Chitinophaga polysaccharea sp. nov., an exopolysaccharide-producing bacterium isolated from the rhizoplane of Dioscorea japonica

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 55-59 ◽  
Author(s):  
Song-Ih Han ◽  
Hyo-Jin Lee ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Dioscorea Japonica ◽  
Established Species ◽  
Type Strains ◽  
Sequence Similarities

A novel strain designated MRP-15T, belonging to the class Sphingobacteriia (phylum Bacteroidetes ), was isolated from the rhizoplane of Dioscorea japonica in South Korea and was characterized taxonomically using a polyphasic approach. The strain was found to comprise Gram-stain-negative, aerobic, non-motile, non-spore-forming rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Chitinophaga but was clearly separated from established species of the genus Chitinophaga . 16S rRNA gene sequence similarities between strain MRP-15T and type strains of established species of the genus Chitinophaga ranged from 90.3 to 97.8 %. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C15 : 0 and C16 : 1ω5c) supported the affiliation of strain MRP-15T with the genus Chitinophaga . Therefore strain MRP-15T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga polysaccharea sp. nov. is proposed. The type strain is MRP-15T ( = KACC 17184T = NCAIMB 02530T).

Reclassification of Parvularcula flava as Aquisalinus luteolus nom. nov. and emended description of the genus Aquisalinus

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Jun-Jie Ying ◽  
Zhi-Cheng Wu ◽  
Yuan-Chun Fang ◽  
Lin Xu ◽  
Cong Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79T and A. flavus D11M-2T, they showed 97.9 % sequence identity, much higher than the sequence identities 92.7–94.3 % between P. flava NH6-79T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79T and A. flavus D11M-2T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79T and A. flavus D11M-2T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79T and other closely related type strains (54.3 %–58.1 % and 68.6–70.4 %, respectively). P. flava NH6-79T and A. flavus D11M-2T also contained summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.

scholarly journals Chryseobacterium gallinarum sp. nov., isolated from a chicken, and Chryseobacterium contaminans sp. nov., isolated as a contaminant from a rhizosphere sample

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1419-1427 ◽  
Author(s):  
Peter Kämpfer ◽  
Marie T. Poppel ◽  
Gottfried Wilharm ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Rhizosphere Sample ◽  
Sequence Similarities

Two yellow-pigmented bacterial strains (100T and C26T), showing 98.4 % 16S rRNA gene sequence similarity to each other and isolated from a chicken in Germany and as a contaminant from an agar plate of a rhizosphere sample in Alabama, were studied by using a polyphasic taxonomic approach. Cells of both isolates were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequences of the two organisms with the sequences of the type strains of the most closely related species of the genus Chryseobacterium showed the highest sequence similarities of strains 100T and C26T to the type strains of Chryseobacterium joostei (respectively 97.5 and 98.2 %), C. viscerum (96.6, 97.8 %), C. gleum (97.1, 97.7 %), C. arthrosphaerae (97.3%, 97.7 %), C. indologenes (97.2, 97.7 %), C. tructae (96.6, 97.6 %), C. jejuense (97.0, 97.6 %) and C. oncorhynchi (96.3, 97.5 %); 16S rRNA gene sequence similarities to members of all other species of the genus Chryseobacterium were below 97.5 %. The fatty acid profiles of both strains consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 1ω9c and iso-C17 : 0 3-OH, but also showed slight differences (absence or presence of C16 : 0 3-OH and iso-C15 : 1 F). DNA–DNA hybridizations between the two strains and between the novel strains and the type strains of C. joostei , C. indologenes , C. jejuense , C. tructae and C. viscerum resulted in relatedness values clearly below 70 %. These DNA–DNA hybridization results and the differentiating biochemical and chemotaxonomic properties showed that both strains 100T and C26T represent novel species, for which the names Chryseobacterium gallinarum sp. nov. (type strain 100T = LMG 27808T = CCM 8493T) and Chryseobacterium contaminans sp. nov. (type strain C26T = LMG 27810T = CCM 8492T) are proposed.

scholarly journals Hymenobacter sediminis sp. nov., isolated from lake sediment

2020 ◽  
Vol 70 (3) ◽  
pp. 1895-1902 ◽  
Author(s):  
Chong Wang ◽  
Bang-Tao Liu ◽  
Rui Zhang ◽  
Chun-Li Liu ◽  
Zong-Jun Du
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Lake Sediment ◽  
Type Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Sequence Similarities

