scholarly journals Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov.

2004 ◽  
Vol 54 (6) ◽  
pp. 2223-2230 ◽  
Author(s):  
Linxian Ding ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Study ◽  
Well Water ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gram Negative ◽  
Morphological Studies ◽  
The 16S Rrna Gene

Two strains of curved bacteria, 7-1T and 7-2T, isolated from well water, were phylogenetically examined to determine their taxonomic position. Strain 7-1T is a Gram-negative, slightly curved rod. Analysis of the 16S rRNA gene sequence showed that strain 7-1T formed a cluster with [Aquaspirillum] delicatum and [Pseudomonas] lanceolata. It has some similar characteristics to [A.] delicatum and [P.] lanceolata, but has sufficient distance to separate it from other genera. DNA–DNA hybridization analysis, as well as chemotaxonomic and morphological studies, demonstrated that strain 7-1T, [A.] delicatum and [P.] lanceolata belong to a new genus, Curvibacter gen. nov. Strain 7-1T (=IAM 15033T=ATCC BAA-807T) is classified as the type strain of Curvibacter gracilis gen. nov., sp. nov., and [A.] delicatum and [P.] lanceolata are classified as Curvibacter delicatus comb. nov. and Curvibacter lanceolatus comb. nov., respectively. Strain 7-2T is a Gram-negative spirillum. Phylogenetic study based on the 16S rRNA gene sequences showed that it formed a cluster with the members of the genus Herbaspirillum, [Pseudomonas] huttiensis and [Aquaspirillum] autotrophicum. The classification is therefore proposed of strain 7-2T (=IAM 15032T=ATCC BAA-806T) as the type strain of Herbaspirillum putei sp. nov., and [P.] huttiensis and [A.] autotrophicum are transferred to the genus Herbaspirillum as Herbaspirillum huttiense comb. nov. and Herbaspirillum autotrophicum comb. nov., respectively.

scholarly journals Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans

2010 ◽  
Vol 60 (12) ◽  
pp. 2710-2714 ◽  
Author(s):  
Vojtěch Kasalický ◽  
Jan Jezbera ◽  
Karel Šimek ◽  
Martin W. Hahn
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Phylogenetic Cluster ◽  
The 16S Rrna Gene

Two bacterial strains, II-B4T and II-D5T, isolated from the meso-eutrophic freshwater Římov reservoir (Czech Republic), were characterized phenotypically, phylogenetically and chemotaxonomically. Both strains were chemo-organotrophic, facultatively anaerobic, non-motile rods, with identical DNA G+C contents of 59.9 mol%. Their major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and their major fatty acids were C16 : 1 ω7c/C16 : 1 ω6c, C16 : 0, C18 : 1 ω7c/C18 : 1 ω6c and C12 : 0. Both strains contained Q-8 as the only respiratory quinone component. The 16S rRNA gene sequences of the two strains possessed 99.1 % similarity; however, the level of DNA–DNA reassociation was only 26.7 %. The strains can also be discriminated from each other by several chemotaxonomic and biochemical traits. Phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of both strains with the genus Limnohabitans within the family Comamonadaceae. The two investigated strains represent the first isolated members of a narrow phylogenetic cluster (the so-called R-BT065 cluster) formed by a large number of environmental sequences and abundant populations detected in the pelagic zones of various freshwater habitats. We propose to place the two strains in separate novel species within the genus Limnohabitans, Limnohabitans planktonicus sp. nov., with the type strain II-D5T (=DSM 21594T =CIP 109844T), and Limnohabitans parvus sp. nov., with the type strain II-B4T (=DSM 21592T =CIP 109845T). The description of the genus Limnohabitans is emended accordingly.

scholarly journals Haloferax profundi sp. nov. and Haloferax marisrubri sp. nov., Isolated from the Discovery Deep Brine-Seawater Interface in the Red Sea

2020 ◽  
Vol 8 (10) ◽  
pp. 1475
Author(s):  
Guishan Zhang ◽  
Xiaoyan Dong ◽  
Yingjiao Sun ◽  
André Antunes ◽  
Tyas Hikmawan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Red Sea ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Negative ◽  
The 16S Rrna Gene

