treatment processes for cheese whey valorisation
    (Elsevier, 2020-08-28) Asunis, Fabiano; De Gioannis, Giorgia; Dessì, Paolo; Isipato, Marco; Lens, Piet N.L.; Muntoni, Aldo; Polettini, Alessandra; Pomi, Raffaella; Rossi, Andreina; Spiga, Daniela; Science Foundation Ireland; Sardinian Regional Government
    With an estimated worldwide production of 190 billion kg per year, and due to its high organic load, cheese whey represents a huge opportunity for bioenergy and biochemicals production. Several physical, chemical and biological processes have been proposed to valorise cheese whey by producing biofuels (methane, hydrogen, and ethanol), electric energy, and/or chemical commodities (carboxylic acids, proteins, and biopolymers). A biorefinery concept, in which several value-added products are obtained from cheese whey through a cascade of biotechnological processes, is an opportunity for increasing the product spectrum of dairy industries while allowing for sustainable management of the residual streams and reducing disposal costs for the final residues. This review critically analyses the different treatment options available for energy and materials recovery from cheese whey, their combinations and perspectives for implementation. Thus, instead of focusing on a specific valorisation platform, in the present review the most relevant aspects of each strategy are analysed to support the integration of different routes, in order to identify the most appropriate treatment train.
  • Publication
    Propionate production by bioelectrochemically-assisted lactate fermentation and simultaneous CO2 recycling
    (Frontiers Media, 2020-12-15) Isipato, Marco; Dessì, Paolo; Sánchez, Carlos; Mills, Simon; Ijaz, Umer Z.; Asunis, Fabiano; Spiga, Daniela; De Gioannis, Giorgia; Mascia, Michele; Collins, Gavin; Muntoni, Aldo; Lens, Piet N. L.; Science Foundation Ireland; European Research Council
    Production of volatile fatty acids (VFAs), fundamental building blocks for the chemical industry, depends on fossil fuels but organic waste is an emerging alternative substrate. Lactate produced from sugar-containing waste streams can be further processed to VFAs. In this study, electrofermentation (EF) in a two-chamber cell is proposed to enhance propionate production via lactate fermentation. At an initial pH of 5, an applied potential of −1 V vs. Ag/AgCl favored propionate production over butyrate from 20 mM lactate (with respect to non-electrochemical control incubations), due to the pH buffering effect of the cathode electrode, with production rates up to 5.9 mM d–1 (0.44 g L–1 d–1). Microbial community analysis confirmed the enrichment of propionate-producing microorganisms, such as Tyzzerella sp. and Propionibacterium sp. Organisms commonly found in microbial electrosynthesis reactors, such as Desulfovibrio sp. and Acetobacterium sp., were also abundant at the cathode, indicating their involvement in recycling CO2 produced by lactate fermentation into acetate, as confirmed by stoichiometric calculations. Propionate was the main product of lactate fermentation at substrate concentrations up to 150 mM, with a highest production rate of 12.9 mM d–1 (0.96 g L–1 d–1) and a yield of 0.48 mol mol–1 lactate consumed. Furthermore, as high as 81% of the lactate consumed (in terms of carbon) was recovered as soluble product, highlighting the potential for EF application with high-carbon waste streams, such as cheese whey or other food wastes. In summary, EF can be applied to control lactate fermentation toward propionate production and to recycle the resulting CO2 into acetate, increasing the VFA yield and avoiding carbon emissions and addition of chemicals for pH control.
