- Volume 70, Issue 1, 2020

Strain KUDC5002T was isolated from soil sampled on the Dokdo Islands, Republic of Korea. This bacterial strain was Gram stain-positive, non-motile, rod-shaped, capable of growing at 25–37°C and pH 5.0–12.0, and showed optimal growth at 30 °C and pH 7.0–8.0. Strain KUDC5002T could be grown in tryptic soy broth containing less than 7.0 % NaCl (w/v). The cell width ranged from 0.5 to 0.6 µm and length ranged from 0.8 to 1.0 µm. Strain KUDC5002T was catalase- and oxidase-positive. Its genomic G+C content was 72.2 mol%. Its major fatty acids were C18 : 1 ω9c (17.3 %), iso-C16 : 0 (16.0 %) and iso-C17 : 0 (11.4 %). Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain KUDC5002T belongs to the genus Nocardioides and is most closely related to strain Nocardioides humi DCY24T (97.0 %). Based on its phenotypic, phylogenetic, genetic and chemotaxonomic features, strain KUDC5002T should be considered a novel species in the genus Nocardioides , for which we have proposed the name Nocardioides sambongensis sp. nov. The type strain is KUDC5002T (=KCTC 39855T=DSM 106604T).

Two previously undescribed, Gram-stain-positive, rod-shaped strains, 410T and 553, were isolated from faeces of the Tibetan antelope (Pantholops hodgsonii) from the Tibet-Qinghai Plateau, PR China. The optimum growth conditions of the two novel strains were 1 % (w/v) NaCl, 37 °C and pH 7. The end products from glucose fermentation included ethanol and lactic acid. Based on results of 16S rRNA gene sequence comparison and phylogenetic and phylogenomic analyses, strains 410T and 553 were classified into the genus Actinomyces , and were closely related to Actinomyces ruminicola (97.6 %), Actinomyces oricola (93.5 %) and Actinomyces dentalis (90.8 %). The genomic G+C content of strain 410T was 67.4 mol%. Digital DNA–DNA hybridization values between strain 410T and each of the closely related species were under 70 %. The respiratory quinones were MK-10 (68 %) and MK-9 (32 %). The main cellular fatty acids of the isolates were C16 : 0, followed by C18 : 1 ω9c. The major polar lipids were diphosphatidylglycerol and phosphatidylinositol-mannoside. The whole-cell sugars contained rhamnose, ribose and glucose. The diagnostic amino acids of cell-wall peptidoglycan included alanine, glutamic acid, lysine and ornithine. The results of biochemical, chemotaxonomic and genotypic analyses revealed that the two novel strains represent a novel species of genus Actinomyces , for which the name Actinomyce s qiguomingii sp. nov. is proposed. The type strain is 410T (=CGMCC 1.16361T= DSM 106201T).

A Gram-stain-positive, aerobic, non-motile, rod-shaped actinobacterium, designated strain 21Sc5-5T, was isolated from a soil sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China and investigated by using a polyphasic approach. Strain 21Sc5-5T grew at 10–37 °C (optimum, 28–30 °C), pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 0–3 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain 21Sc5-5T formed a distinct lineage within the genus Nocardioides and had the highest similarity to Nocardioides albidus THG-S11.7T (97.30 %), followed by Nocardioides kongjuensis A2-4T (97.22 %), Nocardioides nitrophenolicus NSP 41T (97.15 %) and Nocardioides caeni MN8T (97.15 %). The results of chemotaxonomic analyses showed that the isolate possessed ll-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan and MK-8(H4) as the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and three unidentified lipids. The major fatty acids were iso-C16 : 0 and 10-methyl C18 : 0. The genome length of strain 21Sc5-5T was 4.67 Mb containing 372 contigs and with a DNA G+C content of 70.4 mol%. On the basis of data from phylogenetic, phenotypic and chemotaxonomic analyses, strain 21Sc5-5T represents a novel species of the genus Nocardioides , for which the name Nocardioides vastitatis sp. nov. is proposed. The type strain is 21Sc5-5T (=JCM 33365T=CGMCC 4.7608T).

