Chitinophaga taiwanensis sp. nov., isolated from the rhizosphere of Arabidopsis thaliana

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 426-430 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
You-Cheng Liu ◽  
Yi-Han Hsu ◽  
Wei-An Lai ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

An aerobic, Gram-stain-negative, rod-shaped bacterium (strain CC-ALB-1T) was isolated from the rhizosphere of Arabidopsis thaliana. Strain CC-ALB-1T was able to grow at 20–30 °C, pH 5.0–8.0 and with up to 1.0 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain CC-ALB-1T had the highest sequence similarity to Chitinophaga ginsengisegetis Gsoil 040T (96.9 %) and Chitinophaga niastensis JS16-4T (96.7 %); lower levels of similarity (<97.0 %) were observed to strains of all other species of the genus Chitinophaga . The fatty acid profile consisted of iso-C15 : 0, iso-C17 : 0 3-OH, C15 : 1ω5c, C16 : 1ω5c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The predominant quinone system was menaquinone 7 (MK-7). The DNA G+C content was 53.4±0.4 mol%. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-1T is proposed to represent a novel species within the genus Chitinophaga , for which the name Chitinophaga taiwanensis sp. nov. is proposed. The type strain is CC-ALB-1T ( = BCRC 80570T = JCM 18895T).

Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 594-598 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
You-Cheng Liu ◽  
Yi-Han Hsu ◽  
Wei-An Lai ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Type Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Resistant Bacterium ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

An aerobic, Gram-stain-negative, rod-shaped, DDT-resistant bacterium, designated strain CC-ALB-2T, was isolated from the Arabidopsis thaliana rhizosphere. Strain CC-ALB-2T was able to grow at 25–37 °C, at pH 5.0–8.0, with 1.0 % (w/v) NaCl and tolerate up to 200 mg l−1 DDT. 16S rRNA gene sequence analysis of strain CC-ALB-2T showed highest sequence similarity to Novosphingobium stygium KCTC 2891T (97.1 %) and Novosphingobium soli DSM 22821T (96.8 %), and lower levels of similarity (<97.0 %) to other species of the genus Novosphingobium . The major fatty acid profile consisted of C14 : 0 2-OH (13.1 %), C16 : 0 (10.0 %), C15 : 0 iso 3-OH (5.8 %), C16 : 1ω7c/C16 : 1ω6c (summed feature 3, 24.7 %) and C18 : 1ω7c/C18 : 1ω6c (summed feature 8, 42.4 %). The polar lipid profile constitutes sphingoglycolipid, glycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol and phosphatidylcholine. The polyamine pattern showed a predominance of spermidine as the major polyamine. The predominant quinone system was ubiquinone (Q-10). The DNA G+C content was 68.9±0.1 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-2T is proposed to represent a novel species of the genus Novosphingobium for which the name Novosphingobium arabidopsis sp. nov. is proposed. The type strain is CC-ALB-2T ( = BCRC 80571T = JCM 18896T).

scholarly journals Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1241-1244 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Moriya Ohkuma
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Single Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Emended Description

Strains of the recently proposed species Bacteroides chinchillae share more than 99.4 % 16S rRNA gene sequence similarity with the type strain of Bacteroides sartorii although these two species do not appear to be similar from their published descriptions. The aim of this study was to perform phenotypic and genetic analyses of both species to clarify their taxonomic position. B. chinchillae JCM 16497T exhibited high hsp60 gene sequence similarity with B. sartorii JCM 17136T (100 %) as well as B. chinchillae JCM 16498 (100 %). The hsp60 gene sequence analysis and levels of DNA–DNA relatedness observed demonstrated B. sartorii JCM 17136T, B. chinchillae JCM 16497T, and B. chinchillae JCM 16498 are members of a single species. Based on these data, we propose Bacteroides chinchillae as a later heterotypic synonym of Bacteroides sartorii . An emended description of B. sartorii is provided.

Nibribacter koreensis gen. nov., sp. nov., isolated from estuarine water

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4663-4668 ◽  
Author(s):  
Ji Young Kang ◽  
Jeesun Chun ◽  
Kwang Yeop Jahng
Keyword(s):  
Type Species ◽  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-reaction-negative, rod-shaped, non-motile, red-pigmented bacterium, designated strain GSR3061T, was isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment in JEOLlabuk-do of South Korea, and characterized using a polyphasic approach. 16S rRNA gene sequence analysis of strain GSR3061T indicated that the isolate belonged to the phylum Bacteroidetes and exhibited similarity levels of 94.7 % to Rufibacter tibetensis NRRL B-51285T, 92.4 % to Adhaeribacter terreus KACC 14257T and 91.9 % to Pontibacter korlensis KACC 15371T. Growth was observed at 15–40 °C and pH 6.5–9.5. The major cellular fatty acids of the novel strain were summed feature 4 (comprising iso-C17 : 1 I and/or anteiso-C17 : 1 B), iso-C15 : 0, C17 : 1ω6c and iso-C16 : 1 H. Flexirubin-type pigments were absent. The DNA G+C content of strain GSR3061T was 44.9 mol% and the major quinone was MK-7. The polar lipid profile consisted mainly of phosphatidylethanolamine; three unidentified lipids, two unknown aminolipids, two unknown phospholipids, an unknown aminophospholipid and an unknown glycolipid were also present. On the basis of the evidence presented, it is concluded that strain GSR3061T represents a novel species of a new genus, for which the name Nibribacter koreensis gen. nov., sp. nov. is proposed. The type strain of Nibribacter koreensis is GSR3061T ( = KACC 16450T = JCM 17917T).

