- Volume 68, Issue 1, 2018

A novel Gram-stain-positive, strictly aerobic, non-endospore-forming bacterium, designated CAU 9143T, was isolated from a hydric soil sample collected from Seogmo Island in the Republic of Korea. Strain CAU 9143T grew optimally at 30 °C, at pH 7.0 and in the presence of 1 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain CAU 9143T belonged to the genus Arthrobacter and was closely related to Arthrobacter ginkgonis SYP-A7299T (97.1 % similarity). Strain CAU 9143T contained menaquinone MK-9 (H2) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids and two unidentified phospholipids as the major polar lipids. The whole-cell sugars were glucose and galactose. The peptidoglycan type was A4a (l-Lys–D-Glu2) and the major cellular fatty acid was anteiso-C15 : 0. The DNA G+C content was 64.4 mol% and the level of DNA–DNA relatedness between CAU 9143T and the most closely related strain, A. ginkgonis SYP-A7299T, was 22.3 %. Based on phenotypic, chemotaxonomic and genetic data, strain CAU 9143T represents a novel species of the genus Arthrobacter , for which the name Arthrobacter paludis sp. nov. is proposed. The type strain is CAU 9143T (=KCTC 13958T,=CECT 8917T).

An actinomycete strain M4I47T was isolated from sediment from Megas Gialos, Syros, Greece. The results of phylogenetic analysis of the 16S rRNA gene sequence of M4I47T indicated that the highest similarity was with Actinoplanes atraurantiacus Y16T (98.9 %), Actinoplanes deccanensis IFO 13994T (98.8 %), Actinoplanes digitatis IFO 12512T (98.1 %) and Actinoplanes abujensis A4029T (98.0 %). The cell wall of the novel isolate contained meso-diaminopimelic acid and the whole-cell sugars were xylose, arabinose and glucose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H2). The phospholipid profile comprised phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unknown phospholipid. The DNA G+C content was 71.5 mol%. Furthermore, a combination of DNA–DNA relatedness and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the most closely related species. On the basis of these phenotypic and genotypic data, M4I47T represents a novel species of the genus Actinoplanes , for which the name Actinoplanes sediminis sp. nov. is proposed. The type strain is M4I47T (=CCTCC AA 2016022T=DSM 100965T).

A novel actinomycete, designated strain 1H-SSA4T, was isolated from the head of an ant (Camponotus japonicus Mayr) and was found to produce angucyclinone antibiotics. A polyphasic approach was used to determine the taxonomic status of strain 1H-SSA4T. The DNA G+C content of the draft genome sequence, consisting of 11.4 Mbp, was 70.0 mol%. 16S rRNA gene sequence similarity studies showed that strain 1H-SSA4T belongs to the genus Streptomyces with the highest sequence similarity to Streptomyces hygroscopicus subsp. ossamyceticus NBRC 13983T (98.9 %), and phylogenetically clustered with this species, Streptomyces torulosus LMG 20305T (98.8 %), Streptomyces ipomoeae NBRC 13050T (98.5 %) and Streptomyces decoyicus NRRL 2666T (98.4 %). The morphological and chemotaxonomic properties of the strain were also consistent with those members of the genus Streptomyces . A combination of DNA–DNA hybridization experiments and phenotypic tests were carried out between strain 1H-SSA4T and the above-mentioned strains, which further clarified their relatedness and demonstrated that strain 1H-SSA4T could be distinguished from these strains. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces , for which the name Streptomyces capitiformicae sp. nov. is proposed. The type strain is 1H-SSA4T (=CGMCC 4.7403T=DSM 104537T).

