scholarly journals Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2586-2592 ◽  
Author(s):  
C. E. King ◽  
G. M. King
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Thermomicrobium Roseum ◽  
Ph Range

Two thermophilic, Gram-stain-positive, rod-shaped, non-spore-forming bacteria (strains KI3T and KI4T) were isolated from geothermally heated biofilms growing on a tumulus in the Kilauea Iki pit crater on the flank of Kilauea Volcano (Hawai‘i, USA). Strain KI3T grew over an examined temperature range of 50–70 °C (no growth at 80 °C) and a pH range of 6.0–9.0, with optimum growth at 70 °C and pH 7.0. Strain KI4T grew at temperatures of 55–70 °C and a pH range of 5.8–8.0, with optimum growth at 65 °C and pH 6.7–7.1. The DNA G+C contents of strains KI3T and KI4T were 66.0 and 60.7 mol%, respectively. The major fatty acid for both strains was 12-methyl C18 : 0. Polar lipids in strain KI3T were dominated by glycolipids and phosphatidylinositol, while phosphatidylinositol and phosphoglycolipids dominated in strain KI4T. Strain KI3T oxidized carbon monoxide [6.7±0.8 nmol CO h−1 (mg protein)−1], but strain KI4T did not. 16S rRNA gene sequence analyses determined that the strains belong to the class Thermomicrobia , and that strains KI3T and KI4T are related most closely to Thermomicrobium roseum DSM 5159T (96.5 and 91.1 % similarity, respectively). 16S rRNA gene sequence similarity between strain KI3T and strain KI4T was 91.4 %. Phenotypic features and phylogenetic analyses supported the affiliation of strain KI3T to the genus Thermomicrobium , while results of chemotaxonomic, physiological and biochemical assays differentiated strains KI3T and KI4T from Thermomicrobium roseum . Strain KI3T ( = DSM 27067T = ATCC BAA-2535T) is thus considered to be the type strain of a novel species, for which the name Thermomicrobium carboxidum sp. nov. is proposed. Additionally, the characterization and phylogenetic position of strain KI4T showed that it represents a novel species of a new genus, for which the name Thermorudis peleae gen. nov., sp. nov. is proposed. The type strain of Thermorudis peleae is KI4T ( = DSM 27169T = ATCC BAA-2536T).

Sneathia vaginalis sp. nov. (Fusobacteriales, Leptotrichiaceae) as a replacement of the species ‘Sneathia amnii’ Harwich et al. 2012 and ‘Leptotrichia amnionii’ Shukla et al. 2002, and emended description of Sneathia Collins et al. 2001

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Tobias Eisenberg ◽  
Sabine Gronow ◽  
Jane Falgenhauer ◽  
Can Imirzalioglu ◽  
Kristin Mühldorfer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Members of the genus Sneathia are fastidious bacteria that predominantly colonise the female genital tract and are significantly associated with reproductive disorders and genital and neonatal disease. From a taxonomical perspective, the genus only comprises the species Sneathia sanguinegens . Numerous reports on a second species, ‘Sneathia amnii’, have been published, but the name has never been validated. The same is the case for ‘Leptotrichia amnionii’, which was previously shown to belong to the same species as ‘Sneathia amnii’. We studied strains DSM 16631T and DSM 16630, which have been identified and deposited as ‘Leptotrichia amnionii’ previously. At the time of isolation, these strains were found to be most closely related to, but clearly different from, Sneathia sanguinegens based on 16S rRNA gene sequence similarities. Both strains proved to be almost indistinguishable from ‘Sneathia amnii’ based on molecular, morphological and physiological traits. The 16S rRNA gene sequence analysis revealed that strain DSM 16631T was assigned to the genus Sneathia with a sequence similarity of 95.47 % to Sneathia sanguinegens CCUG 41628T, followed by type strains of Caviibacter abscessus (93.03 %), Oceanivirga salmonicida (92.68 %) and Oceanivirga miroungae (91.97 %) as the next closely related members of the Leptotrichiaceae . The novel species was also clearly differentiated from other related taxa by core genome phylogeny, average nucleotide and amino acid identities, in silico DNA–DNA hybridization and MALDI-TOF MS. With respect to chemotaxonomic and physiological patterns, strains DSM 16631T and DSM 16630 were again highly similar to Sneathia sanguinegens . On the basis of these data, we propose the novel species Sneathia vaginalis sp. nov. with the type strain DSM 16631T (=CCUG 52977T=CCUG 52889AT) and a second strain DSM 16630 (=CCUG 52976=CCUG 52888) that were both isolated from bloodstream infections in women with puerperal fever in France. The G+C content of the DNA of the type strain is 28.4 mol% and the genome size is 1.28 Mbp. Based on the observed extremely high similarities of genotypic and phenotypic traits of the novel proposed species to those reported for ‘Sneathia amnii’, we recommend using this new name in all further publications on this taxon.

