scholarly journals Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2642-2649 ◽  
Author(s):  
Maria V. Sizova ◽  
Paul A. Muller ◽  
David Stancyk ◽  
Nicolai S. Panikov ◽  
Manolis Mandalakis ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Sequence Similarity ◽  
Anaerobic Bacteria ◽  
Distinct Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type

Three strictly anaerobic, Gram-positive, non-spore-forming, rod-shaped, motile bacteria, designated strains ACB1T, ACB7T and ACB8, were isolated from human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1T and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin and raffinose; strain ACB7T grew weakly on sucrose only. The growth temperature range was 30–42 °C with optimum growth at 37 °C. Major metabolic fermentation end products of strain ACB1T were acetate and lactate; the only product of strains ACB7T and ACB8 was acetate. Major fatty acids of strain ACB1T were C14 : 0, C16 : 0, C16 : 1ω7c dimethyl aldehyde (DMA) and C18 : 1ω7c DMA. Major fatty acids of strain ACB7T were C12 : 0, C14 : 0, C16 : 0, C16 : 1ω7c and C16 : 1ω7c DMA. The hydrolysate of the peptidoglycan contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. Genomic DNA G+C content varied from 42 to 43.3 % between strains. According to 16S rRNA gene sequence phylogeny, strains ACB1T, ACB8 and ACB7T formed two separate branches within the genus Oribacterium , with 98.1–98.6 % sequence similarity to the type strain of the type species, Oribacterium sinus . Predicted DNA–DNA hybridization values between strains ACB1T, ACB8, ACB7T and O. sinus F0268 were <70 %. Based on distinct genotypic and phenotypic characteristics, strains ACB1T and ACB8, and strain ACB7T are considered to represent two distinct species of the genus Oribacterium , for which the names Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov. are proposed. The type strains are ACB1T ( = DSM 24637T = HM-481T = ATCC BAA-2638T) and ACB7T ( = DSM 24638T = HM-482T = ATCC BAA-2639T), respectively.

scholarly journals Actinokineospora soli sp. nov., a thermotolerant actinomycete isolated from soil, and emended description of the genus Actinokineospora

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1845-1849 ◽  
Author(s):  
Xia Tang ◽  
Yu Zhou ◽  
Jing Zhang ◽  
Hong Ming ◽  
Guo-Xing Nie ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Genomic Dna ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A strain of thermotolerant actinomycete, designated YIM 75948T, was isolated from a soil sample in Yunnan province, China. The strain grew at 25–55 °C (optimum 37 °C). The substrate mycelium and aerial mycelium produced on Czapek’s agar were both pale yellow to white. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid, and the whole-cell sugars were mannose, ribose, glucose, galactose and arabinose. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and C16 : 0 and the predominant respiratory quinone was MK-9(H4). The polar lipids consisted of phosphatidylethanolamine, phosphatidylethanolamine with hydroxy fatty acids, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The genomic DNA G+C content was 73.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 75948T belonged in the genus Actinokineospora and that its closest relative among recognized species was Actinokineospora fastidiosa DSM 43855T (97.6 % sequence similarity). The mean level of DNA–DNA relatedness between the novel strain and A. fastidiosa DSM 43855T was, however, only 47.8 %. Based on the phenotypic, chemotaxonomic and phylogenetic data and the results of the DNA–DNA hybridizations, strain YIM 75948T represents a novel species of the genus Actinokineospora for which the name Actinokineospora soli sp. nov. is proposed. The type strain is YIM 75948T ( = JCM 17695T = DSM 45613T). The description of the genus Actinokineospora is emended to reflect the fact that the genomic DNA G+C contents of A. fastidiosa DSM 43855T and the type strain of Actinokineospora soli sp. nov. recorded in the present study fell above the range given in previous descriptions of this genus.

