APC Microbiome Irelandhttps://hdl.handle.net/10468/1072024-03-28T12:22:04Z2024-03-28T12:22:04Z931116S rRNA gene sequencing of mock microbial populations-impact of DNA extraction method, primer choice and sequencing platformFouhy, FionaClooney, Adam G.Stanton, CatherineClaesson, Marcus J.Cotter, Paul D.https://hdl.handle.net/10468/41262023-04-05T09:28:42Z2016-06-24T00:00:00Zdc.title: 16S rRNA gene sequencing of mock microbial populations-impact of DNA extraction method, primer choice and sequencing platform
dc.contributor.author: Fouhy, Fiona; Clooney, Adam G.; Stanton, Catherine; Claesson, Marcus J.; Cotter, Paul D.
dc.description.abstract: Background: Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results: The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions: Microbiota compositional data differed depending on the primers and sequencing platform that were used. The results demonstrate the risks in comparing data generated using different sequencing approaches and highlight the merits of choosing a standardised approach for sequencing in situations where a comparison across multiple sequencing runs is required.
2016-06-24T00:00:00ZA bioengineered nisin derivative to control biofilms of Staphylococcus pseudintermediusField, DesGaudin, NoemieLyons, FrancyO'Connor, Paula M.Cotter, Paul D.Hill, ColinRoss, R. Paulhttps://hdl.handle.net/10468/23142023-04-05T09:32:13Z2015-01-01T00:00:00Zdc.title: A bioengineered nisin derivative to control biofilms of Staphylococcus pseudintermedius
dc.contributor.author: Field, Des; Gaudin, Noemie; Lyons, Francy; O'Connor, Paula M.; Cotter, Paul D.; Hill, Colin; Ross, R. Paul
dc.description.abstract: Antibiotic resistance and the shortage of novel antimicrobials are among the biggest challenges facing society. One of the major factors contributing to resistance is the use of frontline clinical antibiotics in veterinary practice. In order to properly manage dwindling antibiotic resources, we must identify antimicrobials that are specifically targeted to veterinary applications. Nisin is a member of the lantibiotic family of antimicrobial peptides that exhibit potent antibacterial activity against many gram-positive bacteria, including human and animal pathogens such as Staphylococcus, Bacillus, Listeria, and Clostridium. Although not currently used in human medicine, nisin is already employed commercially as an anti-mastitis product in the veterinary field. Recently we have used bioengineering strategies to enhance the activity of nisin against several high profile targets, including multi-drug resistant clinical pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) and also against staphylococci and streptococci associated with bovine mastitis. However, newly emerging pathogens such as methicillin resistant Staphylococcus pseudintermedius (MRSP) pose a significant threat in terms of veterinary health and as a reservoir for antibiotic resistance determinants. In this study we created a nisin derivative with enhanced antimicrobial activity against S. pseudintermedius. In addition, the novel nisin derivative exhibits an enhanced ability to impair biofilm formation and to reduce the density of established biofilms. The activities of this peptide represent a significant improvement over that of the wild-type nisin peptide and merit further investigation with a view to their use to treat S. pseudintermedius infections.