Three Gram-stain-positive, non-spore-forming, microaerophilic and fructose-6-phosphate phosphoketolase positive strains were isolated from a faecal sample of an adult subject of the emperor tamarin (Saguinus imperator). Given that the isolates revealed identical BOX PCR profiles, strain TRI 5T was selected as a representative and characterized further. Comparative analysis of 16S rRNA gene sequence similarity revealed that strain TRI 5T was closely related to Bifidobacterium saguini DSM 23967T (96.4 %) and to Bifidobacterium longum subsp. longum ATCC 15708 (96.2 %). Multilocus sequence analyses of five housekeeping genes showed the close phylogenetic relatedness of this strain to Bifidobacterium breve DSM 20213T (hsp60 94.1 %), Bifidobacterium saguini DSM 23967T (clpC 91 %), Bifidobacterium avesanii DSM 100685T (dnaG 80.3 %), Bifidobacterium longum subsp. infantis ATCC 15697T (dnaJ 85.3 %) and Bifidobacterium longum subsp. longum ATCC 15708 (rpoB 93 %), respectively. The peptidoglycan type was A3β, with an interpeptide bridge comprising l-Orn (Lys) – l-Ser – l-Ala – l-Thr – l-Ala. The DNA G+C content of strain TRI 5T was 60.9 mol%. Based on the data provided, strain TRI 5T represents a novel species of the genus Bifidobacterium for which the name Bifidobacterium callitrichidarum sp. nov. is proposed. The type strain is TRI 5T (=DSM 103152T=JCM 31790T).

An actinomycete strain, designated KLBMP S0039T, was isolated from the rhizosphere soil of Lycium Linn., collected from the coastal region in Lianyungang, Jiangsu Province, eastern PR China, and was studied to determine its taxonomic position. The isolate showed a combination of morphological and chemotaxonomic properties typical of the members of the genus Nocardia . The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were galactose, arabinose, glucose and ribose. The predominant menaquinone was identified as MK-8(H4ω-cycl). The diagnostic phospholipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and unknown lipids. The predominant cellular fatty acids were identified as C16 : 0, C18 : 0, C18 : 1ω9c, and 10-methyl C18 : 0 [tuberculostearic acid (TBSA)]. The G+C content of the genomic DNA was determined to be 68.2 mol%. The 16S rRNA gene sequence similarity indicated that KLBMP S0039T was most closely related to Nocardia neocaledoniensis NBRC 108232T (99.4 % 16S rRNA gene sequence similarity) and Nocardia asteroides NBRC 15531T (99.2 %), similarities to other type strains of species of the genus Nocardia were found to be less than 98.6 %. However, DNA–DNA relatedness values and phenotypic data indicated that KLBMP S0039T could be clearly distinguished from the closely related species of the genus Nocardia . On the basis of polyphasic taxonomic data, it is concluded that KLBMP S0039T represents a novel species of the genus Nocardia , for which the name Nocardia rhizosphaerihabitans sp. nov. is proposed. The type strain is KLBMP S0039T (=KCTC 39693T=CGMCC 4.7329T).

A Gram-stain-positive, rod-shaped, non-motile bacterial strain, designated JW-1T, was isolated from activated sludge collected from the outlet of an aeration tank in a prometryn-manufacturing plant, located in Binzhou City, Shandong province, PR China. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain JW-1T belongs to the genus Leucobacter and its closest neighbours are ‘ Leucobacter kyeonggiensis ’ F3-P9 (98.95 % similarity), Leucobacter celer subsp . astrifaciens CBX151T (98.62 %), Leucobacter celer subsp . celer NAL101T (98.53 %), Leucobacter chromiiresistens JG31T (97.86 %) and Leucobacter chironomi DSM 19883T (97.37 %). DNA–DNA hybridization values with the above strains were <55 %. The DNA G+C content of strain JW-1T was 72.6 mol%. The major fatty acids of strain JW-1T were iso-C16 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipid. The predominant menaquinone was MK-11. The cell wall amino acids were 2,4-diaminobutyric acid, alanine, glutamic acid, glycine and threonine. Based on the molecular and chemotaxonomic data, as well as the physiological and biochemical characteristics, strain JW-1T is considered to represent a novel species of the genus Leucobacter , for which the name Leucobacter triazinivorans is proposed. The type strain is JW-1T (=DSM 105188T=LMG 30083T).

