In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database

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dc.contributor.author Walsh, Calum J.
dc.contributor.author Guinane, Caitriona M.
dc.contributor.author Hill, Colin
dc.contributor.author Ross, R. Paul
dc.contributor.author O'Toole, Paul W.
dc.contributor.author Cotter, Paul D.
dc.date.accessioned 2016-01-13T16:49:53Z
dc.date.available 2016-01-13T16:49:53Z
dc.date.issued 2015-09-16
dc.identifier.citation WALSH, C. J., GUINANE, C. M., HILL, C., ROSS, R. P., O’TOOLE, P. W. & COTTER, P. D. 2015. In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database. BMC Microbiology, 15:183, 1-11. http://dx.doi.org/10.1186/s12866-015-0515-4 en
dc.identifier.volume 15 en
dc.identifier.issued 1 en
dc.identifier.startpage 1 en
dc.identifier.endpage 11 en
dc.identifier.issn 1471-2180
dc.identifier.uri http://hdl.handle.net/10468/2182
dc.identifier.doi 10.1186/s12866-015-0515-4
dc.description.abstract The human gut microbiota comprises approximately 100 trillion microbial cells which significantly impact many aspects of human physiology - including metabolism, nutrient absorption and immune function. Disturbances in this population have been implicated in many conditions and diseases, including obesity, type-2 diabetes and inflammatory bowel disease. This suggests that targeted manipulation or shaping of the gut microbiota, by bacteriocins and other antimicrobials, has potential as a therapeutic tool for the prevention or treatment of these conditions. With this in mind, several studies have used traditional culture-dependent approaches to successfully identify bacteriocin-producers from the mammalian gut. In silico-based approaches to identify novel gene clusters are now also being utilised to take advantage of the vast amount of data currently being generated by next generation sequencing technologies. In this study, we employed an in silico screening approach to mine potential bacteriocin clusters in genome-sequenced isolates from the gastrointestinal tract (GIT). More specifically, the bacteriocin genome-mining tool BAGEL3 was used to identify potential bacteriocin producers in the genomes of the GIT subset of the Human Microbiome Project’s reference genome database. Each of the identified gene clusters were manually annotated and potential bacteriocin-associated genes were evaluated. en
dc.description.sponsorship Science Foundation Ireland (SFI PI award to PDC “Obesibiotics” (11/PI/1137)) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Biomed Central Ltd. en
dc.rights © Walsh et al. 2015. ; licensee BioMed Central Ltd. 2015. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. en
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en
dc.subject Bacteriocin en
dc.subject Bacteriolysin en
dc.subject Lantibiotic en
dc.subject Sactipeptide en
dc.subject Unclassified drug en
dc.subject Actinobacteria en
dc.subject Bacterial genome en
dc.subject Bacteriocin gene en
dc.subject Bacterium en
dc.subject Bacterium isolate en
dc.subject Bacteroidetes en
dc.subject Bifidobacterium en
dc.subject Firmicutes en
dc.subject Fusobacteria en
dc.subject Gene cluster en
dc.subject Gram positive bacterium en
dc.subject Intestine flora en
dc.subject Proteobacteria en
dc.subject Roseburia en
dc.subject Ruminococcus en
dc.subject Synergistetes en
dc.subject Human Microbiome Project en
dc.subject Human gut microbiota en
dc.title In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Paul W. O'Toole, Microbiology,University College Cork , Cork, Ireland. +353-21-490-3997 Email: pwotoole@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Science Foundation Ireland en
dc.description.status Peer reviewed en
dc.identifier.journaltitle BMC Microbiology en
dc.internal.copyrightchecked Open Access articles licensed via CC-BY 4.0 with UCC affiliated authors. Uploaded Jan 2016. en
dc.internal.IRISemailaddress pwotoole@ucc.ie en
dc.identifier.articleid 183


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©  Walsh et al. 2015. ; licensee BioMed Central Ltd. 2015. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Except where otherwise noted, this item's license is described as © Walsh et al. 2015. ; licensee BioMed Central Ltd. 2015. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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