A Gram-stain-negative, facultatively aerobic, rod-shaped, motile by gliding and pink-pigmented bacterial strain, designated ELS1360T, was isolated from a lake sediment sample collected in Inner Mongolia, PR China. Strain ELS1360T grew optimally at 33 °C, at pH 6.5–7.0 and without NaCl. Strain ELS1360T exhibited 97.3, 97.1 and 96.9 % 16S rRNA gene sequence similarities to Hymenobacter aquatilis HMF3095T, Hymenobacter luteus JCM 30328T and Hymenobacter latericoloratus JCM 30327T, respectively, and 90.4–96.9 % to other members of the genus Hymenobacter . Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain ELS1360T belonged to the genus Hymenobacter and clustered with H. luteus JCM 30328T and H. latericoloratus JCM 30327T. The predominant cellular fatty acids were iso-C15:0, summed feature 3 and C16:1ω5c. Strain ELS1360T contained MK-7 as the sole menaquinone. The major polar lipids contained phosphatidylethanolamine and two unidentified lipids. The genomic DNA G+C content of strain ELS1360T was 57.1 mol%. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain ELS1360T represents a novel species within the genus Hymenobacter , for which the name Hymenobacter sediminis sp. nov. is proposed. The type strain is ELS1360T (=KCTC 62449T=MCCC 1H00319T).

Streptomyces genisteinicus sp. nov., a novel genistein-producing actinomycete isolated from a Chinese medicinal plant and proposal of Streptomyces michiganensis Corbaz et al. 1957 as a later heterotypic synonym of Streptomyces xanthochromogenes Arishima et al. 1956

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Siren Hu ◽  
Kaiqin Li ◽  
Yinfeng Wang ◽  
Yihui Guo ◽  
Meiliang Zhou ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Threshold Values ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Sequence Similarities

A novel genistein-producing actinobacterial strain, designated strain CRPJ-33T, was isolated from the healthy leaves of a medicinal plant Xanthium sibiricum collected from Hunan Province, PR China. 16S rRNA gene sequence analysis indicated strain CRPJ-33T belonged to the genus Streptomyces and had 99.7, 99.0, 98.9, 98.9, 98.8 and 98.7% sequence similarities to Streptomyces zhihengii YIM T102T, Streptomyces eurocidicus NRRL B-1676T, Streptomyces xanthochromogenes NRRL B-5410T, Streptomyces michiganensis NBRC 12797T, Streptomyces mauvecolor LMG 20100T and Streptomyces lavendofoliae NBRC 12882T, respectively. Phylogenetic analysis of 16S rRNA gene sequences showed that strain CRPJ-33T was most closely related to S. zhihengii YIM T102T. However, digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between them were much less than the recommended threshold values. Furthermore, differential comparisons of the phenotypic characteristics were enough to distinguish strain CRPJ-33T from S. zhihengii YIM T102T. Meanwhile, the ANI and dDDH values or MLSA distances between strain CRPJ-33T and other type strains, which exhibited ≥98.7 % 16S rRNA gene sequence similarities to strain CRPJ-33T, were far away from the recommended threshold values. Based on these results, it is thought that strain CRPJ-33T should represent a novel species of the genus Streptomyces , for which the name Streptomyces genisteinicus sp. nov. is proposed. The type strain is CRPJ-33T (=MCCC 1K04965T=JCM 34526T). In addition, the phenotypic, chemotaxonomic and genotypic characteristics, as well as phylogenetic information revealed that the type strains of S. xanthochromogenes and S. michiganensis should belong to same genomic species. Consequently, it is proposed that S. michiganensis is a heterotypic synonym of S. xanthochromogenes for which an emended description is given.

scholarly journals Cellulophaga geojensis sp. nov., a member of the family Flavobacteriaceae isolated from marine sand

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1354-1358 ◽  
Author(s):  
Sooyeon Park ◽  
Ki-Hoon Oh ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Marine Sand ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-negative, aerobic, non-flagellated, non-spore-forming, motile (by gliding) bacterial strain, designated M-M6T, was isolated from marine sand of Geoje island, Korea. Strain M-M6T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain M-M6T fell within the clade comprising Cellulophaga species, forming a coherent cluster with Cellulophaga lytica ATCC 23178T and Cellulophaga fucicola NN015860T, with which it shared 16S rRNA gene sequence similarities of 98.1 and 98.2 %, respectively. Sequence similarities between strain M-M6T and the type strains of other recognized Cellulophaga species were in the range 92.4–93.8 %. Strain M-M6T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The major polar lipids detected in strain M-M6T and the type strains of C. lytica and C. fucicola were two unidentified lipids, one unidentified aminolipid and one unidentified aminophospholipid. The DNA G+C content of strain M-M6T was 35.4 mol%. Levels of DNA–DNA relatedness between strain M-M6T and C. lytica JCM 8516T and C. fucicola JCM 21778T were 33 and 35 %, respectively. Differential phenotypic properties and phylogenetic and genetic distinctiveness distinguished strain M-M6T from all recognized Cellulophaga species. On the basis of the data presented, strain M-M6T is considered to represent a novel species of the genus Cellulophaga , for which the name Cellulophaga geojensis sp. nov. is proposed. The type strain is M-M6T ( = KCTC 23498T = CCUG 60801T).

