scholarly journals Streptomyces cahuitamycinicus sp. nov., isolated from desert soil and reclassification of Streptomyces galilaeus as a later heterotypic synonym of Streptomyces bobili

2020 ◽  
Vol 70 (4) ◽  
pp. 2750-2759 ◽  
Author(s):  
Hayrettin Saygin ◽  
Hilal Ay ◽  
Kiymet Guven ◽  
Demet Cetin ◽  
Nevzat Sahin
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Sequence Similarity ◽  
Single Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A novel actinobacterial strain, designated 13K301T, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. The taxonomic position of strain 13K301T was revealed by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain 13K301T belongs to the genus Streptomyces and had highest sequence similarity to ‘Streptomyces qaidamensis’ S10T (99.2 %), Streptomyces flavovariabilis NRRL B-16367T (98.9 %) and Streptomyces phaeoluteigriseus DSM 41896T (98.8 %), but the strain formed a distinct clade in the phylogenetic tree. The DNA–DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain 13K301T and closely related type strains were significantly lower than the recommended threshold values. The cell wall contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose and ribose. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were determined as the predominant polar lipids. The major menaquinones were identified as MK-9(H8) and MK-9(H6). On the basis of these genotypic and phenotypic data, it is proposed that strain 13K301T should be classified as representative of a novel species of the genus Streptomyces , for which the name Streptomyces cahuitamycinicus sp. nov. is proposed. The type strain is 13K301T (=DSM 106873T=KCTC 49110T). In addition, the whole genome-based comparisons as well as the multilocus sequence analysis revealed that the type strains of Streptomyces galilaeus and Streptomyces bobili belong to a single species. It is, therefore, proposed that S. galilaeus be recognised as a heterotypic synonym of S. bobili for which an emended description is given.

scholarly journals Streptomyces catbensis sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2146-2151 ◽  
Author(s):  
Yayoi Sakiyama ◽  
Nguyen M. Giang ◽  
Shinji Miyadoh ◽  
Dao Thi Luong ◽  
Duong Van Hop ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biochemical Traits ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Physiological And Biochemical

Strain VN07A0015T was isolated from soil collected on Cat Ba Island, Vietnam. The taxonomic position of strain VN07A0015T was near Streptomyces aomiensis M24DS4T (98.5 % 16S rRNA gene sequence similarity) and Streptomyces scabrisporus NBRC 100760T (95.6 %), and it clustered within them; however, this cluster was distant from the type strains of other species of the genus Streptomyces . The aerial mycelia of strain VN07A0015T were greyish and formed imperfect spiral spore chains (retinaculiaperti type) with smooth-surfaced spores. The morphological features of strain VN07A0015T were different from those of the type strains of S. aomiensis and S. scabrisporus . The chemotaxonomic characteristics of strain VN07A0015T were typical for all members of the genus Streptomyces , which possessed ll-type diaminopimelic acid, menaquinone MK-9(H6, H8) and the major fatty acids iso-C16 : 0 and iso-C15 : 0. DNA–DNA relatedness between strain VN07A0015T and S. aomiensis NBRC 106164T was less than 30 %. In addition, some physiological and biochemical traits differed from those of S. aomiensis . Therefore, we propose that strain VN07A0015T be classified in the genus Streptomyces as a representative of Streptomyces catbensis sp. nov. (type strain VN07A0015T = VTCC-A-1889T = NBRC 107860T).

scholarly journals Reclassification of Deinococcus xibeiensis Wang et al. 2010 as a heterotypic synonym of Deinococcus wulumuqiensis Wang et al. 2010

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 1083-1085 ◽  
Author(s):  
Sunhee Hong ◽  
Christine E. Farrance ◽  
Anne Russell ◽  
Hana Yi
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Taxonomic Status ◽  
Single Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Genomic Relatedness

Two species of the genus Deinococcus , namely Deinococcus wulumuqiensis Wang et al. 2010 and Deinococcus xibeiensis Wang et al. 2010, were simultaneously proposed and described in the same publication. However, the identical 16S rRNA gene sequence of the two type strains strongly raised the probability of their relatedness at the species level. Thus, the genomic relatedness of the two species of the genus Deinococcus was investigated here to clarify their taxonomic status. The high (99.9 %) average nucleotide identity (ANI) between the genome sequences of the two type strains suggested that the two species are synonymous. Additional phenotypic data including enzymic activities and substrate-utilization profiles showed no pronounced differences between the type strains of the two species. Data from this study demonstrated that the two taxa constitute a single species. According to Rule 42 of the Bacteriological Code, we propose that D. xibeiensis Wang et al. 2010 should be reclassified as a subjective heterotypic synonym of D. wulumuqiensis Wang et al. 2010.