Anoxybacillus calidus sp. nov., a thermophilic bacterium isolated from soil near a thermal power plant

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 211-219 ◽  
Author(s):  
Arzu Coleri Cihan ◽  
Cumhur Cokmus ◽  
Melih Koc ◽  
Birgul Ozcan
Keyword(s):  
Fatty Acids ◽  
Power Plant ◽  
Type Species ◽  
Sequence Similarity ◽  
Thermal Power ◽  
Thermophilic Bacterium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A novel thermophilic, Gram-stain-positive, facultatively anaerobic, endospore-forming, motile, rod-shaped bacterium, strain C161abT, was isolated from a soil sample collected near Kizildere, Saraykoy-Buharkent power plant in Denizli. The isolate could grow at temperatures between 35 and 70 °C (optimum 55 °C), at pH 6.5–9.0 (optimum pH 8.0–8.5) and with 0–2.5 % NaCl (optimum 0.5 %, w/v). The strain formed cream-coloured, circular colonies and tolerated up to 70 mM boron. Its DNA G+C content was 37.8 mol%. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. Strain C161abT contained menaquinones MK-7 (96 %) and MK-6 (4 %). The major cellular fatty acids were iso-branched fatty acids: iso-C15 : 0 (52.2 %) and iso-C17 : 0 (28.0 %,) with small amounts of C16 : 0 (7.4 %). Phylogenetic analysis based on the 16S rRNA gene revealed 94.6–96.8 % sequence similarity with all recognized species of the genus Anoxybacillus . Strain C161abT showed the greatest sequence similarity to Anoxybacillus rupiensis DSM 17127T and Anoxybacillus voinovskiensis DSM 17075T, both had 96.8 % similarity to strain C161abT, as well as to Anoxybacillus caldiproteolyticus DSM 15730T (96.6 %). DNA–DNA hybridization revealed low levels of relatedness with the closest relatives of strain C161abT, A. rupiensis (21.2 %) and A. voinovskiensis (16.5 %). On the basis of the results obtained from phenotypic, chemotaxonomic, genomic fingerprinting, phylogenetic and hybridization analyses, the isolate is proposed to represent a novel species, Anoxybacillus calidus sp. nov. (type strain C161abT = DSM 25520T = NCIMB 14851T).

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).

Nocardiopsis coralli sp. nov. a novel actinobacterium isolated from the coral Galaxea astreata

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Fenfa Li ◽  
Qingyi Xie ◽  
Shuangqing Zhou ◽  
Fandong Kong ◽  
Yun Xu ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Phosphatidylinositol Mannosides

Strain HNM0947T, representing a novel actinobacterium, was isolated from the coral Galaxea astreata collected from the coast of Wenchang, Hainan, China. The strain was found to have morphological and chemotaxonomic characteristics consistent with the genus Nocardiopsis . The organism formed abundant fragmented substrate mycelia and aerial mycelia which differentiated into non-motile, rod-shaped spores. Whole-cell hydrolysates contained meso-diaminopimelic acid and no diagnostic sugars. The major menaquinones were MK-10(H8), MK-10(H6) and MK-10(H4). The major phospholipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16:0, anteiso-C17:0, C18:0, C18:0 10-methyl (TBSA) and anteiso-C15:0. The G+C content was 71.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HNM0947T belonged to the genus Nocardiopsis and shared highest sequence similarity to Nocardiopsis salina YIM 90010T (98.8%), Nocardiopsis xinjiangensis YIM 90004T(98.5%) and Nocardiopsis kunsanensis DSM 44524T (98.3%). The strain HNM0947T was distinguished from its closest type strain by low average nucleotide identity (90.8%) and dDDH values (60.4%) respectively. Based on genotypic, chemotaxonomic and phenotypic characteristics, it was concluded that strain HNM0947T represents a novel species of the genus Nocardiopsis whose name was proposed as Nocardiopsis coralli sp. nov. The type strain was HNM0947T (=CCTCC AA 2020015 T=KCTC 49525 T).

scholarly journals Haloactinopolyspora alkaliphila sp. nov., and emended description of the genus Haloactinopolyspora

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1945-1951 ◽  
Author(s):  
Yong-Guang Zhang ◽  
Qing Liu ◽  
Hong-Fei Wang ◽  
Dao-Feng Zhang ◽  
Yuan-Ming Zhang ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
North West ◽  
Link Type ◽  
Hybridization Data ◽  
Actinomycete Strain ◽  
Diamino Acid

