Comamonas suwonensis sp. nov., isolated from stream water in the Republic of Korea

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Kyu-Hyun Park ◽  
Zhi Yu ◽  
Ke Dong ◽  
Sang-Seob Lee
Keyword(s):  
Dna Hybridization ◽  
Stream Water ◽  
Optimal Growth ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Republic ◽  
Taxonomic Approach

A novel bacterial strain, EJ-4T, isolated from stream water collected at Seo-ho in Suwon, Republic of Korea, was characterized based on a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EJ-4T belonged to the genus Comamonas . The isolate is Gram-stain-negative, non-motile, aerobic, rod-shaped and forms pale yellow colonies on trypticase soy agar. The optimal growth of this strain was observed aerobically at 30 °C, pH 7 and 0.5 % NaCl. The major fatty acids were summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c; 39.7 %) and C16 : 0 (32.0 %). The G+C content of strain EJ-4T was 58.4mol %. The average nucleotide identity and digital DNA–DNA hybridization values between strain EJ-4T and Comamoas testosteroni were 91.8 and 31.2 %, respectively. The major polar lipids detected in the isolate were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was ubiquinone-8. Based on the results of polyphasic taxonomic analysis of strain EJ-4T, we describe a novel species of the genus Comamonas , for which the name Comamonas suwonensis sp. nov. has been proposed, with EJ-4T (=KCTC 82074T=JCM 34179T=KEMB 1602-279T) as the type strain.

scholarly journals Adhaeribacter radiodurans sp. nov., isolated from the rhizospheric soil of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea

2020 ◽  
Author(s):  
Ye-Ji Hwang ◽  
Jin-Soo Son ◽  
Soo-Yeong Lee ◽  
Min-Ji Kim ◽  
Jong Myong Park ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Optimal Growth ◽  
Amino Acid Identity ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
Cell Width ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Type Strains

KUDC8001T was isolated from the rhizosperic soil of Elymus tsukushiensis in the Dokdo Islands, Republic of Korea. Strain KUDC8001T was Gram-stain-negative, non-motile and rod-shaped. KUDC8001T was catalase- and oxidase-positive. This strain is capable of growing at 4–37 °C and pH 7.0–8.0 and exhibited optimal growth at 25 °C and pH 7.0. It could be grown in R2A, nutrient agar and ISP2 agar plates. The cell width ranged from 0.7 to 1.0 µm, and length ranged from 2.5 to 5.5 µm. The genomic G+C content was 40.8 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that the strain KUDC8001T belongs to the genus Adhaeribacter , which is most closely related to the strain A. pallidiroseus HMF7616T (97.5%). The DNA relatedness of KUDC8001T with the type strains of A. pallidiroseus HMF7616T, A. swui 17 mud1-7T and A. arboris HMF7605T was ≤80.3 % based on average nucleotide identity calculations and ≤86.9 % based on average amino acid identity calculations. In silico DNA–DNA hybridization values of the strain KUDC8001T with the most closely related strains were 22.1, 24.0 and 24.4 %. Based on its phenotypic, phylogenetic, genetic and chemotaxonomic features, the strain KUDC8001T should be considered as a novel species in the genus Adhaeribacter , for which we have proposed the name Adhaeribacter radiodurans sp. nov. The type strain is KUDC8001T (=KCTC 82078T=CGMCC 1.18475T).

scholarly journals Paenibacillus dongdonensis sp. nov., isolated from rhizospheric soil of Elymus tsukushiensis

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2865-2870 ◽  
Author(s):  
Jin-Soo Son ◽  
Hyun-Uk Kang ◽  
Sa-Youl Ghim
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-positive, endospore-forming and rod-shaped bacterial strain, designated KUDC0114T, was isolated from rhizospheric soil of Elymus tsukushiensis from Dongdo Island, one of the largest of the Dokdo Islands, South Korea. The strain displayed optimal growth at 37 °C, pH 8.5 in the absence of NaCl. Based on phylogenetic analysis of 16S rRNA gene sequences, strain KUDC0114T represented a member of the genus Paenibacillus and was most closely related to Paenibacillus taichungensis BCRC 17757T (98.46 %). The cell-wall peptidoglycan was A1γ type, and the predominant quinone was menaquinone-7 (MK-7). The major cellular fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA–DNA hybridization of strain KUDC0114T with nine other strains indicated less than 23 % relatedness, and its DNA G+C content was 44.30 mol%. Based on genomic, phenotypic and phylogenetic analyses, KUDC0114T should be classified as representing novel species within the genus Paenibacillus . The name Paenibacillus dongdonensis sp. nov. is proposed. The type strain is KUDC0114T ( = DSM27607T = KCTC33221T).