Strains SYSU D8007T and SYSU D8014T were isolated from desert soil collected from Saudi Arabia. The two isolates were Gram-stain-positive, non-motile, aerobic and non-spore-forming. These strains were able to grow at 4–45 °C and in the presence of up to 8 % (w/v) NaCl. Strain SYSU D8007T could grow at pH 6.0–10.0, and strain SYSU D8014T at pH 5.0–10.0. They shared highest 16S rRNA gene sequence similarities with Microbacterium marinilacus YM11-607T and Microbacterium paludicola US15T. Menaquinones MK-11 and MK-12 were detected as the respiratory quinones. The polar lipid profiles of strains SYSU D8007T and SYSU D8014T consisted of diphosphatidylglycerol and phosphatidylglycerol, but differed in the number of unidentified glycolipids. Strain SYSU D8007T contained anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as the predominant fatty acids, while strain SYSU D8014T contained anteiso-C15 : 0 and anteiso-C17 : 0 as the major fatty acids (>10 %). While glucose, rhamnose and ribose were detected in strain SYSU D8007T as the whole-cell sugars, galactose, glucose and rhamnose were present in strain SYSU D8014T. The genomic DNA G+C content of strains SYSU D8007T and SYSU D8014T was 72.2 and 73.6 mol%, respectively. Based on phenotypic, genotypic and phylogenetic characteristics, it can be concluded that strains SYSU D8007T and SYSU D8014T represent two novel species of the genus Microbacterium , for which the names Microbacterium album sp. nov. and Microbacterium deserti sp. nov. are proposed, respectively. The type strains are SYSU D8007T (=CGMCC 1.15794T=KCTC 39990T) and SYSU D8014T (=CPCC 204619T=KCTC39991T).

Two actinomycete strains, NEAU-C11T and NEAU-C8, isolated from rhizosphere soil and wheat root, respectively, collected from Langfang, Hebei Province, China. A polyphasic study was carried out to establish the taxonomic position of the two strains. Morphological and chemotaxonomic characteristics of the isolates coincided with the genus Glycomyces . Sequences analysis of the 16S rRNA gene also showed that the organisms belong to the genus Glycomyces and Glycomyces algeriensis is the highest sequence match for both strains. Furthermore, a combination of DNA–DNA hybridization results and some differential physiological and biochemical properties indicated that they were distinguishable from the phylogenetically closest relatives. Therefore, the two strains represent a novel species, for which the name Glycomyces rhizosphaerae sp. nov. is proposed. The type strain is NEAU-C11T (=CGMCC 4.7396T=DSM 104646T).

Although the genus Clavibacter was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2γ diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, Clavibacter michiganensis , has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA–DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the C. michiganensis subspecies to species status. On the basis of whole genome and MLSA data, we propose the establishment of two new species and three new combinations: Clavibacter capsici sp. nov., comb. nov. and Clavibacter tessellarius sp. nov., comb. nov., and Clavibacter insidiosus comb. nov., Clavibacter nebraskensis comb. nov. and Clavibacter sepedonicus comb. nov.

A Gram-stain-positive, rod-shaped, non-motile bacterium, strain PRD07T, was isolated from Godavari river, India during the world’s largest spiritual and religious mass bathing event ‘Kumbh Mela’. Molecular analysis using 16S rRNA gene sequencing and phylogenetic analysis reveals the distinct phylogenetic positioning of strain PRD07T within the genus Corynebacterium . The strain demonstrated highest sequence similarity to Corynebacterium imitans DSM 44264T (97.9 %), Corynebacterium appendicis DSM 44531T (97.1 %) and <96.7 % with all other members of the genus Corynebacterium . The G+C content of PRD07T was 68.5 mol% (Tm) and the DNA–DNA hybridization depicts 61.09 % genomic relatedness with C. imitans DSM 44264T. Chemotaxonomic assessment of strain PRD07T suggested presence of C16 : 0 (31.6 %), C18 : 0 (3.5 %) and C18 : 1ω9c (58.6 %) as the major cellular fatty acids. The major polar lipids of strain PRD07T were phosphatidylglycerol, diphosphatidylglycerol and glycophospholipid. Differentiating molecular, phylogenetic and chemotaxonomic characteristics of strain PRD07T with its closest relatives necessitated the description of strain PRD07T as a novel species of genus Corynebacterium for which the name Corynebacterium godavarianum sp. nov., has been proposed. The type strain is PRD07T (=MCC 3388T=KCTC 39803T=LMG 29598T).