  • Publication
    Organic waste biorefineries: Looking towards implementation
    (Elsevier, 2020-07-16) Alibardi, Luca; Astrup, Thomas F.; Asunis, Fabiano; Clarke, William P.; De Gioannis, Giorgia; Dessì, Paolo; Lens, Piet N.L.; Lavagnolo, Maria Cristina; Lombardi, Lidia; Muntoni, Aldo; Pivato, Alberto; Polettini, Alessandra; Pomi, Raffaella; Rossi, Andreina; Spagni, Alessandro; Spiga, Daniela
    The concept of biorefinery expands the possibilities to extract value from organic matter in form of either bespoke crops or organic waste. The viability of biorefinery schemes depends on the recovery of higher-value chemicals with potential for a wide distribution and an untapped marketability. The feasibility of biorefining organic waste is enhanced by the fact that the biorefinery will typically receive a waste management fee for accepting organic waste. The development and implementation of waste biorefinery concepts can open up a wide array of possibilities to shift waste management towards higher sustainability. However, barriers encompassing environmental, technical, economic, logistic, social and legislative aspects need to be overcome. For instance, waste biorefineries are likely to be complex systems due to the variability, heterogeneity and low purity of waste materials as opposed to dedicated biomasses. This article discusses the drivers that can make the biorefinery concept applicable to waste management and the possibilities for its development to full scale. Technological, strategic and market constraints affect the successful implementations of these systems. Fluctuations in waste characteristics, the level of contamination in the organic waste fraction, the proximity of the organic waste resource, the markets for the biorefinery products, the potential for integration with other industrial processes and disposal of final residues are all critical aspects requiring detailed analysis. Furthermore, interventions from policy makers are necessary to foster sustainable bio-based solutions for waste management.
  • Publication
    Fermentative hydrogen production from cheese whey with in-line, concentration gradient-driven butyric acid extraction
    (Elsevier, 2020-08-01) Dessì P, Asunis F, Ravishankar H, Cocco FG, De Gioannis G, Muntoni A, Lens PNL; Dessì, Paolo; Asunis, Fabiano; Ravishankar, Harish; Cocco, Francesco Giuseppe; De Gioannis, Giorgia; Muntoni, Aldo; Lens, Piet N.L.; Science Foundation Ireland; Sardinian Regional Government
    Hydrogen (H2) generation from cheese whey with simultaneous production and extraction of volatile fatty acids (VFAs) was studied in UASB reactors at two temperatures (20 and 35 °C) and pH values (5.0 and 4.5). The extraction module, installed through a recirculation loop, was a silicone tube coil submerged in water, which allows concentration-driven extraction of undissociated VFAs. Operating conditions were selected as a compromise for the recovery of both H2 and VFAs. Batch experiments showed a higher yield (0.9 mol H2 mol−1 glucoseeq.) at 35 °C and pH 5.0, regardless of the presence of the extraction module, whereas lower yields were obtained at pH 4.5 and 20 °C (0.5 and 0.3 mol H2 mol−1 glucoseeq., respectively). VFAs crossed the silicone membrane, with a strong preference for butyric over propionic and acetic acid due to its higher hydrophobicity. Sugars, lactic acid and nutrients were retained, resulting in an extracted solution of up to 2.5 g L−1 butyric acid with more than 90% purity. Continuous experiment confirmed those results, with production rates up to 2.0 L H2 L−1 d−1 and butyric acid extraction both in-line (from the UASB recirculation) and off-line (from the UASB effluent). In-line VFA extraction can reduce the operating costs of fermentation, facilitating downstream processing for the recovery of marketable VFAs without affecting the H2 production.