Two extremely halophilic archaeal strains, designated SB29T and SB3T, were isolated from the brine-seawater interface of Discovery Deep in the Red Sea. Cells of both strains were pleomorphic (irregular polyhedrals, ovals, and rods) and stained Gram-negative; colonies were pigmented pink. The sequence similarity of the 16S rRNA gene of strain SB29T with that of its most closely related validly described species (Hfx. sulfurifontis DSM 16227T) and that of strain SB3T with its closest validly described relative (Hfx. denitrificans ATCC 35960T) was 98.1% and 98.6%, respectively. The incomplete draft genomes of SB29T and SB3T are 3,871,125 bp and 3,904,985 bp in size, respectively, and their DNA G + C contents are 60.75% and 65.64%, respectively. The highest ANI values between the genomes of SB29T and SB3T and the most closely related genomes in GenBank were determined as 82.6% (Hfx. sulfurifontis ATCC BAA-897T, GenBank accession no. GCA_000337835.1) and 92.6% (Haloferax denitrificans ATCC 35960T, GenBank accession no. GCA_000337795.1), respectively. These data indicate that the two new isolates cannot be classified into any recognized species of the genus Haloferax, and, therefore, two novel species of the genus Haloferax are proposed: Haloferax profundi sp. nov. (type strain SB29T = JCM 19567T = CGMCC 1.14960T) and Haloferax marisrubri sp. nov. (type strain SB3T = JCM 19566T = CGMCC 1.14958T).

Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Hisami Kobayashi ◽  
Yasuhiro Tanizawa ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
Masanori Tohno
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

The taxonomic status of the species Clostridium methoxybenzovorans was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection ( C. methoxybenzovorans ATCC 700855T) is a member of the species Eubacterium callanderi . Hence, C. methoxybenzovorans ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of Lacrimispora indolis (recently reclassified from Clostridium indolis ) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA–DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis .

Calditerricola satsumensis gen. nov., sp. nov. and Calditerricola yamamurae sp. nov., extreme thermophiles isolated from a high-temperature compost

2011 ◽  
Vol 61 (3) ◽  
pp. 631-636 ◽  
Author(s):  
Toshiyuki Moriya ◽  
Tomohisa Hikota ◽  
Isao Yumoto ◽  
Takashi Ito ◽  
Yusuke Terui ◽  
...  
Keyword(s):  
High Temperature ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Synthetic Medium ◽  
Rrna Gene ◽  
Isoleucine Leucine ◽  
Micro Organisms ◽  
The 16S Rrna Gene

Two novel thermophilic micro-organisms, designated YMO81T and YMO722T, were isolated from a high-temperature compost (internal temperature >95 °C). The isolates were able to grow at 80 °C in a nutrient broth and in a synthetic medium. Cells were aerobic, Gram-negative rods (0.3×4.0 μm). Spore formation was not observed. Strain YMO81T grew at 83 °C and pH 6.9–8.9 and grew optimally at 78 °C and pH 7.5 with 2 % NaCl. For growth in a synthetic minimal medium at 70 °C, the vitamins biotin, folic acid and thiamine and the amino acids glutamine and methionine were essential for growth of both strains; at 80 °C, strain YMO81T also required histidine, isoleucine, leucine, lysine, phenylalanine, serine, tryptophan and valine. Cellular fatty acids of the isolates comprised mainly iso-C17 : 0 and anteiso-C17 : 0. The DNA G+C contents of strains YMO81T and YMO722T were 70 and 64 mol%, respectively. When the 16S rRNA gene sequences of the isolates were compared with those of other bacteria, highest similarity was observed with Planifilum yunnanense LA5T (90 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain YMO722T and strain YMO81T was 55 %. N 4-Aminopropylspermine was identified as a major polyamine, which suggested that the isolates were distinct from other related taxa. On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, we propose a new genus, Calditerricola gen. nov., and two novel species, the type species Calditerricola satsumensis sp. nov., with type strain YMO81T (=ATCC BAA-1462T =JCM 14719T =DSM 45223T), and Calditerricola yamamurae sp. nov., with type strain YMO722T (=ATCC BAA-1461T =JCM 14720T =DSM 45224T).

scholarly journals Emended description of the genus Actinokineospora Hasegawa 1988 and transfer of Amycolatopsis fastidiosa Henssen et al. 1987 as Actinokineospora fastidiosa comb. nov.

