scholarly journals Nocardioides nanhaiensis sp. nov., an actinobacterium isolated from a marine sediment sample

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2718-2722 ◽  
Author(s):  
Dao-Feng Zhang ◽  
Jing-Mei Zhong ◽  
Xiao-Mei Zhang ◽  
Zhao Jiang ◽  
En-Min Zhou ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Marine Sediment ◽  
Sediment Sample ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Minor Amount ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample

A rod- to coccus-shaped, non-spore-forming actinobacterium, strain YIM M13091T, was isolated from a marine sediment sample collected from the South China Sea and examined by a polyphasic approach to clarify its taxonomic position. This Gram-staining-positive, aerobic actinobacterium did not produce substrate mycelium and aerial hyphae, and no diffusible pigments were produced on the media tested. The optimum growth occurred at 30 °C, 1 % (w/v) NaCl and pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Nocardioides , with low levels (≤96.2 %) of sequence similarity with respect to Nocardioides kribbensis KSL-2T and other members of the genus Nocardioides . Whole-organism hydrolysates of the strain contained ll-2,6-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4), with MK-8 in a minor amount. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, hydroxyphosphatidylinositol and phosphatidylcholine, were the main polar lipids detected, while iso-C16 : 0 and C18 : 1ω9c were the major fatty acids. The G+C content of the genomic DNA was 68.5 mol%. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a member of the genus Nocardioides , and the name Nocardioides nanhaiensis sp. nov. (Type strain YIM M13091T = JCM 18127T = CCTCC AA 2011020T) is proposed for the novel species.

Gulosibacter sediminis sp. nov., isolated from Indian Ocean marine sediment

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Zhao Jiang ◽  
Wei-Hua Zhang ◽  
Dan Song ◽  
Min Xiao ◽  
Dorji Phurbu ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Marine Sediment ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample ◽  
Unknown Lipid ◽  
Unknown Phospholipid

A novel Gram-stain-positive, catalase-positive, oxidase-negative, aerobic, non-motile, rod-shaped bacterium, designated strain YIM M12148T, was isolated from a marine sediment sample collected from the Indian Ocean. The strain grew optimally at 28 °C, pH 8.0 and in the presence of 1–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M12148T belongs to the genus Gulosibacter , with the highest sequence similarity to Gulosibacter faecalis NBRC 15706T (96.12 %). The cell-wall sugars of strain YIM M12148T were rhamnose, ribose, glucose and mannose. The predominant isoprenoid quinones were MK-8 and MK-9. The polar lipids consisted of major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and one unknown lipid. Major fatty acids (>5 % of the total) of the novel isolate were anteiso-C15 : 0, iso-C15 : 0, iso-C13 : 0 and anteiso-C13 : 0. The genomic DNA G+C content of strain YIM M12148T was 67.15 mol%. On the basis of genotypic and phenotypic data, it is apparent that strain YIM M12148T represents a novel species of the genus Gulosibacter , for which the name Gulosibacter sediminis sp. nov. is proposed. The type strain is YIM M12148T (=KCTC 29660T=DSM 29154T).

Clostridium vitabionis sp. nov., isolated from the large intestine of a mini-pig

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Yeseul Shin ◽  
Jayoung Paek ◽  
Hongik Kim ◽  
Joong-Ki Kook ◽  
Young Hyo Chang
Keyword(s):  
Large Intestine ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Minor Amount ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Clostridium Symbiosum ◽  
A Minor

An obligately anaerobic, Gram-stain-negative, spore-forming, short rod-shaped bacterium, designated strain YH- T4B42T, was isolated from the large intestine of a mini-pig. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Clostridium and is most closely related to Clostridium aminophilum KCTC 5424T, Clostridium symbiosum KCTC 15329T and Clostridium butyricum KCTC 1871T, with 95.5, 92.4 and 83.0 % sequence similarity, respectively. The average nucleotide identity values for strain YH-T4B42T and the closest related strains were lower than 72 %. The G+C content of the isolate was 55.8 mol%. The cell-wall peptidoglycan was A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C16 : 0, C18 : 1 cis 9, C14 : 0 and C18 : 0. The major end products of glucose fermentation were lactate, formate and acetate, with a minor amount of butyrate. Based on its phenotypic, phylogenetic and chemotaxonomic properties, a novel species, Clostridium vitabionis sp. nov., is proposed for strain YH-T4B42T (=KCTC 25105T=NBRC 114767T).