  • Publication
    Microbial electrosynthesis: Towards sustainable biorefineries for production of green chemicals from CO2 emissions
    (Elsevier, 2020-12-01) Dessì, Paolo; Rovira-Alsina, Laura; Sánchez, Carlos; Dinesh, G. Kumaravel; Tong, Wenming; Chatterjee, Pritha; edesco, MicheleT; Farràs, Pau; Hamelers, Hubertus M.V.; Puig, Sebastià; Science Foundation Ireland; Horizon 2020
    Decarbonisation of the economy has become a priority at the global level, and the resulting legislative pressure is pushing the chemical and energy industries away from fossil fuels. Microbial electrosynthesis (MES) has emerged as a promising technology to promote this transition, which will further benefit from the decreasing cost of renewable energy. However, several technological challenges need to be addressed before the MES technology can reach its maturity. The aim of this review is to critically discuss the bottlenecks hampering the industrial adoption of MES, considering the whole production process (from the CO2 source to the marketable products), and indicate future directions. A flexible stack design, with flat or tubular MES modules and direct CO2 supply, is required for site-specific decentralised applications. The experience gained for scaling-up electrochemical cells (e.g. electrolysers) can serve as a guideline for realising pilot MES stacks to be technologically and economically evaluated in industrially relevant conditions. Maximising CO2 abatement rate by targeting high-rate production of acetate can promote adoption of MES technology in the short term. However, the development of a replicable and robust strategy for production and in-line extraction of higher-value products (e.g. caproic acid and hexanol) at the cathode, and meaningful exploitation of the currently overlooked anodic reactions, can further boost MES cost-effectiveness. Furthermore, the use of energy storage and smart electronics can alleviate the fluctuations of renewable energy supply. Despite the unresolved challenges, the flexible MES technology can be applied to decarbonise flue gas from different sources, to upgrade industrial and wastewater treatment plants, and to produce a wide array of green and sustainable chemicals. The combination of these benefits can support the industrial adoption of MES over competing technologies.
  • Publication
    Carboxylic acids production and electrosynthetic microbial community evolution under different CO2 feeding regimes
    (Elsevier, 2020-10-15) Dessì, Paolo; Sánchez, Carlos; Mills, Simon; Cocco, Francesco Giuseppe; Isipato, Marco; Ijaz, Umer Z.; Collins, Gavin; Lens, Piet N.L.; Science Foundation Ireland; Sardinian Regional Government
    Microbial electrosynthesis (MES) is a potential technology for CO2 recycling, but insufficient information is available on the microbial interactions underpinning electrochemically-assisted reactions. In this study, a MES reactor was operated for 225 days alternately with bicarbonate or CO2 as carbon source, under batch or continuous feeding regimens, to evaluate the response of the microbial communities, and their productivity, to dynamic operating conditions. A stable acetic acid production rate of 9.68 g m-2 d-1, and coulombic efficiency up to 40%, was achieved with continuous CO2 sparging, higher than the rates obtained with bicarbonate (0.94 g m-2 d-1) and CO2 under fed-batch conditions (2.54 g m-2 d-1). However, the highest butyric acid production rate (0.39 g m-2 d-1) was achieved with intermittent CO2 sparging. The microbial community analyses focused on differential amplicon sequence variants (ASVs), allowing detection of ASVs significantly different across consecutive samples. This analysis, combined with co-occurence network analysis, and cyclic voltammetry, indicated that hydrogen-mediated acetogenesis was carried out by Clostridium, Eubacterium and Acetobacterium, whereas Oscillibacter and Caproiciproducens were involved in butyric acid production. The cathodic community was spatially inhomogeneous, with potential electrotrophs, such as Sulfurospirillum and Desulfovibrio, most prevalent near the current collector. The abundance of Sulfurospirillum positively correlated with that of Acetobacterium, supporting the syntrophic metabolism of both organisms.
  • Publication
    Eight rules for improving the quality of papers on the antimicrobial susceptibility of bacteria isolated from aquatic animals
    (Inter-Research Science Publisher, 2020-04-30) Smith, Peter
    The methods for antimicrobial susceptibility testing of bacteria, although relatively simple, are not robust. As a consequence, if the data generated in such tests are to be commensu- rate, all susceptibility tests must be performed using standard protocols. A review of the published literature of antimicrobial susceptibility testing of bacteria from aquatic animals revealed a fre- quent occurrence of significant errors, particularly with regard to testing methodology, quality control and the use of appropriate interpretive criteria in the performance and reporting of sus- ceptibility tests. This opinion piece provides a set of rules that, if followed, would help authors to avoid these frequently detected shortcomings.
