Amycolatopsis mongoliensis sp. nov., a novel actinobacterium with antifungal activity isolated from a coal mining site in Mongolia

A novel filamentous actinobacterium designated strain 4-36T showing broad-spectrum antifungal activity was isolated from a coal mining site in Mongolia, and its taxonomic position was determined using polyphasic approach. Optimum growth occurred at 30 °C, pH 7.5 and in the absence of NaCl. Aerial and substrate mycelia were abundantly formed on agar media. The colour of aerial mycelium was white and diffusible pigments were not formed. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain 4-36T formed a distinct clade within the genus Amycolatopsis. The 16S rRNA gene sequence similarity showed that the strain was mostly related to Amycolatopsis lexingtonensis DSM 44544T and Amycolatopsis rifamycinica DSM 46095T with 99.3 % sequence similarity. However, the highest digital DNA-DNA hybridization value to closest species was 44.1 %, and the highest average nucleotide identity value was 90.2 %, both of which were well below the species delineation thresholds. Chemotaxonomic properties were typical of the genus Amycolatopsis, as the major fatty acids were C15 : 0, iso-C16 : 0 and C16 : 0, the cell-wall diamino acid was meso-diaminopimelic acid, the quinone was MK-9(H4), and the main polar lipids were diphosphatidylglycerol, phosphatidylmethanolamine and phosphatidylethanolamine. The in silico prediction of chemotaxonomic markers was also carried out by phylogenetic analysis. The genome mining for biosynthetic gene clusters of secondary metabolites in strain 4-36T revealed the presence of 34 gene clusters involved in the production of polyketide synthase, nonribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, lanthipeptide, terpenes, siderophore and many other unknown clusters. Strain 4-36T showed broad antifungal activity against several filamentous fungi. The phenotypic, biochemical and chemotaxonomic properties indicated that the strain could be clearly distinguished from other species of Amycolatopsis, and thus the name Amycolatopsis mongoliensis sp. nov. is proposed accordingly (type strain, 4-36T=KCTC 39526T=JCM 30565T).

Description of Chryseobacterium fluminis sp. nov., a keratinolytic bacterium isolated from a freshwater river

A Gram-stain-negative, aerobic, rod-shaped bacterial strain, designated MMS21-Ot14T, was isolated from a freshwater river, and shown to represent a novel species of the genus Chryseobacterium on the basis of the results from a polyphasic approach. The 16S rRNA gene sequence analysis revealed that MMS21-Ot14T represented a member of the genus Chryseobacterium of the family Weeksellaceae and was closely related to Chryseobacterium hagamense RHA2-9T (97.52 % sequence similarity), Chryseobacterium gwangjuense THG A18T (97.46 %) and Chryseobacterium gregarium P 461/12T (97.27 %). The optimal growth of MMS21-Ot14T occurred at 25-30 °C, pH 6.0-7.0 and in the absence of NaCl. MMS21-Ot14T was capable of hydrolysing casein, starch, DNA, Tween 20 and tyrosine. The strain also showed keratinolytic activity with keratin azure and decolourising activity with remazol brilliant blue R (RBBR), which indicated potential ability to degrade keratin and lignin. The main polar lipids of MMS21-Ot14T were phosphatidylethanolamine, unidentified aminophospholipids, unidentified aminolipids, an unidentified phospholipid and several unidentified lipids. The predominant fatty acids of MMS21-Ot14T were iso-C15 : 0 and iso-C17 : 0 3-OH, and the major isoprenoid quinone was menaquinone 6 (MK-6). The whole genome of MMS21-Ot14T was 5 062 016 bp in length with a DNA G+C content of 37.7 %. The average nucleotide identity and digital DNA-DNA hybridisation values between MMS21-Ot14T and phylogenetically related members of the genus Chryseobacterium were well below the threshold values for species delineation. It is evident from the results of this study that MMS21-Ot14T should be classified as representing a novel species of the genus Chryseobacterium, for which the name Chryseobacterium fluminis sp. nov. (type strain, MMS21-Ot14T = KCTC 92255T = LMG 32529T) is proposed.

Description of Microcella humidisoli sp. nov. and Microcella daejeonensis sp. nov., isolated from riverside soil, reclassification of Marinisubtilis pacificus as Microcella pacifica comb. nov., and emended description of the genus Microcella

Three Gram-positive, aerobic and rod shaped actinobacteria, designated strains MMS21-STM10T, MMS21-STM12T and MMS21-STM26, were isolated from riverside soil and subjected to polyphasic taxonomic analysis. The strains grew optimally at mesophilic temperatures (25-30 °C) and neutral to slightly alkaline pH (7-8), and NaCl was not required for growth. Best growth was observed on nutrient agar or marine agar media. The strains contained diphosphatidylglycerol, phosphatidylglycerol and a series of unidentified phospholipids, glycolipids and aminolipids, and anteiso-C15 : 0 and iso-C16 : 0 as the main fatty acids in common. The genome sizes ranged between 2.65 and 2.78 Mbp, and the DNA G+C contents between 70.4 and 72.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS21-STM10T showed highest sequence similarity of 98.3 % to Microcella putealis CV-2T, and MMS21-STM12T and MMS21-STM26 of 99.2-99.3 % to Microcella flavibacter WY83T, respectively. In the whole genome-based comparison using the orthologous average nucleotide identity and digital DNA-DNA hybridization, each of strains MMS21-STM10T and MMS21-STM12T could be separated from other species of Microcella. The genome analysis also indicated that both strains contained gene clusters involved in the biosynthesis of alkylresorcinol, microansamycin and carotenoids. The phenotypic characteristics again differentiated the strains from related species, and two new species of Microcella, Microcella humidisoli sp. nov. (type strain, MMS21-STM10T=KCTC 49773T=LMG 32522T) and Microcella daejeonensis sp. nov. (type strain, MMS21-STM12T=KCTC 49750T=LMG 32523T) are proposed accordingly. It was also evident that Marinisubtilis pacificus KN1116T should be reclassified as a new species of Microcella, and Microcella pacifica comb. nov. (type strain, KN1116T=CGMCC 1.17143T=KCTC 49299T) is proposed. In addition, an emended description of Microcella is proposed based on this study.

Erratum: Search for Cosmic-Ray Boosted Sub-GeV Dark Matter Using Recoil Protons at Super-Kamiokande [Phys. Rev. Lett. 130, 031802 (2023)]

This corrects the article DOI: 10.1103/PhysRevLett.130.031802.

Targeted and Logical Discovery of Piperazic Acid-Bearing Natural Products Based on Genomic and Spectroscopic Signatures

A targeted and logical discovery method was devised for natural products containing piperazic acid (Piz), which is biosynthesized from ornithine by l-ornithine N-hydroxylase (KtzI) and N-N bond formation enzyme (KtzT). Genomic signature-based screening of a bacterial DNA library (2020 strains) using polymerase chain reaction (PCR) primers targeting ktzT identified 62 strains (3.1%). The PCR amplicons of KtzT-encoding genes were phylogenetically analyzed to classify the 23 clades into two monophyletic groups, I and II. Cultivating hit strains in media supplemented with 15NH4Cl and applying 1H-15N heteronuclear multiple bond correlation (HMBC) along with 1H-15N heteronuclear single quantum coherence (HSQC) and 1H-15N HSQC-total correlation spectroscopy (HSQC-TOCSY) NMR experiments detected the spectroscopic signatures of Piz and modified Piz. Chemical investigation of the hit strains prioritized by genomic and spectroscopic signatures led to the identification of a new azinothricin congener, polyoxyperuin B seco acid (1), previously reported chloptosin (2) in group I, depsidomycin D (3) incorporating two dehydropiperazic acids (Dpz), and lenziamides A and B (4 and 5), structurally novel 31-membered cyclic decapeptides in group II. By consolidating the phylogenetic and chemical analyses, clade-structure relationships were elucidated for 19 of the 23 clades. Lenziamide A (4) inhibited STAT3 activation and induced G2/M cell cycle arrest, apoptotic cell death, and tumor growth suppression in human colorectal cancer cells. Moreover, lenziamide A (4) resensitized 5-fluorouracil (5-FU) activity in both in vitro cell cultures and the in vivo 5-FU-resistant tumor xenograft mouse model. This work demonstrates that the genomic and spectroscopic signature-based searches provide an efficient and general strategy for new bioactive natural products containing specific structural motifs.

Development of digital mirror therapy for stroke-severe patients

Mirror therapy (MT), which is used in the existing stroke rehabilitation environment, has significant limitations for use with severe stroke patients. Since mirrors only reflect symmetrical movement, allowing a patient to observe precise asymmetrical movement is impossible. This study proposes a new MT system by developing a pyramid hologram technology that uses delayed motion to create realistic images. Significant differences, observed via electroencephalogram, were shown in all motor cortex channels immediately after the event in the delayed condition when compared to before the event (C3: p < 0.001; Cz: p < 0.001, C4: p < 0.001). The illusion of asymmetrical movement using the proposed system can be applied to severe stroke patients to increase the positive outcome of rehabilitation.

