Comparative genomic analysis reveals a diverse repertoire of genes involved in prokaryote-eukaryote interactions within the Pseudovibrio Genus

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dc.contributor.author Romano, Stefano
dc.contributor.author Fernàndez-Guerra, Antonio
dc.contributor.author Reen, F. Jerry
dc.contributor.author Glöckner, Frank O.
dc.contributor.author Crowley, Susan P.
dc.contributor.author O'Sullivan, Orla
dc.contributor.author Cotter, Paul D.
dc.contributor.author Adams, Claire
dc.contributor.author Dobson, Alan D. W.
dc.contributor.author O'Gara, Fergal
dc.date.accessioned 2017-06-20T11:39:46Z
dc.date.available 2017-06-20T11:39:46Z
dc.date.issued 2016-03-30
dc.identifier.citation Romano, S., Fernàndez-Guerra, A., Reen, F. J., Glöckner, F. O., Crowley, S. P., O'Sullivan, O., Cotter, P. D., Adams, C., Dobson, A. D. W. and O'Gara, F. (2016) 'Comparative genomic analysis reveals a diverse repertoire of genes involved in prokaryote-eukaryote interactions within the Pseudovibrio Genus', Frontiers in Microbiology, 7, 387 (20pp.). doi: 10.3389/fmicb.2016.00387 en
dc.identifier.volume 7
dc.identifier.startpage 1
dc.identifier.endpage 20
dc.identifier.issn 1664-302X
dc.identifier.uri http://hdl.handle.net/10468/4114
dc.identifier.doi 10.3389/fmicb.2016.00387
dc.description.abstract Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its microbiota. Our data suggest the presence of a sponge-specific lineage of Pseudovibrio. The reduction in genome size and the loss of some systems potentially used to successfully enter the host, leads to the hypothesis that P. axinellae strain AD2 may be a lineage that presents an ancient association with the host and that may be vertically transmitted to the progeny. en
dc.description.sponsorship Science Foundation Ireland (SSPC-2, 12/RC/2275; 13/TIDA/B2625; 12/TIDA/B2411; 12/TIDA/B2405; 14/TIDA/2438); Department of Agriculture, Food and the Marine (FIRM/RSF/CoFoRD; FIRM 08/RDC/629; FIRM 1/F009/MabS; FIRM 13/F/516); Irish Research Council for Science, Engineering and Technology (PD/2011/2414;<s></s>GOIPG/2014/647); Health Research Board/Irish Thoracic Society (MRCG-2014-6); Marine Institute (Beaufort award C2CRA 2007/082); Teagasc (Walsh Fellowship 2013) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Frontiers Media en
dc.relation.uri http://journal.frontiersin.org/article/10.3389/fmicb.2016.00387/full
dc.rights © 2016, Romano, Fernàndez-Guerra, Reen, Glöckner, Crowley, O'Sullivan, Cotter, Adams, Dobson and O'Gara. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms en
dc.rights.uri https://creativecommons.org/licenses/by/4.0/ en
dc.subject Pseudovibrio en
dc.subject Comparative genomics en
dc.subject Symbiosis en
dc.subject Secretion systems en
dc.subject Toxins en
dc.subject Core-genome en
dc.subject Phylogenesis en
dc.title Comparative genomic analysis reveals a diverse repertoire of genes involved in prokaryote-eukaryote interactions within the Pseudovibrio Genus en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Fergal O’Gara, BIOMERIT Research Centre, University College Cork, Cork, Ireland +353-21-490-3000 E-mail: f.ogara@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder European Commission
dc.contributor.funder Science Foundation Ireland
dc.contributor.funder Department of Agriculture, Food and the Marine
dc.contributor.funder Irish Research Council for Science, Engineering and Technology
dc.contributor.funder Health Research Board
dc.contributor.funder Irish Thoracic Society
dc.contributor.funder Marine Institute
dc.contributor.funder Teagasc
dc.description.status Peer reviewed en
dc.identifier.journaltitle Frontiers in Microbiology en
dc.internal.IRISemailaddress f.ogara@ucc.ie en
dc.identifier.articleid 387
dc.relation.project info:eu-repo/grantAgreement/EC/FP7::SP3::PEOPLE/607786/EU/BluePharmTrain/BLUEPHARMTRAIN
dc.relation.project info:eu-repo/grantAgreement/EC/FP7::SP1::KBBE/312184/EU/Increasing Value and Flow in the Marine Biodiscovery Pipeline/PHARMASEA
dc.relation.project info:eu-repo/grantAgreement/EC/FP7::SP1::KBBE/311975/EU/Marine Microorganisms: Cultivation Methods for Improving their Biotechnological Applications/MACUMBA
dc.relation.project info:eu-repo/grantAgreement/EC/FP7::SP1::KBBE/287589/EU/Marine Microbial Biodiversity, Bioinformatics and Biotechnology/MICRO B3
dc.relation.project info:eu-repo/grantAgreement/EC/FP7::SP3::PEOPLE/256596/EU/Dissecting the role of a novel transcriptional regulator in microbial-host interactomes./MEXT REGULATION
dc.relation.project info:eu-repo/grantAgreement/EC/H2020::IA/634486/EU/Industrial Applications of Marine Enzymes: Innovative screening and expression platforms to discover and use the functional protein diversity from the sea/INMARE


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© 2016, Romano, Fernàndez-Guerra, Reen, Glöckner, Crowley, O'Sullivan, Cotter, Adams, Dobson and O'Gara. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms Except where otherwise noted, this item's license is described as © 2016, Romano, Fernàndez-Guerra, Reen, Glöckner, Crowley, O'Sullivan, Cotter, Adams, Dobson and O'Gara. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms
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