O'Sullivan, O, O'Callaghan, J, Sangrador-Vegas, A, McAuliffe, O, Slattery, L, Kaleta, P, Callanan, M, Fitzgerald, GF, Ross, RP, Beresford, T;

2009

March

BMC Microbiology

Comparative Genomics of Lactic Acid Bacteria Reveals A Niche-Specific Gene Set

Validated

()

9

NA

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..

DOI 10.1186/1471-2180-9-50