scholarly journals Paenibacillus rigui sp. nov., isolated from a freshwater wetland

2011 ◽  
Vol 61 (3) ◽  
pp. 529-534 ◽  
Author(s):  
Keun Sik Baik ◽  
Chae Hong Lim ◽  
Han Na Choe ◽  
Eun Mi Kim ◽  
Chi Nam Seong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Freshwater Wetland ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Diamino Acid

A rod-shaped, endospore-forming, Gram-reaction-variable bacterial strain, designated WPCB173T, was isolated from freshwater collected from the Woopo wetland, Republic of Korea. Based on its phenotypic characteristics and phylogenetic position inferred from 16S rRNA gene sequence analysis, the isolate was identified as being a member of the genus Paenibacillus. Major polar lipids present in strain WPCB173T included phosphatidylethanolamine and several unidentified phospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C15 : 0 (65.2 %). The DNA G+C content was 48.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WPCB173T clustered with species of the genus Paenibacillus, its closest neighbours being Paenibacillus chinjuensis WN9T (96.7 %) and Paenibacillus soli DCY03T (96.4 %). DNA–DNA hybridization of strain WPCB173T with P. soli DCY03T and P. chinjuensis WN9T showed relatedness values of only 10 and 19 %, respectively. On the basis of the phenotypic and phylogenetic evidence, strain WPCB173T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus rigui sp. nov. is proposed. The type strain of the novel species is WPCB173T (=KCTC 13282T =JCM 16352T).

scholarly journals Paenibacillus wooponensis sp. nov., isolated from wetland freshwater

2011 ◽  
Vol 61 (11) ◽  
pp. 2763-2768 ◽  
Author(s):  
Keun Sik Baik ◽  
Han Na Choe ◽  
Seong Chan Park ◽  
Eun Mi Kim ◽  
Chi Nam Seong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Type Strains

A rod-shaped, endospore-forming, Gram-reaction-positive bacterium, designated strain WPCB018T, was isolated from a fresh water sample collected from Woopo wetland, Korea. The isolate was identified as a member of the genus Paenibacillus on the basis of phenotypic characteristics and phylogenetic inference based on 16S rRNA gene sequence analysis. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and unknown aminophospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 (32.2 %), C16 : 0 (20.1 %) and C18 : 0 (18.1 %). The DNA G+C content was 56.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WPCB018T belongs to a cluster comprising species of the genus Paenibacillus, its closest neighbours being Paenibacillus humicus PC-147T (97.5 %) and Paenibcillus pasadenensis SAFN-007T (96.2 %). Genomic DNA–DNA hybridizations performed with strain WPCB018T and type strains of the species P. humicus, P. pinihumi, P. phyllosphaerae, P. pasadenensis and P. tarimensis showed relatedness values of only 10, 17, 18, 19 and 20 %, respectively. On the basis of phenotypic, molecular and genetic evidence, strain WPCB018T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus wooponensis sp. nov. is proposed. The type strain of the novel species is WPCB018T ( = KCTC 13280T  = JCM 16350T).

scholarly journals Erwinia oleae sp. nov., isolated from olive knots caused by Pseudomonas savastanoi pv. savastanoi

2011 ◽  
Vol 61 (11) ◽  
pp. 2745-2752 ◽  
Author(s):  
Chiaraluce Moretti ◽  
Taha Hosni ◽  
Katrien Vandemeulebroecke ◽  
Carrie Brady ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Hybridization Data ◽  
Gene Sequence Analysis ◽  
Phenotypic Tests

Three endophytic bacterial isolates were obtained in Italy from olive knots caused by Pseudomonas savastanoi pv. savastanoi. Phenotypic tests in combination with 16S rRNA gene sequence analysis indicated a phylogenetic position for these isolates in the genera Erwinia or Pantoea, and revealed two other strains with highly similar 16S rRNA gene sequences (>99 %), CECT 5262 and CECT 5264, obtained in Spain from olive knots. Rep-PCR DNA fingerprinting of the five strains from olive knots with BOX, ERIC and REP primers revealed three groups of profiles that were highly similar to each other. Multilocus sequence analysis (MLSA) based on concatenated partial atpD, gyrB, infB and rpoB gene sequences indicated that the strains constituted a single novel species in the genus Erwinia. The strains showed general phenotypic characteristics typical of the genus Erwinia and whole genome DNA–DNA hybridization data confirmed that they represented a single novel species of the genus Erwinia. The strains showed DNA G+C contents ranging from 54.7 to 54.9 mol%. They could be discriminated from phylogenetically related species of the genus Erwinia by their ability to utilize potassium gluconate, l-rhamnose and d-arabitol, but not glycerol, inositol or d-sorbitol. The name Erwinia oleae sp. nov. (type strain DAPP-PG 531T = LMG 25322T = DSM 23398T) is proposed for this novel taxon.

scholarly journals Parabacteroides johnsonii sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (2) ◽  
pp. 293-296 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Maki Kitahara ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Gene Sequence Analysis

A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for l-arabinose and l-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).

scholarly journals Antricoccus suffuscus gen. nov., sp. nov., isolated from a natural cave