2010 ◽  
Vol 60 (6) ◽  
pp. 1444-1449 ◽  
Author(s):  
D. P. Labeda ◽  
N. P. Price ◽  
G. Y. A. Tan ◽  
M. Goodfellow ◽  
H.-P. Klenk
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Careful Evaluation ◽  
Emended Description

The species Amycolatopsis fastidiosa (ex Celmer et al. 1977) Henssen et al. 1987 was proposed, based on morphological and chemotaxonomic observations, for a strain originally described as ‘Pseudonocardia fastidiosa’ Celmer et al. 1977 in a US patent. In the course of a phylogenetic study of the taxa with validly published names within the suborder Pseudonocardineae based on 16S rRNA gene sequences, it became apparent that this species was misplaced in the genus Amycolatopsis. After careful evaluation of the phylogeny, morphology, chemotaxonomy and physiology of the type strain, it was concluded that this strain represents a species of the genus Actinokineospora that is unable to produce motile spores. The description of the genus Actinokineospora is therefore emended to accommodate species that do not produce motile spores, and it is proposed that Amycolatopsis fastidiosa be transferred to the genus Actinokineospora as Actinokineospora fastidiosa comb. nov. The type strain is NRRL B-16697T =ATCC 31181T =DSM 43855T =JCM 3276T =NBRC 14105T =VKM Ac-1419T.

scholarly journals Paenibacillus sabinae sp. nov., a nitrogen-fixing species isolated from the rhizosphere soils of shrubs

2007 ◽  
Vol 57 (1) ◽  
pp. 6-11 ◽  
Author(s):  
Yuchao Ma ◽  
Zhiqiang Xia ◽  
Xuming Liu ◽  
Sanfeng Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Significant Feature ◽  
Rrna Gene ◽  
The Novel ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Rhizosphere Soils

Five novel endospore-forming, nitrogen-fixing bacterial strains were isolated from the rhizosphere soils of plants of the species Sabina squamata, Weigela florida and Zanthoxylum simulans. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the five strains formed a distinct cluster within the genus Paenibacillus. These novel strains showed the highest levels (96.2–98.2 %) of 16S rRNA gene sequence similarity with Paenibacillus azotofixans. However, the DNA–DNA relatedness between these novel strains and P. azotofixans was 12.9–29.5 %. The DNA G+C contents of the five strains were found to be 51.9–52.9 mol%. Phenotypic analyses showed that a significant feature of the novel strains (differentiating them from P. azotofixans and other Paenibacillus species) is that all of them were unable to produce acid and gas from various carbohydrates such as glucose, sucrose, lactose and fructose. Anteiso-branched C15 : 0 was the major fatty acid present in the novel type strain. On the basis of these data, the five novel strains represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sabinae sp. nov. is proposed. The type strain is T27T (=CCBAU 10202T=DSM 17841T).

scholarly journals Idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer Pseudidiomarina aestuarii to the genus Idiomarina as Idiomarina aestuarii comb. nov.

2011 ◽  
Vol 61 (4) ◽  
pp. 969-973 ◽  
Author(s):  
Liping Wang ◽  
Qiliang Lai ◽  
Yuanyuan Fu ◽  
Hua Chen ◽  
Wanpeng Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Surface Seawater ◽  
Chromosomal Dna ◽  
16S Rrna Gene Sequences ◽  
Pr China ◽  
The 16S Rrna Gene

A taxonomic study was carried out on strain 10-D-4T, which was isolated from a crude oil-degrading consortium enriched from surface seawater collected around Xiamen Island, PR China. Strain 10-D-4T grew optimally at pH 7.0–8.0 and at 25 °C. The 16S rRNA gene sequence of strain 10-D-4T showed the highest similarity to those of Idiomarina salinarum ISL-52T (94.6 %), Idiomarina tainanensis PIN1T (94.2 %) and Idiomarina seosinensis CL-SP19T (94.1 %), and showed lower similarity (92.3–94.0 %) to other members of the genus Idiomarina. The major isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were iso-C13 : 0 (5.2 %), iso-C15 : 0 (15.3 %), C16 : 0 (14.3 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (6.6 %), iso-C17 : 0 (15.4 %) and C18 : 1ω7c (13.5 %). The G+C content of the chromosomal DNA was 50.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain 10-D-4T represents a novel species of the genus Idiomarina, for which the name Idiomarina xiamenensis sp. nov. is proposed. The type strain is 10-D-4T ( = CCTCC AB 209061T  = LMG 25227T  = MCCC 1A01370T). We also propose the transfer of Pseudidiomarina aestuarii, described recently, to the genus Idiomarina as Idiomarina aestuarii comb. nov. (type strain KYW314T  = KCTC 22740T  = JCM 16344T).

scholarly journals Pontibacter chinhatensis sp. nov., isolated from pond sediment containing discarded hexachlorocyclohexane isomer waste

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2248-2254 ◽  
Author(s):  
Amit Kumar Singh ◽  
Nidhi Garg ◽  
Rup Lal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Pond Sediment ◽  
The 16S Rrna Gene

