Pustulibacterium marinum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Bashi Channel

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3056-3061 ◽  
Author(s):  
Guanghua Wang ◽  
Danyan Zhou ◽  
Shikun Dai ◽  
Xinpeng Tian ◽  
Jie Li ◽  
...  

A Gram-reaction-negative, non-spore-forming, gliding, non-translucent, colourless or yellow, aerobic and elevated-colony-forming strain, designated E403T, was isolated from the Bashi Channel and subjected to a polyphasic taxonomic study. Strain E403T could grow in the presence of 0.3–8 % (w/v) NaCl, at 16–43 °C and at pH 6–9, and grew optimally at 28 °C, pH 8, in natural seawater medium. The respiratory quinones were MK-6 and MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), iso-C15 : 0 3-OH and C16 : 0. The DNA G+C content of strain E403T was 37.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences of members of the family Flavobacteriaceae showed that strain E403T formed a distinct evolutionary lineage within the stable cluster containing type strains Zhouia amylolytica HN-171T (92.2 % similarity) and Joostella marina En5T (92.4 % similarity). In addition to the large 16S rRNA gene sequence differences, E403T can also be distinguished from the reference type strains J. marina En5T and Sinomicrobium oceani SCSIO 03483T by several phenotypic characteristics and chemotaxonomic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain E403T is suggested to represent a novel species of a new genus in the family Flavobacteriaceae , for which the name Pustulibacterium marinum gen. nov., sp. nov. is proposed. The type strain is E403T ( = CCTCC AB2012862T = CGMCC 1.12333T = KCTC 32192T).

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).


Author(s):  
Peng Wang ◽  
Yuxin Gao

Chakrabartia godavariana PRB40T was compared with Aestuariisphingobium litorale SYSU M10002T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of C. godavariana PRB40T had high similarity (99.8 %) to that of A. litorale SYSU M10002T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Chakrabartia . A draft genomic comparison between the two strains revealed an average nucleotide identity of 97.3 % and a digital DNA–DNA hybridization estimate of 79.5±2.9 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking differences in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Aestuariisphingobium litorale is a later heterotypic synonym of Chakrabartia godavariana .


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1876-1881 ◽  
Author(s):  
Sooyeon Park ◽  
Sung-Min Won ◽  
Doo-Sang Park ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, AH-M5T, which was isolated from a tidal flat sediment at Aphae Island in South Korea, was characterized taxonomically. Strain AH-M5T grew optimally at 25 °C, at pH 7.0–8.0 and in presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain AH-M5T clustered coherently with the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus , showing 93.4–94.3 % sequence similarity. The novel strain exhibited 16S rRNA gene sequence similarity values of less than 93.4 % to the type strains of other recognized species. Strain AH-M5T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The polar lipid profile of strain AH-M5T containing phosphatidylethanolamine and one unidentified lipid as major components was differentiated from those of the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus . The DNA G+C content of strain AH-M5T was 34.8 mol%. Differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrated that strain AH-M5T is distinguished from Mangrovimonas yunxiaonensis and Meridianimaribacter flavus . On the basis of the data presented, strain AH-M5T is considered to represent a novel genus and species within the family Flavobacteriaceae , for which the name Seonamhaeicola aphaedonensis gen. nov., sp. nov. is proposed. The type strain of the type species is AH-M5T ( = KCTC 32578T = CECT 8487T).


2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2363-2370 ◽  
Author(s):  
Hyangmi Kim ◽  
Doo-Sang Park ◽  
Hyun-Woo Oh ◽  
Kang Hyun Lee ◽  
Dong-Ho Chung ◽  
...  

