BIOMERIT Research Centre (BRC) - Journal Articles
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Item Genome sequence of Paracoccus sp. JM45, a bacterial strain isolated from a marine sponge with a dual quorum sensing inhibition activity(American Society for Microbiology, 2019) Gutiérrez-Barranquero, José A.; Parages, María L.; Dobson, Alan D. W.; Reen, F. Jerry; O'Gara, Fergal; Enterprise Ireland; European Commission; Science Foundation Ireland; Department of Agriculture and Food; Irish Research Council for Science, Engineering and Technology; Department of the Marine; Cystic Fibrosis Foundation USA; Health Research Board; Irish Thoracic SocietyThe draft genome sequence of Paracoccus sp. strain JM45, isolated from a marine sponge harvested off the west coast of Ireland, is reported here. Quorum sensing and quorum sensing inhibition activities have been reported recently for this bacterium, and genomic analysis supports its potential use for novel therapeutic development.Item A novel cold active esterase from a deep sea sponge Stelletta normani metagenomic library(Frontiers Media, 2017) Borchert, Erik; Selvin, Joseph; Kiran, Seghal G.; Jackson, Stephen A.; O'Gara, Fergal; Dobson, Alan D. W.; Marine Institute; Seventh Framework ProgrammeEsterases catalyze the hydrolysis of ester bonds in fatty acid esters with short-chain acyl groups. Due to the widespread applications of lipolytic enzymes in various industrial applications, there continues to be an interest in novel esterases with unique properties. Marine ecosystems have long been acknowledged as a significant reservoir of microbial biodiversity and in particular of bacterial enzymes with desirable characteristics for industrial use, such as for example cold adaptation and activity in the alkaline pH range. We employed a functional metagenomic approach to exploit the enzymatic potential of one particular marine ecosystem, namely the microbiome of the deep sea sponge Stelletta normani. Screening of a metagenomics library from this sponge resulted in the identification of a number of lipolytic active clones. One of these encoded a highly, cold-active esterase 7N9, and the recombinant esterase was subsequently heterologously expressed in Escherichia coli. The esterase was classified as a type IV lipolytic enzyme, belonging to the GDSAG subfamily of hormone sensitive lipases. Furthermore, the recombinant 7N9 esterase was biochemically characterized and was found to be most active at alkaline pH (8.0) and displays salt tolerance over a wide range of concentrations. In silico docking studies confirmed the enzyme's activity toward short-chain fatty acids while also highlighting the specificity toward certain inhibitors. Furthermore, structural differences to a closely related mesophilic E40 esterase isolated from a marine sediment metagenomics library are discussed.Item Bile signalling promotes chronic respiratory infections and antibiotic tolerance(Nature Publishing Group, 2016-07-19) Reen, F. Jerry; Flynn, Stephanie; Woods, David F.; Dunphy, Niall; Ní Chróinín, Muireann; Mullane, David; Stick, Stephen; Adams, Claire; O'Gara, Fergal; European Commission; Science Foundation Ireland; Department of Agriculture, Food and the Marine; Irish Research Council for Science, Engineering and Technology; Health Research Board; Marine Institute; Teagasc; Irish Thoracic SocietyDespite aggressive antimicrobial therapy, many respiratory pathogens persist in the lung, underpinning the chronic inflammation and eventual lung decline that are characteristic of respiratory disease. Recently, bile acid aspiration has emerged as a major comorbidity associated with a range of lung diseases, shaping the lung microbiome and promoting colonisation by Pseudomonas aeruginosa in Cystic Fibrosis (CF) patients. In order to uncover the molecular mechanism through which bile modulates the respiratory microbiome, a combination of global transcriptomic and phenotypic analyses of the P. aeruginosa response to bile was undertaken. Bile responsive pathways responsible for virulence, adaptive metabolism, and redox control were identified, with macrolide and polymyxin antibiotic tolerance increased significantly in the presence of bile. Bile acids, and chenodeoxycholic acid (CDCA) in particular, elicited chronic biofilm behaviour in P. aeruginosa, while induction of the pro-inflammatory cytokine Interleukin-6 (IL-6) in lung epithelial cells by CDCA was Farnesoid X Receptor (FXR) dependent. Microbiome analysis of paediatric CF sputum samples demonstrated increased colonisation by P. aeruginosa and other Proteobacterial pathogens in bile aspirating compared to non-aspirating patients. Together, these data suggest that bile acid signalling is a leading trigger for the development of chronic phenotypes underlying the pathophysiology of chronic respiratory disease.Item Evidence of a putative deep sea specific microbiome in marine sponges(Public Library of Science, 2014) Kennedy, Jonathan; Flemer, Burkhardt; Jackson, Stephen A.; Morrissey, John P.; O'Gara, Fergal; Dobson, Alan D. W.; European Commission; Irish Government; Marine InstituteThe microbiota of four individual deep water sponges, Lissodendoryx diversichela, Poecillastra compressa, Inflatella pellicula, and Stelletta normani, together with surrounding seawater were analysed by pyrosequencing of a region of the 16S rRNA gene common to Bacteria and Archaea. Due to sampling constraints at depths below 700 m duplicate samples were not collected. The microbial communities of L. diversichela, P. compressa and I. pellicula were typical of low microbial abundance (LMA) sponges while S. normani had a community more typical of high microbial abundance (HMA) sponges. Analysis of the deep sea sponge microbiota revealed that the three LMA-like sponges shared a set of abundant OTUs that were distinct from those associated with sponges from shallow waters. Comparison of the pyrosequencing data with that from shallow water sponges revealed that the microbial communities of all sponges analysed have similar archaeal populations but that the bacterial populations of the deep sea sponges were distinct. Further analysis of the common and abundant OTUs from the three LMA-like sponges placed them within the groups of ammonia oxidising Archaea (Thaumarchaeota) and sulphur oxidising gamma-Proteobacteria (Chromatiales). Reads from these two groups made up over 70% of all 16S rRNA genes detected from the three LMA-like sponge samples, providing evidence of a putative common microbial assemblage associated with deep sea LMA sponges.Item A novel erythromycin resistance plasmid from Bacillus sp strain HS24, isolated from the marine sponge Haliclona simulans(Public Library of Science, 2014) Barbosa, Teresa M.; Phelan, Robert W.; Leong, Dara; Morrissey, John P.; Adams, Claire; Dobson, Alan D. W.; O'Gara, Fergal; Science Foundation Ireland; Department of Agriculture, Fisheries and Food, Ireland; Environmental Protection Agency; Irish Research Council for Science Engineering and Technology; European Commission; Marine Institute; Teagasc; Health Research BoardA better understanding of the origin and natural reservoirs of resistance determinants is fundamental to efficiently tackle antibiotic resistance. This paper reports the identification of a novel 5.8 kb erythromycin resistance plasmid, from Bacillus sp. HS24 isolated from the marine sponge Haliclona simulans. pBHS24B has a mosaic structure and carries the erythromycin resistance gene erm(T). This is the first report of an erythromycin resistance plasmid from a sponge associated bacteria and of the Erm(T) determinant in the genus Bacillus.