2015-01-01T00:00:00ZA bioengineered nisin derivative to control Streptococcus uberis biofilmsPérez-Ibarreche, MarianaField, DesRoss, R. PaulHill, Colinhttps://hdl.handle.net/10468/145332023-06-01T02:02:45Z2021-07-27T00:00:00Zdc.title: A bioengineered nisin derivative to control Streptococcus uberis biofilms
dc.contributor.author: Pérez-Ibarreche, Mariana; Field, Des; Ross, R. Paul; Hill, Colin
dc.description.abstract: Antimicrobial peptides are evolving as novel therapeutic options against the increasing problem of multidrug-resistant microorganisms, and nisin is one such avenue. However, some bacteria possess a specific nisin resistance system (NSR), which cleaves the peptide reducing its bactericidal efficacy. NSR-based resistance was identified in strains of Streptococcus uberis, a ubiquitous pathogen that causes mastitis in dairy cattle. Previous studies have demonstrated that a nisin A derivative termed nisin PV, featuring S29P and I30V, exhibits enhanced resistance to proteolytic cleavage by NSR. Our objective was to investigate the ability of this nisin derivative to eradicate and inhibit biofilms of S. uberis DPC 5344 and ATCC 700407 () using crystal violet (biomass), 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) (viability) assays, and confocal microscopy (viability and architecture). When preestablished biofilms were assessed, both peptides reduced biofilm biomass by over 60% compared to that of the untreated controls. However, a 42% higher reduction in viability was observed following treatment with nisin PV compared to that of nisin A. Accordingly, confocal microscopy analysis revealed significantly more dead cells on the biofilm upper surface and a reduced thickness following treatment with nisin PV. When biofilm inhibition was assessed, nisin PV inhibited biofilm formation and decreased viability up to 56% and 85% more than nisin A, respectively. Confocal microscopy analysis revealed a lack of biofilm for ATCC 700407 and only dead cells for DPC 5344. These results suggest that nisin PV is a promising alternative to effectively reduce the biofilm formation of strains carrying NSR. One of the four most prevalent species of bovine mastitis-causing pathogens is Its ability to form biofilms confers on the bacteria greater resistance to antibiotics, requiring higher doses to be more effective. In a bid to limit antibiotic resistance development, the need for alternative antimicrobials is paramount. Bacteriocins such as nisin represent one such alternative that could alleviate the impact of mastitis caused by However, many strains of have been shown to possess nisin resistance determinants, such as the nisin resistance protein (NSR). In this study, we demonstrate the ability of nisin and a nisin derivative termed PV that is insensitive to NSR to prevent and remove biofilms of NSR-producing strains. These findings will add new information to the antimicrobial bacteriocins and control of research fields specifically in relation to biofilms and mastitis-associated strains.
2021-07-27T00:00:00ZA bioengineered nisin derivative, M21A, in combination with food grade additives eradicates biofilms of Listeria monocytogenesSmith, Muireann K.Draper, Lorraine A.Hazelhoff, Pieter-JanCotter, Paul D.Ross, R. PaulHill, Colinhttps://hdl.handle.net/10468/33802023-04-05T09:29:48Z2016-11-30T00:00:00Zdc.title: A bioengineered nisin derivative, M21A, in combination with food grade additives eradicates biofilms of Listeria monocytogenes
dc.contributor.author: Smith, Muireann K.; Draper, Lorraine A.; Hazelhoff, Pieter-Jan; Cotter, Paul D.; Ross, R. Paul; Hill, Colin
dc.description.abstract: The burden of foodborne disease has large economic and social consequences worldwide. Despite strict regulations, a number of pathogens persist within the food environment, which is greatly contributed to by a build-up of resistance mechanisms and also through the formation of biofilms. Biofilms have been shown to be highly resistant to a number of antimicrobials and can be extremely difficult to remove once they are established. In parallel, the growing concern of consumers regarding the use of chemically derived antimicrobials within food has led to a drive toward more natural products. As a consequence, the use of naturally derived antimicrobials has become of particular interest. In this study we investigated the efficacy of nisin A and its bioengineered derivative M21A in combination with food grade additives to treat biofilms of a representative foodborne disease isolate of Listeria monocytogenes. Investigations revealed the enhanced antimicrobial effects, in liquid culture, of M21A in combination with citric acid or cinnamaldehyde over its wild type nisin A counterpart. Subsequently, an investigation was conducted into the effects of these combinations on an established biofilm of the same strain. Nisin M21A (0.1 μg/ml) alone or in combination with cinnamaldehyde (35 μg/ml) or citric acid (175 μg/ml) performed significantly better than combinations involving nisin A. All combinations of M21A with either citric acid or cinnamaldehyde eradicated the L. monocytogenes biofilm (in relation to a non-biofilm control). We conclude that M21A in combination with available food additives could further enhance the antimicrobial treatment of biofilms within the food industry, simply by substituting nisin A with M21A in current commercial products such as Nisaplin® (Danisco, DuPont).