scholarly journals Bifidobacterium faecale sp. nov., isolated from human faeces

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3134-3139 ◽  
Author(s):  
Jung-Hye Choi ◽  
Kyung Min Lee ◽  
Myung-Ki Lee ◽  
Chang-Jun Cha ◽  
Geun-Bae Kim
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bifidobacterium Adolescentis ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Gene Sequence Analysis

A novel strain, designated strain CU3-7T, was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7T was phylogenetically affiliated with members of the genus Bifidobacterium . Strain CU3-7T showed the highest level of sequence similarity with Bifidobacterium adolescentis KCTC 3216T (98.4 %), followed by Bifidobacterium ruminantium KCTC 3425T (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7T was closely related to B. adolescentis KCTC 3216T (94.0 %) and B. ruminantium KCTC 3425T (92.5 %). The DNA–DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with B. ruminantium KCTC 3425T and 14.9 % with B. adolescentis KCTC 3216T. Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7T should be classified as the type strain of a novel species within the genus Bifidobacterium , for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904T = JCM 19861T).

scholarly journals Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates

2019 ◽  
Vol 69 (4) ◽  
pp. 964-969 ◽  
Author(s):  
Masanori Tohno ◽  
Yasuhiro Tanizawa ◽  
Yoichiro Kojima ◽  
Mitsuo Sakamoto ◽  
Yasukazu Nakamura ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, strain YK43T, isolated from spent mushroom substrates stored in Nagano, Japan was performed. Growth was detected at 15–45 °C, pH 5.0–8.5, and 0–10 % (w/v) NaCl. The genomic DNA G+C content of strain YK43T was 43.6 mol%. The predominant fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 8. Based on 16S rRNA gene sequence analysis, the type strains of Lactobacillus acidipiscis (sequence similarity, 97.6 %) and Lactobacillus pobuzihii (97.4 %) were most closely related to YK43T. The average nucleotide identities were 74.1 % between strain YK43T and L. acidipiscis DSM 15836T and 74.0 % between YK43T and L. pobuzihii E100301T. Based on a multilocus sequence analysis, comparative genomic analysis and a range of phenotypic and chemotaxonomic characteristics, strain YK43T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus salitolerans sp. nov. is proposed. The type strain is YK43T (=JCM 31331T = DSM 103433T).

Parabacteroides faecis sp. nov., isolated from human faeces

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1342-1346 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Yoshiki Tanaka ◽  
Yoshimi Benno ◽  
Moriya Ohkuma
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Human Faeces ◽  
Link Type ◽  
Gene Sequence Analysis

A bacterial strain, designated 157T, isolated from human faeces was characterized by using a polyphasic taxonomic approach, which included analysis of physiological and biochemical features, cellular fatty acid profiles, menaquinone profiles and its phylogenetic position, based on 16S rRNA gene sequence analysis. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. The isolate was able to grown on medium containing 20 % (w/v) bile. 16S rRNA gene sequence analysis showed that the strain was a member of the genus Parabacteroides . Strain 157T was closely related to Parabacteroides gordonii JCM 15724T (96 % sequence similarity). The results of hsp60 gene sequence analysis indicated that strain 157T was different from P. gordonii JCM 15724T, with a hsp60 gene sequence similarity of 96.1 %. The major cellular fatty acids of strain 157T were anteiso-C15 : 0, iso-C17 : 0 3-OH, C18 : 1ω9c and anteiso-C17 : 0 3-OH. The major menaquinone of the isolate was MK-9. The DNA G+C content of strain 157T was 41.8 mol%. On the basis of these data, strain 157T represents a novel species of the genus Parabacteroides , for which the name Parabacteroides faecis sp. nov. is proposed; the type strain is 157T ( = JCM 18682T = CCUG 66681T).

Luteimonas vadosa sp. nov., isolated from seashore sediment

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1261-1266 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Vassilii I. Svetashev ◽  
Valeriya V. Kurilenko ◽  
Valery V. Mikhailov
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

An aerobic, Gram-stain-negative, yellow-pigmented, non-motile, rod-shaped bacterium designated strain KMM 9005T was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis showed that strain KMM 9005T belonged to the genus Luteimonas and was most closely related to Luteimonas cucumeris KCTC 23627T (96.5 % sequence similarity) and Luteimonas aquatica LMG 24212T (96.1 % sequence similarity). Strain KMM 9005T was characterized by the presence of thin fimbriae, the major ubiquinone Q-8, by the predominance of iso-C17 : 1 followed by iso-C16 : 0, iso-C15 : 0 and iso-C17 : 0 in its fatty acid profile, weak hydrolytic capacity and the inability to assimilate most organic substrates. Based on these distinctive phenotypic characteristics and phylogenetic analysis, strain KMM 9005T represents a novel species of the genus Luteimonas , for which the name Luteimonas vadosa sp. nov. is proposed. The type strain is KMM 9005T ( = NRIC 0881T = JCM 18392T).