scholarly journals Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3010-3015 ◽  
Author(s):  
Avinash Sharma ◽  
Sunil Kumar Dhar ◽  
Om Prakash ◽  
Venkata Ramana Vemuluri ◽  
Vishal Thite ◽  
...  
Keyword(s):  
Cell Wall ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Marine Sediment Sample

A novel Gram-stain-positive, spore-forming, aerobic, non-motile, rod-shaped bacterium designated strain SD111T that forms red-pigmented colonies was isolated from a marine sediment sample (collected from 5 m depth) from Lakshadweep, India. Strain SD111T grew well on seawater agar at pH 6–10 (optimum pH 7.5±0.2). It showed maximum (97.6 %) 16S rRNA gene sequence similarity and formed a monophyletic clade with Domibacillus robiginosus WS 4628T ( = DSM 25058T). The genomic DNA G+C content was 37.4 mol% and the strain showed 37.7 % DNA–DNA relatedness to D. robiginosus DSM 25058T. The major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and iso-C16 : 0 and MK-6 was the predominant quinone. The polar lipid profile of strain SD111T consisted of unidentified phospholipids (PL1 and PL2), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The cell wall contained meso-diaminopimelic acid and the peptidoglycan was of A1γ type. Glucose and ribose were detected as major cell-wall sugars. Results from polyphasic studies indicated that SD111T represents a novel species of the genus Domibacillus for which the name Domibacillus indicus sp. nov. is proposed. The type strain is SD111T ( = MCC 2255T = DSM 28032T).

scholarly journals Brevibacillus migulae sp. nov., isolated from a Yellow River sediment sample

2020 ◽  
Vol 70 (11) ◽  
pp. 5693-5700 ◽  
Author(s):  
Mingming Niu ◽  
Hong Ming ◽  
Li-jiao Cheng ◽  
Bing-fang Yi ◽  
Ting-ting Xia ◽  
...  
Keyword(s):  
Sediment Sample ◽  
Type Species ◽  
Yellow River ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Pr China

Strain CFH S0501T, a novel Gram-stain-positive, aerobic, rod-shaped, endospore-forming and motile micro-organism with peritrichous flagella, was isolated from a sediment sample collected from the Yellow River in Henan Province, PR China. Optimum growth was observed at 28 °C, pH 7.0 and without NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain belonged to the genus Brevibacillus and was closely related to Brevibacillus centrosporus DSM 8445T and Brevibacillus ginsengisoli Gsoil 3088T (with 96.8 and 96.7 % sequence similarity, respectively). The predominant menaquinone was MK-7. Major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unidentified phospholipids and an unidentified polar lipid. The cell-wall peptidoglycan was found to contain meso-diaminopimelic acid. The genome size was 5.26 Mbp with a G+C content of 49.7 mol%. The average nucleotide identity (ANI) and in silico DNA–DNAhybridization (DDH) values between CFH S0501T and the other species of the genus Brevibacillus were found to be low (ANIm <86.11 %, ANIb <70.30 % and DDH <25.00 %). Based on physiological properties, chemotaxonomic characteristics and low ANI and DDH results, strain CFH S0501T is considered to represent a novel species, for which the name Brevibacillus migulae sp. nov. is proposed. The type strain is CFH S0501T (=DSM 29940T=BCRC 80809T).

scholarly journals Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis)

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1561-1566 ◽  
Author(s):  
Jin-Hua Chen ◽  
Xiang-Rong Tian ◽  
Ying Ruan ◽  
Ling-Ling Yang ◽  
Ze-Qiang He ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Crassostrea Hongkongensis ◽  
Link Type

A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118T, was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118T was able to grow with 0–13 % (w/v) NaCl (optimum 2–5 %), at pH 5.5–10.0 (optimum pH 7.5) and at 5–50 °C (optimum 30–35 °C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and C16 : 1ω11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 100118T belonged to the genus Bacillus , and was most closely related to Bacillus litoralis SW-211T (98.9 % 16S rRNA gene sequence similarity), Bacillus halosaccharovorans E33T (98.3 %), Bacillus niabensis 4T19T (97.8 %) and Bacillus herbersteinensis D-1,5aT (97.1 %). The combination of results from the phylogenetic analysis, DNA–DNA hybridization, and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 100118T represents a novel species of the genus Bacillus , for which the name Bacillus crassostreae sp. nov. is proposed. The type strain is JSM 100118T ( = CCTCC AB 2010452T = DSM 24486T = JCM 17523T).

