scholarly journals Halalkalicoccus jeotgali sp. nov., a halophilic archaeon from shrimp jeotgal, a traditional Korean fermented seafood

2007 ◽  
Vol 57 (10) ◽  
pp. 2296-2298 ◽  
Author(s):  
Seong Woon Roh ◽  
Young-Do Nam ◽  
Ho-Won Chang ◽  
Youlboong Sung ◽  
Kyoung-Ho Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Biochemical Tests ◽  
Extremely Halophilic Archaeon ◽  
Physiological And Biochemical

A novel, extremely halophilic archaeon B3T was isolated from shrimp-salted seafood. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Strain B3T is non-motile, Gram-variable, requires at least 10 % (w/v) NaCl for growth and grows in the ranges of 21–50 °C and pH 6.5–9.0. The DNA G+C content of strain B3T was 63.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain B3T belonged to the genus Halalkalicoccus and was phylogenetically closely related to the type strain Halalkalicoccus tibetensis (98.64 %). However, DNA–DNA hybridization experiments showed 7.0 % relatedness between strain B3T and a strain of a reference species of the genus Halalkalicoccus. Combined analysis of 16S rRNA gene sequences, DNA–DNA relatedness data, physiological and biochemical tests indicated that the genotypic and phenotypic characteristics differentiate strain B3T from other Halalkalicoccus species. On the basis of the evidence presented in this report, strain B3T represents a novel species of the genus Halalkalicoccus, for which the name Halalkalicoccus jeotgali. sp. nov. is proposed. The type strain is B3T (=KCTC 4019T=DSM 18796T=JCM 14584T=CECT 7217T).

scholarly journals Halovarius luteus gen. nov., sp. nov., an extremely halophilic archaeon from a salt lake

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2420-2425 ◽  
Author(s):  
Maliheh Mehrshad ◽  
Mohammad Ali Amoozegar ◽  
Ali Makhdoumi ◽  
Mehrnoosh Rasooli ◽  
Basaer Asadi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hypersaline Environment ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Brine Sample ◽  
The Family ◽  
Extremely Halophilic Archaeon

An extremely halophilic archaeon, strain DA50T, was isolated from a brine sample of Urmia lake, a hypersaline environment in north-west Iran. Strain DA50T was orange-pigmented, motile, pleomorphic and required at least 2.5 M NaCl but not MgCl2 for growth. Optimal growth was achieved at 4.0 M NaCl and 0.3 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 45 °C, while it was able to grow over a pH range of 6.5–8.0 and a temperature range of 25–50 °C. Analysis of 16S rRNA gene sequences revealed that strain DA50T is a member of the family Halobacteriaceae, showing a low level of similarity with other members of this family. Highest similarities, 94.4, 94.0 and 93.9 %, were obtained with the 16S rRNA gene sequences of the type strains of Natrialba aegyptia, Halobiforma lacisalsi and Halovivax asiaticus, respectively. Polar lipid analyses revealed that strain DA50T contains phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Four unidentified glycolipids and two minor phospholipids were also observed. The only quinone present was MK-8(II-H2). The G+C content of its DNA was 62.3 mol%. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain DA50T is thus considered to represent a novel species of a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Halovarius luteus gen. nov., sp. nov. is proposed. The type strain of Halovarius luteus is DA50T ( = IBRC-M 10912T = CECT 8510T).

scholarly journals Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex

2011 ◽  
Vol 61 (7) ◽  
pp. 1606-1611 ◽  
Author(s):  
Enrico Tortoli ◽  
Erik C. Böttger ◽  
Anna Fabio ◽  
Enevold Falsen ◽  
Zoe Gitti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polyphasic Analysis ◽  
Mycobacterium Simiae

Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228T ( = DSM 45397T  = CCUG 58464T) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the ‘Mycobacterium simiae complex’ for this group.

Anaerostipes butyraticus sp. nov., an anaerobic, butyrate-producing bacterium from Clostridium cluster XIVa isolated from broiler chicken caecal content, and emended description of the genus Anaerostipes

2010 ◽  
Vol 60 (5) ◽  
pp. 1108-1112 ◽  
Author(s):  
Venessa Eeckhaut ◽  
Filip Van Immerseel ◽  
Frank Pasmans ◽  
Evie De Brandt ◽  
Freddy Haesebrouck ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Broiler Chicken ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Caecal Content ◽  
Emended Description ◽  
Bacterial Clone

Four butyrate-producing isolates were obtained from the caecal content of a 4-week-old broiler chicken. The 16S rRNA gene sequences were determined and confirmed the close relatedness of the four isolates, which suggested that they were derived from a single bacterial clone. Phylogenetic analysis based on 16S rRNA gene sequences showed that its closest relatives were members of cluster XIVa of the Clostridium subphylum of Gram-positive bacteria and that the closest related type strain was Anaerostipes caccae L1-92T (94.5 % similarity). Similarity levels of 96–98 % with sequences from uncultured bacteria from human stool samples were observed. On the basis of morphological, biochemical and phylogenetic characteristics, this strain is assigned to a novel species in the genus Anaerostipes, for which the name Anaerostipes butyraticus sp. nov. is proposed. The type strain is 35-7T (=LMG 24724T =DSM 22094T). An emended description of the genus Anaerostipes is also provided.

