Genome-based reclassification of Paenibacillus jamilae Aguilera et al. 2001 as a later heterotypic synonym of Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994.

Paenibacillus is one of the genera that has high species diversity and Paenibacillus polymyxa, the type species of the genus, is mainly isolated from plant-associated environments. Among the plant-associated species, Paenibacillus jamilae B.3T (=CECT 5266T=DSM 13815T=KACC 10925T=KCTC 13919T) was proposed to be a novel species according to 16S rRNA gene similarity and DNA-DNA relatedness with related species, including Paenibacillus polymyxa. Nevertheless, in the description of Paenibacillus jamilae the used strain of Paenibacillus polymyxa was not the type strain of this species. In this work we found that the type strains of both species showed 16S rRNA gene similarity of 99.6 %. Therefore, in this study, we sequenced the genome of Paenibacillus jamilae KACC 10925T and compared it with those of the type strain of Paenibacillus polymyxa ATCC 842T and other phylogenetically related species. Genome relatedness value calculated by DNA-DNA hybridization between type strains of Paenibacillus polymyxa and Paenibacillus jamilae was 73.5 %, which is higher than the threshold value (70 %). For more objective and repeatable results of genome relatedness, we analysed an average nucleotide identity (ANI) between two strains. Our results showed that ANI value between the type strains of Paenibacillus jamilae and Paenibacillus polymyxa is 98.5 %, a phylogenetic distance also higher than the threshold values (95~96 %). These values were proposed by Yoon et al. (2017). In addition, their phylogenetic distance based on 92 bacterial core genes is highly close compared to other species. These mean that Paenibacillus jamilae and Paenibacillus polymyxa should be reclassified as a single species. Based on the results from genomic level comparison as well as reexamination results of physiological and chemotaxonomic features, we propose reclassification of Paenibacillus jamilae as a later heterotypic synonym of Paenibacillus polymyxa.

Genome-based reclassification of Weissella jogaejeotgali as a later heterotypic synonym of Weissella thailandensis.

Members of the genus Weissella are mostly found in fermented plant material. Among the Weissella species, two species, Weissella thailandensis and Weissella jogaejeotgali, were isolated from foods fermented from marine animals. The two species showed a high level of 16S rRNA gene similarity (99.39 %), whereas they exhibited a moderate level of DNA-DNA hybridization relatedness (63.9 %) in an earlier study. In this study, we determined the whole genome sequence of W. thailandensis KCTC 3751T and compared it to those of W. jogaejeotgali FOL01T and other related species. The average nucleotide identity value between the type strains of W. thailandensis and W. jogaejeotgali was 96.4 %, which is clearly higher than the cut-off proposed for bacterial species. We, therefore, propose to reclassify W. jogaejeotgali as a later heterotypic synonym of W. thailandensis.

Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems.

BACKGROUND: Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing. METHODS: Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l'Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com). RESULTS: TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level. CONCLUSIONS: TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.

Growth of wurtzite CdTe nanowires on fluorine-doped tin oxide glass substrates and room-temperature bandgap parameter determination.

The growth of CdTe nanowires, catalyzed by Sn, was achieved on fluorine-doped tin oxide glass by physical vapor transport. CdTe nanowires grew along the 〈0001〉 direction, with a very rare and phase-pure wurtzite structure, at 290 °C. CdTe nanowires grew under Te-limited conditions by forming SnTe nanostructures in the catalysts and the wurtzite structure was energetically favored. By polarization-dependent and power-dependent micro-photoluminescence measurements of individual nanowires, heavy and light hole-related transitions could be differentiated, and the fundamental bandgap of wurtzite CdTe at room temperature was determined to be 1.562 eV, which was 52 meV higher than that of zinc-blende CdTe. From the analysis of doublet photoluminescence spectra, the valence band splitting energy between heavy hole and light hole bands was estimated to be 43 meV.

Wurtzite ZnTe Nanotrees and Nanowires on Fluorine-Doped Tin Oxide Glass Substrates.

ZnTe nanotrees and nanowires were grown on fluorine-doped tin oxide glass by physical vapor transport. Sn from a fluorine-doped tin oxide layer catalyzed the growth at a growth temperature of 320 °C. Both the stem and branch nanowires grew along ⟨0001⟩ in the rarely observed wurtzite structure. SnTe nanostructures were formed in the liquid catalyst and simultaneously ZnTe nanowire grew under Te-limited conditions, which made the formation of the wurtzite structure energetically favorable. Through polarization-dependent and power-dependent microphotoluminescence measurements from individual wurtzite nanowires at room temperature, we could determine the so far unknown fundamental bandgap of wurtzite ZnTe, which was 2.297 eV and thus 37 meV higher than that of zinc-blend ZnTe. From the analysis of doublet photoluminescence spectra, the valence band splitting energy between heavy hole and light hole bands is estimated to be 69 meV.

Leeuwenhoekiella polynyae sp. nov., isolated from a polynya in western Antarctica.

A Gram-stain-negative, motile by gliding, rod-shaped bacterial strain, designated SOJ2014-1(T) was isolated from surface water of a polynya in the Antarctic Ocean. A comparative 16S rRNA gene sequence analysis showed that strain SOJ2014-1(T) belongs to the genus Leeuwenhoekiella and is most closely related to Leeuwenhoekiella marinoflava DSM 3653(T) (97.5% 16S rRNA gene sequence similarity). The G+C content of the genomic DNA of strain SOJ2014-1(T) was 38.8 mol%. Its predominant cellular fatty acids were summed feature 3 (composed of C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, iso-C15 : 0, iso-C15 : 1 G and summed feature 9 (composed of iso-C17 : 1ω9c and/or 10-methyl C16 : 0). DNA-DNA relatedness between strain SOJ2014-1(T) and close relatives, L. marinoflava DSM 3653(T) and Leeuwenhoekiella aequorea LMG 22550(T), was below 49%. The respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. The strain grew at 0-35 °C (optimum, 25 °C) with 0-14.0% (w/v) NaCl (optimum, 1.0-5.0%). It was strictly aerobic and had different carbohydrate utilization traits compared with L. marinoflava DSM 3653(T). Based on the phenotypic, chemotaxonomic and phylogenetic analyses, strain SOJ2014-1(T) is proposed as a representative of a novel species, Leeuwenhoekiella polynyae. The type strain is SOJ2014-1(T) ( =KCTC 42185(T) =JCM 30387(T)).