scholarly journals Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s

Author(s):  
Estelle Mühle ◽  
Chloé Abry ◽  
Priscilla Leclerc ◽  
Gogoa-Marthe Goly ◽  
Alexis Criscuolo ◽  
...  

Genome sequence analysis of two strains collected in Canada at the end of the 1970s and deposited in 1998 at the Collection de l’Institut Pasteur has led to the taxonomic description of a novel fish-associated species in the genus Flavobacterium . Both strains, CIP 105534T and CIP 105535, were yellow-pigmented, Gram-stain-negative, non-spore-forming rod-shaped bacteria that exhibited gliding motility. They grew aerobically in a temperature range from 5 to 30 °C with optimal growth at 25 °C on trypticase soy or Reasoner's 2A agar but they did not grow on marine agar. Their major fatty acid profiles were similar, consisting of iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH (shown as summed feature 3), C16 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 0. The major polyamine was sym-homospermidine. Phosphatidylethanolamine and, most notably, ornithine-containing lipid OL2 and unidentified aminophospholipid APL1 were major polar lipids. A yellow pigment spot was visible after chromatographic analysis. The predominant respiratory quinone was MK-6. The G+C content of the two genomes was 34 mol% and their size was around 5.8 Mb. Comparison of the 16S rRNA gene sequences with those of the closely related type strains showed high levels of relatedness with Flavobacterium collinsii and Flavobacterium pectinovorum . All average nucleotide identity (ANI) and digital DNA–DNA hybridization values estimated against publicly available Flavobacterium genome assemblies were lower than 90 and 30 %, respectively. Phylogenetic, phenotypic and chemotaxonomic data indicated that the two strains represent a novel species of the genus Flavobacterium , for which the name Flavobacterium bizetiae sp. nov. is proposed. The type strain is CIP 105534T (=LMG 1342T). The unique ability of F. bizetiae to use melibiose as a sole source of carbon could provide a simple phenotypic test to discriminate F. bizetiae from its closest relatives.

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1991-1997 ◽  
Author(s):  
Zenghu Zhang ◽  
Tong Yu ◽  
Tingting Xu ◽  
Xiao-Hua Zhang

A Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic bacterium with gliding motility, designated strain SW150T, was isolated from surface seawater of the South Pacific Gyre (39° 19′ S 139° 48′ W) during the Integrated Ocean Drilling Program Expedition 329. Optimal growth occurred in the presence of 2–4 % (w/v) NaCl, at pH 7–8 and at 28–30 °C. The dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, C16 : 1ω6c and/or C16 : 1ω7c and 10-methyl C16 : 0 and/or iso-C17 : 1ω9c. The polar lipids of strain SW150T comprised phosphatidylethanolamine, three unknown polar lipids and one unknown aminolipid. The major respiratory quinone was MK-6. The DNA G+C content of strain SW150T was 33.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina macrocephali JAMB N27T and Aquimarina muelleri KMM 6020T with 97.8 and 96.8 % sequence similarities, respectively. The estimated DNA–DNA hybridization values were 21.00±2.33 % between strain SW150T and A. macrocephali JAMB N27T and 20.60±2.32 % between strain SW150T and Aquimarina megaterium XH134T. On the basis of polyphasic analyses, strain SW150T represents a novel species of the genus Aquimarina , for which the name Aquimarina pacifica sp. nov. is proposed. The type strain is SW150T ( = JCM 18214T = CGMCC 1.12180T).


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1037-1044 ◽  
Author(s):  
Bi He Kong ◽  
Qun Fang Liu ◽  
Min Liu ◽  
Yang Liu ◽  
Lei Liu ◽  
...  

A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain xj7T, was isolated from roots of Typha angustifolia L. growing in Beijing Cuihu Wetland, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inference. The novel strain was spore-forming, motile, catalase-positive and oxidase-negative. Optimal growth of strain xj7T occurred at 28–30 °C and pH 7.0–7.5. Diphosphatidylglycerol was the most abundant polar lipid and occurred along with phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and three unknown aminophospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant isoprenoid quinone was MK-7. The major fatty acid components were anteiso-C15 : 0 (56.1 %), iso-C16 : 0 (9.1 %), C16 : 0 (8.0 %), iso-C14 : 0 (6.3 %) and iso-C15 : 0 (5.1 %). The G+C content of genomic DNA was 47.9 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain xj7T fell within the evolutionary radiation encompassed by the genus Paenibacillus , its closest neighbours were Paenibacillus borealis KK19T (97.5 %) and Paenibacillus durus DSM 1735T (97.1 %). However, the DNA–DNA relatedness values between strain xj7T and P. borealis KK19T and between strain xj7T and P. durus DSM 1735T, were both 35 %. Based on phenotypic, chemotaxonomic and phylogenetic properties, strain xj7T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus typhae sp. nov. is proposed. The type strain is xj7T ( = CGMCC 1.11012T = DSM 25190T).