scholarly journals Halorubrum ezzemoulense sp. nov., a halophilic archaeon isolated from Ezzemoul sabkha, Algeria

2006 ◽  
Vol 56 (7) ◽  
pp. 1583-1588 ◽  
Author(s):  
Karima Kharroub ◽  
Teresa Quesada ◽  
Raquel Ferrer ◽  
Susana Fuentes ◽  
Margarita Aguilera ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
16S Rrna Gene Sequences ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Extremely Halophilic Archaeon ◽  
Derivatives Of

A novel extremely halophilic archaeon was isolated from Ezzemoul sabkha, Algeria. The strain, designated 5.1T, was neutrophilic, motile and Gram-negative. At least 15 % (w/v) NaCl was required for growth. The isolate grew at pH 6.5–9.0, with optimum growth at pH 7.0–7.5. Mg2+ was required for growth. Polar lipids were C20C20 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, and phosphatidylglycerol sulfate and sulfated diglycosyl diether. The genomic DNA G+C content of strain 5.1T was 61.9 mol% (T m). Phylogenetic analysis based on comparison of 16S rRNA gene sequences revealed that strain 5.1T clustered with Halorubrum species. The results of DNA–DNA hybridization and biochemical tests allowed genotypic and phenotypic differentiation of strain 5.1T from other Halorubrum species. The name Halorubrum ezzemoulense sp. nov. (type strain 5.1T=CECT 7099T=DSM 17463T) is proposed.

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 Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet

2007 ◽  
Vol 57 (10) ◽  
pp. 2221-2227 ◽  
Author(s):  
Sören Muurholm ◽  
Sylvie Cousin ◽  
Orsola Päuker ◽  
Evelyne Brambilla ◽  
Erko Stackebrandt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Hard Water ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Close Relationship ◽  
Metabolic Properties ◽  
North Germany

Five isolates that were related phylogenetically to members of the genus Pedobacter were isolated from freshwater of the hard-water creek Westerhöfer Bach, North Germany. The five strains (WB 2.1-25T, WB 2.3-71T, WB 3.3-3T, WB 3.3-22T and WB 2.3-45T) were Gram-negative and chemoheterotrophic, with rod-shaped cells. Most of their metabolic properties matched those given in the description of the genus Pedobacter. Consistent with the genus description, their fatty acids included mainly iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c, iso-C15 : 0 2-OH or both); C16 : 1 ω5c, C16 : 0, iso-C15 : 0 3-OH, C16 : 0 3-OH and iso-C17 : 0 3-OH were present in smaller amounts. The major isoprenoid quinone was menaquinone 7. With one exception, binary similarity values of the almost complete 16S rRNA gene sequences determined among the isolates as well as between the isolates and type strains of Pedobacter species were lower than 98.5 %. The only exception was the close relationship between Pedobacter caeni DSM 16990T and strain WB 2.3-45T (99.2 % similarity). DNA–DNA reassociation values determined for this pair of strains was 29.8 %, indicating that strain WB 2.3-45T represents a unique genospecies. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WB 2.1-25T and WB 2.3-71T form a group that is moderately related to P. caeni and strain WB 2.3-45T (98.5 % similarity). Strains WB 3.3-3T and WB 3.3-22T (98.5 % similarity) branched separately from these four organisms. The five phylogenetically isolated strains differed from each other as well as from the type strain of the type species (Pedobacter heparinus DSM 2366T) and some related representatives of the genus in several metabolic reactions and cultural parameters. On the basis of phenotypic and phylogenetic distinctiveness, five novel species are proposed: Pedobacter duraquae sp. nov., with WB 2.1-25T (=DSM 19034T=CIP 109481T) as the type strain; Pedobacter westerhofensis sp. nov., with WB 3.3-22T (=DSM 19036T=CIP 109479T) as the type strain; Pedobacter metabolipauper sp. nov., with WB 2.3-71T (=DSM 19035T=CIP 109480T) as the type strain; Pedobacter hartonius sp. nov., with WB 3.3-3T (=DSM 19033T=CIP 109468T) as the type strain; and Pedobacter steynii sp. nov., with WB 2.3-45T (=DSM 19110T=CIP 109507T) as the type strain.