Pan-Asian adapted ESMO Clinical Practice Guidelines for the diagnosis, staging and treatment of patients with metastatic breast cancer

The most recent version of the European Society for Medical Oncology (ESMO) Clinical Practice Guidelines for the diagnosis, staging and treatment of patients with metastatic breast cancer (MBC) was published in 2021. A special, hybrid guidelines meeting was convened by ESMO and the Korean Society of Medical Oncology (KSMO) in collaboration with nine other Asian national oncology societies in May 2022 in order to adapt the ESMO 2021 guidelines to take into account the differences associated with the treatment of MBC in Asia. These guidelines represent the consensus opinions reached by a panel of Asian experts in the treatment of patients with MBC representing the oncological societies of China (CSCO), India (ISMPO), Indonesia (ISHMO), Japan (JSMO), Korea (KSMO), Malaysia (MOS), the Philippines (PSMO), Singapore (SSO), Taiwan (TOS) and Thailand (TSCO). The voting was based on the best available scientific evidence and was independent of drug access or practice restrictions in the different Asian countries. The latter were discussed when appropriate. The aim of these guidelines is to provide guidance for the harmonisation of the management of patients with MBC across the different regions of Asia, drawing from data provided by global and Asian trials whilst at the same time integrating the differences in genetics, demographics and scientific evidence, together with restricted access to certain therapeutic strategies.

Nocardioides okcheonensis sp. nov., isolated from riverside soil

An actinobacterial strain designated MMS20-HV4-12^T, displaying a high hydrolytic potential for various substrates, was isolated from a riverside soil sample and characterized by polyphasic taxonomic analysis. Growth occurred at 10-37 °C (optimum, 30°C), with NaCl concentrations of 0-4 % (optimum, 0 %) and at pH 7-9 (optimum, pH 8). MMS20-HV4-12^T was catalase-positive, oxidase-negative, rod-shaped and formed creamy white-coloured colonies. Based on the results of 16S rRNA gene sequence analysis, MMS20-HV4-12^T was found to be mostly related to the type strains of Nocardioides alpinus (98.3 % sequence similarity), Nocardioides furvisabuli (98.1 %) and Nocardioides zeicaulis (98.0 %). MMS20-HV4-12^T showed optimal growth on Reaoner's 2A agar, forming white-coloured colonies. The diagnostic polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, the major fatty acids were iso-C_16 : 0, C_17 : 1 ω8c and 10-methyl-C_17 : 0, the major isoprenoid quinone was MK-8(H₄), the diagnostic cell-wall sugar was galactose, and the cell-wall diamino acid was ll-diaminopimelic acid. The genome of MMS20-HV4-12^T was 4.47 Mbp in size with a G+C content of 72.9 mol%. The genome based analysis indicated low relatedness between MMS20-HV4-12^T and all compared species of Nocardioides, as the highest digital DNA-DNA hybridization and the orthologous average nucleotide identity values were 26.8 and 83.8% respectively. Based on genotypic, phenotypic and phylogenomic characterization, MMS20-HV4-12^T evidently represents a novel species of genus Nocardioides, for which the name Nocardioides okcheonensis sp. nov. (type strain=MMS20-HV4-12^T=KCTC 49651^T=LMG 32360^T) is proposed.

Flavobacterium humidisoli sp. nov., isolated from riverside soil

A novel Gram-stain-negative, yellow-pigmented, non-motile and rod-shaped bacterial strain designated MMS21-Er5^T was isolated and subjected to polyphasic taxonomic characterization. MMS21- Er5^T could grow at 4-34 °C (optimum, 30 °C), at pH 6-8 (optimum, pH 7) and in the presence of 0-2% NaCl (optimum, 1 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that MMS21- Er5^T showed low levels of sequence similarities with other species, as the highest similarity of 97.83 % was observed with Flavobacterium tyrosinilyticum THG DN8.8^T, then 97.68 % with 'Flavobacterium ginsengiterrae' DCY 55 and 97.63 % with Flavobacterium banpakuense 15F3^T, which were well below the suggested cutoff for species distinction. The whole genome sequence of MMS21-Er5^T consisted of a single contig of 5.63 Mbp, and the DNA G+C content was 34.06 mol%. The in-silico DNA-DNA hybridization and orthologous average nucleotide identity values were highest with Flavobacterium tyrosinilyticum KCTC 42726^T (45.7 and 91.92% respectively). The predominant respiratory quinone for the strain was menaquinone-6 (MK-6), the major cellular fatty acid was iso-C_15 : 0, and the diagnostic polar lipids were phosphatidylethanolamine and phosphatidyldiethanolamine. The combination of physiological and biochemical tests clearly distinguished the strain from related species of the genus Flavobacterium. On the basis of these results, strain MMS21-Er5^T evidently represents a novel species of the genus Flavobacterium, for which the name Flavobacterium humidisoli sp. nov. is proposed (type strain=MMS21-Er5^T=KCTC 92256^T =LMG 32524^T).

Brevibacillus humidisoli sp. nov., a moderately thermoalkaliphilic and halotolerant species isolated from riverside soil

A Gram-stain-positive, aerobic, rod-shaped, motile, and endospore-forming bacterial strain designated MMS20-4M-10-Y^T was isolated from riverside soil and subjected to taxonomic characterization. Strain MMS20-4M-10-Y^T was moderately thermophilic, alkaliphilic and halotolerant, as the strain grew at 25-50 °C (optimum, 45 °C), at pH 7.0-10.0 (optimum, pH 8.0) and in the presence of 0-6 % NaCl (optimum, 0 %). Analysis of 16S rRNA gene sequences indicated that MMS20-4M-10-Y^T fell into a phylogenetic cluster belonging to the genus Brevibacillus. Strain MMS20-4M-10-Y^T showed the highest 16S rRNA gene sequence similarity to Brevibacillus marinus SCSIO 07484^T (96.7 %). Based on the reults of orthologous average nucleotide identity analysis, MMS20-4M-10-Y^T was again mostly related to B. marinus SCSIO 07484^T with 78.0 % identity, which also shared the highest average nucleotide identity of 68.0 %. In contrast, the digital DNA-DNA relatedness analysis indicated that Aneureibacillus migulanus DSM 2895^T was the closest species with 29.5 % similarity. The genome-based analyses indicated that all compared species showed low genomic relatedness with MMS20-4M-10-Y^T. The major fatty acids of the strain were anteiso-C_15 : 0, iso-C_15 : 0, iso-C_16 : 0 and iso-C_17 : 0, the major respiratory quinone was MK-7, the diagnostic polar lipids were phosphatidyl-N-methylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, and diagnostic cell-wall diamino acid was meso-diaminopimelic acid, which was consistent with the general chemotaxonomic features of the genus. The total length of the genome was 4.91 Mbp and the DNA G+C content was 51.8 mol%. Based on both phenotypic and phylogenetic evidence, strain MMS20-4M-10-Y^T should be classified as representing a novel species of the genus Brevibacillus, for which a name Brevibacillus humidisoli sp. nov. (type strain=MMS20-4M-10-Y^T=KCTC 43333^T=LMG 32359^T) is proposed.

Agromyces seonyuensis sp. nov., isolated from island soil

A Gram-positive, non-motile, pale yellow coloured actinobacterial strain designated MMS17-SY077^T was isolated from island soil, and its taxonomic position was investigated using a polyphasic approach. Strain MMS17-SY077^T grew optimally at 30 °C, at pH 7 and in the absence of NaCl on Reasoner's 2A agar. Based on the 16S rRNA gene sequence analysis, the strain was assigned to the genus Agromyces of the family Microbacteriaceae, and the most related species were Agromyces italicus DSM 16388^T (98.8 % sequence similarity), Agromyces allii UMS-62^T (98.1 %) and Agromyces terreus DS-10^T (97.8 %). Strain MMS17-SY077^T formed a distinct cluster within the Agromyces clade in the phylogenetic tree. Genome-based comparative analyses confirmed a clear distinction between the strain and neighbouring species, as the highest orthologous average nucleotide identity and digital DNA-DNA hybridization values with other related species were 77.2 and 21.4% respectively, which were far below the cutoffs for species distinction. The diagnostic polar lipids of MMS17-SY077^T were diphosphatidylglycerol and phosphatidylglycerol, and unidentified glycolipids and an unidentified aminolipid were also present. The main isoprenoid quinones were menaquinones with 11 and 12 isoprene units (MK-11 and MK-12), and main fatty acids were anteiso-C_15 : 0 (34.4 %) and iso-C_16 : 0 (33.2 %). The whole-cell hydrolysates contained rhamnose, ribose and galactose as diagnostic sugars, and l-2,4-diaminobutyric acid as the major diamino acid. The DNA G+C content was 72.1 mol %. Based on phenotypic, chemotaxnomic and phylogenetic characterization, strain MMS17-SY077^T should be classified as representing a new species of the genus Agromyces, for which the name Agromyces seonyunensis sp. nov. is proposed (type strain MMS17-SY077^T=KCTC 49423^T=LMG 31762^T).