2016-11-30T00:00:00ZA biological framework for emotional dysregulation in alcohol misuse: from gut to brainCarbia, CarinaLannoy, SéverineMaurage, PierreLópez-Caneda, EduardoO'Riordan, Kenneth J.Dinan, Timothy G.Cryan, John F.https://hdl.handle.net/10468/145842023-06-15T02:03:45Z2020-12-07T00:00:00Zdc.title: A biological framework for emotional dysregulation in alcohol misuse: from gut to brain
dc.contributor.author: Carbia, Carina; Lannoy, Séverine; Maurage, Pierre; López-Caneda, Eduardo; O'Riordan, Kenneth J.; Dinan, Timothy G.; Cryan, John F.
dc.description.abstract: Alcohol use disorder (AUD) has been associated with impairments in social and emotional cognition that play a crucial role in the development and maintenance of addiction. Repeated alcohol intoxications trigger inflammatory processes and sensitise the immune system. In addition, emerging data point to perturbations in the gut microbiome as a key regulator of the inflammatory cascade in AUD. Inflammation and social cognition are potent modulators of one another. At the same time, accumulating evidence implicates the gut microbiome in shaping emotional and social cognition, suggesting the possibility of a common underlying loop of crucial importance for addiction. Here we propose an integrative microbiome neuro-immuno-affective framework of how emotional dysregulation and alcohol-related microbiome dysbiosis could accelerate the cycle of addiction. We outline the overlapping effects of chronic alcohol use, inflammation and microbiome alterations on the fronto-limbic circuitry as a convergence hub for emotional dysregulation. We discuss the interdependent relationship of social cognition, immunity and the microbiome in relation to alcohol misuse- from binge drinking to addiction. In addition, we emphasise adolescence as a sensitive period for the confluence of alcohol harmful effects and emotional dysregulation in the developing gut-brain axis.
2020-12-07T00:00:00ZA brief guide to studying fear in developing rodents: important considerations and common pitfalls.Cowan, Caitlin S. M.Richardson, Rickhttps://hdl.handle.net/10468/74582024-03-13T16:46:41Z2018-04-26T00:00:00Zdc.title: A brief guide to studying fear in developing rodents: important considerations and common pitfalls.
dc.contributor.author: Cowan, Caitlin S. M.; Richardson, Rick
dc.description.abstract: Development is a time of rapid change that sets the pathway to adult functioning across all aspects of physical and mental health. Developmental studies can therefore offer insight into the unique needs of individuals at different stages of normal development as well as the etiology of various disease states. The aim of this overview is to provide an introduction to the practical implementation of developmental studies in rats and mice, with an emphasis on the study of learned fear. We first discuss how developmental factors may influence experimental outcomes for any study. This is followed by a discussion of methodological issues to consider when conducting studies of developing rodents, highlighting examples from the literature on learned fear. Throughout, we offer some recommendations to guide researchers on best practice in developmental studies.