scholarly journals Rhodococcus enclensis sp. nov., a novel member of the genus Rhodococcus

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2693-2697 ◽  
Author(s):  
Syed G. Dastager ◽  
Rahul Mawlankar ◽  
Shan-Kun Tang ◽  
Srinivasan Krishnamurthi ◽  
V. Venkata Ramana ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel actinobacterial strain, designated, NIO-1009T, was isolated from a marine sediment sample collected from Chorao Island, Goa, India. Phylogenetic analysis comparisons based on 16S rRNA gene sequences between strain NIO-1009T and other members of the genus Rhodococcus revealed that strain NIO-1009T had the closest sequence similarity to Rhodococcus kroppenstedtii DSM 44908T and Rhodococcus corynebacterioides DSM 20151T with 99.2 and 99.1 %, respectively. Furthermore, DNA–DNA hybridization results showed that R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T were 39.5 (3.0 %) and 41.7 (2.0 %) with strain NIO-1009T, respectively, which were well below the 70 % limit for any novel species proposal. Phylogenetically strain NIO-1009T forms a stable clade with and R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T with 100 % bootstrap values. Strain NIO-1009T contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose as the cell wall sugars. The major fatty acids were C16 : 0, C18 : 1ω9c, C16 : 1(ω6c and/or ω7c) and 10-methyl C18 : 0. The only menaquinone detected was MK-8(H2), while the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. The G+C content of the genomic DNA was 66.9 mol%. The phenotypic and genotypic data showed that strain NIO-1009T warrants recognition as a novel species of the genus Rhodococcus for which the name Rhodococcus enclensis sp. nov., is proposed; the type strain is NIO-1009T ( = NCIM 5452T = DSM 45688T).

scholarly journals Bacillus tianshenii sp. nov., isolated from a marine sediment sample

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1998-2002 ◽  
Author(s):  
Zhao Jiang ◽  
Dao-Feng Zhang ◽  
Thi-Nhan Khieu ◽  
Chu Ky Son ◽  
Xiao-Mei Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Sediment Sample ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Marine Sediment Sample

A novel Gram-stain-positive, motile, catalase- and oxidase-positive, aerobic, endospore-forming, peritrichous, rod-shaped bacterium, designated YIM M13235T, was isolated from a marine sediment sample collected from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M13235T belonged to the genus Bacillus . The strain grew optimally at 30 °C, pH 7.0 and in the presence of 2–4 % (w/v) NaCl. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. Strain YIM M13235T exhibited a menaquinone system with MK-7, and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown glycolipid. The major fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 1ω10c and summed feature 4 (anteiso-C17 : 1 and/or iso-C17 : 1). The genomic DNA G+C content was 42.1 mol%. The DNA–DNA relatedness values between strain YIM M13235T and its close relatives (16S rRNA gene sequence similarities >97 %) including Bacillus halmapalus DSM 8723T, Bacillus horikoshii DSM 8719T and Bacillus zhanjiangensis JSM 099021T were 41 %, 44 % and 44 %, respectively. On the basis of genotypic, phenotypic and DNA–DNA relatedness data, it is apparent that strain YIM M13235T represents a novel species of the genus Bacillus , for which the name Bacillus tianshenii sp. nov. is proposed. The type strain is YIM M13235T ( = DSM 25879T = KCTC 33044T).

scholarly journals Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4115-4119 ◽  
Author(s):  
Parisa Zarparvar ◽  
Mohammad Ali Amoozegar ◽  
Mahdi Moshtaghi Nikou ◽  
Peter Schumann ◽  
Antonio Ventosa
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

