Comparative genomics of lactic acid bacteria reveals a niche-specific gene set
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
BMC Microbiology 2009, 9:50 doi:10.1186/1471-2180-9-50Published: 5 March 2009
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.
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.
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.