Streptomyces guryensis sp. nov. exhibiting antimicrobial activity, isolated from riverside soil

A novel Gram-stain-positive, aerobic actinobacterial strain designated NR30^T was isolated from riverside soil. A polyphasic approach was employed for the taxonomic characterization of NR30^T. The strain developed extensively branched light brown to light pink substrate mycelia and light grey aerial mycelia, and produced spiny spores in loose spiral spore chains on ISP 3 and 4 agars. NR30^T grew at 10-40°C (optimum, 30°C), at pH 6.0-9.0 (optimum, pH 8.0) and in the presence of 0-3 % NaCl (optimum, 0 %). Analysis of 16S rRNA gene sequences indicated that NR30^T represents a member of the genus Streptomyces. NR30^T shared the highest 16S rRNA gene sequence similarity with Streptomyces cyaneus NRRL B-2296^T (98.6 %). On the basis of orthologous average nucleotide identity, NR30^T was most closely related to Streptomyces panaciradicis NBRC 109811^T with 86.3 % identity. The results of the digital DNA-DNA hybridization analysis also indicated low levels of relatedness with other species, as the highest value was observed with Streptomyces panaciradicis NBRC 109811^T (31.1 %). The major fatty acids of the strain were anteiso-C_15 : 0, C_16 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. The major respiratory quinones were MK-9(H₈) and MK-9(H₆). The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol mannoside. The major cell wall diamino acid was ll-diaminopimelic acid, and the characteristic whole-cell sugars were rhamnose, ribose and glucose. The DNA G+C content was 70.3 mol %. NR30^T exhibited antimicrobial activity against several Gram-negative bacteria and yeasts. On the basis of the results of both phenotypic and phylogenetic analyses, strain NR30^T evidently represents a novel species of the genus Streptomyces, and the name Streptomyces guryensis sp. nov. (type strain=NR30^T =KCTC 49653^T=LMG 32476^T) is proposed accordingly.

Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction

Concerns over Klebsiella pneumoniae resistance to the last-line antibiotic treatment have prompted a reconsideration of bacteriophage therapy in public health. Biotechnological application of phages and their gene products as an alternative to antibiotics necessitates the understanding of their genomic context. This study sequenced, annotated, characterized, and compared two Klebsiella phages, KP1 and KP12. Physiological validations identified KP1 and KP12 as members of Myoviridae family. Both phages showed that their activities were stable in a wide range of pH and temperature. They exhibit a host specificity toward K. pneumoniae with a broad intraspecies host range. General features of genome size, coding density, percentage GC content, and phylogenetic analyses revealed that these bacteriophages are distantly related. Phage lytic proteins (endolysin, anti-/holin, spanin) identified by the local alignment against different databases, were subjected to further bioinformatic analyses including three-dimensional (3D) structure prediction by AlphaFold. AlphaFold models of phage lysis proteins were consistent with the published X-ray crystal structures, suggesting the presence of T4-like and P1/P2-like bacteriophage lysis proteins in KP1 and KP12, respectively. By providing the primary sequence information, this study contributes novel bacteriophages for research and development pipelines of phage therapy that ultimately, cater to the unmet clinical and industrial needs against K. pneumoniae pathogens.

Search for Cosmic-Ray Boosted Sub-GeV Dark Matter Using Recoil Protons at Super-Kamiokande

We report a search for cosmic-ray boosted dark matter with protons using the 0.37  megaton×years data collected at Super-Kamiokande experiment during the 1996-2018 period (SKI-IV phase). We searched for an excess of proton recoils above the atmospheric neutrino background from the vicinity of the Galactic Center. No such excess is observed, and limits are calculated for two reference models of dark matter with either a constant interaction cross section or through a scalar mediator. This is the first experimental search for boosted dark matter with hadrons using directional information. The results present the most stringent limits on cosmic-ray boosted dark matter and exclude the dark matter-nucleon elastic scattering cross section between 10^{-33}cm^{2} and 10^{-27}cm^{2} for dark matter mass from 1  MeV/c^{2} to 300  MeV/c^{2}.

ESO-ESMO fifth international consensus guidelines for breast cancer in young women (BCY5)

We dedicate this manuscript in memory of a dear friend and colleague Bella Kaufman. The fifth International Consensus Symposium for Breast Cancer in Young Women (BCY5) took place virtually in October 2020, organized by the European School of Oncology (ESO) and the European Society of Medical Oncology (ESMO). Consensus recommendations for the management of breast cancer in young women were updated from BCY4 with incorporation of new evidence to inform the guidelines. Areas of research priorities as well as specificities in different geographic and minority populations were identified. This manuscript summarizes the ESO-ESMO international consensus recommendations, which are also endorsed by the European Society of Breast Specialists (EUSOMA).

Micromonospora antibiotica sp. nov. and Micromonospora humidisoli sp. nov., two new actinobacterial species exhibiting antimicrobial potential

Two novel actinobacterial strains, designated MMS20-R2-23T and MMS20-R2-29T, were isolated from riverside soil and subjected to taxonomic characterization. Both strains were Gram-stain-positive, aerobic, non-motile and filamentous, and formed orange to strong orange-brown coloured colonies, which later turned black. Both strains grew optimally at mesophilic temperatures, neutral to slightly alkaline pH and in the absence of NaCl. Analysis of 16S rRNA gene sequences indicated that the two novel strains fell into phylogenetic clusters belonging to the genus Micromonospora . Strains MMS20-R2-23T and MMS20-R2-29T showed the highest 16S rRNA gene sequence similarity to Micromonospora phytophila SG15T (99.3 %) and Micromonospora humida MMS20-R1-14T (99.4 %), respectively. Based on the comparative genome analysis, strain MMS20-R2-23T had the highest orthologous average nucleotide identity (orthoANI) value of 92.70 % with Micromonospora matsumotoense DSM 44100T, and MMS20-R2-29T shared 94.99 % with Micromonospora wenchangensis CCTCC AA 2012002T. Besides, the digital DNA–DNA hybridization (dDDH) values of MMS20-R2-23T and MMS20-R2-29T with the same species were 47.6 and 59.2% respectively, which were also highest among the compared species, thus confirming the separation of each strain at species level from related species. The orthoANI and dDDH values between MMS20-R2-23T and MMS20-R2-29T were 92.18 and 44.9% respectively. The genomes of strains MMS20-R2-23T and MMS20-R2-29T were estimated as 7.56 Mbp and 7.13 Mbp in size, and the DNA G+C contents were 72.5 and 72.9 mol%, respectively. The chemotaxonomic properties of both strains were consistent with those of the genus. The novel strains showed antimicrobial activity against a broad range of microbes, in particular Gram-positive bacteria and yeasts. It is evident that each of the isolated strains merits recognition as representing novel species of Micromonospora , for which the names Micromonospora antibiotica sp. nov. (type strain=MMS20-R2-23T=KCTC 49542T=JCM 34495T) and Micromonospora humidisoli sp. nov. (type strain=MMS20-R2-29T=KCTC 49543T=JCM 34496T) are proposed.

Identification of distinct subgroups in moderately severe rheumatic mitral stenosis using data-driven phenotyping of longitudinal hemodynamic progression

Background

Rheumatic mitral stenosis (MS) is a significant cause of valvular heart disease. Pulmonary artery systolic pressure (PASP) reflects the hemodynamic consequences of MS and is used to determine treatment strategies. However, PASP progression and expected outcomes in patients with moderately severe MS remain unclear.

Purpose

We aimed to examine the impact of progression rate of PASP in moderately severe MS.

Methods

A cohort of 866 consecutive patients with moderately severe rheumatic MS (1.0 cm2.