A halophilic actinomycete, strain R4S8T, was isolated from soil of Inche-Broun hypersaline wetland in the north of Iran. The isolate grew aerobically at temperatures of 30–50 °C (optimum 40 °C), pH 6–10 (optimum pH 7.0) and in the presence of 1–15 % (w/v) NaCl (optimum 3–5 %). It formed short and straight to moderately flexuous aerial mycelium without motile elements. The cell wall of strain R4S8T contained meso-diaminopimelic acid as the diamino acid without any diagnostic sugars. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylmonomethylethanolamine two unknown phospholipids and one unknown aminophospholipid. It synthesized anteiso-C15 : 0 (44.8 %), iso-C15 : 0 (28.8 %) and iso-C14 : 0 (8.5 %) as major fatty acids. MK-6 was the predominant respiratory quinone. The G+C content of the genomic DNA was 52.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R4S8T belongs to the family Thermoactinomycetaceae and showed the closest 16S rRNA gene sequence similarity with Desmospora activa IMMIB L-1269T (95.5 %) and Marininema mesophilum SCSIO 10219T (95.3 %). On the basis of phylogenetic analysis and phenotypic characteristics, strain R4S8T represents a novel species in a new genus within the family Thermoactinomycetaceae , for which the name Salinithrix halophila gen. nov., sp. nov. is proposed. The type strain of the type species is R4S8T ( = IBRC-M 10813T = CECT 8506T).

Micromonospora sediminicola sp. nov., isolated from marine sediment

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 570-575 ◽  
Author(s):  
Khomsan Supong ◽  
Chanwit Suriyachadkun ◽  
Somboon Tanasupawat ◽  
Khanit Suwanborirux ◽  
Pattama Pittayakhajonwut ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Andaman Sea ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample ◽  
Actinomycete Strain

An actinomycete strain, designated strain SH2-13T, was isolated from a marine sediment sample collected from the Andaman Sea of Thailand. Applying a polyphasic approach, the isolate was identified as a member of the genus Micromonospora using morphological and chemotaxonomic characteristics, including the presence of meso-diaminopimelic acid in the peptidoglycan. Whole-cell sugars were arabinose, galactose, glucose, rhamnose, ribose and xylose. Diagnostic polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and phosphoglycolipids. The major menaquinones were MK-10(H2), MK-10(H4) and MK-10(H6). 16S rRNA gene sequence analysis revealed similarity to Micromonospora marina JSM1-1T (99.1 %), Micromonospora coxensis 2-30-b(28)T (99.1 %), Micromonospora aurantiaca DSM 43813T (98.8 %) and Micromonospora chalcea DSM 43026T (98.7 %). However, a combination of DNA–DNA hybridization results and phenotypic properties indicated that strain SH2-13T ( = NBRC 107934T = BCC 45601T) should be classified as the type strain of a novel species, with the proposed name Micromonospora sediminicola sp. nov.

scholarly journals Streptomyces pharmamarensis sp. nov. isolated from a marine sediment

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1165-1170 ◽  
Author(s):  
Lorena Carro ◽  
Paz Zúñiga ◽  
Fernando de la Calle ◽  
Martha E. Trujillo
Keyword(s):  
Fatty Acids ◽  
Marine Sediment ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Physiological Data ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-positive actinobacterium, strain PM267T, was isolated from a marine sediment sample in the Mediterranean Sea. The novel strain produced extensively branched substrate and aerial hyphae that carried spiral spore chains. Substrate and aerial mycelia were cream–white and white, respectively. Diffusible pigments were not observed. 16S rRNA gene sequence analysis revealed that strain PM267T belonged to the genus Streptomyces and shared a gene sequence similarity of 97.1 % with Streptomyces artemisiae YIM 63135T and Streptomyces armeniacus JCM 3070T. Values <97 % were obtained with other sequences representing members of the genus Streptomyces . The cell wall peptidoglycan contained ll -diaminopimelic acid. MK-9(H8) was the major menaquinone. The phospholipid pattern included phosphatidylethanolamine as diagnostic lipid (type II). Major fatty acids found were iso- and anteiso- fatty acids. The G+C content of the DNA was 71.2 mol%. The strain was halotolerant and was able to grow in the presence of 9 % (w/v) NaCl (with an optimum of 2 %). On the basis of these results and additional physiological data obtained in the present study, strain PM267T represents a novel species within the genus Streptomyces for which the name Streptomyces pharmamarensis sp. nov. is proposed (type strain PM267T  = CECT 7841T  = DSM 42032T).

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