Streptomyces spirodelae sp. nov., isolated from duckweed

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Yuparat Saimee ◽  
Kannika Duangmal
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid

A novel actinobacterium, designated strain DW4-2T, was isolated from duckweed (Spirodela sp.) collected from an agricultural pond in Kasetsart University, Bangkok, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces . Strain DW4-2T showed the highest 16S rRNA gene sequence similarity values to Streptomyces qinglanensis DSM 42035T (98.5 %), S treptomyces smyrnaeus DSM 42105T (98.4 %) and Streptomyces oryzae S16-07T (98.4 %). Digital DNA–DNA hydridization and average nucleotide identity values between the genome sequences of strain DW4-2T with S. qinglanensis DSM 42035T (29.8 and 87.8 %), S. smyrnaeus DSM 42105T (33.1 and 89.0 %) and S. oryzae S16-07T (33.0 and 88.9 %) were below the thresholds of 70 and 95–96 % for prokaryotic conspecific assignation. Chemotaxonomic data revealed that strain DW4-2T possessed MK-9(H6) and MK-9(H8) as the predominant menaquinones. It contained ll -diaminopimelic acid as the diagnostic diamino acid and glucose, ribose and trace amount of madurose in whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid, an unidentified lipid and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The genomic DNA size of the strain DW4-2T was 7 310 765 bp with DNA G+C content 71.0 mol%. Genomic analysis of the genome indicated that the strain DW4-2T had the potential to produce bioactive compounds. On the basis of these genotypic and phenotypic data, it is supported that strain DW4-2T represents a novel species of the genus Streptomyces , for which the name Streptomyces spirodelae sp. nov. is proposed. The type strain is strain DW4-2T (=TBRC 13095T=NBRC 114803T).

scholarly journals Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1199-1203 ◽  
Author(s):  
Sung-Geun Woo ◽  
Sathiyaraj Srinivasan ◽  
Jihoon Yang ◽  
Yong-An Jung ◽  
Myung Kyum Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Sewage Disposal ◽  
Phenotypic Properties ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Strain MJ31T, a Gram-reaction-positive, aerobic, rod-shaped, non-motile bacterium, was isolated from a sludge sample collected at the Daejeon sewage-disposal plant, in South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MJ31T belonged to the genus Nocardioides , appearing most closely related to Nocardioides dubius KSL-104T (98.6 % sequence similarity), Nocardioides jensenii DSM 20641T (97.6 %), Nocardioides daedukensis MDN22T (97.2 %) and Nocardioides mesophilus MSL-22T (97.0 %). The chemotaxonomic properties of strain MJ31T were consistent with those of the genus Nocardioides : MK-8(H4) was the predominant menaquinone, iso-C16 : 0, iso-C17 : 0 and C18 : 1ω9c were the predominant cellular fatty acids, and the cell-wall peptidoglycan was based on ll-2,6-diaminopimelic acid. The genomic DNA G+C content of strain MJ31T was 71.2 mol%. Some differential phenotypic properties and low DNA–DNA relatedness values (<28 %) with the type strains of closely related species indicated that strain MJ31T represents a novel species, for which the name Nocardioides daejeonensis sp. nov. is proposed. The type strain is MJ31T ( = KCTC 19772T = JCM 16922T).

scholarly journals Nocardioides daecheongensis sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4109-4114 ◽  
Author(s):  
Jun-Muk Lim ◽  
Soo-Jin Kim ◽  
Moriyuki Hamada ◽  
Jae-Hyung Ahn ◽  
Hang-Yeon Weon ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Gene Sequence Analysis ◽  
Type Strains

Strain KIS2-16T was isolated from a soil sample collected from Daecheong Island of Incheon region, South Korea. KIS2-16T was Gram-staining-positive, aerobic, non-spore-forming, non-motile, catalase-positive, oxidase-negative and mesophilic. On the basis of 16S rRNA gene sequence analysis, strain KIS2-16T represented a member of the genus Nocardioides , being most closely related to the type strains of species of the genus Nocardioides , Nocardioides maradonensis RP-B30T (97.8 % sequence similarity) and Nocardioides ultimimeridianus RP-B26T (97.0 %). The fatty acid profile of KIS2-16T was dominated by C18 : 1ω9c, C17 : 1ω8c, C16 : 0, C18 : 0 10-methyl (TBSA), C16 : 0 2-OH and C17 : 0 2-OH. The major isoprenoid quinone was MK-8(H4), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The peptidoglycan structure was A3γ-type with ll-diaminopimelic acid. The genomic DNA G+C content of KIS2-16T was 64.9 mol%. Strain KIS2-16T showed DNA–DNA hybridization values of less than 70 % with the closely related species of the genus Nocardioides . Based on phenotypic, genotypic and phylogenetic data, the isolate represents a novel species of the genus Nocardioides , for which the name Nocardioides daecheongensis sp. nov. (type strain KIS2-16T = DSM 27136T = KACC 17297T = NBRC 109597T) is proposed.

