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.

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 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 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.

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 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).

scholarly journals New insight into diversity in the genus Xenorhabdus, including the description of ten novel species

2006 ◽  
Vol 56 (12) ◽  
pp. 2805-2818 ◽  
Author(s):  
Patrick Tailliez ◽  
Sylvie Pagès ◽  
Nadège Ginibre ◽  
Noël Boemare
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Typing ◽  
Type Strain ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Group ◽  
The 16S Rrna Gene

We investigated the diversity of a collection of 76 Xenorhabdus strains, isolated from at least 27 species of Steinernema nematodes and collected in 32 countries, using three complementary approaches: 16S rRNA gene sequencing, molecular typing and phenotypic characterization. The 16S rRNA gene sequences of the Xenorhabdus strains were highly conserved (similarity coefficient >95 %), suggesting that the common ancestor of the genus probably emerged between 250 and 500 million years ago. Based on comparisons of the 16S rRNA gene sequences, we identified 13 groups and seven unique sequences. This classification was confirmed by analysis of molecular typing profiles of the strains, leading to the classification of new isolates into the Xenorhabdus species described previously and the description of ten novel Xenorhabdus species: Xenorhabdus cabanillasii sp. nov. (type strain USTX62T=CIP 109066T=DSM 17905T), Xenorhabdus doucetiae sp. nov. (type strain FRM16T=CIP 109074T=DSM 17909T), Xenorhabdus griffiniae sp. nov. (type strain ID10T=CIP 109073T=DSM 17911T), Xenorhabdus hominickii sp. nov. (type strain KE01T=CIP 109072T=DSM 17903T), Xenorhabdus koppenhoeferi sp. nov. (type strain USNJ01T=CIP 109199T=DSM 18168T), Xenorhabdus kozodoii sp. nov. (type strain SaVT=CIP 109068T=DSM 17907T), Xenorhabdus mauleonii sp. nov. (type strain VC01T=CIP 109075T=DSM 17908T), Xenorhabdus miraniensis sp. nov. (type strain Q1T=CIP 109069T=DSM 17902T), Xenorhabdus romanii sp. nov. (type strain PR06-AT=CIP 109070T=DSM 17910T) and Xenorhabdus stockiae sp. nov. (type strain TH01T=CIP 109067T=DSM 17904T). The Xenorhabdus strains studied here had very similar phenotypic patterns, but phenotypic features nonetheless differentiated the following species: X. bovienii, X. cabanillasii, X. hominickii, X. kozodoii, X. nematophila, X. poinarii and X. szentirmaii. Based on phenotypic analysis, we identified two major groups of strains. Phenotypic group GA comprised strains able to grow at temperatures of 35–42 °C, whereas phenotypic group GB comprised strains that grew at temperatures below 35 °C, suggesting that some Xenorhabdus species may be adapted to tropical or temperate regions and/or influenced by the growth and development temperature of their nematode host.

Flavobacterium lotistagni sp. nov. and Flavobacterium celericrescens sp. nov., isolated from freshwater habitats

2021 ◽  
Author(s):  
Jia-Hong Wu ◽  
Ya-Xiu You ◽  
Chiu-Chung Young ◽  
Soon-Wo Kwon ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Freshwater Habitats

This study presents taxonomic descriptions of strains CYK-4T and TWA-26T isolated from freshwater habitats in Taiwan. Both strains were Gram-stain-negative, strictly aerobic, motile by gliding and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that both strains belonged to the genus Flavobacterium . Analysis of 16S rRNA gene sequences showed that strains CYK-4T and TWA-26T shared 92.7 % sequence similarity and were most closely related to Flavobacterium ovatum W201ET (95.6 %) and Flavobacterium aquaticum JC164T (96.7 %), respectively. Both strains shared common chemotaxonomic characteristics comprising MK-6 as the main isoprenoid quinone, iso-C15 : 0 and iso-C15 : 1 G as the predominant fatty acids, phosphatidylethanolamine as the principal polar lipid, and homospermidine as the major polyamine. The DNA G+C contents of strains CYK-4T and TWA-26T were 41.5 and 31.8 mol%, respectively. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95–96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus Flavobacterium , for which the names Flavobacterium lotistagni sp. nov. (type strain CYK-4T=BCRC 81192T=LMG 31330T) and Flavobacterium celericrescens sp. nov. (type strain TWA-26T=BCRC 81200T=LMG 31333T) are proposed.

scholarly journals Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 90-94 ◽  
Author(s):  
P. García-Fraile ◽  
M. Chudíčková ◽  
O. Benada ◽  
J. Pikula ◽  
M. Kolařík
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

During the study of bacteria associated with bats affected by white-nose syndrome hibernating in caves in the Czech Republic, we isolated two facultatively anaerobic, Gram-stain-negative bacteria, designated strains 12T and 52T. Strains 12T and 52T were motile, rod-like bacteria (0.5–0.6 µm in diameter; 1–1.3 µm long), with optimal growth at 20–35 °C and pH 6–8. On the basis of the almost complete sequence of their 16S rRNA genes they should be classified within the genus Serratia ; the closest relatives to strains 12T and 52T were Serratia quinivorans DSM 4597T (99.5 % similarity in 16S rRNA gene sequences) and Serratia ficaria DSM 4569T (99.5 % similarity in 16S rRNA gene sequences), respectively. DNA–DNA relatedness between strain 12T and S. quinivorans DSM 4597T was only 37.1 % and between strain 52T and S. ficaria DSM 4569T was only 56.2 %. Both values are far below the 70 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Serratia as representatives of Serratia myotis sp. nov. (type strain 12T = CECT 8594T = DSM 28726T) and Serratia vespertilionis sp. nov. (type strain 52T = CECT 8595T = DSM 28727T).

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