Results

Data-driven phenotyping identified two distinct trajectories based on PASP progression: a rapid progression group (N=38, 8.7%) and a slow progression group (N=398, 91.3%). Patients in the rapid progression group were older and had more comorbidities than patients in the slow progression group, including diabetes, and atrial fibrillation (all P&lt;0.05). The initial mean diastolic pressure gradient and PASP were higher in the rapid progression group than in the slow progression group (6.2±2.4 mmHg vs. 5.1±2.0 mmHg, P=0.001, and 42.3±13.3 mmHg vs. 33.0±9.2 mmHg, P&lt;0.001, respectively). During a mean follow-up of 7.0±3.0 years, the event-free survival rate was significantly lower in the rapid progression group than in the slow progression group (log-rank P&lt;0.001). Rapid PASP progression was a significant risk factor for composite outcomes even after adjusting for comorbidities (hazard ratio: 3.08, 95% confidence interval (CI): 1.68–5.64, P&lt;0.001). Multivariate regression analysis revealed that PASP&gt;40 mmHg was independently associated with the probability of rapid progression group allocation (odds ratio: 4.95, 95% CI: 2.08–11.99, P&lt;0.001).

Conclusions

Two groups with distinct patterns of PASP progression were identified. Rapid PASP progression was associated with a significantly higher risk of the composite outcomes. The main independent echocardiographic predictor for rapid progression group allocation was initial PASP&gt;40 mmHg.

Funding Acknowledgement

Type of funding sources: Private hospital(s). Main funding source(s): This study was supported by a Severance Hospital Research fund for Clinical excellence (SHRC) (C-2020-0041) and a faculty research grant of Yonsei University College of Medicine (6-2020-0156).

Streptomyces montanisoli sp. nov., exhibiting antimicrobial activity, isolated from mountain soil around a decaying tree

A Gram-stain-positive, aerobic actinobacterial strain designated MMS17-BM035T isolated from mountain soil around a decaying tree was subjected to taxonomic characterization. The isolate developed extensively branched substrate mycelia and white aerial hyphae on International Streptomyces Project 2 agar. Strain MMS17-BM035T grew at 15–34 °C (optimum, 30 °C), at pH 5.0–8.0 (optimum, pH 7.0) and in the presence of 0–6 % NaCl (optimum, 0 %). Analysis of 16S rRNA gene sequences indicated that MMS17-BM035T fell into a phylogenetic cluster belonging to the genus Streptomyces . MMS17-BM035T shared the highest sequence similarity of 99.45 % with Streptomyces fuscigenes JBL-20T, and no higher than 98.7 % with other species of Streptomyces . Based on the orthologous average nucleotide identity, MMS17-BM035T was again mostly related to S. fuscigenes JBL-20T with 84.14 % identity, and less than 80 % with other species. The digital DNA–DNA hybridization analysis also indicated low levels of relatedness with related species, as the highest value was observed with S. fuscigenes JBL-20T (28.8 %). The major fatty acids of the strain were anteiso-C15 : 0, a summed feature (consisting of C18 : 1 ω7c/C18 : 1 ω6c), iso-C15 : 0, C16 : 0 and C20 : 0. The major respiratory quinones were MK-9(H4) and MK-9(H6). The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositolmannoside. The major cell-wall diamino acid was ll-diaminopimelic acid, and the characteristic whole-cell sugars were glucose and ribose. The DNA G+C content was 72.1 mol%. Strain MMS17-BM035T exhibited antimicrobial activity against several Gram-positive bacteria and yeasts. Based on both phenotypic and phylogenetic evidences, strain MMS17-BM035T should be classified as representing a novel species, for which the name Streptomyces montanisoli sp. nov. (type strain=MMS17-BM035T=KCTC 49544T=JCM 34528T) is proposed.

High-precision measurement of the W boson mass with the CDF II detector

The mass of the W boson, a mediator of the weak force between elementary particles, is tightly constrained by the symmetries of the standard model of particle physics. The Higgs boson was the last missing component of the model. After observation of the Higgs boson, a measurement of the W boson mass provides a stringent test of the model. We measure the W boson mass, M_W, using data corresponding to 8.8 inverse femtobarns of integrated luminosity collected in proton-antiproton collisions at a 1.96 tera-electron volt center-of-mass energy with the CDF II detector at the Fermilab Tevatron collider. A sample of approximately 4 million W boson candidates is used to obtain [Formula: see text], the precision of which exceeds that of all previous measurements combined (stat, statistical uncertainty; syst, systematic uncertainty; MeV, mega-electron volts; c, speed of light in a vacuum). This measurement is in significant tension with the standard model expectation.

Metabacillus bambusae sp. nov., isolated from bamboo grove soil

A bacterial strain designated BG109T was isolated from bamboo grove soil, and subjected to polyphasic taxonomic characterization. BG109T is an aerobic, non-motile, Gram-stain-positive and endospore-forming bacterium. BG109T showed growth at 10–40 °C (optimum, 37 °C), at pH 4–10 (optimum, 8), and in the presence of 0–7 % NaCl concentration (optimum, 0–1 %). The predominant menaquinone of BG109T was MK-7, and the cell wall peptidoglycan contained major amounts of meso–diaminopimelic acid as the diagnostic diamino acid. The diagnostic polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and unidentified phospholipids and glycolipids were also present. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0, iso-C16 : 0 and C16 : 0. The chemotaxonomic properties of BG109T were generally consistent with those of members of the genus Metabacillus . BG109T shared highest 16S rRNA gene sequence similarities with ‘Metabacillus elymi’ KUDC1714 (99.26 %), Metabacillus sediminilitoris DSL-17T (98.17 %), Metabacillus litoralis SW-211T (98.16 %) and Metabacillus crassostreae JSM 100118T (97.13 %), all of which were well below the suggested cutoff level for species distinction. The genome level relatedness also confirmed the separation of BG109T from other species of the genus Metabacillus . Thus, it is evident that BG109T merits recognition as representing a novel species of the genus Metabacillus , for which the name Metabacillus bambusae sp. nov. is proposed. The type strain is BG109T (=KCTC 43190T=JCM 34515T).

Determination of the baseline tritium concentrations (HTO, TFWT and OBT) in soil and plants in Ontario, Canada

Tritiated water (HTO), tissue free water tritium (TFWT) and organically bound tritium (OBT) activity concentrations in soil and plant leaves, collected at background areas in Ontario, were measured to quantify the current tritium baseline. Five representative background sites, based on their geological characteristics and residential populations, have been selected for this study. Undisturbed soils, plant leaves and surface water samples were collected at 5 sites (London, Kapuskasing, Thunder Bay, Elliot Lake and Cornwall areas) in 2015. Water sample HTO activity concentrations were measured using Liquid Scintillation Counting (LSC, ALOKA), and HTO activity concentrations for soil and TFWT for plant leaves were measured by LSC (Quantulus 1220) on water extracted from frozen samples using a freeze-drying vacuum system equipped with a liquid nitrogen trap. Plant leaf OBT levels were obtained by combustion of rinsed freeze-dried samples using a Parr combustion system, while soil OBT values were obtained using a tube furnace combustion system. Combustion water was distilled before being counted by LSC (Quantulus 1220). HTO activity concentrations were found to range between 1.4 and 2.0 Bq/L (MDA = 0.5 Bq/L) in surface water and soil samples. TFWT values were less than the minimum detectable activity (MDA = 3.5 Bq/L) in plant leaves. In contrast, OBT activity concentrations (MDA = 5 Bq/L) ranged from 5.7 to 17.1 Bq/L in plant leaves and 8.3-20.7 Bq/L in surface soil (0-5 cm depth). The overall OBT activity concentrations were higher in the London and the Cornwall areas. Lower levels were measured near Thunder Bay, Kapuskasing and Elliot Lake. There was no obvious relationship between soil OBT activity concentrations and soil types. The results provide the current tritium (HTO, TFWT and OBT) baseline values in Ontario. These values will be helpful for use as background locations for the evaluation of past and future environmental tritium inputs associated with nuclear facilities, and will be taken into account when evaluating the environmental impact of nuclear facilities in Ontario. Since samples in this study were primarily taken in wooded areas, some questions remain regarding the possibility that soil samples in open, non-wooded areas could show different HTO and OBT contents than those presented in this study.