2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2512-2516 ◽  
Author(s):  
Jie Pan ◽  
Cong Sun ◽  
Xin-Qi Zhang ◽  
Ying-Yi Huo ◽  
Xu-Fen Zhu ◽  
...  

Strain CMB17T was a short rod-shaped bacterium isolated from marine sediment of the Pacific Ocean. Cells were Gram-stain-negative and non-motile. Optimal growth occurred at 25–30 °C, pH 6.5–7 and 0.5–1 % (w/v) NaCl. The major fatty acid was C18 : 1ω7c (87.59 %), and ubiquinone-10 was detected as the only isoprenoid quinone. The DNA G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CMB17T is most closely related to Paracoccus stylophorae KTW-16T (96.7 %), P. solventivorans DSM 6637T (96.4 %) and P. saliphilus YIM 90738T (96.4 %). Based on phenotypic, genotypic and phylogenetic characteristics, strain CMB17T is proposed to represent a novel species, denominated Paracoccus sediminis sp. nov. (type strain CMB17T = JCM 18467T = DSM 26170T = CGMCC 1.12681T).


2020 ◽  
Vol 70 (8) ◽  
pp. 4569-4575 ◽  
Author(s):  
Qian Wang ◽  
Feng Liu ◽  
De-Chao Zhang

The Gram-stain-negative, orange-pigmented, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated TP-CH-4T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. The optimal growth conditions were determined to be at pH 7–8, 25–30 °C and in the presence of 2 % (w/v) NaCl. The major respiratory quinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and three unidentified polar lipids. The predominant cellular fatty acids were iso-C15 : 0 and summed feature 1 (composed of C13 : 03-OH and/or iso-C15 : 1H). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TP-CH-4T was a member of the family Flavobacteriaceae and formed a distinct lineage. Strain TP-CH-4T displayed highest sequence similarities to Pseudozobellia thermophila KMM 3531T (95.1 %) and Flagellimonas flava A11T (93.9 %). Genome sequencing revealed the strain TP-CH-4T has a genome size of 4.5 Mbp and a G+C content of 44.5 mol%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence, strain TP-CH-4T represents a novel species of a novel genus of the family Flavobacteriaceae , for which the name Pelagihabitans pacificus gen. nov., sp. nov. is proposed. The type strain of Pelagihabitans pacificus is TP-CH-4T (=CGMCC 1.17120T=KCTC 72434T).


2020 ◽  
Vol 70 (3) ◽  
pp. 1720-1728 ◽  
Author(s):  
Anusha Rai ◽  
Smita N ◽  
Suresh G ◽  
Shabbir A ◽  
Deepshikha G ◽  
...  

A Gram-stain-negative, non-motile, coccoid-shaped, catalase- and oxidase-positive, non-denitrifying, neutrophilic bacterium designated as strain JC501T was isolated from an epiphytic rhizosphere of an orchid, Aerides maculosa, growing in the Western Ghats of India. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain JC501T belonged to the genus Paracoccus and had the highest levels of sequence identity with Paracoccus marinus KKL-A5T (98.9 %), Paracoccus contaminans WPAn02T (97.3 %) and other members of the genus Paracoccus (<97.3 %). Strain JC501T produced indole-3 acetic acid and other indole derivatives from tryptophan. The dominant respiratory quinone was Q-10 and the major fatty acid was C18 : 1ω7c/C18 : 1ω6c, with significant quantities of C18 : 1ω9c, C17 : 0 and C16 : 0. The polar lipids of strain JC501T comprised phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid, two unidentified aminolipids, two unidentified lipids and four unidentified phospholipids. The genome of strain JC501T was 3.3 Mbp with G+C content of 69.4 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of eight housekeeping genes. Based on the results of phylogenetic analyses, low (<85.9 %) average nucleotide identity, digital DNA–DNA hybridization (<29.8 %), chemotaxonomic analysis and physiological properties, strain JC501T could not be classified into any of the recognized species of the genus Paracoccus . Strain JC501T represents a novel species, for which the name Paracoccus aeridis sp. nov. is proposed. The type strain is JC501T (=LMG 30532T=NBRC 113644T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3528-3533 ◽  
Author(s):  
Yan-lin Zhong ◽  
Xun-Ke Sun ◽  
Jian-Gang Hui ◽  
Hui-ling Teng ◽  
Zong-Jun Du