Strains RU-16T, RU-28, RU-04T and PU-02T were isolated from the gut of the African mole cricket, Gryllotalpa africana. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belonged to the family Microbacteriaceae . All four strains were most closely related to Curtobacterium ginsengisoli DCY26T (below 97 % 16S rRNA gene sequence similarity). These isolates were Gram-stain-positive, motile (by gliding), rod-shaped and exhibited ivory-coloured colonies. Their chemotaxonomic properties included MK-11 as the major respiratory quinone, ornithine as the cell-wall diamino acid, acetyl as the acyl type of the peptidoglycan, cyclohexyl-C17 : 0 as the major fatty acid and phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, we propose a new genus in the family Microbacteriaceae , Gryllotalpicola gen. nov., with three novel species, Gryllotalpicola daejeonensis sp. nov. (type strain RU-04T  = KCTC 13809T  = JCM 17590T), Gryllotalpicola koreensis sp. nov. (type strain RU-16T  = KCTC 13810T  = JCM 17591T) and Gryllotalpicola kribbensis sp. nov. (type strain PU-02T  = KCTC 13808T  = JCM 17593T). Gryllotalpicola koreensis is the type species of the genus. Additionally, we propose that Curtobacterium ginsengisoli should be reclassified in the genus as Gryllotalpicola ginsengisoli comb. nov. (type strain DCY26T  = KCTC 13163T  = JCM 14773T).


2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 1972-1981 ◽  
Author(s):  
Taishi Tsubouchi ◽  
Yasuhiro Shimane ◽  
Kozue Mori ◽  
Keiko Usui ◽  
Toshiki Hiraki ◽  
...  

A novel filamentous bacterium, designated strain JIR-001T, was isolated from hemipelagic sediment in deep seawater. This strain was non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form and ivory coloured with wrinkles between the centre and the edge of the colony on ISP2 medium. The isolate grew aerobically at 55–73 °C with the formation of aerial mycelia; spores were produced singly along the aerial mycelium. These morphological features show some similarities to those of the type strains of some species belonging to the family Thermoactinomycetaceae . Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain JIR-001T belongs to the family Thermoactinomycetaceae within the class Bacilli . Similarity levels between the 16S rRNA gene sequence of strain JIR-001T and those of the type strains of Thermoactinomycetaceae species were 85.5–93.5 %; highest sequence similarity was with Melghirimyces algeriensis NariEXT. In the DNA–DNA hybridization assays between strain JIR-001T and its phylogenetic neighbours the mean hybridization levels with Melghirimyces algeriensis NariEXT, Planifilum fimeticola H0165T, Planifilum fulgidum 500275T and Planifilum yunnanense LA5T were 5.3–7.5, 2.3–4.7, 2.1–4.8 and 2.5–4.9 %, respectively. The DNA G+C content of strain JIR-001T was 55.1 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and C16 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, glucolipid, phosphatidylserine, an amino-group containing phospholipid, an unknown phospholipid and two unknown lipids. The predominant menaquinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, strain JIR-001T is considered to represent a novel species in a new genus of the family Thermoactinomycetaceae , for which the name Polycladomyces abyssicola gen. nov., sp. nov. is proposed. The type strain of Polycladomyces abyssicola is JIR-001T ( = JCM 18147T = CECT 8074T).


Author(s):  
Rui Yin ◽  
Yan-Jun Yi ◽  
Zhuo Chen ◽  
Guan-Jun Chen ◽  
Yan-Xia Zhou ◽  
...  

A Gram-stain-negative, aerobic, yellow, non-motile, rod-shaped and alginate-degrading bacterium, designated Dm15T, was isolated from marine alga collected in Weihai, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Dm15T represents a distinct line of the family Flavobacteriaceae . Strain Dm15T had the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Arcticiflavibacter luteus (96.7 %) and 93.7–96.4 % sequence similarity to other phylogenetic neighbours ( Bizionia paragorgiae , Winogradskyella thalassocola , Ichthyenterobacterium magnum , Psychroserpens burtonensis and Arcticiflavibacter luteus ) in the family Flavobacteriaceae . The novel isolate was able to grow at 10–40 °C (optimum, 30–33 °C), pH 7.0–9.0 (optimum, pH 7.0–7.5) and with 0.5–6.0 % NaCl (optimum 2.0–3.0 %, w/v). It could grow at 40 °C, and degrade alginate and cellulose, which were different from the neighbour genera. The draft genome consisted of 3395 genes with a total length of 3 798 431 bp and 34.1mol% G+C content. Especially, there were some specific genes coding for cellulase and alginate lyase, which provided a basis for the above phenotypic characteristics. The strain's genome sequence showed 71.1–80.2 % average amino acid identity values and 71.8–77.7 % average nucleotide identity values compared to the type strains of related genera within the family Flavobacteriaceae . It shared digital DNA–DNA hybridization identity of 19.8 and 20.9 % with I. magnum and A. luteus , respectively. The sole menaquinone was MK-6. The major fatty acids were iso-C15 : 0 and iso-C15 : 1 G. The polar lipids included six unidentified polar lipids, four unidentified aminolipids and phosphatidylethanolamine. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain Dm15T represents a novel species of a new genus in the family Flavobacteriaceae , phylum Bacteroidetes , for which the name Flavihalobacter algicola gen. nov., sp. nov. is proposed. The type strain is Dm15T (KCTC 42256T=CICC 23815T).