  • Publication
    The performance of antimicrobial susceptibility testing programmes relevant to aquaculture and aquaculture products
    (Food and Agriculture Organization of the United Nations (FAO), 2019) Smith, Peter
    Antimicrobial susceptibility testing of bacteria isolated from aquatic animals and their environments may be performed either as part of a monitoring or surveillance programme or to provide guidance for clinical treatments of diseased animals. This technical paper addresses best practice guidelines for the performance of these susceptibility tests. Section 1 discusses the relevance of this document to The FAO Action Plan on Antimicrobial Resistance 2016- 2020. Section 2 provides a general background to the principles of antimicrobial susceptibility testing. It stresses the absolute need for the use of internationally agreed standardized test protocols and the adherence to the quality control requirement of those protocols. It also stresses the importance of the use of consensus-based, internationally harmonized criteria in the interpretation of the meanings that can be given to in-vitro susceptibility data. It provides a discussion of the theory of interpretive criteria and the methods by which they can be calculated. Section 3 discusses the current status of the standard protocols that can be recommended for use in antimicrobial susceptibility testing of bacteria isolated from aquatic animals. Following a consideration of 44 species of bacteria that represent those most frequently isolated from aquatic animals, it demonstrates that the currently available standardized protocols are adequate for the determination of the antimicrobial susceptibility of 37 of them (84 percent). Section 4 discusses the importance of the design of programmes aimed at monitoring or surveillance of antimicrobial resistance associated with the use of antimicrobial agents in the rearing of aquatic animals. These programmes may be performed to address various questions. It is important that the design adopted in any programme generates data appropriate to the question being asked. In this paper four designs are outlined, each of which will provide data for programmes aimed at answering different questions. Section 5 provides some conclusions, while Section 6 gives a list of references. The technical paper is supported by four annexes that provide: (i) a listing of Clinical and Laboratory Standards Institute (CLSI) documents cited in the paper; (ii) a list of the antimicrobial agents most commonly used in aquaculture; (iii) notes on the selection of test protocols for selected Gram-positive cocci; and (iv) guidance on the possible use of epidemiological cut-off values in a clinical context.
  • Publication
    Setting epidemiological cut-off values for bacteria isolated from aquatic animals: a toolbox for designing a 96-well plate for microdilution MIC assays
    (European Association of Fish Pathologists, 2020-06-02) Baron, Sandrine; Smith, Peter; Verner-Jeffreys, David W.
    A workshop was held at the EAFP meeting in Porto to initiate discussion on the design of studies that could generate the data needed to set epidemiological cut-off values appropriate for application to antimicrobial susceptibility data for bacteria isolated from aquatic animals. To set such cut-off values, consortia of at least five laboratories are needed. The work required from individual laboratories, although not a relatively large number, was the susceptibility testing of approximately 30 isolates of each species. What is essential is, however, that the activities of the laboratories, and the experimental protocols that they use, are coordinated. A major aim of this workshop was to encourage the formation of informal groups of laboratories that could form consortia and coordinate their activities to produce the data needed to generate cut-off values for various species that were of interest to them. All laboratories with an interest in the possibility of joining such a consortia were, and are still, invited to contact Sandrine Baron (Sandrine.BARON@anses.fr) who has agreed to facilitate this activity
  • Publication
    A review of the shortcomings in the testing methods used and reporting of data in the literature on antimicrobial susceptibility
    (European Association of Fish Pathologists, 2020-06-02) Smith, Peter; Egan, Sarah
    The susceptibility test protocols used in 186 published papers that reported 203 studies of the antimicrobial susceptibility of non-cholera Vibrio spp were examined. Only a very small percentage of the studies provided explicit evidence that they had used standardised susceptibility protocols. Although all 203 reported frequencies of resistance in the isolates they studied, 185 of them either did not provide the criteria they used to determine resistance, used criteria that had not been validated or used criteria that were inappropriate. Less than 10% of the studies used internationally-harmonised consensus-based interpretive criteria that were appropriate to their data. These shortcomings in the performance and/or the reporting of susceptibility had results such that it was difficult or impossible to compare the data generated in the various studies. It is argued that compliance with the recommendations of OIE Aquatic Animal Code for the performing and reporting of susceptibility studies would be a major step towards limiting the frequency of these shortcomings in the scientific literature