2018-04-26T00:00:00ZA cell wall-associated polysaccharide is required for bacteriophage adsorption to the Streptococcus thermophilus cell surfaceMcDonnell, BrianHanemaaijer, LaurensBottacini, FrancescaKelleher, PhilipLavelle, KatherineSadovskaya, IrinaVinogradov, EvgenyVer Loren van Themaat, EmielKouwen, ThijsMahony, Jennifervan Sinderen, Douwehttps://hdl.handle.net/10468/97292024-03-13T16:51:27Z2020-01-01T00:00:00Zdc.title: A cell wall-associated polysaccharide is required for bacteriophage adsorption to the Streptococcus thermophilus cell surface
dc.contributor.author: McDonnell, Brian; Hanemaaijer, Laurens; Bottacini, Francesca; Kelleher, Philip; Lavelle, Katherine; Sadovskaya, Irina; Vinogradov, Evgeny; Ver Loren van Themaat, Emiel; Kouwen, Thijs; Mahony, Jennifer; van Sinderen, Douwe
dc.description.abstract: Streptococcus thermophilus strain ST64987 was exposed to a member of a recently discovered group of S. thermophilus phages (the 987 phage group), generating phage-insensitive mutants, which were then characterized phenotypically and genomically. Decreased phage adsorption was observed in selected bacteriophage-insensitive mutants, and was partnered with a sedimenting phenotype and increased cell chain length or aggregation. Whole genome sequencing of several bacteriophage-insensitive mutants identified mutations located in a gene cluster presumed to be responsible for cell wall polysaccharide production in this strain. Analysis of cell surface-associated glycans by methylation and NMR spectroscopy revealed a complex branched rhamno-polysaccharide in both ST64987 and phage-insensitive mutant BIM3. In addition, a second cell wall-associated polysaccharide of ST64987, composed of hexasaccharide branched repeating units containing galactose and glucose, was absent in the cell wall of mutant BIM3. Genetic complementation of three phage-resistant mutants was shown to restore the carbohydrate and phage resistance profiles of the wild-type strain, establishing the role of this gene cluster in cell wall polysaccharide production and phage adsorption and, thus, infection.
2020-01-01T00:00:00ZA comparative analysis of the genus Faecalibacterium and the utilisation of an enrichment based strategy for the isolation of gut phageFitzgerald, Cormac Brianhttps://hdl.handle.net/10468/113372023-04-04T11:05:28Z2020-12-11T00:00:00Zdc.title: A comparative analysis of the genus Faecalibacterium and the utilisation of an enrichment based strategy for the isolation of gut phage
dc.contributor.author: Fitzgerald, Cormac Brian
dc.description.abstract: Faecalibacterium prausnitzii is a Gram negative member of the Ruminococcaceae family and is highly oxygen sensitive. F. prausnitzii has been shown to have the ability to reduce inflammation in the human gut. It can produce a number of anti- inflammatory substances, including butyrate. A reduction in the abundance of F. prausnitzii has also been identified in patients with CRC, type 2 diabetes and IBD.
This thesis describes the most extensive comparative analysis done to date on F. prausnitzii. Chapter 3 reports the analysis of all 31 sequenced strains of F. prausnitzii, including 11 strains that were sequenced specifically for this project. We were able to confirm the two phylogroups of F. prausnitzii that had previously been determined by 16s rRNA analysis. We also examined the differential abundance of COG categories between phylogroups. A striking lack of synteny between strains of F. prausnitzii was also described in Chapter 3.
In Chapter 4 we increased the number of F. prausnitzii strains to 78 which confirmed the presence of a third phylogroup. In this chapter questions regarding the lack of synteny between strains was also addressed. In order to determine if the genomic rearrangement of the species happened frequently or only over many generations, F. prausnitzii strain A2-165 was grown in duplicate and isolates were sequenced before and following 13 passages in broth. A large inversion was observed in one of the duplicates. We next determined whether rearrangements could be detected in individual reads discarded by the assembler. BLAST was employed to view alignments of all reads against the assembled genomes. The results from this analysis showed that a significant number of reads had been rearranged across the genome. When this is compared to Bacteroides it was possible to even more clearly note that the rearrangements of reads in F. prausnitzii were dispersed throughout the genome whereas in Bacteroides they were much more localised.
Chapter 5 briefly explores the varying levels of synteny across 240 different bacterial genera. We see in this chapter that F. prausnitzii is indeed on the lower end of the spectrum with relation to synteny. We can also see that there is a wide variety of different levels of synteny present for the genera that were included in the analysis.
Chapter 6 explores a non-plaque based method for the identification and propagation of novel bacteriophage from the intestinal tract. The isolation strategy involved two stages. The first required the pooling of 20 faecal filtrates (viromes) and propagating them on purified bacterial hosts obtained from culture collections as well as a number of strains that were isolated in the laboratory. This protocol was modified slightly for the second stage of the isolation procedure where three faecal filtrates were processed from faecal samples and potential bacterial hosts were isolated from the same samples from which the filtrates were created. Several previously unknown phage were isolated using this method including the discovery of the first cultured representative of the CrAssphage family of viruses.