scholarly journals Gordonia iterans sp. nov., isolated from a patient with pneumonia

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3520-3525 ◽  
Author(s):  
Ying-Qian Kang ◽  
Hong Ming ◽  
Tohru Gonoi ◽  
Yuru Chen ◽  
Yu Cao ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A second novel clinical actinobacterial strain, designated IFM 10348T, was isolated from the sputum of the same Japanese patient with bacterial pneumonia from whom the type strain of Gordonia araii had been isolated. The strains differed in phylogenetic position and drug-resistance profiles. The taxonomic position of strain IFM 10348T was clarified by phenotypic, chemotaxonomic and phylogenetic studies. Phylogenetic analyses based on 16S rRNA gene sequences clearly demonstrated that strain IFM 10348T occupied a distinct clade within the genus Gordonia and was related closely to Gordonia malaquae DSM 45064T and Gordonia hirsuta DSM 44140T (97.3 and 97.1 % similarities, respectively). Strain IFM 10348T was also clearly differentiated from G. malaquae DSM 45064T and G. hirsuta DSM 44140T based on gyrB and secA1 gene sequence similarity values. Strain IFM 10348T had MK-9(H2) as the predominant menaquonine, contained meso-diaminopimelic acid, arabinose, galactose and glucosamine as cell-wall components, and contained C18 : 1ω9c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major cellular fatty acids. Mycolic acids were present. The DNA G+C content of strain IFM 10348T was 68.0 mol%. DNA–DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that strain IFM 10348T represents a novel species of the genus Gordonia , for which the name Gordonia iterans sp. nov. is proposed. The type strain is IFM 10348T ( = CCTCC M2011245T = NCCB 100436T).

Streptomyces kebangsaanensis sp. nov., an endophytic actinomycete isolated from an ethnomedicinal plant, which produces phenazine-1-carboxylic acid

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3733-3738 ◽  
Author(s):  
Nurul’ Izzah Mohd Sarmin ◽  
Geok Yuan Annie Tan ◽  
Christopher M. M. Franco ◽  
RuAngelie Edrada-Ebel ◽  
Jalifah Latip ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Ethnomedicinal Plant ◽  
Phyletic Line

A spore-forming streptomycete designated strain SUK12T was isolated from a Malaysian ethnomedicinal plant. Its taxonomic position, established using a polyphasic approach, indicates that it is a novel species of the genus Streptomyces . Morphological and chemical characteristics of the strain were consistent with those of members of the genus Streptomyces . Analysis of the almost complete 16S rRNA gene sequence placed strain SUK12T in the genus Streptomyces where it formed a distinct phyletic line with recognized species of this genus. The strain exhibited highest sequence similarity to Streptomyces corchorusii DSM 40340T (98.2 %) followed by Streptomyces chrestomyceticus NRRL B-3310T (98.1 %). The G+C content of the genomic DNA was 74 mol%. Chemotaxonomic data [MK-9(H8) as the major menaquinone; LL-diaminopimelic acid as a component of cell-wall peptidoglycan; C12 : 0, C14 : 0, C15 : 0 and C17 : 1 as the major fatty acids; phospholipid type II] supported the affiliation of strain SUK12T to the genus Streptomyces . The results of the phylogenetic analysis and phenotypic data derived from this and previous studies allowed the genotypic and phenotypic differentiation of strain SUK12T from the related species of the genus Streptomyces . The DNA–DNA relatedness value between strain SUK12T and S. corchorusii DSM 40340T is 18.85±4.55 %. Strain SUK12T produces phenazine-1-carboxylic acid, known as tubermycin B, an antibacterial agent. It is proposed, therefore, that strain SUK12T ( = DSM 42048T = NRRL B-24860T) be classified in the genus Streptomyces as the type strain of Streptomyces kebangsaanensis sp. nov.