  • Publication
    Standard protocols for antimicrobial susceptibility testing of Vibrionaceae isolated from aquatic animals
    (European Association of Fish Pathologists, 2018-07-18) Smith, Peter; Egan, Sarah
    A review of the relevant literature has shown that it is safe to recommend that the antimicrobial susceptibility of the species of the Vibrionaceae most commonly isolated from aquatic animals can be established using internationally standardised protocols that specify the use of Mueller-Hinton media that has not been supplemented with additional NaCl
  • Publication
    Influence of incubation time on antimicrobial susceptibility testing of pathogenic Vibrio anguillarum and Vibrio vulnificus isolated from fish
    (Elsevier, 2020-07-15) Baron, Sandrine; Ceccarelli, Daniela; Dalsgaard, Inger; Granier, Sophie A.; Haenen, Olga; Jansson, Eva; Madsen, Lone; Jouy, Eric; Kempf, Isabelle; Larvor, Emeline; Morin, Thierry; Testerink, Joop; Veldman, Kees; Mouritsen, Kári Karbech; Van Gelderen, Betty; Voorbergen-Laarman, Michal; Säker, Eva; Blomkvist, Eva; Smith, Peter
    A multi-laboratory study was performed to investigate the most suitable incubation time for susceptibility tests of fish pathogens Vibrio anguillarum and Vibrio vulnificus performed at 28 degrees C. An isolate set consisting of 30 V. anguillarum and 26 V. vulnificus was used by four participating laboratories in Denmark, France, Sweden, and the Netherlands. Inhibition zone diameters were determined by agar disc diffusion for eight agents and Minimum Inhibitory Concentration (MIC) values were determined for seven agents using the standard CLSI testing protocols for non-fastidious organisms that specify 24-28 h incubation. In this work an additional set of readings was made after 48 h incubation. In total, 1120 paired zone sizes and 399 paired MIC observations were made at the two incubation times. Examination of the data demonstrated that incubation time had a small but statistically significant effect on the numerical values of susceptibility measures. However, the effects of incubation time on the precision of the data sets and the categorisation of isolates based on the application of epidemiological cutoff values were slight and statistically non significant. These analyses suggest that the susceptibility of these Vibrio species could be established using protocols that specify either 24-28 h or 44-48 h incubation.This study does not provide evidence that prolonged incubation to 48 h improves the quality of data generated by the tests. Therefore, it is recommended that the existing standard CLSI protocols with 24-28 h at 28 degrees C should be adopted for susceptibility testing of V. anguillarum and V. vulnificus.
  • Publication
    Glycomics microarrays reveal differential in situ presentation of the biofilm polysaccharide Poly-N-acetylglucosamine on Acinetobacter baumannii and Staphylococcus aureus cell surfaces
    (MDPI, 2020-04-02) Flannery, Andrea; Le Berre, Marie; Pier, Gerald B.; O’Gara, James P.; Kilcoyne, Michelle; Irish Research Council; Royal Society of Chemistry Analytical Chemistry Trust Fund; Health Research Board
    The biofilm component poly-N-acetylglucosamine (PNAG) is an important virulence determinant in medical-device-related infections caused by ESKAPE group pathogens including Gram-positive Staphylococcus aureus and Gram-negative Acinetobacter baumannii. PNAG presentation on bacterial cell surfaces and its accessibility for host interactions are not fully understood. We employed a lectin microarray to examine PNAG surface presentation and interactions on methicillin-sensitive (MSSA) and methicillin-resistant S. aureus (MRSA) and a clinical A. baumannii isolate. Purified PNAG bound to wheatgerm agglutinin (WGA) and succinylated WGA (sWGA) lectins only. PNAG was the main accessible surface component on MSSA but was relatively inaccessible on the A. baumannii surface, where it modulated the presentation of other surface molecules. Carbohydrate microarrays demonstrated similar specificities of S. aureus and A. baumannii for their most intensely binding carbohydrates, including 3′ and 6′sialyllactose, but differences in moderately binding ligands, including blood groups A and B. An N-acetylglucosamine-binding lectin function which binds to PNAG identified on the A. baumannii cell surface may contribute to biofilm structure and PNAG surface presentation on A. baumannii. Overall, these data indicated differences in PNAG presentation and accessibility for interactions on Gram-positive and Gram-negative cell surfaces which may play an important role in biofilm-mediated pathogenesis.