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4410-4416 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel actinobacterium, designated strain C4-31T, was isolated from soil collected from a cave. Cells were aerobic, Gram-reaction-positive, oxidase-negative, catalase-positive and non-motile cocci. Comparison of 16S rRNA gene sequences showed that the organism occupied a distinct phylogenetic position within the suborder Frankineae, with sequence similarity values of less than 93.2 % to members of this suborder. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unknown aminophospholipid and an unknown phospholipid. The major fatty acids were iso-C16 : 0, C17 : 1ω6c and C16 : 0. The G+C content of the DNA was 62.8 mol%. On the basis of morphological and chemotaxonomic data as well as phylogenetic evidence, strain C4-31T ( = KCTC 39556T = DSM 100065T) is considered to represent the type strain of a novel species of a new genus in the suborder Frankineae, for which the name Antricoccus suffuscus gen. nov., sp. nov. is proposed.

scholarly journals Paenibacillus ripae sp. nov., isolated from bank side soil

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4757-4762 ◽  
Author(s):  
Ying Sun ◽  
Zhaohui Guo ◽  
Qi Zhao ◽  
Qiyu Gao ◽  
QinJian Xie ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Pr China ◽  
Diamino Acid

A Gram-stain-variable, rod-shaped, non-motile and endospore-forming bacterium, designated strain HZ1T, was isolated from a sample of bank side soil from Hangzhou city, Zhejiang province, PR China. On the basis of 16S rRNA gene sequence analysis, strain HZ1T was closely related to members of the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus agarexedens DSM 1327T (94.4 %), Paenibacillus sputi KIT00200-70066-1T (94.4 %). Growth occurred at 15–42 °C (optimum 30–37 °C), pH 5.0–9.5 (optimum pH 7.0–8.0) and NaCl concentrations of up to 6.0 % (w/v) were tolerated (optimum 0.5 %). The dominant respiratory quinone was MK-7 and the DNA G+C content was 40.1 mol%. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids of strain HZ1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain HZ1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus ripae sp. nov. (type strain HZ1T = CCTCC AB 2014276T = LMG 28639T) is proposed.

scholarly journals Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan

2004 ◽  
Vol 54 (6) ◽  
pp. 1927-1931 ◽  
Author(s):  
Akiko Kageyama ◽  
Katsukiyo Yazawa ◽  
Akira Mukai ◽  
Mari Kinoshita ◽  
Nobukatsu Takata ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Morphological Criteria ◽  
Respective Type ◽  
Type Strains

Three actinomycete strains isolated from soils and one strain isolated from a patient with lung nocardiosis in 1999 and 2001 in Japan have been provisionally assigned to the genus Nocardia on the basis of morphological criteria. These isolates were further investigated to determine their specific taxonomic status. Detailed chemotaxonomic characterization and 16S rRNA gene sequence analysis of these isolates confirmed that they belong to the genus Nocardia. The 16S rRNA gene sequences of the four strains were most similar to that of Nocardia farcinica. However, the sequence similarity values between these four strains and N. farcinica were <98·9 %. These four strains were susceptible to 5-fluorouracil, and they have the ability to decompose urea, which is a very characteristic trait. Furthermore, DNA–DNA relatedness data revealed that IFM 10311T, IFM 10312 and IFM 10313 comprise a single novel species of Nocardia, that IFM 10084T represents another novel species of Nocardia and that these two novel species could be distinguished from N. farcinica. The names Nocardia shimofusensis sp. nov. and Nocardia higoensis sp. nov. are proposed, with IFM 10311T (=NBRC 100134T=JCM 12122T=DSM 44733T) and IFM 10084T (=NBRC 100133T=JCM 12121T=DSM 44732T) as the respective type strains.

scholarly journals Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae

2004 ◽  
Vol 54 (5) ◽  
pp. 1669-1676 ◽  
Author(s):  
Yi-Chueh Lin ◽  
Kazunori Uemori ◽  
Dominique A. de Briel ◽  
Vallapa Arunpairojana ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
Hexadecanoic Acid ◽  
16S Rrna Gene Analysis ◽  
Separate Branch ◽  
The Family ◽  
Diamino Acid

Seven strains of actinobacteria, isolated from soil, wounds, urine, cow faeces, human blood and butter, were characterized by a polyphasic approach to clarify their taxonomic position. On the basis of chemotaxonomy, 16S rRNA gene analysis and DNA relatedness, strain IAM 14851T can be classified within the cluster of the genus Leucobacter and is proposed as a novel species, Leucobacter albus sp. nov., with strain IAM 14851T (=TISTR 1515T) as the type strain. The other six strains formed a phylogenetically separate branch in the family Microbacteriaceae, having the following characteristics: the major menaquinones are MK-8 to MK-10, the DNA G+C content ranges from 62 to 68 mol%, the diamino acid in the cell wall is diaminobutyric acid and the muramic acid in the peptidoglycan is of the acetyl type. The major fatty acids are 12-methyltetradecanoic acid (anteiso-C15 : 0), hexadecanoic acid (C16 : 0), 14-methyl-pentadecanoic acid (iso-C16 : 0) and 14-methyl-hexadecanoic acid (anteiso-C17 : 0). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA hybridization and 16S rRNA gene sequence comparison, the novel genus Zimmermannella gen. nov. is proposed for these six strains. Four novel species are proposed: Zimmermannella helvola sp. nov. (type species; type strain IAM 14726T=NBRC 15775T=DSM 20419T=TISTR 1509T), Zimmermannella alba sp. nov. (type strain IAM 14724T=NBRC 15616T=TISTR 1510T), Zimmermannella bifida sp. nov. (type strain IAM 14848T=TISTR 1511T) and Zimmermannella faecalis sp. nov. (type strain IAM 15030T=NBRC 15706T=ATCC 13722T=TISTR 1514T).