Bombella favorum sp. nov. and Bombella mellum sp. nov., two novel species isolated from the honeycombs of Apis mellifera

2021 ◽  
Author(s):  
Maik Hilgarth ◽  
Johannes Redwitz ◽  
Matthias A. Ehrmann ◽  
Rudi F. Vogel ◽  
Frank Jakob
Keyword(s):  
Apis Mellifera ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

As part of a study investigating the microbiome of bee hives and honey, two novel strains (TMW 2.1880T and TMW 2.1889T) of acetic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they cannot be assigned to known species. The isolates are Gram-stain-negative, aerobic, pellicle-forming, catalase-positive and oxidase-negative. Cells of TMW 2.1880T are non-motile, thin/short rods, and cells of TMW 2.1889T are motile and occur as rods and long filaments. Morphological, physiological and phylogenetic analyses revealed a distinct lineage within the genus Bombella . Strain TMW 2.1880T is most closely related to the type strain of Bombella intestini with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 94.16 and 56.3 %, respectively. The genome of TMW 2.1880T has a size of 1.98 Mb and a G+C content of 55.3 mol%. Strain TMW 2.1889T is most closely related to the type strain of Bombella apis with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 85.12 and 29.5 %, respectively. The genome of TMW 2.1889T has a size of 2.07 Mb and a G+C content of 60.4 mol%. Ubiquinone analysis revealed that both strains contained Q-10 as the main respiratory quinone. Major fatty acids for both strains were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8, respectively, and additionally C14 : 0 2-OH only for TMW 2.1880T and C14 : 0 only for TMW 2.1889T. Based on polyphasic evidence, the two isolates from honeycombs of Apis mellifera represent two novel species of the genus Bombella , for which the names Bombella favorum sp. nov and Bombella mellum sp. nov. are proposed. The designated respective type strains are TMW 2.1880T (=LMG 31882T=CECT 30114T) and TMW 2.1889T (=LMG 31883T=CECT 30113T).

Paraburkholderia acidiphila sp. nov., Paraburkholderia acidisoli sp. nov. and Burkholderia guangdongensis sp. nov., isolated from forest soil, and reclassification of Burkholderia ultramafica as Paraburkholderia ultramafica comb. nov.