  • Publication
    Generation of a panel of high affinity antibodies and development of a biosensor-based immunoassay for the detection of okadaic acid in shellfish
    (Elsevier, 2015-07-10) Le Berre, Marie; Kilcoyne, Michelle; Kane, Marian; Enterprise Ireland; Programme for Research in Third Level Institutions (PRTLI)
    Okadaic acid (OA) and its derivatives, DTX-1 and DTX-2, are marine biotoxins associated with diarrhetic shellfish poisoning. Routine monitoring of these toxins relies on the mouse bioassay. However, due to the technical unreliability and animal usage of this bioassay, there is always a need for convenient and reliable alternative assay methods. A panel of monoclonal antibodies against OA was generated and the most suitable was selected for biosensor-based assay development using surface plasmon resonance. The cross reactivity of the selected antibody with DTX-1 was found to be 73%, confirming the antibody suitability for both OA and DTX detection. The OA and derivative assay was designed as an inhibition assay covering the concentrations 1-75 ng/ml, with a sensitivity of 22.4 ng/ml. The assay was highly reproducible and preliminary validation showed no matrix interference from mussel extracts and good recovery of added standard in mussel extracts, with %CV of
  • Publication
    Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale
    (Public Library of Science, 2019-09-26) Goertz, Sarah; de Menezes, Alexandre B.; Birtles, Richard J.; Fenn, Jonathan; Lowe, Ann E.; MacColl, Andrew D. C.; Poulin, Benoit; Young, Stuart; Bradley, Janette E.; Taylor, Christopher H.; Natural Environment Research Council; Biotechnology and Biological Sciences Research Council
    The composition of the mammalian gut microbiota can be influenced by a multitude of environmental variables such as diet and infections. Studies investigating the effect of these variables on gut microbiota composition often sample across multiple separate populations and habitat types. In this study we explore how variation in the gut microbiota of the house mouse (Mus musculus domesticus) on the Isle of May, a small island off the east coast of Scotland, is associated with environmental and biological factors. Our study focuses on the effects of environmental variables, specifically trapping location and surrounding vegetation, as well as the host variables sex, age, body weight and endoparasite infection, on the gut microbiota composition across a fine spatial scale in a freely interbreeding population. We found that differences in gut microbiota composition were significantly associated with the trapping location of the host, even across this small spatial scale. Sex of the host showed a weak association with microbiota composition. Whilst sex and location could be identified as playing an important role in the compositional variation of the gut microbiota, 75% of the variation remains unexplained. Whereas other rodent studies have found associations between gut microbiota composition and age of the host or parasite infections, the present study could not clearly establish these associations. We conclude that fine spatial scales are important when considering gut microbiota composition and investigating differences among individuals.
  • Publication
    Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study
    (Frontiers Media, 2018-11-21) Storey, Sean; Ashaari, Mardiana Mohd; Clipson, Nicholas; Doyle, Evelyn; de Menezes, Alexandre B.; Environmental Protection Agency, Ireland; Malaysian Ministry of Higher Education; International Islamic University Malaysia
    Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDa) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDa gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased similar to 20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.