The work described in this thesis contributes to the body of knowledge relating to the important gut commensal, F. prausnitzii. In addition, a protocol was successfully developed for the isolation of bacteriophage from the gut which resulted in the description of the first culturable representative of the CrAssphage family.
2020-12-11T00:00:00ZA comparative study of gluten-free sprouts in the gluten-free bread-making processHorstmann, Stefan W.Atzler, Jonas J.Heitmann, MareileZannini, EmanueleLynch, Kieran M.Arendt, Elke K.https://hdl.handle.net/10468/78292024-03-13T16:48:08Z2018-11-14T00:00:00Zdc.title: A comparative study of gluten-free sprouts in the gluten-free bread-making process
dc.contributor.author: Horstmann, Stefan W.; Atzler, Jonas J.; Heitmann, Mareile; Zannini, Emanuele; Lynch, Kieran M.; Arendt, Elke K.
dc.description.abstract: The addition of sprouted grains and seeds to cereal products has been identified as one of the upcoming trends in recent market reports. In this study, seven types of sprouts (amaranth, brown millet, corn, lentil, lupin, pea, quinoa) were milled and characterised with respect to their compositional (starch, protein, fat, ash, fibre, moisture) and functional properties (water hydration properties). These sprouted flours were included in a gluten-free bread formulation at a level of 5% and the impact on dough (temperature-dependent rising behaviour, pasting and rheological properties) and bread quality parameters (volume, crumb structure and texture) was evaluated. Factors such as the method of germination and the botanical origin influenced the chemical composition of the applied raw material. The functional properties of the different malts and sprouts are affected by the chemical composition of the individual grains. The differences in functional properties were, in turn, found to affect the dough properties and the quality parameters of the baked gluten-free breads. However, statistical analysis showed no correlation between the various factors. Based on this, effects on dough and bread properties were hypothesised to be caused by a combination of multiple factors. All bread formulations containing sprouted flour had significantly improved bread quality parameters in comparison to the control (without sprouted flour). The addition of amaranth sprouted flour, however, resulted in the highest loaf volume and the softest breadcrumb, suggesting its potential for further investigations in further studies.
2018-11-14T00:00:00ZA comprehensive review on the impact of β-glucan metabolism by Bacteroides and Bifidobacterium species as members of the gut microbiotaFernandez-Julia, Pedro J.Munoz-Munoz, Josevan Sinderen, Douwehttps://hdl.handle.net/10468/144392023-05-06T02:02:17Z2021-04-20T00:00:00Zdc.title: A comprehensive review on the impact of β-glucan metabolism by Bacteroides and Bifidobacterium species as members of the gut microbiota
dc.contributor.author: Fernandez-Julia, Pedro J.; Munoz-Munoz, Jose; van Sinderen, Douwe
dc.description.abstract: β-glucans are polysaccharides which can be obtained from different sources, and which have been described as potential prebiotics. The beneficial effects associated with β-glucan intake are that they reduce energy intake, lower cholesterol levels and support the immune system. Nevertheless, the mechanism(s) of action underpinning these health effects related to β-glucans are still unclear, and the precise impact of β-glucans on the gut microbiota has been subject to debate and revision. In this review, we summarize the most recent advances involving structurally different types of β-glucans as fermentable substrates for Bacteroidetes (mainly Bacteroides) and Bifidobacterium species as glycan degraders. Bacteroides is one of the most abundant bacterial components of the human gut microbiota, while bifidobacteria are widely employed as a probiotic ingredient. Both are generalist glycan degraders capable of using a wide range of substrates: Bacteroides spp. are specialized as primary degraders in the metabolism of complex carbohydrates, whereas Bifidobacterium spp. more commonly metabolize smaller glycans, in particular oligosaccharides, sometimes through syntrophic interactions with Bacteroides spp., in which they act as secondary degraders.
2021-04-20T00:00:00Z