scholarly journals Alkalibacillus flavidus sp. nov., isolated from a marine solar saltern

2010 ◽  
Vol 60 (2) ◽  
pp. 434-438 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Marine Solar Saltern ◽  
Phenotypic Properties ◽  
Diamino Acid

A Gram-stain-positive, motile, rod-shaped bacterial strain, ISL-17T, was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain ISL-17T grew optimally at pH 8.5–9.0, at 37 °C and in the presence of approximately 10 % (w/v) NaCl. It contained meso-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, MK-7 as the predominant menaquinone and iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids. The DNA G+C content was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-17T fell within the genus Alkalibacillus, clustering with Alkalibacillus salilacus BH163T with a bootstrap resampling value of 100 %. Strain ISL-17T exhibited 98.2 % 16S rRNA gene sequence similarity to A. salilacus BH163T and 95.8–96.5 % similarity to the type strains of the other Alkalibacillus species. The mean DNA–DNA relatedness value between strain ISL-17T and A. salilacus KCTC 3916T was 19 %. The phenotypic properties of strain ISL-17T, together with its phylogenetic and genetic distinctiveness, enable this strain to be differentiated from recognized Alkalibacillus species. On the basis of phenotypic, phylogenetic and genetic data, strain ISL-17T represents a novel species within the genus Alkalibacillus, for which the name Alkalibacillus flavidus sp. nov. is proposed; the type strain is ISL-17T (=KCTC 13258T =CCUG 56753T).

scholarly journals Nonomuraea wenchangensis sp. nov., isolated from mangrove rhizosphere soil

2011 ◽  
Vol 61 (6) ◽  
pp. 1304-1308 ◽  
Author(s):  
Fan Wang ◽  
Xiao-Xiong Xu ◽  
Zhi Qu ◽  
Cheng Wang ◽  
Hai-Peng Lin ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Strain 210417T, which forms highly branched substrate and aerial mycelia, is a Gram-positive, aerobic and non-motile actinomycete isolated from mangrove rhizosphere soil. 16S rRNA gene sequence analysis showed that the strain should be classified in the genus Nonomuraea, being most closely related to the type strains of Nonomuraea coxensis (99.6 %) and Nonomuraea bangladeshensis (99.3 %). Chemotaxonomic properties [madurose as the major sugar in the cell wall; meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan; MK-9(H4) as the major menaquinone; iso-C16 : 0 (24.1 %) as major fatty acid; and phospholipid pattern type IV] are consistent with the assignment of strain 210417T to the genus Nonomuraea. Strain 210417T could be differentiated from the closely related species N. coxensis and N. bangladeshensis by morphological, physiological, biochemical and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA–DNA hybridization results. It is therefore proposed that strain 210417T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea wenchangensis sp. nov. is given; the type strain is 210417T ( = CGMCC 4.5598T  = DSM 45477T).

scholarly journals Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India

2005 ◽  
Vol 55 (1) ◽  
pp. 91-94 ◽  
Author(s):  
S. Mayilraj ◽  
G. S. Prasad ◽  
K. Suresh ◽  
H. S. Saini ◽  
S. Shivaji ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cold Desert ◽  
Gene Sequence Analysis

The taxonomic position of a bacterium isolated from a cold desert of the Himalayas, India, was analysed by using a polyphasic approach. The isolated strain, designated K22-03T, had phenotypic characteristics that matched those of the genus Planococcus and it represents a novel species. The almost-complete 16S rRNA gene sequence (1464 bases) of the novel strain was compared with those of previously studied Planococcus type strains and confirmed that the strain belongs to the genus Planococcus. 16S rRNA gene sequence analysis indicated that strain K22-03T differs from all other species of Planococcus by at least 2·5 %. DNA–DNA hybridization showed that it had low genomic relatedness with Planomicrobium mcmeekinii (MTCC 3704T, 23 %), Planococcus psychrophilus (MTCC 3812T, 61 %), Planococcus antarcticus (MTCC 3854T, 45 %) and Planomicrobium okeanokoites (MTCC 3703T, 51 %), the four species with which it was most closely related based on 16S rRNA gene sequence analysis (97–97·5 % similarity). Therefore, strain K22-03T should be recognized as a novel species, for which the name Planococcus stackebrandtii sp. nov. is proposed. The type strain is K22-03T (=MTCC 6226T=DSM 16419T=JCM 12481T).

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