A halotolerant, Gram-negative, rod-shaped and light-red-pigmented bacterium, designated LP51T, was isolated from pond sediment near a hexachlorocyclohexane dumpsite located at Chinhat, Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LP51T formed a distinct phyletic clade along with the members of the genus Pontibacter. The 16S rRNA gene sequence similarity to members of the genus Pontibacter ranged from 94.2 to 99.4  %. The cells were motile, aerobic and catalase- and oxidase-positive. The major fatty acids were iso-C15  :  0 (17.8  %), iso-C15  :  0 3-OH (8.8  %), iso-C17  :  0 3-OH (5.7  %), summed feature 3 (C16  :  1ω7c and/or C16  :  1ω6c; 6.5  %) and summed feature 4 (iso-C17  :  1 I and/or anteiso-C17  :  1 B; 30.7  %). The polar lipid profile of strain LP51T showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, unknown aminolipids, unknown polar lipids and unknown glycolipids. DNA–DNA relatedness of strain LP51T with respect to the most closely related type strain, Pontibacter korlensis X14-1T, was 47.2  %. On the basis of this information, it is proposed that the isolate be assigned to a novel species of the genus Pontibacter, for which the name Pontibacter chinhatensis sp. nov. is proposed. The type strain is LP51T ( = CCM 8436T = MCC 2070T).

scholarly journals Lactobacillus hayakitensis sp. nov., isolated from intestines of healthy thoroughbreds

2007 ◽  
Vol 57 (12) ◽  
pp. 2836-2839 ◽  
Author(s):  
Hidetoshi Morita ◽  
Chiharu Shiratori ◽  
Masaru Murakami ◽  
Hideto Takami ◽  
Yukio Kato ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Biochemical Characterization ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Reassociation ◽  
The 16S Rrna Gene

Two strains, KBL13T and GBL13, were isolated as one of intestinal lactobacilli from the faecal specimens from different thoroughbreds of the same farm where they were born in Hokkaido, Japan. They were Gram-positive, facultatively anaerobic, catalase-negative, non-spore-forming and non-motile rods. KBL13T and GBL13 homofermentatively metabolize glucose, and produce lactate as the sole final product from glucose. The 16S rRNA gene sequence, DNA–DNA hybridization, DNA G+C content and biochemical characterization indicated that these two strains, KBL13T and GBL13, belong to the same species. In the representative strain, KBL13T, the DNA G+C content was 34.3 mol%. Lactobacillus salivarius JCM 1231T (=ATCC 11741T; AF089108) is the type strain most closely related to the strain KBL13T as shown in the phylogenetic tree, and the 16S rRNA gene sequence identity showed 96.0 % (1425/1484 bp). Comparative 16S rRNA gene sequence analysis of this strain indicated that the two isolated strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives, L. salivarius, Lactobacillus aviarius, Lactobacillus saerimneri and Lactobacillus acidipiscis. DNA–DNA reassociation experiments with L. salivarius and L. aviarius confirmed that KBL13T represents a novel species, for which the name Lactobacillus hayakitensis sp. nov. is proposed. The type strain is KBL13T (=JCM 14209T=DSM 18933T).

scholarly journals Haloargentinum marplatensis gen. nov., sp. nov., a novel extremely halophilic bacterium isolated from salted-ripened anchovy (Engraulis anchoita)

2020 ◽  
Author(s):  
Silvina Perez ◽  
Margarita Gomila ◽  
Silvia Elena Murialdo ◽  
Irene Mabel Ameztoy ◽  
Narjol Gonzalez-Escalona ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Type Strain ◽  
Close Relationships ◽  
Halophilic Bacterium ◽  
Rrna Gene ◽  
Gram Negative ◽  
Novel Genus And Species ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

ABSTRACTA facultative aerobic, Gram-negative, motile, non-endospore forming and extremely halophilic bacterium, strain 11aii⊺, isolated from salted-ripened anchovy, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA gene revealed close relationships to species of the genera Lentibacillus and Virgibacillus (94.2% similarity). The organism grew optimally in the presence of 20-35 % NaCl. The major fatty acids of strain 11aii⊺ were C16:0 (42.1%) and anteiso-C15:0 (31.2%) and also presented iso-C16:0 (11.0%), anteiso-C17:0 (10.4%) and C18:0 (5.2%). Based on data presented here, strain 11aii⊺ is considered to represent a novel genus and species, for which the name Haloargentinum marplatensis gen. nov. sp. nov. is proposed with the strain 11aii⊺ as type strain.

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