Paenibacillus artemisiicola sp. nov. and Paenibacillus lignilyticus sp. nov., two new endophytic bacterial species isolated from plant roots

Two Gram-positive, endospore-forming, rod-shaped bacterial strains designated MWE-103^T and DLE-14^T were isolated from plant roots. The 16S rRNA gene sequence analysis indicated that strain MWE-103^T was closely related to Paenibaillus sacheonensis SY01^T with a sequence similarity of 97.82 %, and strain DLE-14^T to Paenibacillus rhizoryzae IZS3-5^T with 99.09 % similarity. The orthologous average nucleotide identity and digital DNA-DNA hybridization values using whole genome data indicated that strains MWE-103^T and DLE-14^T could be readily distinguished from the mostly related species. Both strains grew at mesophilic temperature ranges, and grew best at pH 6 and in the absence of NaCl. The major fatty acid in both strains was anteiso-C_15 : 0, but their relative proportions differed. The predominant quinone of both strains was menaquinone 7, the cell-wall diamino acid was meso-diaminopimelic acid, and the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, which were consistent with those of related species. Amylase and cellulase activities were positive for both strains. Strain DLE-14^T exhibited the potential for lignin degradation. The DNA G+C contents of strain MWE-103^T and DLE-14^T were 60.9 and 50.8 mol% respectively. The genomes of the two strains revealed potential plant-growth-promoting characteristics such as nitrogen fixation, siderophore production and phosphate solubilization. Based on phylogenetic and phenotypic evidence, strains MWE-103^T and DLE-14^T should each be recognized as a novel species of Paenibacillus, for which the names Paenibacillus artemisiicola sp. nov. (type strain: MWE-103^T=KCTC 43287^T=JCM 34503^T) and Paenibacillus lignilyticus sp. nov. (type strain: DLE-14^T=KCTC 43288^T=JCM 34504^T) are proposed.

Micromonospora humida sp. nov., exhibiting antimicrobial potential, isolated from riverside soil

An actinobacterial strain designated MMS20-R1-14^T was isolated from a riverside soil sample. Colonies on agar plates were orange to strong orange brown in colour, which later became black. The cells grew at 10-40 °C (optimum, 37 °C), pH 5.0-11.0 (pH 8.0) and in the presence of 0-4 % NaCl (1 %). The 16S rRNA gene sequence of strain MMS20-R1-14^T showed highest similarities to Micromonospora wenchangensis CCTCC AA 2012002^T (99.51 %) and Micromonospora rifamycinica AM105^T (99.37 %). The orthoANI values between strain MMS20-R1-14^T and the two type strains were 95.72 and 90.99 %, and the digital DNA-DNA hybridization values were 63.6 and 40.8 %, respectively, thus confirming the distinction of strain MMS20-R1-14^T from its mostly related species. The DNA G+C content of strain MMS20-R1-14^T was 72.9 mol%. The strain contained meso-diaminopimelic acid as the major cell-wall amino acid, and the characteristic whole-cell sugars were arabinose, xylose, glucose, ribose and rhamnose. The main cellular fatty acids were C_18 : 1  ω9c, iso-C_15 : 0 and iso-C_16 : 0, the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the predominant menaquinones were MK-10(H₄) and MK-10(H₆), all of which were consistent with those of Micromonospora. Strain MMS20-R1-14^T showed antimicrobial activity against a range of bacterial and yeast species. The genome of the strain was found to contain 33 potential biosynthetic gene clusters for secondary metabolites, thus showing a high potential as a producer of bioactive compounds. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain MMS20-R1-14^T merits recognition as representing a novel species of the genus Micromonospora, for which the name Micromonospora humida sp. nov. (type strain=MMS20 R1-14^T=KCTC 49541^T=JCM 34494^T) is proposed.

Pseudomonas guryensis sp. nov. and Pseudomonas ullengensis sp. nov., isolated from soil

Two Gram-staining-negative, aerobic, rod-shaped bacteria designated strains SR9^T and UL070^T, were isolated from soil and subjected to taxonomic characterization. Strain SR9^T grew at 10-37 °C (optimum 30 °C), at pH 4.0-10.0 (optimum pH 8.0) and in the presence of 0-1 % NaCl (optimum 0 %), and UL070^T at 4-33 °C (optimum 30 °C), at pH 4.0-10.0 (optimum pH 7.0) and in the presence of 0-2 % NaCl (optimum 0 %), respectively. Strain UL070^T was motile with flagella. Analysis of 16S rRNA gene sequences indicated that the two strains fell into phylogenetic clusters belonging to the genus Pseudomonas. Both strains SR9^T and UL070^T were mostly related to Pseudomonas campi S1-A32-2^T with 99.70 and 99.01% sequence similarities, and the similarity between the two isolates was 98.90 %. The genome-based in silico analyses indicated that each of the strains SR9^T and UL070^T was clearly separated from other species of Pseudomonas, as the orthologous average nucleotide identity (OrthoANI) and the digital DNA-DNA hybridization (dDDH) values were no higher than 93.09 and 50.03% respectively with any related species, which were clearly below the cutoff for species distinction. The fatty acid profiles of the two strains mainly consisting of unsaturated components, the presence of ubiquinone 9 (Q-9) as the major respiratory quinone, and phosphatidylethanolamine (PE) and diphosphatidylglycerol (DPG) as the diagnostic polar lipids were consistent with their classification into Pseudomonas. The DNA G+C contents of strains SR9^T and UL070^T were 63.2 mol% and 63.6 mol% respectively. On the basis of both phenotypic and phylogenetic evidences, each of the isolated strains should be classified as a novel species, for which the names Pseudomonas guryensis sp. nov. (type strain=SR9^T=KCTC 82228^T=JCM 34509^T) and Pseudomonas ullengensis sp. nov. (type strain=UL070^T=KCTC 82229^T=JCM 34510^T) are proposed.

Comparison of 16S rRNA Gene Based Microbial Profiling Using Five Next-Generation Sequencers and Various Primers

Microbial community analysis based on the 16S rRNA-gene is used to investigate both beneficial and harmful microorganisms in various fields and environments. Recently, the next-generation sequencing (NGS) technology has enabled rapid and accurate microbial community analysis. Despite these advantages of NGS based metagenomics study, sample transport, storage conditions, amplification, library preparation kits, sequencing, and bioinformatics procedures can bias microbial community analysis results. In this study, eight mock communities were pooled from genomic DNA of Lactobacillus acidophilus KCTC 3164^T, Limosilactobacillus fermentum KCTC 3112^T, Lactobacillus gasseri KCTC 3163^T, Lacticaseibacillus paracasei subsp. paracasei KCTC 3510^T, Limosilactobacillus reuteri KCTC 3594^T, Lactococcus lactis subsp. lactis KCTC 3769^T, Bifidobacterium animalis subsp. lactis KCTC 5854^T, and Bifidobacterium breve KCTC 3220^T. The genomic DNAs were quantified by droplet digital PCR (ddPCR) and were mixed as mock communities. The mock communities were amplified with various 16S rRNA gene universal primer pairs and sequenced by MiSeq, IonTorrent, MGIseq-2000, Sequel II, and MinION NGS platforms. In a comparison of primer-dependent bias, the microbial profiles of V1-V2 and V3 regions were similar to the original ratio of the mock communities, while the microbial profiles of the V1-V3 region were relatively biased. In a comparison of platform-dependent bias, the sequence read from short-read platforms (MiSeq, IonTorrent, and MGIseq-2000) showed lower bias than that of long-read platforms (Sequel II and MinION). Meanwhile, the sequences read from Sequel II and MinION platforms were relatively biased in some mock communities. In the data of all NGS platforms and regions, L. acidophilus was greatly underrepresented while Lactococcus lactis subsp. lactis was generally overrepresented. In all samples of this study, the bias index (BI) was calculated and PCA was performed for comparison. The samples with biased relative abundance showed high BI values and were separated in the PCA results. In particular, analysis of regions rich in AT and GC poses problems for genome assembly, which can lead to sequencing bias. According to this comparative analysis, the development of reference material (RM) material has been proposed to calibrate the bias in microbiome analysis.

Flavobacterium hydrocarbonoxydans sp. nov., isolated from polluted soil

This paper presents a polyphasic taxonomic study of a Gram-stain-negative bacterium designated GA093^T, a soil isolate capable of benzo(α)pyrene degradation. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain GA093^T is a member of the genus Flavobacterium, and formed an independent phylogenetic line while clustering with the type strains of Flavobacterium hibernum, Flavobacterium branchiarum and Flavobacterium hydatis. Strain GA093^T was facultatively anaerobic, and could grow at 4-33 °C (optimum, 30 °C), at pH 6-11 (optimum, pH 7) and in the presence of 0-2 % (w/v) NaCl (optimum, 0 %). Strain GA093^T was capable of producing acid from various carbon sources, which was comparable to other related species of Flavobacterium. The strain contained MK-6 as the only isoprenoid quinone, iso-C_15 : 0 as the major cellular fatty acid, phosphatidylethanolamine and phosphatidylinositol as diagnostic polar lipids, and sym-homospermidine as the major polyamine. The chemotaxonomic properties of strain GA093^T were consistent with the general properties of Flavobacterium except the presence of phosphatidylinositol, which distinguished it from other related species. The total stretch of the obtained genome of GA093^T was 5.05 Mbp, and the DNA G+C content was 34.79 mol%. The genome contained genes potentially related to the degradation of aromatic hydrocarbons. On the basis of the present polyphasic analysis, strain GA093^T was found to have properties that distunguished it as representing a novel species of the genus Flavobacterium, for which the name Flavobacterium hydrocarbonoxydans sp. nov. is proposed. The type strain is GA093^T (=KCTC 72594^T=LMG 31760^T).