A Gram-stain-negative, rod-shaped, facultative anaerobic bacterium, designated strain 3539T, was isolated from coastal sediment of Weihai, PR China. Optimal growth occurred at 28 °C, pH 7.5–8.0 and in the presence of 3.0 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 3539T formed a robust clade with members of the genus Marinicella and was closely related to Marinicella litoralis JCM 16154T, Marinicella sediminis F2T and Marinicella pacifica sw153T with 97.7, 96.2 and 95.4 % sequence similarity, respectively. The average amino acid identity, percentage of conserved proteins, average nucleotide identity and digital DNA–DNA hybridization values between strain 3539T and M. litoralis JCM 16154T were 64.9, 68.3, 72.8 and 18.9 %, respectively. The genomic DNA G+C content of strain 3539T was 42.0 mol%. The dominant respiratory quinone was ubiquinone-8, and the major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c). The polar lipids of strain 3539T consisted of phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified lipid and three unidentified phospholipids. Based on the combination of phylogenetic, phenotypic and chemotaxonomic data, strain 3539T is considered to represent a novel species within the genus Marinicella in he family Alcanivoracaceae , for which the name Marinicella rhabdoformis sp. nov. is proposed. The type strain of the new species is 3539T (=KCTC 72414T=MCCC 1H00388T).


2020 ◽  
Vol 70 (12) ◽  
pp. 6133-6141 ◽  
Author(s):  
Chan-Yeong Park ◽  
Seong-Jun Chun ◽  
Chunzhi Jin ◽  
Ve Van Le ◽  
Yingshun Cui ◽  
...  

A novel Gram-stain-negative, aerobic, non-spore-forming, non-motile, and rod-shaped bacterium, strain ETT8T was isolated from a chemostat culture of microalga Ettlia sp. YC001. Optimal growth was with 0–2% NaCl and at 25–37 °C on R2A medium. Phylogenetic analysis based on the 16S rRNA gene and genome sequence showed that strain ETT8T belongs to the genus Tabrizicola , with the close neighbours being T. sediminis DRYC-M-16T (98.1 %), T. alkalilacus DJCT (97.6 %), T. fusiformis SY72T (96.9 %), T. piscis K13M18T (96.8 %), and T. aquatica RCRI19T (96.5 %). The genomic comparison of strain ETT8T with type species in the genus Tabrizicola was analysed using the genome-to-genome distance calculator (GGDC), average nucleotide identity (ANI), and average amino acid identity (AAI) (values indicated ≤17.7, ≤75.4 and ≤71.9 %, respectively). The genomic DNA G+C content of strain ETT8T was 64.4 %, plus C18 : 1  ω6c and C18 : 0-iso were the major fatty acids and Q-10 the major respiratory quinone. Strain ETT8T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine aminolipid, and four unidentified lipids as the major polar lipids. Based on the chemotaxonomic, genotypic, and phenotype results, strain ETT8T was recognized as a novel species of the genus Tabrizicola for which the name Tabrizicola algicola sp. nov. is proposed. The type strain is ETT8T (=KCTC 72206T=JCM 31893T=MCC 4339T).


2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 400-405 ◽  
Author(s):  
Yong Min Kwon ◽  
Sung-Hyun Yang ◽  
Kae Kyoung Kwon ◽  
Sang-Jin Kim

A Gram-negative, proteorhodopsin-containing, orange pigmented, rod-shaped and strictly aerobic bacterium, designated strain AKS622T, was isolated from a glacier core collected from the coast of King George Island, Antarctica. 16S rRNA gene sequence analysis revealed that strain AKS622T was affiliated to the genus Nonlabens of the family Flavobacteriaceae and showed highest similarity to Nonlabens marinus S1-08T (97.9 %). The level of DNA–DNA relatedness between strain AKS622T and N. marinus S1-08T was 46 %. Optimal growth of strain AKS622T was observed at pH 7.0, at 15 °C and with 2.0 % NaCl. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C16 : 0 3-OH, C17 : 0 2-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content was 37.9 mol%. The major respiratory quinone was MK-6. Phosphatidylethanolamine, four unidentified glycolipids, three unidentified aminolipids and one unidentified lipid were detected as major polar lipids. On the basis of the data from this polyphasic taxonomic study, it was concluded that strain AKS622T represents a novel species within the genus Nonlabens , for which the name Nonlabens antarcticus sp. nov. is proposed. The type strain is AKS622T ( = KCCM 43019T = JCM 14068T). Emended descriptions of N. marinus Park et al. 2012 and Nonlabens agnitus Yi and Chun 2012 are given.


