KEO assisted in the design of the study, acquired funding

for the project, and provided critical analysis of the manuscript.”
“Background The LAB represents a group of organisms that are functionally related by their general ability to produce lactic acid during homo- or hetro-fermentative Emricasan metabolism. They are predominantly Gram-positive, non-sporulating facultative anaerobic bacteria and have been isolated from sources as diverse as plants, animals and humans (for recent reviews on LAB see [3–7]). LAB can be sub-classified 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). Some LAB, such as Lb. rhamnosus ATCC 53013 and Lb. acidophilus NCFM have been shown to be probiotic, which is defined by the World Health Organisation as: ‘Live microorganisms which when administered in adequate amounts confer a health benefit on the host’. [9] LAB are also a reservoir for antimicrobial peptides, such as bacteriocins. There are numerous examples XAV 939 of bacteriocin producing LAB -one

of the most recent being Lb. salivarius UCC118, which was shown to be effective in reducing L. monocytogenes infections in mice [10]. However, members of the LAB can also be important pathogens, e.g. several Streptococcus and Enterococcus species. Such species are commonly found in the human and animal GI tract Evodiamine and can occasionally cause disease. Diseases caused by colonisation of pathogenic LAB include urinary tract infections,

bacteremia, bacterial endocarditis, diverticulitis, and meningitis. Members of the LAB group have close phylogenetic relationships largely due to their sharing relatively small, AT-rich genomes (~2.4 Mb) and common metabolic pathways [8]. Despite their phylogenetic closeness, the LAB occupy a diverse set of ecological niches including fermenting plants, milk, wine, sour-dough, the human and animal GI tract and the oral cavities of vertebrates. Such niche diversity among closely-related species suggests considerable genetic adaptation during their evolution. The recently sequenced dairy culture Lb. helveticus DPC4571 [1], has 98.4% 16s ribosomal RNA identity to the gut organism Lb. acidophilus NCFM [2]. This gave us a unique opportunity to investigate two very similar organisms occupying extremely different niches and led us to investigate if we could define a specific gene set which is associated with niche adaptation in LAB. LY2835219 Phylogenetically, both Lb. helveticus and Lb. acidophilus branch together with other gut bacteria.