Phylogenomic reconstruction of lactic acid bacteria: an update

<p>Abstract</p> <p>Background</p> <p>Lactic acid bacteria (LAB) are important in the food industry for the production of fermented food products and in human health as commensals in the gut. However, the phylogenetic relationships among LAB species remain under intensive debate owing to disagreements among different data sets.</p> <p>Results</p> <p>We performed a phylogenetic analysis of LAB species based on 232 genes from 28 LAB genome sequences. Regardless of the tree-building methods used, combined analyses yielded an identical, well-resolved tree topology with strong supports for all nodes. The LAB species examined were divided into two groups. Group 1 included families Enterococcaceae and Streptococcaceae. Group 2 included families Lactobacillaceae and Leuconostocaceae. Within Group 2, the LAB species were divided into two clades. One clade comprised of the acidophilus complex of genus <it>Lactobacillus </it>and two other species, <it>Lb. sakei </it>and <it>Lb. casei</it>. In the acidophilus complex, <it>Lb. delbrueckii </it>separated first, while <it>Lb. acidophilus</it>/<it>Lb. helveticus </it>and <it>Lb. gasseri</it>/<it>Lb. johnsonii </it>were clustered into a sister group. The other clade within Group 2 consisted of the salivarius subgroup, including five species, <it>Lb. salivarius</it>, <it>Lb. plantarum</it>, <it>Lb. brevis</it>, <it>Lb. reuteri</it>, <it>Lb. fermentum</it>, and the genera <it>Pediococcus, Oenococcus</it>, and <it>Leuconostoc</it>. In this clade, <it>Lb. salivarius </it>was positioned most basally, followed by two clusters, one corresponding to <it>Lb. plantarum</it>/<it>Lb. brevis </it>pair and <it>Pediococcus</it>, and the other including <it>Oenococcus</it>/<it>Leuconostoc </it>pair and <it>Lb. reuteri</it>/<it>Lb. fermentum </it>pair. In addition, phylogenetic utility of the 232 genes was analyzed to identify those that may be more useful than others. The genes identified as useful were related to translation and ribosomal structure and biogenesis (TRSB), and a three-gene set comprising genes encoding ultra-violet resistance protein B (<it>uvrB</it>), DNA polymerase III (<it>polC</it>) and penicillin binding protein 2B (<it>pbpB</it>).</p> <p>Conclusions</p> <p>Our phylogenomic analyses provide important insights into the evolution and diversification of LAB species, and also revealed the phylogenetic utility of several genes. We infer that the occurrence of multiple, independent adaptation events in LAB species, have resulted in their occupation of various habitats. Further analyses of more genes from additional, representative LAB species are needed to reveal the molecular mechanisms underlying adaptation of LAB species to various environmental niches.</p

A search for 95 GHz class I methanol masers in molecular outflows

We have observed a sample of 288 molecular outflow sources including 123 high-mass and 165 low-mass sources to search for class I methanol masers at 95 GHz transition and to investigate relationship between outflow characteristics and class I methanol maser emission with the PMO-13.7m radio telescope. Our survey detected 62 sources with 95 GHz methanol masers above 3$\sigma$ detection limit, which include 47 high-mass sources and 15 low-mass sources. Therefore the detection rate is 38% for high-mass outflow sources and 9% for low-mass outflow sources, suggesting that class I methanol maser is relatively easily excited in high-mass sources. There are 37 newly detected 95 GHz methanol masers (including 27 high-mass and 10 low-mass sources), 19 of which are newly identified (i.e. first identification) class I methanol masers (including 13 high-mass and 6 low-mass sources). Statistical analysis for the distributions of maser detections with the outflow parameters reveals that the maser detection efficiency increases with outflow properties (e.g. mass, momentum, kinetic energy and mechanical luminosity of outflows etc.). Systematic investigations of relationships between the intrinsic luminosity of methanol maser and the outflow properties (including mass, momentum, kinetic energy, bolometric luminosity and mass loss rate of central stellar sources) indicate a positive correlations. This further supports that class I methanol masers are collisionally pumped and associated with shocks, where outflows interact with the surrounding ambient medium.Comment: 32 pages, 5 figures, accepted by Ap