Author(s):  
Lina Lyu ◽  
Qiliang Lai ◽  
Jianyang Li ◽  
Zhiqiang Yu ◽  
Zongze Shao

Strain 11-3T was isolated from the surface seawater along the coast of Xiamen Island, China. Cells were Gram-stain-negative, oxidase- and catalase-positive, short and rod-shaped, nonmotile, 0.5-1.0 μm in width and 1.0-2.0 μm in length. Growth of strain 11-3T was at temperature of 15–37°C (optimum 28–35°C), at pH of 5.0-11.0 (optimum 7.0-9.0) and at salinity range of 0-10 (optimum 0.5–1). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 11-3T belonged to the genus Paracoccus and had the highest similarity with Paracoccus caeni MJ17T (98.1 %), followed by Paracoccus xiamenensis 12-3T (97.1 %), Paracoccus zeaxanthinifaciens ATCC 21588T (97.1 %), Paracoccus aestuarii DSM 19484T (97.0 %), Paracoccus liaowanqingii 2251T (97.0 %), Paracoccus fistulariae KCTC 22803T (97.0 %) and other species of the genus Paracoccus (95.2–96.8 %). The DNA-DNA hybridization values between strain 11-3T and the selected strains ( P. caeni MJ17T, P. xiamenensis 12-3T, P. zeaxanthinifaciens ATCC 21588T, P. aestuarii DSM 19484T and P. liaowanqingii 2251T) were 19.4, 19.5, 21.6, 19.3 and 19.8 %, respectively. Corresponding, their ANI values were 77.53, 75.61, 75.36, 75.73 and 75.33 %, respectively. The major fatty acid was summed feature 8 (C18:1 ω6c/ω7c). The major respiratory quinone was Q10. The polar lipids included phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), unidentified glycolipid (GL) and unidentified aminolipid (AL). The DNA G+C content of strain 11-3T was 60.1 %. Based on results of the phylogenetic analysis, phenotypic and chemotaxonomic characteristics, strain 11-3T represents a novel species of the genus Paracoccus , for which the name Paracoccus amoyensis sp. nov. is proposed. The type strain is 11-3T (=MCCC 1A16380T=KCTC 72689T).


2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4277-4283 ◽  
Author(s):  
Ruo-Xi Pi ◽  
Wen-Wu Zhang ◽  
Ming-Xu Fang ◽  
Yan-Zhou Zhang ◽  
Tian-Tian Li ◽  
...  

A novel anaerobic bacterium, designated NH-JN4T was isolated from a sediment sample collected in the South China Sea. Cells were Gram-stain-positive, spore-forming, peritrichous and rod-shaped (0.5–1.2×2.2–7 µm). The temperature and pH ranges for growth were 22–42 °C and pH 6.0–8.5. Optimal growth occurred at 34–38 °C and pH 6.5–7.0. The NaCl concentration range for growth was 0.5–6 % (w/v) with an optimum of 2.5 %. Catalase and oxidase were not produced. Substrates which could be utilized were peptone, tryptone, yeast extract, beef extract and glycine. Main fermentation products from PYG medium were formate, acetate, butyrate and ethanol. Strain NH-JN4T could utilize sodium sulfite as an electron acceptor. No respiratory quinone was detected. The predominant fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0 DMA. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The DNA G+C content was 35.8 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain NH-JN4T was a member of family Clostridiaceae , and was most closely related to Clostridium limosum ATCC 25620T, Clostridium proteolyticum DSM 3090T, Clostridium histolyticum ATCC 19401T and Clostridium tepidiprofundi SG 508T, showing 94.0, 93.0, 92.9 and 92.3 % sequence similarity, respectively. On the basis of phenotypic, genotypic and chemotaxonomic properties, strain NH-JN4T represents a novel species of a new genus in the family Clostridiaceae , for which the name Oceanirhabdus sediminicola gen. nov., sp. nov. is proposed. The type strain of the type species is NH-JN4T ( = JCM 18501T = CCTCC AB 2013103T = KCTC 15322T).


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