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

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dc.contributor.authorO'Sullivan, Orla
dc.contributor.authorO'Callaghan, John
dc.contributor.authorSangrador-Vegas, Amaia
dc.contributor.authorMcAuliffe, Olivia
dc.contributor.authorSlattery, Lydia
dc.contributor.authorKaleta, Pawel
dc.contributor.authorCallanan, Michael
dc.contributor.authorFitzgerald, Gerald F.
dc.contributor.authorRoss, R. Paul
dc.contributor.authorBeresford, Thomas P.
dc.contributor.funderDepartment of Agriculture, Food and the Marineen
dc.date.accessioned2012-11-09T07:01:20Z
dc.date.available2012-11-09T07:01:20Z
dc.date.copyright2009-03
dc.date.issued2009-03-05
dc.description.abstractBackground: 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.sponsorshipDepartment of Agriculture and Food, Ireland (Food Institutional Research Measure, 04/R&D/TD/311)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationO'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: 10.1186/1471-2180-9-50en
dc.identifier.doi10.1186/1471-2180-9-50
dc.identifier.issn1471-2180
dc.identifier.journaltitleBMC Microbiologyen
dc.identifier.startpage50en
dc.identifier.urihttps://hdl.handle.net/10468/749
dc.identifier.volume9en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urihttp://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 9:50en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjectLactobacillus helveticusen
dc.subjectLatctobacillus acidophilusen
dc.subjectDairyen
dc.subjectProbiotic bacteriaen
dc.subjectLactic aciden
dc.subjectHomologen
dc.subjectGuten
dc.subjectNicheen
dc.titleComparative genomics of lactic acid bacteria reveals a niche-specific gene seten
dc.typeArticle (peer-reviewed)en
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