scholarly journals Loktanella variabilis sp. nov., isolated from a tidal flat

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2579-2585 ◽  
Author(s):  
Ja-Min Park ◽  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Jae Yeol Cho ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Type Strains

Two Gram-negative, aerobic and rod-shaped or ovoid bacterial strains with different colony colours (greyish yellow and moderate orange), designated J-MR2-YT and J-MR2-O, were isolated from a tidal flat in the South Sea of South Korea. The two novel strains grew optimally at 35–37 °C. Strains J-MR2-YT and J-MR2-O showed no difference in their 16S rRNA gene sequences, and the mean DNA–DNA relatedness between them was 94 %. Phylogenetic trees based on 16S rRNA gene sequences revealed that strains J-MR2-YT and J-MR2-O clustered consistently with the type strains of Loktanella soesokkakensis , L. hongkongensis and L. cinnabarina , with which it exhibited 97.83–99.06 % sequence similarity. Sequence similarities to the type strains of the other recognized species of the genus Loktanella were 94.01–96.26 %. Both strains contained Q-10 as the predominant ubiquinone, C18 : 1ω7c as the major fatty acid and phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and one unidentified aminolipid as the major polar lipids. The DNA G+C contents of strains J-MR2-YT and J-MR2-O were 68.1 and 68.4 mol%, respectively, and DNA–DNA relatedness values with the type strains of L. soesokkakensis , L. hongkongensis and L. cinnabarina were 19–37 %. Differential phenotypic properties, together with their phylogenetic and genetic distinctiveness, revealed that the two novel strains are separated from other species of the genus Loktanella . On the basis of the data presented, strains J-MR2-YT and J-MR2-O are proposed to represent a novel species of the genus Loktanella , for which the name Loktanella variabilis sp. nov. is proposed. The type strain is J-MR2-YT ( = KCTC 42074T = CECT 8572T).

Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1402-1408 ◽  
Author(s):  
P. Kämpfer ◽  
N. Lodders ◽  
K. Martin ◽  
R. Avendaño-Herrera
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Three Gram-staining-negative non-endospore-forming strains were isolated from farmed fish in Chile: one (LM-09-FpT) from a rainbow trout (Oncorhynchus mykiss) and the others (LM-19-FpT and LM-20-Fp) from two Atlantic salmon (Salmo salar). Phylogenetic analyses based on 16S rRNA gene sequences indicated that all three isolates belonged to the genus Flavobacterium . In these analyses, strain LM-09-FpT appeared most closely related to the type strains of Flavobacterium chungangense (98.5 % sequence similarity), Flavobacterium glaciei (98.2 %), Flavobacterium aquidurense (97.6 %), Flavobacterium saccharophilum (97.6 %) and Flavobacterium hercynium (97.6 %). The 16S rRNA gene sequences of strains LM-19-FpT and LM-20-Fp were found to be identical and most similar to the corresponding sequences of the type strains of Flavobacterium aquidurense (98.6 %), Flavobacterium frigidimaris (98.5 %), Flavobacterium hercynium (97.9 %), Flavobacterium saccharophilum (97.7 %) and Flavobacterium pectinovorum (97.7 %). For each of the three novel strains, menaquinone (MK-6) was the predominant respiratory quinone and the major compounds in the polar lipid profile were phosphatidylethanolamine, an unidentified aminolipid, phosphatidylserine and two or three unknown lipids. The fatty acid profile of each strain, which comprised major amounts of iso-C15 : 0, C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as well as smaller amounts of various hydroxylated fatty acids (e.g. iso-C16 : 0 3-OH, iso-C17 : 0 3-OH, C16 : 0 3-OH and C15 : 0 3-OH), indicated that each belonged to the genus Flavobacterium . Based on their physiological and biochemical characteristics and the results of DNA–DNA hybridizations, which showed relatively low levels of relatedness between the novel strains and the most closely related Flavobacterium species, strain LM-09-FpT ( = LMG 26360T = CCM 7940T) represents a novel species within the genus Flavobacterium , for which the name Flavobacterium chilense sp. nov. is proposed, and strains LM-19-FpT ( = LMG 26359T = CCM 7939T) and LM-20-Fp ( = LMG 26331) represent a second novel species within the same genus, for which the name Flavobacterium araucananum sp. nov. is proposed.