Roseomonas aerophila sp. nov., isolated from air

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2334-2337 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Jae-Hyung Ahn ◽  
Seung-Beom Hong ◽  
Soon-Ja Seok ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
16S Rna

An aerobic, Gram-stain-negative, motile, mesophilic bacterium, designated strain 7515T-07T, was isolated from an air sample in the Taean region, Republic of Korea. The strain grew at 4–40 °C (optimum, 30 °C) and pH 5.0–9.0 (optimum, pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 7515T-07T was related to members of the genus Roseomonas and had highest 16S rRNA gene sequence similarity with Roseomonas ludipueritiae 170/96T (96.7 %). 16S RNA gene sequence similarity between strain 7515T-07T and Roseomonas gilardii ATCC 49956T (the type species of the genus Roseomonas ) was 93.4 %. Strain 7515T-07T contained Q-10 as the ubiquinone and C18 : 1ω7c and C19 : 0 cyclo ω8c as the dominant fatty acids (>10 %). The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified aminolipids. The DNA G+C content was 73.0 mol%. Combined data from phenotypic, phylogenetic and chemotaxonomic studies demonstrated that strain 7515T-07T is a representative of a novel species of the genus Roseomonas , for which the name Roseomonas aerophila sp. nov. is proposed. The type strain is 7515T-07T ( = KACC 16529T = NBRC 108923T).

Stappia taiwanensis sp. nov., isolated from a coastal thermal spring

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1350-1354 ◽  
Author(s):  
P. Kämpfer ◽  
A. B. Arun ◽  
A. Frischmann ◽  
H.-J. Busse ◽  
Chiu-Chung Young ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A beige-coloured, Gram-stain-negative, aerobic, non-motile moderately thermotolerant, rod-shaped organism, strain CC-SPIO-10-1T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on Marine Agar 2216. Based on 16S rRNA gene sequence analysis, this organism was grouped into the genus Stappia , showing 98.3 % sequence similarity to Stappia indica B106T and 98.2 % gene sequence similarity to Stappia stellulata IAM 12621T . Ubiquinone Q-10 was the major respiratory quinone and C18 : 1ω7c and C18 : 1ω7c 11-methyl were detected as the major fatty acids. The hydroxylated fatty acid C18 : 0 3-OH was detected as well. Predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, unidentified aminolipid AL1 and unidentified phospholipid PL1. Minor amounts of several unidentified lipids (PL2 and L1–L7) were present as well. The polyamine pattern contained the major compounds spermidine and spermine. Strain CC-SPIO-10-1T could be differentiated from the type strains of S. stellulata and S. indica by a set of biochemical tests. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain CC-SPIO-10T represents a novel species of the genus Stappia for which the name Stappia taiwanensis sp. nov. is proposed. The type strain is CC-SPIO-10 T ( = CCUG 59208T = LMG 25538 T = CCM 7757T).

Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp.

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 435-441 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Jui-Hsing Chou ◽  
Cyril Bontemps ◽  
Geoffrey N. Elliott ◽  
Eduardo Gross ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

Five strains, JPY461T, JPY359, JPY389, DPU-3 and STM4206 were isolated from nitrogen-fixing nodules on the roots of Mimosa spp. and their taxonomic positions were investigated using a polyphasic approach. All five strains grew at 15–40 °C (optimum, 30–37 °C), at pH 4.0–8.0 (optimum, pH 6.0–7.0) and with 0–1 % (w/v) NaCl [optimum, 0 % (w/v)]. On the basis of 16S rRNA gene sequence analysis, a representative strain (JPY461T) showed 97.2 % sequence similarity to the closest related species Burkholderia acidipaludis SA33T, a similarity of 97.2 % to Burkholderia terrae KMY02T, 97.1 % to Burkholderia phymatum STM815T and 97.1 % to Burkholderia hospita LMG 20598T. The predominant fatty acids of the five novel strains were summed feature 2 (comprising C16 : 1 iso I and/or C14 : 0 3-OH), summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 , C16 : 0 3-OH, C17 : 0 cyclo, C18 : 1 ω7c and C19 : 0 cyclo ω8c. The major isoprenoid quinone was Q-8 and the DNA G+C content of the strains was 63.0–65.0 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, an unidentified aminolipid and several unidentified phospholipids. The DNA–DNA relatedness of the novel strain with respect to recognized species of the genus Burkholderia was less than 54 %. On the basis of 16S rRNA and recA gene sequence similarities, chemotaxonomic and phenotypic data, the five strains represent a novel species in the genus Burkholderia , for which the name Burkholderia diazotrophica sp. nov. is proposed with the type strain, JPY461T ( = LMG 26031T = BCRC 80259T = KCTC 23308T).

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