Auritidibacter ignavus is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from Auritidibacter ignavus IMMIB L-1656T (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a novel species of the genus Auritidibacter . Auritidibacter ignavus DSM 45359T (=IMMIB L-1656T) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with A. ignavus DSM 45359T by WGS (ANIb scores >98 %), MALDI-TOF (Bruker), cellular fatty acid analysis and biochemically (some differences were observed). A nearly full 16S rRNA gene sequence could not be readily prepared from A. ignavus DSM 45359T, even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of A. ignavus DSM 45359T had only 97.5 % similarity to that of A. ignavus IMMIB L-1656T, implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus Auritidibacter were consistent with A. ignavus DSM 45359T, did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, A. ignavus DSM 45359T had genome of 2.53×106 bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59×106 bp with DNA G+C contents of 59.3–59.52 %. A. ignavus NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. Emendation of Auritidibacter ignavus was proposed based on these results.

A genome-based phylogeny of the publicly available genomes of the genus Nocardiopsis reveals that Nocardiopsis baichengensis YIM 90130T is closely related to Nocardiopsis halophila DSM 44494T. Overall genome relatedness indices between the genomes of the two species were above the threshold values necessary for defining a new species (dDDH, 82.9 %; ANIb, 97.8 %; ANIm, 98.3 %; AAI, 97.7 %). Both species showed a similar G+C content of 73.6 mol% in their genomes. Considering the high similarity between the genomes of the two species, we propose that Nocardiopsis baichengesis Li et al. 2006 should be reclassified as a later heterotypic synonym of Nocardiopsis halophila Al-Tai and Ruan 1994.

A Gram-positive, aerobic, non-spore-forming, non-pigmented and non-motile actinobacterial strain was isolated from a soil sample collected in Guangzhou, China. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain 130T is most closely related to the type strain Nocardioides iriomotensis NBRC 105384T, with a sequence similarity of 97.69 %. The isolate was distinguished from this phylogenetically related type strain by DNA–DNA hybridization (33.3 %), digital DNA–DNA hybridization (21.2 %), average nucleotide identity (75.7 %) and by a range of physiological and biochemical characteristics. Strain 130T contained MK-8(H4) and MK-7 as the major menaquinones, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol as the main polar lipids, and iso-C16 : 0, C17 : 1ω8c, anteiso-C17 : 0, C18 : 1ω9c, C17 : 0 and iso-C14 : 0 as the major cellular fatty acids. The novel strain grew at 20–36 °C, at pH 6.0–8.0 and in the presence of 0–6 % (w/v) NaCl. The genomic DNA G+C content was 72.9 mol%. The genome contained 4817 putative protein-coding sequences, and 45 tRNA and three rRNA genes. Phylogenomic analysis confirmed that strain 130T belongs to the genus Nocardioides and distinguished it from recognized Nocardioides species with available genomes. Based on these polyphasic taxonomic data, strain 130T represents a new species of the genus Nocardioides , for which the name Nocardioides guangzhouensis sp. nov. is proposed. The type strain is 130T (=CICC 24668T=JCM 33269T).

A novel actinobacterial strain, designated SYSU K10008T, was isolated from a soil sample collected from a karst cave in Xingyi County, Guizhou Province, south-western PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and the results of phylogenetic analysis, strain SYSU K10008T was most closely related to Streptomyces cyaneus CGMCC 4.1671T, and shared the highest sequence identity of 98.3 % based on the NCBI database. In addition, ll-diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were glucose and rhamnose. The major isoprenoid quinone was MK-9(H6), while the major fatty acids (>10 %) were C16 : 0, iso-C16 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16  : 1 ω6c). The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10008T was 70.5 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10008T represents a novel species of the genus Streptomyces , for which the name Streptomyces cavernae sp. nov. is proposed. The type strain is SYSU K10008T (=KCTC 39850T=DSM 104115T).