Amycolatopsis magusensis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1254-1260 ◽  
Author(s):  
Mustafa Camas ◽  
Nevzat Sahin ◽  
Anil Sazak ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A novel actinomycete, designated strain KT2025T, was isolated from arid soil collected from Magusa, northern Cyprus. The taxonomic position of the novel strain was established by using a polyphasic approach. The organism had chemical and morphological features consistent with its classification in the genus Amycolatopsis . Phylogenetic analyses based on 16S rRNA gene sequences supported the classification of the isolate in the genus Amycolatopsis and showed that the organism formed a cluster with Amycolatopsis nigrescens CSC17-Ta-90T, Amycolatopsis minnesotensis 32U-2T, Amycolatopsis sacchari DSM 44468T and Amycolatopsis dongchuanensis YIM 75904T. 16S rRNA gene sequence similarity analysis indicated that strain KT2025T was most closely related to Amycolatopsis lurida DSM 43134T (97.5 %), Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409T (97.4 %), Amycolatopsis keratiniphila subsp. nogabecina DSM 44586T (97.1 %), Amycolatopsis nigrescens DSM 44992T (97.1 %), Amycolatopsis azurea DSM 43854T (97.1 %) and Amycolatopsis minnesotensis DSM 44988T (96.9 %). The organism was found to have chemical features typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and hydroxy-phosphatidylethanolamine. The major fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The G+C content of the genomic DNA was 70.8 mol%. Phenotypic data clearly distinguished the isolate from its closest relatives. The combined genotypic and phenotypic data and low levels of DNA–DNA relatedness with its closest relatives indicated that strain KT2025T represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis magusensis sp. nov. is proposed. The type strain is KT2025T ( = DSM 45510T = KCTC 29056T).

scholarly journals Sneathiella aquimaris sp. nov., isolated from aquaculture seawater

2020 ◽  
Vol 70 (6) ◽  
pp. 3824-3831 ◽  
Author(s):  
Guizhen Li ◽  
Qiliang Lai ◽  
Peisheng Yan ◽  
Li Gu ◽  
Zongze Shao
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Type Strains

A novel marine bacterium, designated strain 216LB-ZA1-12T, was isolated from a Penaeus vannamei aquaculture seawater sample. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 216LB-ZA1-12T belonged to the genus Sneathiella , with the highest sequence similarity to Sneathiella glossodoripedis MKT133T (97.7 %), followed by Sneathiella limimaris GH1-24T (97.0 %), Sneathiella chungangensis CAU 1294T (96.6 %) and Sneathiella chinensis LMG 23452T (96.1 %). The average nucleotide identity and the DNA–DNA hybridization estimate values between strain 216LB-ZA1-12T and four close type strains were between 69.2–71.3% and 16.7–17.8 %, respectively. The bacterium was Gram-stain-negative, facultatively anaerobic, oxidase and catalase positive, oval- to rod-shaped, and motile. Growth was observed at pH 7–9, salinities of 1–15% and temperatures of 4–42 °C. The G+C content of the chromosomal DNA was 48.50 mol%. The major respiratory quinone was determined to be Q-10. The principal fatty acids were summed feature 8 (C18 : 1  ω7c/ω6c) and C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and aminophospholipid. The combined genotypic and phenotypic data show that strain 216LB-ZA1-12T represents a novel species within the genus Sneathiella , for which the name Sneathiella aquimaris sp. nov. is proposed, with the type strain 216LB-ZA1-12T (=MCCC 1A14570T=KCTC 72144T).

Friedmanniella flava sp. nov., a soil actinomycete

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1771-1775 ◽  
Author(s):  
Xuefang Zhang ◽  
Jianli Zhang ◽  
Yabo Zhang ◽  
Yuhua Xin ◽  
Hongju He
Keyword(s):  
Type Species ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Chemical Properties ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type

A novel actinomycete, strain W6T, was isolated from a soil sample of Yunnan Province, China. The bacterium was aerobic, non-motile, non-spore-forming and Gram-stain-positive. Genetic, phenotypic and chemical properties of the isolate were studied. 16S rRNA gene sequence data suggested that the novel isolate belonged to the genus Friedmanniella and shared 98.6 % sequence similarity with Friedmanniella antarctica DSM 11053T and Friedmanniella okinawensis DSM 21744T, the most closely related species. The cell-wall peptidoglycan contained ll-diaminopimelic acid, and mycolic acids were absent. The main menaquinone was MK-9(H4) and the predominant fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The phospholipid profile contained phosphatidylglycerol, phosphatidylinositol, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content of strain W6T was 72 mol%. Strain W6T showed 30.0 % and 28.5 % DNA–DNA relatedness, respectively, to F. antarctica DSM 11053T and F. okinawensis DSM 21744T. The combined genotypic and phenotypic data showed that strain W6T should be assigned to the genus Friedmanniella as a representative of a novel species, for which the name Friedmanniella flava sp. nov. is proposed. The type strain is W6T ( = CGMCC 4.6856T = JCM 17701T).

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