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Open Access Highly Accessed Research article

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

Orla O'Sullivan1, John O'Callaghan1, Amaia Sangrador-Vegas1, Olivia McAuliffe1, Lydia Slattery1, Pawel Kaleta1, Michael Callanan1, Gerald F Fitzgerald23, R Paul Ross123* and Tom Beresford1

Author Affiliations

1 Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland

2 Alimentary Pharmabiotic Centre, Cork, Ireland

3 Department of Microbiology, University College Cork, Ireland

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BMC Microbiology 2009, 9:50  doi:10.1186/1471-2180-9-50

Published: 5 March 2009

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.