Two actinobacterial isolates, strains SG15T and SGB14T, were recovered through a microbial diversity study of nitrogen fixing nodules from Pisum sativum plants collected in Salamanca (Spain). The taxonomic status of these isolates was determined using a polyphasic approach and both presented chemotaxonomic and morphological properties consistent with their classification in the genus Micromonospora . For strains SG15T and SGB14T, the highest 16S rRNA gene sequence similarities were observed with Micromonospora coxensis JCM 13248T (99.2 %) and Micromonospora purpureochromogenes DSM 43821T (99.4 %), respectively. However, strains SG15T and SGB14T were readily distinguished from their phylogenetic neighbours both genetically and phenotypically indicating that they represent two new Micromonospora species. The following names are proposed for these species: Micromonospora phytophila sp. nov. type strain SG15T (=CECT 9369T; =DSM 105363T), and Micromonospora luteiviridis sp. nov. type strain SGB14T (=CECT 9370T; =DSM 105362T).

A novel actinomycete strain PS42-9T, which formed short chains of spores borne on the tip of long sporophores arising from the substrate mycelium, was isolated from soil in Phu-Sang National Park, Phayao province, Thailand. The isolate contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The whole-cell sugars of strain PS42-9T were glucose, madurose, mannose, rhamnose and ribose. The characteristic phospholipids were phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine and ninhydrin-positive glycophospholipids. The major menaquinone was MK-10(H4). The main cellular fatty acids were C17 : 1ω8c and C17 : 0. The G+C content of the genomic DNA was 71.5 mol%. Phylogenetic analysis using 16S rRNA gene sequences revealed that strain PS42-9T should be classified in the genus Herbidospora and was closely related to Herbidospora sakaeratensis DMKUA 205T (99.10 %) and Herbidospora yilanensis NBRC 106371T (98.61 %). The result of DNA–DNA hybridization and some physiological and biochemical properties indicated that strain PS42-9T could be readily distinguished from its closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, this strain represents a novel species, for which the name Herbidospora soli sp. nov. is proposed. The type strain is PS42-9T (=BCC 46909T=NBRC 108780T).

The species within the Mycobacterium tuberculosis Complex (MTBC) have undergone numerous taxonomic and nomenclatural changes, leaving the true structure of the MTBC in doubt. We used next-generation sequencing (NGS), digital DNA–DNA hybridization (dDDH), and average nucleotide identity (ANI) to investigate the relationship between these species. The type strains of Mycobacterium africanum , Mycobacterium bovis , Mycobacterium caprae , Mycobacterium microti and Mycobacterium pinnipedii were sequenced via NGS. Pairwise dDDH and ANI comparisons between these, previously sequenced MTBC type strain genomes (including ‘Mycobacterium canettii’, ‘Mycobacterium mungi’ and ‘Mycobacterium orygis’) and M. tuberculosis H37RvT were performed. Further, all available genome sequences in GenBank for species in or putatively in the MTBC were compared to H37RvT. Pairwise results indicated that all of the type strains of the species are extremely closely related to each other (dDDH: 91.2–99.2 %, ANI: 99.21–99.92 %), greatly exceeding the respective species delineation thresholds, thus indicating that they belong to the same species. Results from the GenBank genomes indicate that all the strains examined are within the circumscription of H37RvT (dDDH: 83.5–100 %). We, therefore, formally propose a union of the species of the MTBC as M. tuberculosis . M. africanum , M. bovis , M. caprae , M. microti and M. pinnipedii are reclassified as later heterotypic synonyms of M. tuberculosis . ‘M. canettii’, ‘M. mungi’, and ‘M. orygis’ are classified as strains of the species M. tuberculosis . We further recommend use of the infrasubspecific term ‘variant’ (‘var.’) and infrasubspecific designations that generally retain the historical nomenclature associated with the groups or otherwise convey such characteristics, e.g. M. tuberculosis var. bovis.

