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

Walsh, Calum J.; Guinane, Caitriona M.; Hill, Colin; Ross, R. Paul; O'Toole, Paul W.; Cotter, Paul D.

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

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.contributor.funder	Science Foundation Ireland	en
dc.date.accessioned	2016-01-13T16:49:53Z
dc.date.available	2016-01-13T16:49:53Z
dc.date.issued	2015-09-16
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.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	183
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.doi	10.1186/s12866-015-0515-4
dc.identifier.endpage	11	en
dc.identifier.issn	1471-2180
dc.identifier.issued	1	en
dc.identifier.journaltitle	BMC Microbiology	en
dc.identifier.startpage	1	en
dc.identifier.uri	https://hdl.handle.net/10468/2182
dc.identifier.volume	15	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