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

Semi-inclusive decays of BB meson into a dark anti-baryon and baryons

Using the recently developed $B$-Mesogenesis scenario, we studied the semi-inclusive decays of $B$ meson into a dark anti-baryon $\psi$ plus any possible states $X$ containing $u/c$ and $d/s$ quarks with unit baryon number. The two types of effective Lagrangians proposed by the scenario are both considered in the study. The semi-inclusive decay branching fractions of $B\to X \psi$ are calculated by the method of heavy quark expansion, where the non-perturbative contributions from the matrix elements of dimension-5 operators are included. We obtained the branching fractions as functions of the dark anti-baryon mass. Using the experimental upper limits of the branching fractions, we presented the constraints of the coupling constants in the $B$-Mesogenesis scenario.Comment: 17 pages, 4 figures and 1 tabl