Muriicola soli sp. nov., isolated from soil

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002^T was isolated from island soil. The isolate grew at 20-37 °C (optimum, 30 °C), at pH 6.0-9.5 (optimum, pH 7) and in the presence of 0.5-4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002^T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8^T and Muriicola jejuensis EM44^T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C_15 : 1 G and iso-C_15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002^T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002^T and M. jejuensis and that between the strain and M. marianensis A6B8^T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002^T should be recognized as a novel species of the genus Muriicola, for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002^T (=KCTC 62790^T=JCM 32370^T).

Heminiphilus faecis gen. nov., sp. nov., a member of the family Muribaculaceae, isolated from mouse faeces and emended description of the genus Muribaculum

The novel strain AM35^T was isolated from the faeces of C57BL/6 mice. These cells are strictly anaerobic, gram negative, oxidase negative, catalase positive, rod-shaped and non-motile. The strain produced creamy yellowish colonies on brain heart infusion (BHI) agar with hemin. Growth was investigated at 30-41 °C in the presence of 0.5-1.5% (w/v) NaCl at pH 6.5-8.5. Taxonomic analysis based on 16S rRNA gene sequencing revealed that strain AM35^T is affiliated with the family Muribaculaceae and closely related to the genus Muribaculum. The genomic DNA G + C content of strain AM35^T was 47.8 mol%. We detected the whole-cell sugars ribose and galactose; meso-2,6-diaminopimelic acid was absent. The major fatty acids (> 10%) were anteiso-C_15:0 and iso-C_15:0; the major polar lipid was phosphatidylethanolamine. The major respiratory quinones were MK-10 and MK-11. Based on our phylogenetic, phenotypic and chemotaxonomic analyses, strain AM35^T represents a novel genus within the family Muribaculaceae, for which we propose the name Heminiphilus faecis gen. nov., sp. nov. The type strain of Heminiphilus faecis gen. nov., sp. nov. is AM35^T (= KCTC 15907 ^T = DSM 110151 ^T).

Search for Sub-eV Sterile Neutrinos at RENO

We report a search result for a light sterile neutrino oscillation with roughly 2200 live days of data in the RENO experiment. The search is performed by electron antineutrino (ν[over ¯]_{e}) disappearance taking place between six 2.8 GW_{th} reactors and two identical detectors located at 294 m (near) and 1383 m (far) from the center of the reactor array. A spectral comparison between near and far detectors can explore reactor ν[over ¯]_{e} oscillations to a light sterile neutrino. An observed spectral difference is found to be consistent with that of the three-flavor oscillation model. This yields limits on sin^{2}2θ_{14} in the 10^{-4}≲|Δm_{41}^{2}|≲0.5  eV^{2} region, free from reactor ν[over ¯]_{e} flux and spectrum uncertainties. The RENO result provides the most stringent limits on sterile neutrino mixing at |Δm_{41}^{2}|≲0.002  eV^{2} using the ν[over ¯]_{e} disappearance channel.

Experimental investigation of D2 conversion to DHO in soil near the Cernavoda nuclear power plant site in Romania

The current Canadian and Romanian model predictions for tritium dose following an atmospheric tritiated hydrogen gas (HT) release is based on a default Canadian Standards Association (CSA) conversion factor of HT to tritiated water (HTO) of 4.3%. The determination of an empirical site specific value for the conversion factor was essential for the CANDU Cernavoda Nuclear Power Plant (NPP) in Romania to verify if the CSA value is appropriate for use at this site. Given the role of soil characteristics on the conversion of HT to HTO, on-site experiments would provide the best evaluation of the conversion factor. The objective of the study was to define the soil HT to HTO conversion parameters specific to the Cernavoda NPP site. In June 2016, a series of experiments were conducted to meet this objective. First, the in situ deposition velocity of D₂ gas, as a surrogate for HT gas, was obtained using an exposure chamber. Diffusion of D₂ into the soil was then evaluated based on the measurements of DHO concentrations in the exposed soil. As soil microbes play a role in the conversion of HT to HTO, this work included a microbiological characterization of the soil, which targeted total soil bacteria (cultivable and gene-based) and hydrogen oxidizing bacteria (cultivable and gene-based). The fraction of hydrogen oxidizing cultivable soil bacteria represented 14-20% of the total cultivable bacteria population estimated as 2.8-29.2 × 10⁵ cfu/g of soil. The empirically derived HT to HTO conversion factor was lower than the default value (4.3%). It fell between 0.9% and 2.0%. The default value is therefore more conservative than the Cernavoda site-specific derived value obtained from the study.

Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential

The genus Streptacidiphilus represents a group of acidophilic actinobacteria within the family Streptomycetaceae, and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely Streptomyces and Kitasatospora, these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 Streptacidiphilus species were subjected to the comparative analysis together with selected Streptomyces and Kitasatospora genomes. This study represents the first comprehensive comparative genomic analysis of the genus Streptacidiphilus. The results indicate that the genomes of Streptacidiphilus contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in Streptacidiphilus only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of Streptacidiphilus were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919^T were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each Streptacidiphilus species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities.

Kitasatospora acidiphila sp. nov., isolated from pine grove soil, exhibiting antimicrobial potential

A polyphasic study was carried out to establish the taxonomic position of an acidophilic isolate designated MMS16-CNU292T (=JCM 32302T) from pine grove soil, and provisionally assigned to the genus Kitasatospora . On the basis of 16S rRNA gene sequence similarity, the strain formed a novel evolutionary lineage within Kitasatospora and showed highest similarities to Kitasatospora azatica KCTC 9699T (98.75 %), Kitasatospora kifunensis IFO 15206T (98.74 %), Kitasatospora purpeofusca NRRL B-1817T (98.61 %) and Kitasatospora nipponensis HKI 0315T (98.42 %), respectively. Strain MMS16-CNU292T possessed MK-9(H6) and MK-9(H8) as the major menaquinones, and a major amount of meso-diaminopimelic acid in the cell-wall peptidoglycan. The whole-cell hydrolysates were rich in galactose, glucose and mannose, and the polar lipids mainly consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannosides. The major fatty acids were anteiso-C15 : 1-A, anteiso-C15 : 0, and iso-C15 : 0, and the DNA G+C content was 71.5 mol%. The strain exhibited antibacterial activity against a number of bacterial strains, and the activity was generally greater when grown in acidic conditions. The phylogenetic, chemotaxonomic and phenotypic properties enabled distinction of MMS16-CNU292T from related species, and thus the isolate should be recognized as a new species of the genus Kitasatospora , for which the name Kitasatospora acidiphila sp. nov. (type strain=MMS16-CNU292T=KCTC 49011T=JCM 32302T) is proposed.

Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil

Three aerobic, rod-shaped actinobacterial strains, designated MMS17-SY117^T, MMS17-SY207-3^T and MMS17-SY213^T, were isolated from soil and their taxonomic positions were analysed using a polyphasic approach. The isolates showed best growth at 30 °C, pH 7 and 0-1 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolates were affiliated to the genus Nocardioides, and the closest species to MMS17-SY117^T, MMS17-SY207-3^T and MMS17-SY213^T were Nocardioides aestuarii JC2056^T (97.76%), Nocardioides currus IB-3^T (97.41%) and Nocardioides exalbidus RC825^T (98.71%), respectively. Each isolate formed a distinct cluster within the Nocardioides clade in the phylogenetic tree. The orthologous average nucleotide identity and digital DNA-DNA hybridization values were in the range of 74.4-85.7 % and 16.6-39.2 %, respectively, with the type strains of related species. The major polar lipids in all three strains were phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids were iso-C_16 : 0 and C_17 : 1 ω8c. MK-8(H₄) was the major isoprenoid quinone and ll-DAP was the major diamino acid. Galactose, glucose and rhamnose were present in the whole-cell hydrolysate, and MMS17-SY213^T also contained mannose and ribose. The DNA G+C contents of MMS17-SY117^T, MMS17-SY207-3^T and MMS17-SY213^T were 72.2, 70.4 and 71.5 mol%, respectively. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of each strain as representing a new species of Nocardioides, for which the names Nocardioides euryhalodurans sp. nov. (MMS17-SY117^T=KCTC 49175^T=JCM 32831^T), Nocardioides seonyuensis sp. nov. (MMS17-SY207-3^T=KCTC 49176^T=JCM 32832^T) and Nocardioides eburneiflavus sp. nov. (MMS17-SY213^T=KCTC 49177^T=JCM 32833^T) are proposed accordingly.

Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium

BACKGROUND

Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment.