Two novel Actinobacteria , designated strains NEAU-YY421T and NEAU-YY642T, were isolated from the rhizosphere soil of wheat (Triticum aestivum L.) collected from Zhumadian, Henan Province, PR China and characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains NEAU-YY421T and NEAU-YY642T belonged to the genus Streptomyces and strain NEAU-YY421T was most closely related to Streptomyces fumanus CGMCC 4.1732T (97.9 % sequence similarity) and Streptomyces naganishii DSM 40282T (97.8 %), and that of strain NEAU-YY642T to Streptomyces zhaozhouensis LZS-5T (98.0 %) and Streptomyces sedi YIM 65188T (97.5 %). The cell walls of the two strains contained ll-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysates were glucose and ribose. Multilocus sequence analysis using the concatenated sequences of the atp D, gyr B, rec A, rpo B and trp B genes showed that the two strains formed separate branches in the genus Streptomyces . Moreover, a combination of DNA–DNA hybridization results and cultural and physiological properties indicated that the two strains can be distinguished from their closest phylogenetic relatives. Therefore, strains NEAU-YY421T and NEAU-YY642T belong to two novel species in the genus Streptomyces , for which the names Streptomyces triticagri sp. nov. (NEAU-YY421T=CGMCC 4.7476T=DSM 106775T) and Streptomyces triticirhizae sp. nov. (NEAU-YY642T=CCTCC AA 2018092T=DSM 107172T) are proposed, respectively.

A novel actinomycete, designated strain NEAU-HEGS1-5T, was isolated from the ear of wheat (Triticum aestivum L.) and characterized using a polyphasic approach. The morphological and chemotaxonomic characteristics of the strain coincided with those of members of the genus Microbispora . The results of 16S rRNA gene sequence analysis showed that the isolate was most closely related to Microbispora bryophytorum NEAU-TX2-2T (99.3 %), Microbispora camponoti 2C-HV3T (99.2 %), Microbispora amethystogenes JCM 3021T (99.1 %) and Microbispora rosea subsp. rosea JCM 3006T (98.5 %). However, two tree-making algorithms supported the position that strain NEAU-HEGS1-5T formed a distinct clade with M. bryophytorum NEAU-TX2-2T, M. camponoti 2C-HV3T and M. rosea subsp . rosea JCM 3006T. Furthermore, multilocus sequence analysis based on the 16S-gyr B-rpo B genes and a combination of DNA–DNA hybridization results and some physiological and biochemical properties demonstrated that the strain could be distinguished from its closest relatives. Therefore, it is proposed that strain NEAU-HEGS1-5T should be classified as representative of a novel species of the genus Microbispora , for which the name Microbispora fusca sp. nov. is proposed. The type strain is NEAU-HEGS1-5T (=CCTCC AA 2019030T=DSM 104648T).

A Gram-stain-positive bacterial strain, designated LMM-1653T, was isolated from a uterus swab from a Holstein Frisian dairy cow in the frame of a clinical sampling trial. The isolated strain, which showed a rod to coccoid shape, was catalase-positive and oxidase-negative. Based on 16S rRNA gene sequence similarity, its closest relatives were Corynebacterium flavescens and Corynebacterium argatoratense (96.50 % similarity each), suggesting that this isolate represents a novel species. Strain LMM-1653T had a quinone system consisting mainly of menaquinones MK-8(H2) and MK-9(H2). The polar lipid profile showed presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol-mannoside as well as one unidentified glycolipid and one unidentified aminoglycolipid. Moderate to minor amounts of three unidentified glycolipids, β-gentiobiosyl diacylglycerol, one unidentified aminoglycolipid and three unidentified lipids without a functional group were also found. The cell wall contained meso-diaminopimelic acid and the strain also contained corynemycolic acids. The fatty acid profile was predominantly composed of straight-chain, saturated and mono-unsaturated fatty acids, dominated by C18 : 1ω9c and C16 : 0. Since this isolate differs from the nearest related established Corynebacterium species in its genetic and phenotypic traits, a novel species named Corynebacterium endometrii LMM-1653T (=LMG-31164T=CCM 8952T) of the genus Corynebacterium is proposed.