Brevifollis gellanilyticus gen. nov., sp. nov., a gellan-gum-degrading bacterium of the phylum Verrucomicrobia

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3075-3078 ◽  
Author(s):  
Shigeto Otsuka ◽  
Taku Suenaga ◽  
Hoan Thi Vu ◽  
Hiroyuki Ueda ◽  
Akira Yokota ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gellan Gum ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Degrading Bacterium ◽  
Type Strains ◽  
Sequence Similarities

The taxonomic properties of strain DC2c-G4T, a Gram-staining-negative, ovoid, gellan-gum-degrading bacterial isolate, were examined. Phylogenetic analysis based on 16S rRNA gene sequences identified this isolate as a member of the phylum Verrucomicrobia and closest to the genus Prosthecobacter . The 16S rRNA gene sequence similarities between this isolate and any of the type strains of species of the genus Prosthecobacter were less than 95 %. In addition, the absence of a single prostheca and the predominant menaquinone MK-7(H2) supported the differentiation of this isolate from the genus Prosthecobacter . Here, we propose Brevifollis gellanilyticus gen. nov., sp. nov. to accommodate the isolate. The type strain of the type species is DC2c-G4T ( = NBRC 108608T = CIP 110457T).

scholarly journals Psychrobacter ciconiae sp. nov., isolated from white storks (Ciconia ciconia)

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 772-777 ◽  
Author(s):  
Peter Kämpfer ◽  
Leszek Jerzak ◽  
Gottfried Wilharm ◽  
Jan Golke ◽  
Hans-Jürgen Busse ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
White Storks ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Five beige bacterial strains (176/10T, 178/10, 182/10, 185/7 and 193/8) were isolated from white storks in Poland and found to share identical 16S rRNA gene sequences; they were also investigated in a polyphasic taxonomic study. The cells of all isolates were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequences of these organisms with the sequences of the type strains of the most closely related species of the genus Psychrobacter showed highest sequence similarities to the type strains of Psychrobacter pulmonis and Psychrobacter faecalis (both 97.1 %). The 16S rRNA gene sequence similarities to all other species of the genus Psychrobacter were below 96.3 %. All five isolates showed an identical profile of physiological reactions and almost identical fatty acid profiles consisting of mainly C18 : 1ω9c, but also C12 : 0 3-OH as a characteristic hydroxylated fatty acid. A quinone system with mainly ubiquinone Q-8 was detected and the polar lipid profile of the type strain, 176/10T, was mainly composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and diphosphatidylglycerol, plus some hitherto uncharacterized phospholipids and one aminolipid. The major polyamines were spermidine and putrescine. DNA–DNA hybridizations between 176/10T and the type strains of P. pulmonis and P. faecialis resulted in relatedness values below 70 %. These results indicate that the strains represent a novel species, for which the name Psychrobacter ciconiae sp. nov. (type strain 176/10T = CIP 110777T = LMG 28175T = CCM 8519T) is proposed.

Flavobacterium yanchengense sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2848-2852 ◽  
Author(s):  
Gang Hu ◽  
Jun Zhang ◽  
Guiqin Yang ◽  
Yang-Yang Li ◽  
Yi-Ting Guan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, non-spore-forming, rod-shaped bacterial strain, hgT, resembling members of the genus Flavobacterium , was isolated from soil, and subjected to a taxonomic study using a polyphasic approach. Strain hgT grew optimally at pH 7.0 and 30 °C in the presence of 1 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 34 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain hgT belonged to the genus Flavobacterium . Levels of 16S rRNA gene sequence similarity between strain hgT and the type strains of species of the genus Flavobacterium were below 94.7 %. Strain hgT differed from phylogenetically related species of the genus Flavobacterium in several phenotypic characteristics. On the basis of phenotypic and phylogenetic distinctiveness, strain hgT ( = CCTCC AB 2012099T = KACC 16855T) was classified in the genus Flavobacterium as the type strain of a novel species, for which the name Flavobacterium yanchengense sp. nov. is proposed.

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