Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., isolated from humans.

Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive coccoid bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37 °C in anaerobic conditions. They also metabolize carbohydrates, such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains. The highest digital DNA-DNA hybridization (dDDH) values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. Strains Marseille-P3761 and Marseille-P3195 shared an OrthoANI value of 83.5% which was the highest value found with Peptoniphilus species studied here. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that Peptoniphilus coli sp. nov., and Peptoniphilus urinae sp. nov., are new species for which strains Marseille-P3761 (CSUR P3761 = CCUG 71,569) and Marseille-P3195 (CSUR P3195 = DSM 103,468) are their type strains, respectively of two new Peptoniphilus species, for which we propose the names Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., respectively.

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut.

Human urine was considered sterile for a long time. However, 416 species have been previously cultured, including only 40 anaerobic species. Here, we used culturomics, particularly those targeting anaerobes, to better understand the urinary microbiota. By testing 435 urine samples, we isolated 450 different bacterial species, including 256 never described in urine of which 18 were new species. Among the bacterial species identified, 161 were anaerobes (35%). This study increased the known urine repertoire by 39%. Among the 672 bacterial species isolated now at least once from urine microbiota, 431 (64.1%) were previously isolated from gut microbiota, while only 213 (31.7%) were previously isolated from vagina. These results suggest that many members of the microbiota in the urinary tract are in fact derived from the gut, and a paradigm shift is thus needed in our understanding.

Impact of single atomic defects and vacancies on the magnetic anisotropy energy of CoPt thin films.

The impact of surface vacancies and single adatoms on the magnetic properties of tetragonal L1 0 CoPt thin films is investigated from first principles. We consider Co and Fe single adatoms deposited on a Pt-terminated thin film while a Pt adatom is assumed to be supported by a Co-terminated film. The vacancy is injected in the top-surface layer of the films with both types of termination. After finding the most stable location of the defects, we discuss their magnetic properties tied to those of the substrate and investigate the magnetocrystalline anisotropy energy (MAE). Previous simulations (Brahimi et al 2016 J. Phys.: Condens. Matter 28 496002) predicted a large out-of-plane surface MAE for the Pt-terminated CoPt films (4 meV per f.u.) in contrast to in-plane surface MAE for Co-terminated films (-1 meV per f.u.). Here, we find that the surface MAE is significantly modified upon the presence of the atomic defects. All investigated defects induce an in-plane MAE, which is large enough for Fe adatom and Pt vacancy to switch the surface MAE from out-of-plane to in-plane for the Pt-terminated films. Interestingly, among the investigated defects Pt vacancy has the largest effect on the MAE in contrast to Co vacancy, which induced the smallest but still significant effect. This behavior is explained in terms of the orbital moment anisotropy of the thin films.

Giant perpendicular magnetic anisotropy energies in CoPt thin films: impact of reduced dimensionality and imperfections.

The impact of reduced dimensionality on the magnetic properties of the tetragonal L1 0 CoPt alloy is investigated from ab initio considering several kinds of surface defects. By exploring the dependence of the magnetocrystalline anisotropy energy (MAE) on the thickness of CoPt thin films, we demonstrate the crucial role of the chemical nature of the surface. For instance, Pt-terminated thin films exhibit huge MAEs which can be 1000% larger than those of Co-terminated films. Besides the perfect thin films, we scrutinize the effect of defective surfaces such as stacking faults or anti-sites on the surface layers. Both types of defects reduce considerably the MAE with respect to the one obtained for Pt-terminated thin films. A detailed analysis of the electronic structure of the thin films is provided with a careful comparison to the CoPt bulk case. The behavior of the MAEs is then related to the location of the different virtual bound states utilizing second order perturbation theory.