A novel actinomycete strain, Bv016T, belonging to the genus Streptomyces , was isolated from the bark of tree, Bauhinia variegata Linn., collected in Thailand. The taxonomic position of the strain was characterized by using a polyphasic approach. ll-Diaminopimelic acid, glucose, mannose, ribose and galactose were detected in its whole-cell hydrolysates. The N-acyl type of muramic acid was acetyl. The strain contained anteiso-C15  :  0, iso-C16  :  0, iso-C15  :  0 and iso-C14  :  0 as the major fatty acids and MK-9(H8), MK-9(H6) and MK-9(H4) as the major menaquinones. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The strain was closely related to Streptomyces griseoluteus JCM 4041T (98.4 %), Streptomyces seoulensis JCM 10116T (98.4 %) and Streptomyces recifensis JCM 4408T (98.2 %). The draft genome of Bv016T was 6.74 Mb with 5949 coding sequences with an average G+C content of 71.7 mol%. The ANIb and ANIm values of strain Bv016T were 94.1 and 95.2 %, respectively, and the digital DNA–DNA hybridization value was 60.6 % in comparison with the draft genome of S. griseoluteus JCM 4765T. The results of the taxonomic analysis suggested that strain Bv016T represented a novel species of the genus Streptomyces for which the name Streptomyces bauhiniae sp. nov. is proposed. The type strain is Bv016T (=JCM 33208T=TISTR 2645T).

An isolate, 13K206T, with typical morphological characteristics of the genus Micromonospora was obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliation of the strain. The strain showed chemotaxonomical properties consistent with its classification in the genus Micromonospora such as meso- and 3-OH-A2pm in the cell-wall peptidoglycan, xylose in whole-cell hydrolysate and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain was closely related to ‘ Micromonospora spongicola ’ S3-1T, Micromonospora nigra DSM 43818T and Micromonospora yasonensis DS3186T with sequence similarities of 98.6, 98.5 and 98.4 %, respectively. Digital DNA–DNA hybridization and average nucleotide identity analyses in addition to gyrB gene analysis confirmed the assignment of the strain to a novel species within the genus Micromonospora for which the name Micromonospora deserti sp. nov. is proposed. The type strain is 13K206T (=JCM 32583T=DSM 107532T). The DNA G+C content of the type strain is 72.4 mol%.

A Gram-strain positive, mycelium-forming actinomycete, YIM 121212T, was isolated from an alkaline soil sample collected in Yunnan province, PR China. Classification using a polyphasic approach indicated that YIM 121212T represents a member of the genus Prauserella , and is closely related to Prauserella coralliicola SCSIO 11529T (99.31 %), Prauserella endophytica SP28S-3T (99.17 %), Prauserella soli 12-833T (97.43 %), Prauserella oleivorans RIPIT (97.03 %), Prauserella marina MS498T (96.74 %), Prauserella rugosa DSM 43194T (96.54 %) and Prauserella muralis 05-Be-005T (95.92 %). Average nucleotide identity values (ANI) of YIM 121212T to P. coralliicola DSM 45821T and P. endophytica CGMCC 4.7182T were 93.1 and 92.8 %, respectively, which were lower than the threshold of 95 %. The digital DNA–DNA hybridization (dDDH) values between YIM 121212T and these two species were 50.8 and 49.9 %, respectively and thus were also well below the cut off value (>70 %) for species delineation. The DNA G+C content of YIM 121212T is 70.8 mol%. Major fatty acids are iso-C16 : 0, iso-C16 : 1H, C16 : 1ω7c/iso-C15 : 0 2OH, C17 : 1ω6c, and C17 : 1ω8c. The predominant menaquinone is MK-9(H4). The polar lipid profile consists of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylmethylethanolamine (PME), phosphatidylinositol (PI), and phosphatidylinositol mannoside (PIM). The draft genomes were further analyzed for the presence of secondary metabolite biosynthesis (SMB) gene clusters. On the basis of the above observations, YIM121212T can be distinguished from closely related species belonging to the genus Prauserella . Thus, YIM121212T represents a novel species of the genus Prauserella , for which the name Prauserella flavalba sp. nov. is proposed. The type strain is YIM121212T (=CCTCC AA 2013011T=DSM 45973T).

