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

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    Author
    O'Sullivan, Orla cc
    O'Callaghan, John
    Sangrador-Vegas, Amaia
    McAuliffe, Olivia
    Slattery, Lydia
    Kaleta, Pawel
    Callanan, Michael J.
    Fitzgerald, Gerald F
    Ross, R Paul
    Beresford, Tom
    Keyword
    Niche specific genes
    lactic acid bacteria
    Date
    05/03/2009
    
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    URI
    http://hdl.handle.net/11019/247
    Citation
    Orla O'Sullivan, John O'Callaghan, Amaia Sangrador-Vegas, Olivia McAuliffe, Lydia Slattery, Pawel Kaleta, Michael Callanan, Gerald F Fitzgerald, R Paul Ross and Tom Beresford. Comparative genomics of lactic acid bacteria reveals a niche-specific gene set. BMC Microbiology. 2009 Mar 05;9(1):50. DOI:10.1186/1471-2180-9-50
    Abstract
    Background: The recently sequenced genome of Lactobacillus helveticus DPC4571 1 revealed a dairy organism with significant homology (75% of genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM 2. 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.
    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.1186/1471-2180-9-50
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    Food Biosciences
    Teagasc publications in Biomed Central
    Teagasc publications in Biomed Central
    Teagasc publications in Biomed Central

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