RESULTS

A high quality draft genome (7.8 Mb) of S. yeochonensis CN732 was obtained with a G + C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites.

CONCLUSIONS

This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.

Gordonia insulae sp. nov., isolated from an island soil

A mycolic acid-containing actinobacterium designated strain MMS17-SY073^T was isolated from island soil. The isolate showed best growth at 25 °C, pH 6, and 0 % (w/v) NaCl. The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS17-SY073^T belongs to the genus Gordonia, and is mostly related to the type strains of Gordonia soli (98.5 % sequence similarity), Gordonia polyisoprenivorans (98.1%), and Gordonia hankookensis (97.8%). The genome-based comparisons showed a clear distinction between the strain and the two neighbouring species, G. soli and G. polyisoprenivorans, with the average nucleotide identities (ANI) of 75.8 and 76.3 %, respectively. Notably, the genome of strain MMS17-SY073^T was the largest in total stretch and gene counts among the complete genomes of Gordonia, and contained a number of biosynthetic gene clusters for secondary metabolites, in particular those for non-ribosomal peptide synthetases. The major polar lipids were diphosphatidyl glycerol (DPG), phosphatidyl glycerol (PG), phosphatidyl ethanolamine (PE), phosphatidyl inositol (PI) and phosphatidyl inositol mannoside (PIM). The isoprenoid quinone was MK-9(H₂), and the main fatty acids were C_16 : 0 (30.2%) and 10-methyl-C_18 : 0 (33.7%). The whole cell hydrolysates contained galactose, arabinose, and meso-diaminopimelic acid. The DNA G+C content was 67.4 mol%. Based on phenotypic, chemotaxonomic and genetic analysis, strain MMS17-SY073^T should be classified as a new species of the genus Gordonia, for which the name Gordonia insulae sp. nov. is proposed (type strain=MMS17-SY073^T=KCTC 49257^T=JCM 33277^T).

Genome based characterization of Kitasatospora sp. MMS16-BH015, a multiple heavy metal resistant soil actinobacterium with high antimicrobial potential

An actinobacterial strain designated Kitasatospora sp. MMS16-BH015, exhibiting high level of heavy metal resistance, was isolated from soil of an abandoned metal mining site, and its potential for metal resistance and secondary metabolite production was studied. The strain was resistant to multiple heavy metals including zinc (up to 100 mM), nickel (up to 2 mM) and copper (up to 0.8 mM), and also showed antimicrobial potential against a broad group of microorganisms, in particular filamentous fungi. The genome of strain MMS16-BH015 was 8.96 Mbp in size with a G + C content of 72.7%, and contained 7270 protein-coding genes and 107 tRNA/rRNA genes. The genome analysis revealed presence of at least 121 metal resistance related genes, which was prominently higher in strain MMS16-BH015 compared to other genomes of Kitasatospora. The genes included those for proteins representing various families involved in the transport of heavy metals, for example dipeptide transport ATP-binding proteins, high-affinity nickel transport proteins, and P-type heavy metal-transporting ATPases. Additionally, 43 biosynthetic gene clusters (BGCs) for secondary metabolites, enriched with those for non-ribosomal peptides, were detected in this multiple heavy metal resistant actinobacterium, which was again the highest among the compared genomes of Kitasatospora. The pan-genome analysis also identified higher numbers of unique genes related to secondary metabolite production and metal resistance mechanism in strain MMS16-BH015. A high level of correlation between the biosynthetic potential and heavy metal resistance could be observed, thus indicating that heavy metal resistant actinobacteria can be a promising source of bioactive compounds.

Distribution of organically bound tritium (OBT) activity concentrations in aquatic biota from eastern Canada

A survey of eastern Canadian biota was conducted to determine the distribution of activity concentrations of organically bound tritium (OBT). Fish samples were collected from Lake Ontario and the St. Lawrence River in areas continuously receiving inputs of tritiated water (HTO) from operating nuclear power plants, and from Lake Nipissing, a background area. Components of their aquatic environments were sampled. The data collected also provides some insight on how tritium activity concentrations in ambient water influence tissue free water tritium (TFWT) and OBT activity concentrations in biological tissues. Using an ALOKA liquid scintillation system, fish TFWT and OBT were quantified. Fish TFWT averaged 1.6 ± 0.1 Bq/L in Lake Nipissing and 3.1 ± 0.3 Bq/L in Lake Ontario. In contrast, TFWT ranged from 11.1 to 80.8 Bq/L in the St. Lawrence River near the Gentilly-2 Canada Deuterium Uranium (CANDU) site. Fish tissue OBT levels were 4.0 ± 0.4 Bq/L and 5.3 ± 0.2 Bq/L for Lake Nipissing and Lake Ontario, respectively, and between 18.1 and 134.2 Bq/L for CANDU sites. The activity concentrations of TFWT and OBT were reviewed for algae, freshwater mussel and various fish samples collected near Gentilly-2, Pickering and Darlington Nuclear Power Generating Stations. TFWT in aquatic biota was found to correlate with the tritium activity concentrations measured in waters at the time of sampling (TFWT/HTO of ambient water was 0.3-4.3). The OBT concentration factors (OBT/HTO of ambient water) were found to be higher in freshwater mussels (between 17 and 47) compared to algae and fish (0.3-10). These results point to a heterogeneous distribution of biota OBT content in these aquatic ecosystems. It was also noted that all fish and algae samples were found to be within the range of tritium activity concentrations that has been historically measured in the same waters. Values in freshwater mussels were above this range.

Organically bound tritium (OBT) activity concentrations in surface soil at the Chalk River Laboratories, Canada

Canadian Nuclear Laboratories (CNL)'s Chalk River Laboratories (CRL) site is home to a large nuclear research complex in Canada. CRL's air tritium releases amount to about 10¹⁵ Bq/year. The objective of the study was to characterize the spatial footprint of the 60 years of tritium atmospheric releases in surface soil by measurement of organically bound tritium (OBT). Soil OBT activity concentrations were of particular interest because soil represents a long-term tritium reservoir that can act as a historical record of tritium releases into the environment. Soil samples to a 5 cm depth were collected within the CRL site from 2012 to 2014. Each sample was analyzed for tritiated water (HTO) and OBT activity concentrations. The highest HTO and OBT measurements obtained during this study were 154.0 ± 7.8 Bq/L and 180.9 ± 37.3 Bq/L, respectively. A developed OBT map indicated that retained tritium in soil was not related to the distance of sources-term but it was related to the prevailing wind direction.

Fuel-Composition Dependent Reactor Antineutrino Yield at RENO

We report a fuel-dependent reactor electron antineutrino (ν[over ¯]_{e}) yield using six 2.8 GW_{th} reactors in the Hanbit nuclear power plant complex, Yonggwang, Korea. The analysis uses 850 666 ν[over ¯]_{e} candidate events with a background fraction of 2.0% acquired through inverse beta decay (IBD) interactions in the near detector for 1807.9 live days from August 2011 to February 2018. Based on multiple fuel cycles, we observe a fuel ^{235}U dependent variation of measured IBD yields with a slope of (1.51±0.23)×10^{-43}  cm^{2}/fission and measure a total average IBD yield of (5.84±0.13)×10^{-43}  cm^{2}/fission. The hypothesis of no fuel-dependent IBD yield is ruled out at 6.6σ. The observed IBD yield variation over ^{235}U isotope fraction does not show significant deviation from the Huber-Mueller (HM) prediction at 1.3 σ. The measured fuel-dependent variation determines IBD yields of (6.15±0.19)×10^{-43} and (4.18±0.26)×10^{-43}  cm^{2}/fission for two dominant fuel isotopes ^{235}U and ^{239}Pu, respectively. The measured IBD yield per ^{235}U fission shows the largest deficit relative to the HM prediction. Reevaluation of the ^{235}U IBD yield per fission may mostly solve the reactor antineutrino anomaly (RAA) while ^{239}Pu is not completely ruled out as a possible contributor to the anomaly. We also report a 2.9 σ correlation between the fractional change of the 5 MeV excess and the reactor fuel isotope fraction of ^{235}U.

Treatment Outcome and Renal Safety of 3-Year Tenofovir Disoproxil Fumarate Therapy in Chronic Hepatitis B Patients with Preserved Glomerular Filtration Rate

Background/Aims

To investigate the treatment efficacy and renal safety of long-term tenofovir disoproxil fumarate (TDF) therapy in chronic hepatitis B (CHB) patients with preserved renal function.

Methods

The medical records of 919 CHB patients who were treated with TDF therapy were reviewed. All patients had preserved renal function with an estimated glomerular filtration rate (eGFR) of at least 60 mL/min/1.73 m².