A novel actinobacterium, designated strain NEAU-C40T, was isolated from the rhizosphere soil of rice (Oryza sativa L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and was characterized using a polyphasic approach. On the basis of results of 16S rRNA gene sequence analysis, strain NEAU-C40T belongs to the genus Streptomyces , and shares highest sequence similarities with Streptomyces polygonati CGMCC 4.7237T (97.9%) and Streptomyces abietis DSM 42080T (97.9%). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Streptomyces . Cell walls contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose, rhamnose and ribose. The major menaquinones were identified as MK-9(H8) and MK-9(H6). The major fatty acids were iso-C16:0, anteiso-C15:0, C16:0 and anteiso-C17:0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and an unidentified lipid. The genomic DNA G+C content of strain NEAU-C40T was 71.8 mol%. Moreover, multilocus sequence analysis based on five other housekeeping genes (atp D, gyr B, rpo B, rec A and trp B) and the low level of DNA–DNA relatedness allowed the isolate to be differentiated from its most closely related strains. On the basis of phenotypic, genotypic and phylogenetic data, strain NEAU-C40T can be characterized to represent a novel species of the genus Streptomyces , for which the name Streptomyces oryziradicis sp. nov. is proposed. The type strain is NEAU-C40T (=DSM 107943T=CCTCC AA 2018038T).

A novel actinobacterial strain, designated NEAU-LL90T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, north-east PR China and characterized by using a polyphasic approach. Morphological and chemotaxonomic characteristics were consistent with those members of the genus Nocardia . The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant menaquinone detected was MK-8(H4, ω-cycl). Major fatty acids (>10 %) were identified as C16:0, C18:1ω9c, C18:0 and 10-methyl C19:0. Mycolic acids were present. The results of 16S rRNA gene sequence analysis showed that strain NEAU-LL90T belongs to the genus Nocardia with high sequence similarity to Nocardia niigatensis JCM11894T (98.1 %), similarities to other type strains of species of the genus Nocardia were found to be lower than 98.0 %. Furthermore, a combination of DNA–DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-LL90T could be distinguished from its closest relative. Therefore, it is proposed that strain NEAU-LL90T represents a novel species of the genus Nocardia , for which the name Nocardia stercoris sp. nov. is proposed. The type strain is NEAU-LL90T (=CGMCC 4.7500T=JCM 32663T).

A Gram-stain-positive, aerobic bacterium, designated CPCC 204705T, was isolated from a desert soil sample, collected from the Badain Jaran desert. Growth of strain CPCC 204705T was observed at pH 6.0–8.0 and 15–37 °C, with optimal growth at 28 °C and pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204705T belonged to the genus Cellulomonas , showing the highest similarity (98.54 %) of 16S rRNA gene sequence to Cellulomonas oligotrophica JCM 17534T. The peptidoglycan type was A4β, containing d-ornithine and d-glutamic acids as diagnostic amino acids. Rhamnose and galactose were detected in the whole-cell hydrolysate as diagnostic sugars. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C15 : 1A, C14 : 0 and C16 : 0. The major menaquinone was MK-9 (H4) and the polar lipid system contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, one unidentified lipid, one unidentified aminolipid and two unidentified aminophospholipids. The DNA–DNA hybridization value between strain CPCC 204705T and C. oligotrophica JCM 17534T was 7.1±0.4 %, and the value of average nucleotide identity between these two strains was 79.8 %. The DNA G+C content of strain CPCC 204705T was 75.4 mol%. Based on the results of physiological experiments, chemotaxonomic data, phylogenetic analysis and DNA–DNA hybridization value, strain CPCC 204705T should be classified as a novel Cellulomonas species. The name Cellulomonas telluris sp. nov. is proposed, with strain CPCC 204705T (=DSM 105430T=KCTC 39974T) as the type strain.

Five actinobacteria isolates, KC201T, KC401, KC310T, KC712T and 6K102T, were recovered from the Karakum Desert during an investigation of novel actinobacteria with biotechnological potential. A polyphasic approach confirmed the affiliation of the strains to the genus Nonomuraea . The strains showed chemotaxonomic and morphological properties consistent with their classification in the genus Nonomuraea . Furthermore, these strains clearly distinguished and formed well supperted clades in phylogenetic and phylogenomic trees. Low ANI and dDDH values and distinguishing phenotypic properties between isolates KC201T, KC310T, KC712T and 6K102T showed that these strains belonged to novel Nonomuraea species, the names proposed for these taxa are Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov., with the type strains KC310T (=CGMCC 4.7331T =DSM 102919T =KCTC 39774T), KC712T (=CGMCC 4.7334T =DSM 102925T =KCTC 39776), KC201T (=CGMCC 4.7339T =DSM 102917T =KCTC 39781T) and 6K102T (=CGMCC 4.7541T =JCM 32916), respectively.