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Zeng-hong Gao ◽  
Qiu-mei Zhang ◽  
Ying-ying Lv ◽  
You-qi Wang ◽  
Bing-nan Zhao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Three Gram-stain-negative, aerobic, motile and rod-shaped bacterial strains, 7Q-K02T, DHF22T and DHOM02T, were isolated from forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, China. Strains 7Q-K02T, DHF22T and DHOM02T grew at 4–37, 4–42 and 12–37 °C, pH 3.0–8.5, 3.5–8.5 and 5.0–8.0, and in the presence of 0–3.0, 0–3.5 and 0–2.5 % (w/v) NaCl; with optima at 28–33, 28 and 28–33 °C, pH 3.5–6.5, 4.0–5.5 and 6.5–7.0, and 0–1.5, 0–1.5 and 0.5–1.5 % (w/v) NaCl, respectively. Strains 7Q-K02T and DHF22T have the highest 16S rRNA gene sequence similarities of 99.0 and 98.0 % to Paraburkholderia sacchari LMG 19450T and 97.7 % between themselves, while strain DHOM02T shares the highest similarity of 98.4 % to ‘Burkholderia rinojensis’ A396T followed by 98.3 % to Burkholderia plantarii ATCC 43733T. In the 16S rRNA gene sequence phylogram, strain 7Q-K02T formed a sister branch with Paraburkholderia sacchari , Paraburkholderia oxyphila and Paraburkholderia paradisi , and strain DHF22T was separated from all other species within the genus Paraburkholderia , while strain DHOM02T formed a separated clade with members of the genus Burkholderia . The DNA G+C contents of strains 7Q-K02T, DHF22T and DHOM02T wwe 64.3, 65.4 and 66.6 %, respectively. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strains 7Q-K02T, DHF22T and closely related Paraburkholderia strains were in the ranges of 25.5–43.7 % and 81.5–91.3 %, respectively. While dDDH and ANI values between strain DHOM02T and Burkholderia strains with genome sequence data were in the ranges of 22.4–31.0 % and 78.2–86.1 %, respectively. These three strains have the same major respiratory quinone: ubiquinone-8. Strains 7Q-K02T, DHF22T and DHOM02T have C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c) as their major fatty acid compositions. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of phenotypic, phylogenetic, genomic analyses and chemotaxonomic data, strains 7Q-K02T and DHF22T represent two novel species of the genus Paraburkholderia , for which the names Paraburkholderia acidiphila sp. nov. (type strain 7Q-K02T=CGMCC 1.15433T=KCTC 62472T=LMG 29209T) and Paraburkholderia acidisoli sp. nov. (type strain DHF22T=GDMCC 1.1448T=LMG 30262T) are proposed, while strain DHOM02T represents a novel species in the genus Burkholderia , for which the name Burkholderia guangdongensis sp. nov. (type strain DHOM02T=KCTC 42625T=LMG 28843T) is proposed. We also propose to transfer Burkholderia ultramafica to the genus Paraburkholderia as Paraburkholderia ultramafica comb. nov. based mainly on the results of phylogenomic analysis.

Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Muhammed Duman ◽  
Hilal Ay ◽  
Soner Altun ◽  
Nevzat Sahin ◽  
Izzet Burcin Saticioglu
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Internal Organs ◽  
Content Type ◽  
Link Type ◽  
Apparently Healthy

Two yellow-pigmented isolates, F-60T and F-392, were isolated from the internal organs of an apparently healthy rainbow trout (Oncorhynchus mykiss). The strains were identified as members of the genus Flavobacterium based on the results of 16S rRNA gene sequence analysis. Strains F-60T and F-392 had the highest 16S rRNA gene sequence identity level of 97.4 % to the type strain of Flavobacterium crassostreae LPB0076T. A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium . Digital DNA–DNA hybridization (dDDH) and average nucleotide identity based on blast (ANIb) values for strains F-60T and F-392 were calculated as 100 %. However, dDDH and ANI analyses between the strains and their close neighbours confirmed that both strains represent a novel species in the genus Flavobacterium . The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain of Flavobacterium frigidarium DSM 17623T while those values for F. crassostreae LPB0076T were obtained as 21.4–21.5 % and 76.3 %. The DNA G+C content of the strains was 34.5 mol%. Chemotaxonomic and phylogenomic analyses of these isolates confirmed that both strains are representatives of a novel species for which the name Flavobacterium muglaense sp. nov. is proposed, with F-60T as the type strain (=JCM 34196T=KCTC 82256T).

Rhodococcus cerastii sp. nov. and Rhodococcus trifolii sp. nov., two novel species isolated from leaf surfaces

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1024-1029 ◽  
Author(s):  
P. Kämpfer ◽  
S. Wellner ◽  
K. Lohse ◽  
N. Lodders ◽  
K. Martin
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two Gram-positive, non-endospore-forming rods, strains C5T and T8T , were isolated from the phyllospheres of Cerastium holosteoides and Trifolium repens, respectively, and were studied in detail for their taxonomic position. 16S rRNA gene sequence analysis allocated both isolates clearly to the genus Rhodococcus . Isolate C5T was most closely related to Rhodococcus fascians and Rhodococcus yunnanensis , showing 99.2 % gene sequence similarity to both species. Strain T8T revealed the highest 16S rRNA gene sequence similarity to Rhodococcus corynebacterioides (98.8 %) and Rhodococcus kroppenstedtii (98.6 %). The quinone system of both strains was composed of dihydrogenated menaquinones with eight (major amount) as well as nine, seven and six isoprenoid units (MK-8H2, MK-9H2 MK-7H2 MK-6H2).The polar lipid profiles of strains C5T and T8T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. Additionally, strain C5T contained one unknown glycolipid, and strain T8T three unknown aminolipids. The fatty acid profiles contained major amounts of C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0, which supported the grouping of the two isolates in the genus Rhodococcus . Physiological/biochemical characterization and DNA–DNA hybridizations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of both strains. For this reason, we propose strain C5T ( = LMG 26203T  = CCM 7906T) as the type strain of a novel species with the name Rhodococcus cerastii sp. nov., and strain T8T ( = LMG 26204T  = CCM 7905T) as the type strain of a second novel species with the name Rhodococcus trifolii sp. nov.

Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
...  
Keyword(s):  
Zea Mays ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus , most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA–DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK–6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.

scholarly journals Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1866-1875 ◽  
Author(s):  
Katharina J. Huber ◽  
Pia K. Wüst ◽  
Manfred Rohde ◽  
Jörg Overmann ◽  
Bärbel U. Foesel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Acidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the Acidobacteria are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the Acidobacteria were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4HT and Ac_23_E3T were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4HT and Ac_23_E3T were aerobic mesophiles with a broad range of tolerance towards pH (4.0–9.5 and 3.5–10.0, respectively) and temperature (15–44 and 12–47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4HT and Ac_23_E3T were iso-C15 : 0, summed feature 1 (C13 : 0 3-OH/iso-C15 : 1 H), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and anteiso-C17 : 0. The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4HT and Ac_23_E3T were 53.2 and 52.6 mol%, respectively. The closest described relative was Blastocatella fastidiosa A2-16T, with 16S rRNA gene sequence identity of 93.2 and 93.3 %, respectively. Strains A22_HD_4HT and Ac_23_E3T displayed 16S rRNA gene sequence similarity of 97.4 % to each other. On the basis of the low DNA–DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4HT = DSM 26555T = LMG 27985T) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3T = DSM 26558T = LMG 27597T).

scholarly journals Herbidospora mongoliensis sp. nov., isolated from soil, and reclassification of Herbidospora osyris and Streptosporangium claviforme as synonyms of Herbidospora cretacea

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2322-2329 ◽  
Author(s):  
Ismet Ara ◽  
Baljinova Tsetseg ◽  
Damdinsuren Daram ◽  
Manabu Suto ◽  
Katsuhiko Ando
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Analyses ◽  
Content Type ◽  
Link Type ◽  
Phospholipid Profile

A Gram-reaction-positive aerobic actinomycete, designated strain MN08-A0118T, which produced short chains of non-motile spores on the tips of long sporophores and formed yellow–brown colonies with branched substrate mycelium, was studied in detail to determine its taxonomic position. On the basis of 16S rRNA gene sequence analyses, strain MN08-A0118T was grouped into the genus Herbidospora , being most closely related to Streptosporangium claviforme (98.2 %), Herbidospora osyris (98.2 %), Herbidospora daliensis (98.2 %), Herbidospora cretacea (97.9 %) and Herbidospora yilanensis (97.4 %). Chemotaxonomic data supported allocation of the strain to the genus Herbidospora . MK-10(H4) was the predominant menaquinone with minor amounts of MK-10(H6), MK-10(H2) and MK-9(H4); the fatty acid profile contained major amounts of iso-C16 : 0, C17 : 0 10-methyl, iso-C14 : 0 and iso-C16 : 0 2-OH; the phospholipid profile contained phosphatidylethanolamine, phosphatidylmethylethanolamine and glucosamine-containing phospholipids; and the whole-cell sugars included ribose, glucose, galactose, madurose and rhamnose (trace). The phylogenetic data, phenotypic and genotypic properties and DNA–DNA hybridization differentiated this strain from its closely related strains, S. claviforme (35–54 % DNA–DNA relatedness), H. osyris (39–51 %), H. daliensis (3–16 %), H. cretacea (34–39 %) and H. yilanensis (34–42 %). Thus, MN08-A0118T represents a novel species of the genus Herbidospora , for which the name Herbidospora mongoliensis sp. nov. is proposed, with MN08-A0118T ( = NBRC 105882T  = VTCC D9-22T) as the type strain. In addition, DNA–DNA hybridization results showed that S. claviforme and H. osyris are synonyms of H. cretacea .

