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

Orla O'Sullivan,Michael Callanan,Tom Beresford,John O'Callaghan,Olivia Mcauliffe,Pawel Kaleta,Lydia Slattery,Amaia Sangrador-Vegas,R Paul Ross,Gerald F Fitzgerald

doi:10.1186/1471-2180-9-50

Abstract

BackgroundThe 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.ResultsTaking 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.ConclusionComparative 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.

Highlights

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]
Analysis of the completed genome sequences revealed that 75% of predicted DPC4571 ORFs have orthologues in the Lb. acidophilus NCFM genome
Focusing on the differences between the two genomes, DPC4571 has 123 genes which are not found in NCFM while the NCFM strain has 503 genes not found in DPC4571

Summary

Introduction

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]. BMC Microbiology 2009, 9:50 http://www.biomedcentral.com/1471-2180/9/50 into 7 phylogenetic clades:Lactococcus, Lactobacillus, Enterococcus, Pediococcus, Streptococcus, Leuconostoc and Oenococcus [8] They represent the single most exploited group of bacteria in the food industry, playing crucial roles in the fermentation of dairy products, meat and vegetables, as well as in the production of wine, coffee, cocoa and sourdough. This is reflected in the fact that to date (July 2008), 65 LAB genomes are either completely sequenced or in progress (source http://www.ncbi.nlm.nih.gov). Diseases caused by colonisation of pathogenic LAB include urinary tract infections, bacteremia, bacterial endocarditis, diverticulitis, and meningitis

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