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


CONCLUSIONS
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.
O'Sullivan
Orla
O
Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland. orla.osullivan@teagasc.ie
O'Callaghan
John
J
Sangrador-Vegas
Amaia
A
McAuliffe
Olivia
O
Slattery
Lydia
L
Kaleta
Pawel
P
Callanan
Michael
M
Fitzgerald
Gerald F
GF
Ross
R Paul
RP
Beresford
Tom
T
D000220:Adaptation, Biological / Q000235:genetics; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D007779:Lactobacillus acidophilus / Q000235:genetics* / Q000378:metabolism; D052198:Lactobacillus helveticus / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity
D004269:DNA, Bacterial