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Eleven strains of homofermentative, rod-shaped lactic acid bacteria and five strains of heterofermentative, sphere-shaped lactic acid bacteria were isolated from fermented fish (pla-ra and pla-chom) in Thailand. They were identified as new species and named Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., respectively, on the basis of phylogenetic analysis of the 16S rRNA gene sequences, DNA relatedness and phenotypic characteristics. The type strain of L. acidipiscis is FS60-1

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Lactobacillus kunkeei is an inhabitant of fructose-rich niches and is a potential member of the fructophilic lactic acid bacteria. In the present study, the phylogenetic and biochemical characteristics of the type strain and eight isolates of L. kunkeei, originating from wine, flowers and honey, were studied. The nine isolates, including the type strain, formed a well-defined phylogenetic subcluster based on the analysis of 16S rRNA gene sequences. The subcluster was not closely related to other subclusters in the Lactobacillus phylogenetic group. Biochemically, the eight new isolates showed typical fructophilic characteristics. The eight isolates grew poorly on glucose, but grew well on fructose. Good growth on glucose was only recorded in the presence of electron acceptors. The type strain of L. kunkeei differed from the other isolates only on the basis of poor growth on fructose. Although they belong to a group of obligately heterofermentative lactic acid bacteria, all nine isolates, including the type strain, produced almost equimolar amounts of lactic acid and acetic acid and very little ethanol from glucose. Eight of the isolates can thus be regarded as typical 'obligately' fructophilic lactic acid bacteria. Although the type strain of L. kunkeei was phenotypically slightly different from the other isolates, it possessed several important fructophilic characteristics. On the basis of the evidence gathered in this study, the type strain of L. kunkeei is recognized as a member of the 'obligately' fructophilic lactic acid bacteria.

BackgroundSpecific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA) in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background.ResultsThrough genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-κB reporter cells expressing Toll like receptor (TLR)-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-α after stimulation with the WTA mutants as compared to the wild-type.ConclusionsThe study presented here correlates structural differences in WTA to their functional characteristics, thereby providing important information aiding to improve our understanding of molecular host-microbe interactions and probiotic functionality.

Oenococcus oeni is a lactic acid bacteria species encountered particularly in wine, where it achieves the malolactic fermentation. Molecular typing methods have previously revealed that the species is made of several genetic groups of strains, some being specific to certain types of wines, ciders or regions. Here, we describe 36 recently released O. oeni genomes and the phylogenomic analysis of these 36 plus 14 previously reported genomes. We also report three genome sequences of the sister species Oenococcus kitaharae that were used for phylogenomic reconstructions. Phylogenomic and population structure analyses performed revealed that the 50 O. oeni genomes delineate two major groups of 12 and 37 strains, respectively, named A and B, plus a putative group C, consisting of a single strain. A study on the orthologs and single nucleotide polymorphism contents of the genetic groups revealed that the domestication of some strains to products such as cider, wine, or champagne, is reflected at the genetic level. While group A strains proved to be predominant in wine and to form subgroups adapted to specific types of wine such as champagne, group B strains were found in wine and cider. The strain from putative group C was isolated from cider and genetically closer to group B strains. The results suggest that ancestral O. oeni strains were adapted to low-ethanol containing environments such as overripe fruits, and that they were domesticated to cider and wine, with group A strains being naturally selected in a process of further domestication to specific wines such as champagne.

BackgroundFructobacillus spp. in fructose-rich niches belong to the family Leuconostocaceae. They were originally classified as Leuconostoc spp., but were later grouped into a novel genus, Fructobacillus, based on their phylogenetic position, morphology and specific biochemical characteristics. The unique characters, so called fructophilic characteristics, had not been reported in the group of lactic acid bacteria, suggesting unique evolution at the genome level. Here we studied four draft genome sequences of Fructobacillus spp. and compared their metabolic properties against those of Leuconostoc spp.ResultsFructobacillus species possess significantly less protein coding sequences in their small genomes. The number of genes was significantly smaller in carbohydrate transport and metabolism. Several other metabolic pathways, including TCA cycle, ubiquinone and other terpenoid-quinone biosynthesis and phosphotransferase systems, were characterized as discriminative pathways between the two genera. The adhE gene for bifunctional acetaldehyde/alcohol dehydrogenase, and genes for subunits of the pyruvate dehydrogenase complex were absent in Fructobacillus spp. The two genera also show different levels of GC contents, which are mainly due to the different GC contents at the third codon position.ConclusionThe present genome characteristics in Fructobacillus spp. suggest reductive evolution that took place to adapt to specific niches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2339-x) contains supplementary material, which is available to authorized users.

A fructophilic lactic acid bacterium, designated strain F214-1 T , was isolated from a flower of Tropaeolum majus in South Africa. Based on phylogenetic analysis of 16S rRNA gene sequences, the strain formed a subcluster with Fructobacillus ficulneus and Fructobacillus pseudoficulneus and, based on recA gene sequences, the strain formed a subcluster with F. ficulneus. DNA-DNA hybridization studies showed that strain F214-1 T was phylogenetically distinct from its closest relatives. Acid was produced from the fermentation of D-glucose, D-fructose and D-mannitol only. D-Fructose was the preferred sole carbon and energy source and was fermented more rapidly than D-glucose. Growth of the strain on D-glucose under anaerobic conditions was very weak but external electron acceptors such as oxygen and pyruvate enhanced growth on D-glucose. Lactic acid and acetic acid were produced from D-glucose in equimolar amounts. Ethanol was produced at very low levels, despite the strain's obligately heterofermentative metabolism. Based on these data, strain F214-1 T represents a novel species of fructophilic bacteria in the genus Fructobacillus, for which the name Fructobacillus tropaeoli sp. nov. is proposed. and sodium azide (0.05; pH 6.8), was added to the crushed samples and the bags were incubated at 30 u C for 24 h. After incubation, each sample was inoculated into FYP broth by using a loop and incubated at 30 u C under aerobic conditions on an orbital shaker (120 r.p.m.) for 2 days. The culture was then streaked onto FYP agar plates containing (l 21) 5 g CaCO 3 and 12 g agar. The plates were incubated at 30 u C under aerobic conditions until visible colonies were observed. Colonies were selected based on differences in morphology, such as colony size and shape, and the clearance zone formed from hydrolysis of CaCO 3 by lactic acid, inoculated into FYP broth and GYP broth and incubated statically for 24 h at 30 u C. GYP broth differed from FYP broth by containing 10 g l 21 D-glucose instead of D-fructose.Strain F214-1 T grew well in FYP broth but poorly in GYP broth and was, therefore, regarded as a fructophilic lactic acid bacterium. The strain was stored at 280 u C in nutrient broth containing 20 % (v/v) glycerol. Strains F. durionis LMG 22556 T , F. ficulneus JCM 12225 T , F. fructosus NRIC 1058T and F. pseudoficulneus DSM 14568 T were cultured in FYP broth and used as reference strains.The 16S rRNA gene sequence of strain F214-1 T was determined as described previously (Endo & Okada, 2005). The closest recognized relatives of the isolate were determined by performing database searches and sequences of closely related species were retrieved from DDBJ. Multiple sequence alignments were carried out by using CLUSTAL_X, version 1.18 (Thompson et al., 1997). Distance matrices for the aligned sequences were calculated by using the two-parameter method of Kimura (1980) and phylogenetic trees were reconstructed by using the neighbourjoining, maximum-likelihood and maximum-parsimony methods in PHYLIP version 3.65 software as descr...