Comparative genomics of lactic acid bacteria reveals a niche-specific gene set

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dc.contributor.author O'Sullivan, Orla
dc.contributor.author O'Callaghan, John
dc.contributor.author Sangrador-Vegas, Amaia
dc.contributor.author McAuliffe, Olivia
dc.contributor.author Slattery, Lydia
dc.contributor.author Kaleta, Pawel
dc.contributor.author Callanan, Michael
dc.contributor.author Fitzgerald, Gerald F.
dc.contributor.author Ross, R. Paul
dc.contributor.author Beresford, Thomas P.
dc.date.accessioned 2012-11-09T07:01:20Z
dc.date.available 2012-11-09T07:01:20Z
dc.date.copyright 2009-03
dc.date.issued 2009-03-05
dc.identifier.citation O'Sullivan O, O'Callaghan J, Sangrador-Vegas A, McAuliffe O, Slattery L, Kaleta P, Callanan M, Fitzgerald GF, Ross RP, Beresford T. Comparative genomics of lactic acid bacteria reveals a niche-specific gene set. BMC Microbiol. 2009 Mar 5; 9:50. doi: 10.1186/1471-2180-9-50 en
dc.identifier.volume 9 en
dc.identifier.startpage 50 en
dc.identifier.issn 1471-2180
dc.identifier.uri http://hdl.handle.net/10468/749
dc.identifier.doi 10.1186/1471-2180-9-50
dc.description.abstract Background: The recently sequenced genome of Lactobacillus helveticus DPC4571 revealed a dairy organism with significant homology (75% of genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM. This led us to hypothesise that a group of genes could be determined which could define an organism's niche. Results: Taking 11 fully sequenced lactic acid bacteria (LAB) as our target, (3 dairy LAB, 5 gut LAB and 3 multi-niche LAB), we demonstrated that the presence or absence of certain genes involved in sugar metabolism, the proteolytic system, and restriction modification enzymes were pivotal in suggesting the niche of a strain. We identified 9 niche specific genes, of which 6 are dairy specific and 3 are gut specific. The dairy specific genes identified in Lactobacillus helveticus DPC4571 were lhv_1161 and lhv_1171, encoding components of the proteolytic system, lhv_1031 lhv_1152,lhv_1978 and lhv_0028 encoding restriction endonuclease genes, while bile salt hydrolase genes lba_0892 and lba_1078, and the sugar metabolism gene lba_1689 from Lb. acidophilus NCFM were identified as gut specific genes. Conclusion: Comparative analysis revealed that if an organism had homologs to the dairy specific geneset, it probably came from a dairy environment, whilst if it had homologs to gut specific genes, it was highly likely to be of intestinal origin. We propose that this "barcode" of 9 genes will be a useful initial guide to researchers in the LAB field to indicate an organism's ability to occupy a specific niche. en
dc.description.sponsorship Department of Agriculture and Food, Ireland (Food Institutional Research Measure, 04/R&D/TD/311) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher BioMed Central en
dc.relation.uri http://www.biomedcentral.com/1471-2180/9/50
dc.rights © 2009 O'Sullivan et al; licensee BioMed Central Ltd. This article was originally published in BMC Microbiology March 5 2009 9:50 en
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en
dc.subject Lactobacillus helveticus en
dc.subject Latctobacillus acidophilus en
dc.subject Dairy en
dc.subject Probiotic bacteria en
dc.subject Lactic acid en
dc.subject Homolog en
dc.subject Gut en
dc.subject Niche en
dc.title Comparative genomics of lactic acid bacteria reveals a niche-specific gene set en
dc.type Article (peer-reviewed) en
dc.internal.authorurl http://publish.ucc.ie/researchprofiles/D010/gfitzgerald en
dc.internal.authorcontactother Gerald F. Fitzgerald, Microbiology, University College Cork, Cork, Ireland. Tel: +353 21 490 3000 Email: g.fitzgerald@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.internal.rssid 89609029
dc.contributor.funder Department of Agriculture, Food and the Marine en
dc.description.status Peer reviewed en
dc.identifier.journaltitle BMC Microbiology en
dc.internal.copyrightchecked Creative Commons Licence You are free: to Share — to copy, distribute and transmit the work to Remix — to adapt the work to make commercial use of the work Under the following conditions: Attribution — You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). /creativecommons.org/licenses/by/2.0 en
dc.internal.IRISemailaddress g.fitzgerald@ucc.ie en


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© 2009 O'Sullivan et al; licensee BioMed Central Ltd. This article was originally published in BMC Microbiology March 5 2009 9:50 Except where otherwise noted, this item's license is described as © 2009 O'Sullivan et al; licensee BioMed Central Ltd. This article was originally published in BMC Microbiology March 5 2009 9:50
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