Author(s):  
Yong Wu ◽  
Yuxin Gao ◽  
Jiasong Fang ◽  
Yuli Wei

Cellulomonas algicola KZ-21T was compared with Cellulomonas aurantiaca THG-SMD2.3T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of Cellulomonas algicola KZ-21T shared complete similarity (100.0 %) with that of Cellulomonas aurantiaca THG-SMD2.3T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Cellulomonas . Genome comparison between the two strains revealed an average nucleotide identity of 99.2 % and a digital DNA–DNA hybridization estimate of 93.7±1.8 %, strongly indicating that the two strains belong to a single species. In addition, neither strain displayed any striking differences in metabolic, physiological or chemotaxonomic features. Therefore, we propose Cellulomonas aurantiaca as a later heterotypic synonym of Cellulomonas algicola .


2020 ◽  
Vol 70 (4) ◽  
pp. 2178-2185 ◽  
Author(s):  
Wen-Ming Chen ◽  
Cheng-Ye Cai ◽  
Shih-Yi Sheu

A bacterial strain designated FSY-15T was isolated from a freshwater mesocosm in Taiwan and characterised using a polyphasic taxonomic approach. Cells of strain FSY-15T were Gram-negative, aerobic, non-spore forming, non-motile rods and formed orange coloured colonies. Growth occurred at 20–30 °C (optimum, 25 °C), at pH 6–7.5 (optimum, pH 7) and with 0–0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-15T formed a phylogenetic lineage in the the family Cytophagaceae . Strain FSY-15T was most closely related to the genera Pseudarcicella and Arcicella, and the levels of 16S rRNA gene sequence identity with respect to members of related genera are less than 94.1 %. Strain FSY-15T showed less than 68.8 % average nucleotide identity and less than 24.7 % digital DNA–DNA hybridisation identity compared to the type strains of related genera within the family Cytophagaceae . The predominant fatty acids were iso-C15 : 0, C16 : 1ω5c and the major hydroxyl fatty acid was iso-C15 : 0 3-OH. The major isoprenoid quinone was MK-7 and the DNA G+C content was 35.8 mol%. The major polar lipids were phosphatidylethanolamine and several uncharacterised aminophospholipid, aminolipid, phospholipid and lipid. The major polyamine was spermidine. On the basis of the genotypic and phenotypic data, strain FSY-15T represents a novel species of a new genus in the family Cytophagaceae , for which the name Sandaracinomonas limnophila gen. nov., sp. nov. is proposed. The type strain is FSY-15T (=BCRC 81011T =LMG 29732T =KCTC 52445T).


2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1354-1358 ◽  
Author(s):  
Sooyeon Park ◽  
Ki-Hoon Oh ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

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).


2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3254-3263 ◽  
Author(s):  
Martin W. Hahn ◽  
Johanna Schmidt ◽  
Sami J. Taipale ◽  
W. Ford Doolittle ◽  
Ulrike Koll

A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola ’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8T represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8T is noticeable due to its unusually low values of cell size (0.05 µm3), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8T is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8T and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8T was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8T represents a novel species of a new genus in the family Microbacteriaceae , for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8T ( = DSM 23834T = LMG 26932T).


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