Chryseobacterium carnipullorum sp. nov., isolated from raw chicken

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3243-3249 ◽  
Author(s):  
George Charimba ◽  
Piet Jooste ◽  
Jacobus Albertyn ◽  
Celia Hugo
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Processing Plant ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Taxonomic Approach ◽  
The 16S Rrna Gene

Three Gram-staining-negative, rod-shaped, non-spore-forming, non-motile, oxidase-positive, yellow pigmented and aerobic bacterial isolates designated 8_R23573, 9_R23581T and 10_R23577 were isolated from raw chicken at a broiler processing plant in Bloemfontein, South Africa. A polyphasic taxonomic approach was used to determine their exact taxonomic identities. Phylogenetic analysis of the 16S rRNA gene sequences showed that the three strains belonged to the genus Chryseobacterium , exhibiting the highest similarities to Chryseobacterium shigense DSM 17126T (98.6–99.2 %) and Chryseobacterium luteum DSM 18605T (98.3–98.7 %). The most abundant quinone was menaquinone MK-6 and the predominant cellular fatty acids were iso-15 : 0, iso-17 : 1ω9c, iso-17 : 0 3-OH and summed feature 3 (iso-16 : 1ω7c and/or iso-15 : 0 2-OH), which supported the affiliation of the strains to the genus Chryseobacterium . The DNA G+C contents of the strains were 36.9, 36.7 and 36.6 mol% respectively. The DNA–DNA hybridization results gave relatedness values ranging from 78.8 to 87.2 % among the three strains and 23.4 to 56.1 % to the two nearest phylogenetic neighbours C. shigense DSM 17126T and C. luteum LMG 23785T. On the basis of the data from this polyphasic study, the three strains are concluded to represent a novel species of the genus Chryseobacterium for which the name Chryseobacterium carnipullorum sp. nov. is proposed. The type strain is 9_R23581T ( = LMG 26732T = DSM 25581T).

Mariniflexile maritimum sp. nov., isolated from seawater of the South Sea in the Republic of Korea

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
So-Ra Ko ◽  
Ve Van Le ◽  
Long Jin ◽  
Sang-Ah Lee ◽  
Chi-Yong Ahn ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
The South ◽  
Content Type ◽  
Link Type ◽  
South Sea ◽  
The Republic

A novel Gram-stain-negative, rod-shaped, aerobic, non-motile bacterial strain, designated M5A1MT, was isolated from seawater collected from the South Sea of the Republic of Korea. Based on 16S rRNA gene sequence similarity, strain M5A1MT was closely related to Mariniflexile gromovii KMM 6038T (95.3 %), Mariniflexile fucanivorans SW5T (95.2 %), Mariniflexile soesokkakense RSSK-9T (95.1 %), Yeosuana aromativorans GW1-1T (94.6 %) and Confluentibacter lentus HJM-3T (94.6 %). Genome-based phylogenetic analyses revealed that strain M5A1MT formed a distinct cluster with the type strains of the genus Mariniflexile . The major cellular fatty acid constituents (>5 % of the total fatty acids) were iso-C15:0, anteiso-C15 : 0, iso-C15 : 0 3-OH, iso-C15 : 1 G, iso-C16:03-OH and iso-C17 : 0 3-OH. The respiratory quinone was identified as MK-6. The major polar lipids were phosphatidylethanolamine and one unidentified polar lipid. The genomic DNA G+C content of strain M5A1MT was determined to be 37.7 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain M5A1MT is considered to represent a novel species within the genus Mariniflexile , for which the name Mariniflexile maritimum sp. nov. is proposed. The type strain is M5A1MT (=KCTC 72895T=JCM 33982T).