A facultatively alkaliphilic actinomycete strain, designated EGI 80088T, was isolated from a saline-alkali soil sample from Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80088T formed fragmented aerial hyphae and short spore chains, and rod-like spores aggregated at maturity. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and glucosamine, mannose, galactose, glucose and rhamnose as the marker sugars. The major fatty acids identified (>5 %) were anteiso-C15 : 0, iso-C15 : 0, summed feature 4 (iso-C17 : 1I/anteiso-C17 : 1B), iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA of strain EGI 80088T was 70.6 mol%. EGI 80088T showed the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Haloactinopolyspora alba YIM 93246T (98.5 %). The DNA–DNA relatedness value of the strain EGI 80088T and H. alba YIM 93246T was 59.3±5.2 %. On the basis of morphological, chemotaxonomic and phylogenetic characteristics and DNA–DNA hybridization data, strain EGI 80088T represents a novel species of the genus Haloactinopolyspora , for which the name Haloactinopolyspora alkaliphila sp. nov. (type strain EGI 80088T = BCRC 16946T = JCM 19128T) is proposed. The description of the genus Haloactinopolyspora has also been emended.

Thermoanaerobacter pentosaceus sp. nov., an anaerobic, extremely thermophilic, high ethanol-yielding bacterium isolated from household waste

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2396-2404 ◽  
Author(s):  
Ana Faria Tomás ◽  
Dimitar Karakashev ◽  
Irini Angelidaki
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Maximum Yield ◽  
Maximum Growth ◽  
Household Waste ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Phylogenetic Distance ◽  
Content Type ◽  
Link Type

An extremely thermophilic, xylanolytic, spore-forming and strictly anaerobic bacterium, strain DTU01T, was isolated from a continuously stirred tank reactor fed with xylose and household waste. Cells stained Gram-negative and were rod-shaped (0.5–2 µm in length). Spores were terminal with a diameter of approximately 0.5 µm. Optimal growth occurred at 70 °C and pH 7, with a maximum growth rate of 0.1 h−1. DNA G+C content was 34.2 mol%. Strain DTU01T could ferment arabinose, cellobiose, fructose, galactose, glucose, lactose, mannitol, mannose, melibiose, pectin, starch, sucrose, xylan, yeast extract and xylose, but not cellulose, Avicel, inositol, inulin, glycerol, rhamnose, acetate, lactate, ethanol, butanol or peptone. Ethanol was the major fermentation product and a maximum yield of 1.39 mol ethanol per mol xylose was achieved when sulfite was added to the cultivation medium. Thiosulfate, but not sulfate, nitrate or nitrite, could be used as electron acceptor. On the basis of 16S rRNA gene sequence similarity, strain DTU01T was shown to be closely related to Thermoanaerobacter mathranii A3T, Thermoanaerobacter italicus Ab9T and Thermoanaerobacter thermocopriae JT3-3T, with 98–99 % similarity. Despite this, the physiological and phylogenetic differences (DNA G+C content, substrate utilization, electron acceptors, phylogenetic distance and isolation site) allow for the proposal of strain DTU01T as a representative of a novel species within the genus Thermoanaerobacter , for which the name Thermoanaerobacter pentosaceus sp. nov. is proposed, with the type strain DTU01T ( = DSM 25963T = KCTC 4529T = VKM B-2752T = CECT 8142T).

Bacillus gottheilii sp. nov., isolated from a pharmaceutical manufacturing site

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 867-872 ◽  
Author(s):  
Herbert Seiler ◽  
Mareike Wenning ◽  
Verena Schmidt ◽  
Siegfried Scherer
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Acid Type

A novel Gram-staining-positive, rod-shaped, motile, strictly aerobic, endospore-forming bacterium, designated WCC 4585T, was isolated from a pharmaceutical production line. The organism grew optimally at 30 °C, at pH 8 and in the presence of 0.5 % (w/v) NaCl. Oval endospores were formed subterminally and terminally in swollen sporangia. The cell-wall diamino acid was meso-diaminopimelic acid (type A1γ) and the genomic DNA G+C content was 38.7 mol%. The major menaquinone was MK-7. The cellular fatty acid profile contained major amounts of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, and the cellular phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. The isolate was most closely related to Bacillus oceanisediminis H2T, Bacillus infantis SMC 4352-1T, Bacillus firmus NCIMB 9366T, Bacillus circulans ATCC 4513T and Bacillus horneckiae DSM 23495T with which it shared less than 98.0 % 16S rRNA gene sequence similarity. DNA–DNA relatedness values between strain WCC 4585T and five type strains of related species were ≤27 % and sequence similarity values based on groEL sequences were ≤88.7 %. On the basis of the characteristics presented, strain WCC 4585T is proposed to represent a novel species, Bacillus gottheilii sp. nov. The type strain is WCC 4585T( = DSM 23668T = CCUG 59876T = LMG 25856T).