Roseoflavin is the only known riboflavin (vitamin B2) analog with antibiotic properties. It is actively taken up by many micro-organisms and targets flavinmononucleotide riboswitches and flavoproteins. It is described as the product of the tentatively named ‘ Streptomyces davawensis’ JCM 4913. Taxonomic analysis of this strain with a polyphasic approach showed that it is very closely related to Streptomyces cinnabarinus (DSM 40467). The two Streptomyces isolates were obtained from different geographical locations (the Philippines and the Kamchatka Peninsula, respectively), their genomes have been sequenced and the question was whether or not the two isolates were representatives of the same species. As we also worked with another isolate of Streptomyces cinnabarinus JS 360, the producer of the cinnabaramides, we wanted to clarify the taxonomic position of the three isolates by using a polyphasic approach. After analysis of the 16S rRNA gene sequence, we found in total 23 species of the genus Streptomyces that showed a similarity higher than 98.5 % to the three strains. We showed that ‘S. davawensis’ JCM 4913 and S. cinnabarinus DSM 40467 were very closely related but belong to two different species. Hence, we validate ‘S. davawensis’ as Streptomyces davaonensis sp. nov. with the type strain JCM 4913T (=DSM 101723T). In addition, the cinnabaramide producer can be clearly differentiated from S. davaonensis and this isolate is described as Streptomyces cinnabarigriseus sp. nov. with strain JS360T (=NCCB 100590T=DSM 101724T) as the type strain.

A novel extremely halophilic archaeon, designated SAH-A6T, was isolated from a sample of commercial rock salt in Ethiopia. Cells of SAH-A6T were aerobic and pleomorphic. The strain was able to grow at concentrations of 15–30 % (w/v) NaCl (optimum 20–25 % NaCl), at pH 6.0–9.0 (optimum pH 7.0) and in a temperature range of 30–55 °C (optimum 37–45 °C). Mg2+ was not required for growth of SAH-A6T cells. On the basis of 16S rRNA gene sequence analysis, strain SAH-A6T was closely related to Halorubrum halodurans Cb34T (99.1 %), Halorubrum rubrum YC87T (98.9 %), Halorubrum aquaticum EN-2T (98.7 %), Halorubrum cibi JCM 15757T (98.4 %), Halorubrum luteum CGSA15T (97.3 %), Halorubrum lipolyticum 9-3T (97.1 %), Halorubrum tibetense 8W8T (97.1 %), Halorubrum kocurii JCM 1478T (97.1 %), Halorubrum halophilum B8T (97.0 %) and Halorubrum persicum C49T (97.0 %). Phylogenetic analysis based on the rpoB' gene sequences showed that strain SAH-A6T was closely related to Hrr. halodurans Cb34T (99.7 %), Hrr. aquaticum JCM 14031T (99.3 %) and other members of the genus Halorubrum (<99.0 %). The DNA G+C content of the strain was 68.0 mol%. DNA–DNA hybridization between strain SAH-A6T and the most closely related members of the genus Halorubrum were below 55 %, suggesting that the new isolate constitutes a different genospecies. On the bases of chemotaxonomic, phenotypic and genotypic data, strain SAH-A6T (=KCCM 43215T=JCM 31519T) represents a novel species of the genus Halorubrum , for which the name Halorubrum aethiopicum sp. nov. is proposed.

A Gram-stain-negative, oval-shaped and light pink pigmented bacterium, designated XAAS-2T, was isolated from rhizosphere soil of Tamarix ramosissima. The sole respiratory quinone of the type strain XAAS-2T was MK-7, and the principal cellular fatty acids were summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and iso-C15 : 0. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. 16S rRNA gene sequence analysis indicated that strain XAAS-2T belonged to the genus Pontibacter within the family Cytophagaceae with sequence similarities of 93.9–97.1 % to other type species of the genus Pontibacter and to Pontibacter xinjiangensis CCTCC AB 207200T as the closest neighbour. The DNA G+C content of strain XAAS-2T was 50.6 mol%. The level of DNA–DNA relatedness of XAAS-2T and P. xinjiangensis CCTCC AB 207200T was 47.5 % (sd=3.27). Phenotypic and genotypic data suggested that strain XAAS-2T represents a novel species of the genus Pontibacter , for which the name Pontibacter brevis sp. nov. is proposed, with the type strain XAAS-2T (=CCTCC AB 2016135T=JCM 31443T).