[(1S,2S,3R,4R)-3-Hydr­oxy-4,7,7-tri­methyl­bicyclo­[2.2.1]heptan-2-yl]methyl[(E)-3-(trimethyl­silyl)prop-2-enyl]selen­onium bromide

The title compound, a seleno­nium bromide, C17H33OSeSi+·Br−, was obtained from the reaction of enanti­omerically pure 4,7,7-trimethyl-2-methyl­selanylbicyclo­[2.2.1]heptan-3-ol and (3-bromopropen­yl)trimethyl­silane in acetone. Due to the chiral bicyclic substituent, the crystal structure is not centrosymmetric and has no symmetry plane, with four chiral C atoms in the cation. The asymmetric unit contains one seleno­nium cation and one bromide anion. C–H⋯Br and O–H⋯Br hydrogen bonds link the ions, forming a one-dimensional R-helical chain-like supra­molecular structure

Methyl 2-{[2,8-bis­(trifluoro­meth­yl)quinolin-4-yl]­oxy}acetate

In the crystal structure of the title compound, C14H9F6NO3, mol­ecules are connected by inter­molecular C—H⋯O hydrogen bonds. The best planes through the benzene and pyridyl rings make a dihedral angle of 1.59 (12)°

2-Amino-4-(2,4-dichloro­phen­yl)-6-(naphthalen-1-yl)nicotinonitrile

In the crystal structure of the title compound, C22H13Cl2N3, the mol­ecules are connected via inter­molecular C—H⋯N and N—H⋯N hydrogen bonds, forming a three-dimensional network. The dihedral angles between naphthyl ring system and the pyridyl and benzene rings are 55.04 (7) and 75.87 (7)°, respectively, whereas the pyridyl and benzene rings are oriented at a dihedral angle of 59.56 (8)°

2-Benzyl­sulfanyl-3-(2,2,2-trifluoro­ethoxy)pyridine

The title compound, C14H12F3NOS, was synthesized by the reaction of 2-chloro-3-(2,2,2-trifluoro­eth­oxy)pyridine and phenyl­methane­thiol. The dihedral angle between the aromatic rings is 76.7 (2)°. In the crystal structure, weak aromatic π–π stacking between inversion-related pairs of pyridine rings [centroid-to-centroid separation = 3.776 (2) Å] may help to establish the packing

Pd(II) and Zn(II) Based Complexes with Schiff Base Ligands: Synthesis, Characterization, Luminescence, and Antibacterial and Catalytic Activities

Two new metal complexes involving Schiff base ligands, namely, [Pd(L1)2] (1) and [Zn(L2)2] (2), [HL1: 2,4-dibromo-6-((E)-(mesitylimino)methyl)phenol and HL2: 2-((E)-(2,6-diisopropylphenylimino)methyl)-4,6-dibromophenol], have been solvothermally synthesized and characterized by elemental analysis, IR-spectroscopy, thermogravimetric analysis, powder X-ray diffraction, and single-crystal X-ray diffraction. Both 1 and 2 are mononuclear cyclometalated complexes with square planar and tetrahedral coordination geometry, respectively. 1 and 2 display photoluminescence in the solid state at 298 K (fluorescence lifetimes τ = 5.521 μs at 508 nm for 1; τ = 3.697 μs at 506 nm for 2). These Schiff base ligands and their metal complexes have been screened for antibacterial activity against several bacteria strains, and the results are compared with the activity of penicillin. Moreover, the Suzuki reaction of 4-bromoanisole with phenylboronic acid by 1 has also been studied

2-Chloro-5-(chloro­meth­yl)pyridine

The title compound, C6H5Cl2N, is almost planar, with an r.m.s. deviation of 0.0146 Å for all atoms except for the 5-choloromethyl Cl atom. The offset Cl atom lies above this plane with a Cl—C—C angle of 111.11 (17)°. In the crystal, mol­ecules are connected via inter­molecular C—H⋯N hydrogen bonds, forming dimers