scholarly journals Pseudovibrio axinellae sp. nov., isolated from an Irish marine sponge

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 141-145 ◽  
Author(s):  
John A. O’Halloran ◽  
Teresa M. Barbosa ◽  
John P. Morrissey ◽  
Jonathan Kennedy ◽  
Alan D. W. Dobson ◽  
...  
Keyword(s):  
Marine Sponge ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-negative, motile, rod-shaped bacterial strain, designated Ad2T, was isolated from a marine sponge, Axinella dissimilis, which was collected from a semi-enclosed marine lake in Ireland. Strain Ad2T grew optimally at 24 °C, at pH 7.0 and in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Ad2T clustered with members of the genus Pseudovibrio , and showed 97.3–98.2 % sequence similarity to the type strains of recognized Pseudovibrio species. DNA–DNA relatedness values between strain Ad2T and the type strains of other Pseudovibrio species were <27 %. The DNA G+C content of strain Ad2T was 50.5 mol%. The major fatty acid was 18 : 1ω7c. Differences in phenotypic properties, together with phylogenetic and DNA–DNA hybridization analyses, indicated that strain Ad2T represented a novel species of the genus Pseudovibrio . The name Pseudovibrio axinellae sp. nov. is proposed, with Ad2T ( = DSM 24994T = NCIMB 14761T) as the type strain.

Dickeya aquatica sp. nov., isolated from waterways

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2264-2266 ◽  
Author(s):  
Neil Parkinson ◽  
Paul DeVos ◽  
Minna Pirhonen ◽  
John Elphinstone
Keyword(s):  
Dna Hybridization ◽  
Profile Analysis ◽  
Sequence Similarity ◽  
Branch Length ◽  
Rrna Gene ◽  
New Taxon ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Uk

Pectinolytic Gram-negative bacteria were isolated from different waterways in the UK and Finland. Three strains (174/2T, 181/2 and Dw054) had the same 16S rRNA gene sequences which shared 99 % sequence similarity to species of the genus Dickeya , and a phylogeny of related genera confirmed attribution to this genus. Fatty acid profile analysis of all three strains found a high proportion of C16 : 1ω7c/C16 : 1ω7c and C16 : 0 fatty acids, and library profile searches found closest matches to Dickeya chrysanthemi . Production of a concatenated phylogeny using six loci, recA, gapA, atpD, gyrB, infB and rpoB, provided a high-resolution phylogeny which placed strains 174/2T and 181/2 as a distinct clade, separated from the other species of the genus Dickeya by a relatively long branch-length. DNA–DNA hybridization analysis with a limited number of reference species also supported the distinctiveness of strains 174/2T and 181/2 within the genus Dickeya . All three strains could be phenotypically distinguished from other species of the genus by fermentation of melibiose and raffinose but not d-arabinose or mannitol. The name Dickeya aquatica sp. nov. is proposed for the new taxon; the type strain is 174/2T ( = NCPPB 4580T = LMG 27354T).

Sphingobium czechense sp. nov., isolated from a hexachlorocyclohexane dump site

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 723-728 ◽  
Author(s):  
Neha Niharika ◽  
Hana Moskalikova ◽  
Jasvinder Kaur ◽  
Fazlurrahman Khan ◽  
Miroslava Sedlackova ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Dump Site ◽  
Content Type ◽  
Link Type ◽  
Physiological Tests

A yellow-pigmented bacterial strain, designated LL01T, was isolated from hexachlorocyclohexane (HCH)-contaminated soil at Spolana Neratovice, a former Czech producer of lindane. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL01T occupied a distinct phylogenetic position in the Sphingobium cluster, showing highest similarity to Sphingobium rhizovicinum CC-FH12-1T (98.5 %). The DNA G+C content of strain LL01T was 66.1 mol%. The predominant respiratory pigment was ubiquinone Q-10. The polar lipid profile of strain LL01T also corresponded to those reported for other Sphingobium species (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipids), supporting its identification as a member of the genus Sphingobium . Spermidine was the major polyamine observed. The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished strain LL01T from closely related species of the genus Sphingobium . Therefore, strain LL01T represents a novel species of the genus Sphingobium , for which the name Sphingobium czechense sp. nov. is proposed (type strain LL01T = CCM 7979T = DSM 25410T).