Pseudomonas cyclaminis sp. nov., a pathogen causing bacterial bud blight of cyclamen in Japan

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Hiroyuki Sawada ◽  
Takashi Fujikawa ◽  
Shigeru Osada ◽  
Mamoru Satou
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Total Fatty Acids

Five phytopathogenic bacterial strains, MAFF 301449T, MAFF 301450, MAFF 301451, MAFF 301452, and MAFF 301453, which were isolated from bud blight lesions of cyclamen (Cyclamen persicum Mill.) in Miyagi, Japan, were subjected to polyphasic taxonomic characterisation. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one to five polar flagella, and rod-shaped. Analysis of 16S rRNA gene sequences showed that they belong to the genus Pseudomonas , with Pseudomonas extremaustralis 14-3T (99.79 % sequence similarity), Pseudomonas trivialis DSM 14937T (99.79 %), Pseudomonas poae DSM 14936T (99.72 %), and Pseudomonas antarctica CMS 35T (99.72 %) as their relatives. The genomic DNA G+C content was 60.3 mol% and the major fatty acids (>5 % of the total fatty acids) were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), and C17 : 0 cyclo. Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade separated from their relatives. Average nucleotide identity and digital DNA–DNA hybridisation analyses with the closely related Pseudomonas species corroborated their novel species status. The strains were differentiated from their relatives by phenotypic characteristics, pathogenicity towards cyclamen, cellular fatty acid composition, and whole-cell MALDI-TOF mass spectrometry profiles. Based on the phenotypic, chemotaxonomic, and genotypic data obtained, we conclude that the strains represent a novel Pseudomonas species, for which we propose the name Pseudomonas cyclaminis sp. nov.; the type strain is MAFF 301449T (=ICMP 23720T).

Streptomyces chiangmaiensis sp. nov. and Streptomyces lannensis sp. nov., isolated from the South-East Asian stingless bee (Tetragonilla collina)

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1896-1901 ◽  
Author(s):  
Yaowanoot Promnuan ◽  
Takuji Kudo ◽  
Moriya Ohkuma ◽  
Panuwan Chantawannakul
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
East Asian ◽  
Stingless Bee ◽  
Diaminopimelic Acid ◽  
The South ◽  
Content Type ◽  
Link Type

Two novel actinomycetes, strains TA4-1T and TA4-8T, were isolated from the South-East Asian stingless bee (Tetragonilla collina Smith 1857), collected from Chiang Mai Province, Thailand. The morphological and chemotaxonomic properties of strains TA4-1T and TA4-8T were consistent with the genus Streptomyces , i.e. the formation of aerial mycelia bearing spiral spore chains, the presence of the ll-isomer of diaminopimelic acid in cell walls, iso- and anteiso-branched fatty acids with carbon chain lengths 14–17 atoms as the major fatty acids and MK-9(H8) as the predominant menaquinone plus minor amounts of MK-9(H6) and MK-9(H10). Analysis of 16S rRNA gene sequences showed that strains TA4-1T and TA4-8T exhibited 98.8 and 98.1 % sequence similarity, respectively, with Streptomyces chromofuscus NRRL B-12175T and 98.9 % sequence similarity with each other. This study suggested that strains TA4-1T and TA4-8T were distinct from previously described species of the genus Streptomyces . In addition, the low degrees of DNA–DNA relatedness between the isolates and S. chromofuscus JCM 4354T warranted assigning strains TA4-1T and TA4-8T to two novel species. The names Streptomyces chiangmaiensis sp. nov. (type strain TA4-1T  = JCM 16577T  = TISTR 1981T) and Streptomyces lannensis sp. nov. (type strain TA4-8T  = JCM 16578T  = TISTR 1982T) are proposed. The species names indicate the geographical locations where the stingless bees reside.

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).

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