Algoriphagus pacificus sp. nov. and Algoriphagus oliviformis sp. nov., isolated from a mariculture fishpond

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Huibin Lu ◽  
Zhipeng Cai ◽  
Tongchu Deng ◽  
Youfeng Qian ◽  
Meiying Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13CT and H41T) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13CT and H41T shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus Algoriphagus . YJ13CT only shared 93.8 % 16S rRNA gene sequence similarity with H41T. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13CT and H41T clustered closely with species of the genus Algoriphagus . The calculated pairwise orthologous average nucleotide identity with usearch (OrthoANIu) values between strains YJ13CT and H41T and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13CT and H41T was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13CT and H41T and their major cellular fatty acids contained iso-C15 : 0, C16 : 1 ω7c and C17 : 1 ω9c. The polar lipids profiles of YJ13CT and H41T consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13CT and H41T represent two distinct novel species of the genus Algoriphagus , for which the names Algoriphagus pacificus sp. nov. (type strain YJ13CT=GDMCC 1.2178T=KCTC 82450T) and Algoriphagus oliviformis sp. nov. (type strain H41T=GDMCC 1.2179T=KCTC 82451T) are proposed.

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 Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes

2007 ◽  
Vol 57 (9) ◽  
pp. 2073-2078 ◽  
Author(s):  
Jennifer C. Ast ◽  
Ilse Cleenwerck ◽  
Katrien Engelbeen ◽  
Henryk Urbanczyk ◽  
Fabiano L. Thompson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Housekeeping Gene ◽  
Photobacterium Phosphoreum ◽  
Aflp Analysis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Biochemical Tests

Six representatives of a luminous bacterium commonly found in association with deep, cold-dwelling marine fishes were isolated from the light organs and skin of different fish species. These bacteria were Gram-negative, catalase-positive, and weakly oxidase-positive or oxidase-negative. Morphologically, cells of these strains were coccoid or coccoid-rods, occurring singly or in pairs, and motile by means of polar flagellation. After growth on seawater-based agar medium at 22 °C for 18 h, colonies were small, round and white, with an intense cerulean blue luminescence. Analysis of 16S rRNA gene sequence similarity placed these bacteria in the genus Photobacterium. Phylogenetic analysis based on seven housekeeping gene sequences (16S rRNA gene, gapA, gyrB, pyrH, recA, rpoA and rpoD), seven gene sequences of the lux operon (luxC, luxD, luxA, luxB, luxF, luxE and luxG) and four gene sequences of the rib operon (ribE, ribB, ribH and ribA), resolved the six strains as members of the genus Photobacterium and as a clade distinct from other species of Photobacterium. These strains were most closely related to Photobacterium phosphoreum and Photobacterium iliopiscarium. DNA–DNA hybridization values between the designated type strain, Photobacterium kishitanii pjapo.1.1T, and P. phosphoreum LMG 4233T, P. iliopiscarium LMG 19543T and Photobacterium indicum LMG 22857T were 51, 43 and 19 %, respectively. In AFLP analysis, the six strains clustered together, forming a group distinct from other analysed species. The fatty acid C17 : 0 cyclo was present in these bacteria, but not in P. phosphoreum, P. iliopiscarium or P. indicum. A combination of biochemical tests (arginine dihydrolase and lysine decarboxylase) differentiates these strains from P. phosphoreum and P. indicum. The DNA G+C content of P. kishitanii pjapo.1.1T is 40.2 %, and the genome size is approximately 4.2 Mbp, in the form of two circular chromosomes. These strains represent a novel species, for which the name Photobacterium kishitanii sp. nov. is proposed. The type strain, pjapo.1.1T (=ATCC BAA-1194T=LMG 23890T), is a luminous symbiont isolated from the light organ of the deep-water fish Physiculus japonicus.

scholarly journals Neisseria wadsworthii sp. nov. and Neisseria shayeganii sp. nov., isolated from clinical specimens

2011 ◽  
Vol 61 (1) ◽  
pp. 91-98 ◽  
Author(s):  
William J. Wolfgang ◽  
Andrea N. Carpenter ◽  
Jocelyn A. Cole ◽  
Sabine Gronow ◽  
Andrea Habura ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Nearest Neighbours ◽  
23S Rrna Gene ◽  
Additional Support

An analysis of 16S rRNA gene sequences from archived clinical reference specimens has identified two novel Neisseria species. For each species, two strains from independent sources were identified. Amongst species with validly published names, the closest species to the newly identified organisms were Neisseria canis, N. dentiae, N. zoodegmatis, N. animaloris and N. weaveri. DNA–DNA hybridization studies demonstrated that the newly identified isolates represent species that are distinct from these nearest neighbours. Analysis of partial 23S rRNA gene sequences for the newly identified strains and their nearest neighbours provided additional support for the species designation. Bayesian analysis of 16S rRNA gene sequences suggested that the newly identified isolates belong to distinct but related species of the genus Neisseria, and are members of a clade that includes N. dentiae, N. bacilliformis and N. canis. The predominant cellular fatty acids [16 : 0, summed feature 3 (16 : 1ω7c and/or iso-15 : 0 2-OH) and 18 : 1ω7c], as well as biochemical and morphological analyses further support the designation of Neisseria wadsworthii sp. nov. (type strain 9715T =DSM 22247T =CIP 109934T) and Neisseria shayeganii sp. nov. (type strain 871T =DSM 22246T =CIP 109933T).

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