scholarly journals Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1488-1494 ◽  
Author(s):  
Daichi Fujii ◽  
Fumiko Nagai ◽  
Yohei Watanabe ◽  
Yukio Shirasawa
Keyword(s):  
Wastewater Treatment ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two Gram-staining-negative, strictly aerobic, non-endospore-forming, non-motile, rod-shaped bacteria, designated strains YIT 12745T and YIT 12746T, were isolated from sludge from a wastewater treatment plant. 16S rRNA gene sequence analyses indicated that these strains belonged to the genus Flavobacterium . In these analyses, strains YIT 12745T and YIT 12746T were most closely related to the type strains of Flavobacterium caeni and Flavobacterium terrigena , with 16S rRNA gene sequence similarity values of 94.9 % and 96.2 %, respectively. For both novel strains, menaquinone (MK-6) was the only respiratory quinone. The major fatty acids of strain YIT 12745T were iso-C15 : 1 G (14.4 %), iso-C16 : 0 (13.2 %), C15 : 0 (12.9 %), iso-C15 : 0 (12.9 %) and iso-C17 : 0 3-OH (11.5 %). Those of strain YIT 12746T were iso-C15 : 0 (21.5 %), iso-C16 : 0 (13.3 %), C15 : 0 (12.0 %) and iso-C15 : 1 G (11.9 %). The genomic DNA G+C contents of strains YIT 12745T and YIT 12746T were 48.7 and 30.9 mol%, respectively. From their differential phenotypic and phylogenetic characteristics, these strains are considered to represent two novel species of the genus Flavobacterium , for which the names Flavobacterium longum sp. nov. (type strain YIT 12745T = JCM 19141T = DSM 27077T) and Flavobacterium urocaniciphilum sp. nov. (type strain YIT 12746T = JCM 19142T = DSM 27078T) are proposed. Emended descriptions of Flavobacterium caeni and Flavobacterium terrigena are also proposed.

scholarly journals Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov.

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1342-1349 ◽  
Author(s):  
Mareike Jogler ◽  
Hong Chen ◽  
Julia Simon ◽  
Manfred Rohde ◽  
Hans-Jürgen Busse ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A previously undescribed aerobic, non-sporulating bacterium, strain G1A_585T, was isolated from an oligotrophic freshwater lake in Bavaria, Germany. The rod-shaped cells were Gram-stain-negative and non-motile. Based on 16S rRNA gene sequence similarity, strain G1A_585T was a member of the family Sphingomonadaceae and shared <95.2 % similarity with type strains of all members of the most closely related genus, Sphingopyxis . Phyogenetically, the isolate shared a root with strains of three marine species, Sphingopyxis flavimaris DSM 16223T, Sphingopyxis marina DSM 22363T and Sphingopyxis litoris DSM 22379T. The polar lipids of strain G1A_585T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipids, three glycolipids and one unknown lipid. Ubiquinone-10 was the dominant quinone (93.1 %) and ubiquinone-9 (6.5 %) was also detected. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 38.2 %); C16 : 1ω7c (33.6 %) and C14 : 0 2-OH (17.8 %). The major polyamine was spermidine and traces of 1,3-diaminopropane, putrescine and spermine were also detected. The DNA G+C content of strain G1A_585T was 55.7 mol% and the isolate was oxidase- and catalase-positive. Based on the phylogenetic relationship, the low DNA G+C content compared with most other members of the genus Sphingopyxis and the presence of signature nucleotides in the 16S rRNA gene sequence, a novel species in a new genus and species, Sphingorhabdus planktonica gen. nov., sp. nov., is proposed; the type strain of Sphingorhabdus planktonica is G1A_585T ( = DSM 25081T  = LMG 26646T). Because Sphingopyxis flavimaris DSM 16223T, Sphingopyxis marina DSM 22363T and Sphingopyxis litoris DSM 22379T form a phylogenetic group together with strain G1A_585T that is clearly separated from all other known Sphingopyxis strains and share signature nucleotides, these three Sphingopyxis strains are reclassified as members of the proposed novel genus Sphingorhabdus: Sphingorhabdus flavimaris comb. nov. (type strain SW-151T = DSM 16223T = KCTC 12232T), Sphingorhabdus marina comb. nov. (type strain FR1087T = DSM 22363T = IMSNU 14132T = KCTC 12763T = JCM 14161T) and Sphingorhabdus litoris comb. nov. (type strain FR1093T = DSM 22379T = IMSNU 14133T = KCTC 12764T = JCM 14162T).

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