Sphingobacterium caeni sp. nov., isolated from activated sludge

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2260-2264 ◽  
Author(s):  
Li-Na Sun ◽  
Jun Zhang ◽  
Qing Chen ◽  
Jian He ◽  
Shun-Peng Li
Keyword(s):  
Phylogenetic Analysis ◽  
Activated Sludge ◽  
Dna Hybridization ◽  
Type Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach ◽  
Ph Range

The taxonomic status of a bacterium, strain DC-8T, isolated from activated sludge, was determined using a polyphasic taxonomic approach. The cells of strain DC-8T were Gram-negative, non-motile, non-spore-forming and rod-shaped. The isolate grew at temperature range of 10–40 °C (optimum 30–35 °C), pH range of 5.0–10.0 (optimum 6.5–8.0) and NaCl concentrations of 0–5 % (optimum 0–1 %). The predominant menaquinone of strain DC-8T was MK-7 and major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 39.7 %), iso-C15 : 0 (33.7 %) and C16 : 0 (5.2 %). The DNA G+C content was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain DC-8T was a member of the genus Sphingobacterium . Strain DC-8T shared the highest similarity with Sphingobacterium siyangense SY1T (98.4 %), Sphingobacterium multivorum IAM 14316T (98.3 %), Sphingobacterium canadense CR11T (98.0 %) and Sphingobacterium detergens 6.2ST (97.9 %) and shared less than 97 % similarity with other members of the genus Sphingobacterium . DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain DC-8T and its closest phylogenetic neighbours were below 70 %. Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain DC-8T was clearly distinguished from all recognized species of the genus Sphingobacterium and should be classified as a representative of a novel species of the genus Sphingobacterium , for which the name Sphingobacterium caeni sp. nov. is proposed. The type strain is DC-8T ( = CCTCC AB 2012020T = KACC 16850T).

scholarly journals Tangfeifania diversioriginum gen. nov., sp. nov., a representative of the family Draconibacteriaceae

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3473-3477 ◽  
Author(s):  
Qian-Qian Liu ◽  
Xiao-Li Li ◽  
Alejandro P. Rooney ◽  
Zong-Jun Du ◽  
Guan-Jun Chen
Keyword(s):  
New Genus ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Qinghai Province ◽  
Link Type ◽  
The Family

A novel Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and pink-pigmented bacterium, designated G22T, was isolated from Gahai, a saltwater lake in Qinghai province, China. Optimal growth occurred at 33–35 °C, pH 7.0–7.5, and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The major polar lipids were phosphatidylethanolamine and three unknown lipids. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH, and MK-7 was the main respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G22T fell within the class Bacteroidia . Its closest phylogenetic neighbour was the recently described species Draconibacterium orientale , the sole member of the family Draconibacteriaceae , with merely 90.04 % sequence similarity. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence observed, a novel species in a new genus, Tangfeifania diversioriginum gen. nov., sp. nov., is proposed within the family Draconibacteriaceae . The type strain is G22T ( = CICC 10587T = DSM 27063T).

scholarly journals Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 562-569 ◽  
Author(s):  
Hong Cheng ◽  
Shun Zhang ◽  
Ying-Yi Huo ◽  
Xia-Wei Jiang ◽  
Xin-Qi Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Hydrolysis Of ◽  
Sequence Similarities

A taxonomic study was carried out on strain YN3T, which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0–10.0 and 4–32 °C in the presence of 0–9.0 % (w/v) NaCl. Strain YN3T was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3T should be assigned to the genus Gilvimarinus . ‘Gilvimarinus agarilyticus’ KCTC 23325 and Gilvimarinus chinensis QM42T had the closest phylogenetic relationship to strain YN3T, and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA–DNA hybridization studies, we propose that strain YN3T represents a novel species of the genus Gilvimarinus , for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3T ( = KCTC 32438T = JCM 19198T). An emended description of the genus Gilvimarinus is also presented.

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