Results

A total of 426 patients (184 treatment-naïve and 242 treatment-experienced) were included for analysis. A virologic response (VR) was defined as achieving an undetectable serum hepatitis B virus (HBV) DNA level, and the overall VR was 74.9%, 86.7%, and 89.4% at the 1, 2, and 3-year follow-ups, respectively. Achieving a VR was not influenced by previous treatment experience, TDF combination therapy, or antiviral resistance. In a multivariate analysis, being hepatitis B e antigen positive at baseline and having a serum HBV DNA level ≥2,000 IU/mL at 12 months were associated with lower VR rates during the long-term TDF therapy. The overall renal impairment was 2.9%, 1.8%, and 1.7% at the 1, 2, and 3-year follow-ups, respectively. With regard to renal safety, underlying diabetes mellitus (DM) and an initial eGFR of 60 to 89 mL/min/1.73 m² were significant independent predictors of renal impairment.

Conclusions

TDF therapy appears to be an effective treatment option for CHB patients with a preserved GFR. However, patients with underlying DM and initial mild renal dysfunction (eGFR, 60 to 89 mL/min/1.73 m²) have an increased risk of renal impairment.

Streptomyces fodineus sp. nov., an actinobacterium with antifungal activity isolated from mine area soil

A novel actinobacterial strain producing an antifungal substance was isolated from a sample of acidic mine area soil, and its taxonomic position was evaluated. The novel strain, designated TW1S1^T, formed white-grey aerial mycelium and yellow substrate mycelium on oatmeal agar. Growth occurred at 10-45 °C (optimum, 30 °C), pH 4-9 (pH 6-7) and in the presence of up to 8 % (w/v) NaCl. Melanin was produced on peptone-yeast extract-iron agar. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that the novel strain should be assigned to the genus Streptomyces, and the closest species was Streptomyces puniciscabiei S77^T with 99.1 % sequence similarity, which was followed by Streptomyces durhamensis NRRL B-3309^T (99.0 %), Streptomyces filipinensis NBRC 12860^T (98.9 %) and Streptomyces yaanensis Z4^T (98.7 %). The chemotaxonomic properties were consistent with those of Streptomyces. ll-Diaminopimelic acid was the diagnostic diamino acid, and alanine, glutamic acid and glycine were present in the peptidoglycan. The cell-wall hydrolysate also contained galactose, glucose, mannose and ribose. The predominant isoprenoid quinones were MK-9(H4) and MK-9(H6), the major polar lipids were phosphatidylglycerol and an unidentified phospholipid, and the main fatty acids were iso-C16 : 0 and anteiso-C15 : 0. However, strain TW1S1^T could be distinguished from its neighbouring species by its phenotypic properties. In addition, the genome-based comparison with the closest species indicated that strain TW1S1^T should be recognized as a separate species. The phylogenetic, phenotypic and chemotaxonomic as well as genomic evidence supported that TW1S1^T represents a novel species of Streptomyces, for which the name Streptomycesfodineus sp. nov. is proposed (type strain, TW1S1^T = KCTC 49013^T = JCM 32404^T).

Acidiphilamides A-E, Modified Peptides as Autophagy Inhibitors from an Acidophilic Actinobacterium, Streptacidiphilus rugosus

Five new tripeptides, acidiphilamides A-E (1-5), were discovered along with two previously reported compounds, l-isoleucinamide (6) and l-valinamide (7), from Streptacidiphilus rugosus AM-16, an acidophilic actinobacterial strain isolated from acidic forest soil. The structures of 1-5 were elucidated as modified tripeptides bearing phenylalaninol or methioninol fragments with C₃-C₅ acyl chains based mainly on NMR and mass spectroscopic data. The absolute configurations of the amine units were established by advanced Marfey's method and GITC (2,3,4,6-tetra- O-acetyl-β-d-glucopyranosyl isothiocyanate) derivatization followed by LC/MS analysis. Acidiphilamides A and B (1 and 2), the first secondary metabolites isolated from the rare actinobacterial genus Streptacidiphilus, significantly inhibited autophagic flux but not proteasome activity in HeLa cells. These compounds appeared to block mainly the autophagosome-lysosome fusion step in the late stage of cellular autophagy.

Tritium in fish from remote lakes in northwestern Ontario, Canada

Tritium is most commonly generated as a by-product of nuclear reactors. As such, environmental concentrations are typically only reported near regions of interest, and background concentrations in areas unaffected by anthropogenic disturbance are not well characterized. To provide information on background levels of tritium in the natural environment, tissue-free water tritium (TFWT) and organically-bound tritium (OBT) were measured in the flesh of 106 fish collected within three lakes located at the IISD-Experimental Lakes Area (ELA) in Ontario, Canada in 2014. For the three ELA lakes studied, water tritium (HTO) activity concentration was determined to be below reliably detectable levels (0.6 Bq/L). Fish TFWT was found to be below 0.7 Bq/L, similar to the surrounding water tritium activity concentration. Fish OBT activity concentrations, at below 5 Bq/L, were also very low. Fish size was significantly related to OBT activity in Lake Whitefish and White Sucker from Lake 302, but not in other lakes. Though we observed significant differences in potential tritium exposure to humans among lakes, the levels of tritium reported here are below the Canadian natural background radiation of 1.8 mSv/y. These results provide information on background levels of tritium in freshwater fishes in Canada.

Measurement of Reactor Antineutrino Oscillation Amplitude and Frequency at RENO

The RENO experiment reports more precisely measured values of θ_{13} and |Δm_{ee}^{2}| using ∼2200 live days of data. The amplitude and frequency of reactor electron antineutrino (ν[over ¯]_{e}) oscillation are measured by comparing the prompt signal spectra obtained from two identical near and far detectors. In the period between August 2011 and February 2018, the far (near) detector observed 103 212 (850 666) ν[over ¯]_{e} candidate events with a background fraction of 4.8% (2.0%). A clear energy and baseline dependent disappearance of reactor ν[over ¯]_{e} is observed in the deficit of the measured number of ν[over ¯]_{e}. Based on the measured far-to-near ratio of prompt spectra, we obtain sin^{2}2θ_{13}=0.0896±0.0048(stat)±0.0047(syst) and |Δm_{ee}^{2}|=[2.68±0.12(stat)±0.07(syst)]×10^{-3}  eV^{2}.

Streptacidiphilus pinicola sp. nov., isolated from pine grove soil

A moderately acidophilic actinobacterial strain, designated MMS16-CNU450^T, was isolated from pine grove soil, and its taxonomic position was analysed using a polyphasic approach. The isolate showed best growth at 30 °C, pH 6 and 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolate was assigned to the genus Streptacidiphilus, and the closest species were Streptacidiphilus rugosus AM-16^T (sequence similarity, 98.61 %), Streptacidiphilus melanogenes NBRC 103184^T (98.53 %), Streptacidiphilus jiangxiensis NBRC 100920^T (98.19 %) and Streptacidiphilus anmyonensis NBRC 103185^T (98.05 %). The isolate formed a distinct cluster of its own within the Streptacidiphilusclade in the phylogenetic tree. Based on whole-genome comparison between the strain MMS16-CNU450^T and the type strains of related species, the orthologous average nucleotide identity and in silico DNA-DNA hybridization values were in the range of 77.9-87.0 and 22.3-32.7 %, respectively. The DNA G+C content of the isolate was 68.6 mol%. The phylogenetic, phenotypic, chemotaxonomic and genomic data supported the affiliation of the strain to Streptacidiphilus, and the name Streptacidiphilus pinicola sp. nov. (type strain, MMS16-CNU450^T=KCTC 49008^T=JCM 32300^T) is proposed accordingly.

Search for Boosted Dark Matter Interacting with Electrons in Super-Kamiokande

A search for boosted dark matter using 161.9 kt yr of Super-Kamiokande IV data is presented. We search for an excess of elastically scattered electrons above the atmospheric neutrino background, with a visible energy between 100 MeV and 1 TeV, pointing back to the Galactic center or the Sun. No such excess is observed. Limits on boosted dark matter event rates in multiple angular cones around the Galactic center and Sun are calculated. Limits are also calculated for a baseline model of boosted dark matter produced from cold dark matter annihilation or decay. This is the first experimental search for boosted dark matter from the Galactic center or the Sun interacting in a terrestrial detector.

Search for the Exotic Meson X(5568) with the Collider Detector at Fermilab

A search for the exotic meson X(5568) decaying into the B_{s}^{0}π^{±} final state is performed using data corresponding to 9.6  fb^{-1} from pp[over ¯] collisions at sqrt[s]=1960  GeV recorded by the Collider Detector at Fermilab. No evidence for this state is found and an upper limit of 6.7% at the 95% confidence level is set on the fraction of B_{s}^{0} produced through the X(5568)→B_{s}^{0}π^{±} process.