scholarly journals Flavobacterium daemonensis sp. nov., isolated from Daemo Mountain soil

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 983-989 ◽  
Author(s):  
Hien T. T. Ngo ◽  
MooChang Kook ◽  
Tae-Hoo Yi
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Link Type ◽  
Gram Staining ◽  
Bright Yellow

A Gram-staining-negative, catalase- and oxidase-positive, obligately aerobic, motile by gliding, bright yellow and rod-shaped bacterial strain was isolated from soil of Daemo Mountain (Daemosan) in Seoul, Republic of Korea. Its taxonomic position was investigated by using a polyphasic study. On the basis of 16S rRNA gene sequence comparisons, strain THG–DJ7T was found to be most closely related to Flavobacterium denitrificans ED5T (97.9 % sequence similarity), Flavobacterium ginsenosidimutans THG 01T (97.6 %), Flavobacterium kyungheensis THG-107T (97.5 %), Flavobacterium anhuiense D3T (97.1 %) and Flavobacterium ginsengisoli DCY54T (97.0 %). The DNA–DNA relatedness between strain THG–DJ7T and its phylogenetically closest neighbours was below 40.0 %. The G+C content of the genomic DNA was determined to be 32.6 mol%. The only isoprenoid quinone detected in strain THG–DJ7T was menaquinone-6 (MK-6). The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were found to be phosphatidylethanolamine, phosphatidyldimethylethanolamine, an unidentified aminophosphoglycolipid, phosphatidylserine and an unidentified lipid. The major fatty acids were identified as iso-C15 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). These data support the affiliation of strain THG–DJ7T to the genus Flavobacterium . We report the phenotypic, genotypic and phylogenetic characterization of strain THG–DJ7T. Based on the findings presented, a novel species of the genus Flavobacterium , Flavobacterium daemonensis sp. nov. is proposed, with THG–DJ7T ( = KACC 17651T = JCM 19455T) as the type strain.

scholarly journals Sphingopyxis italica sp. nov., isolated from Roman catacombs

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2565-2569 ◽  
Author(s):  
Cynthia Alias-Villegas ◽  
Valme Jurado ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Dna Base ◽  
Physiological Tests

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, strain SC13E-S71T, was isolated from tuff, volcanic rock, where the Roman catacombs of Saint Callixtus in Rome, Italy, was excavated. Analysis of 16S rRNA gene sequences revealed that strain SC13E-S71T belongs to the genus Sphingopyxis , and that it shows the greatest sequence similarity with Sphingopyxis chilensis DSM 14889T (98.72 %), Sphingopyxis taejonensis DSM 15583T (98.65 %), Sphingopyxis ginsengisoli LMG 23390T (98.16 %), Sphingopyxis panaciterrae KCTC 12580T (98.09 %), Sphingopyxis alaskensis DSM 13593T (98.09 %), Sphingopyxis witflariensis DSM 14551T (98.09 %), Sphingopyxis bauzanensis DSM 22271T (98.02 %), Sphingopyxis granuli KCTC 12209T (97.73 %), Sphingopyxis macrogoltabida KACC 10927T (97.49 %), Sphingopyxis ummariensis DSM 24316T (97.37 %) and Sphingopyxis panaciterrulae KCTC 22112T (97.09 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), C14 : 0 2-OH and C16 : 0. The predominant menaquinone was MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. These chemotaxonomic data are common to members of the genus Sphingopyxis . However, a polyphasic approach using physiological tests, DNA base ratios, DNA–DNA hybridization and 16S rRNA gene sequence comparisons showed that the isolate SC13E-S71T belongs to a novel species within the genus Sphingopyxis , for which the name Sphingopyxis italica sp. nov. is proposed. The type strain is SC13E-S71T ( = DSM 25229T = CECT 8016T).

scholarly journals Belliella aquatica sp. nov., isolated from a saline lake

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1622-1627 ◽  
Author(s):  
Zhi-Ping Zhong ◽  
Ying Liu ◽  
Ting-Ting Hou ◽  
Yu-Guang Zhou ◽  
Hong-Can Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Saline Lake ◽  
Qaidam Basin ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-negative bacterium, strain TS-T86T, was isolated from Lake Tuosu, a saline lake (salinity 5.4 %, w/w) in Qaidam basin, China. Its taxonomic position was determined by using a polyphasic approach. Strain TS-T86T was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Cells were non-spore-forming, non-motile rods, 0.4–0.6 µm wide and 1.2–2.3 µm long. Growth was observed in the presence of 0–9.0 % (w/v) NaCl (optimum, 2.0 %), at 4–35 °C (optimum, 25 °C) and at pH 7.0–10.5 (optimum, pH 8.5–9.0). Strain TS-T86T contained MK-7 as the predominant respiratory quinone. The major fatty acids (>10 %) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, an unknown phospholipid, six unidentified aminolipids and two uncharacterized lipids. The DNA G+C content was 35 mol% (T m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T86T was associated with the genus Belliella , and showed the highest sequence similarity to Belliella baltica BA134T (98.5 %) and then to Belliella kenyensis No.164T (95.7 %) and Belliella pelovolcani CC-SAL-25T (95.3 %). DNA–DNA relatedness of strain TS-T86T to Belliella baltica DSM 15883T was 32±3 %. It is concluded that strain TS-T86T represents a novel species of the genus Belliella , for which the name Belliella aquatica sp. nov. is proposed. The type strain is TS-T86T ( = CGMCC 1.12479T = JCM 19468T).

scholarly journals Salinibaculum litoreum gen. nov., sp. nov., isolated from salted brown alga Laminaria

2020 ◽  
Vol 70 (4) ◽  
pp. 2879-2887 ◽  
Author(s):  
Dong Han ◽  
Heng-Lin Cui
Keyword(s):  
Brown Alga ◽  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
A Minor

A novel Gram-stain-negative, aerobic and rod-shaped halophilic archaeon, designated HD8-45T, was isolated from the red brine of salted brown alga Laminaria produced at Dalian, PR China. According to the results of 16S rRNA gene and rpoB′ gene sequence comparisons, strain HD8-45T showed the highest sequence similarity to the corresponding genes of Salinirussus salinus YGH44T (95.1 and 85.2 % similarities, respectively), Halovenus aranensis EB27T (91.2 and 86.0 % similarities, respectively). The low sequence similarity and the phylogeny implied the novel generic status of strain HD8-45T. Genomic relatedness analyses showed that strain HD8-45T were clearly distinguished from other species in the order Halobacteriales , with average nucleotide identity, amino acid identity and in silico DNA–DNA hybridization values not more than 75.1, 65.6 and 21.5 %. The polar lipid pattern contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two major glycolipids and two minor glycolipids. The two major glycolipids and a minor glycolipid were chromatographically identical to disulfated mannosyl glucosyl diether, sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. The major respiratory quinones were menaquinone MK-8 and MK-8(H2). The DNA G+C content was 62.0 mol% (Tm ) and 61.9 mol% (genome). All these results showed that strain HD8-45T represents a novel species of a new genus in the order Halobacteriales , for which the name Salinibaculum litoreum gen. nov., sp. nov. is proposed. The type strain of Salinibaculum litoreum is HD8-45T (=CGMCC 1.15328T=JCM 31107T).

Bacillus gottheilii sp. nov., isolated from a pharmaceutical manufacturing site

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 867-872 ◽  
Author(s):  
Herbert Seiler ◽  
Mareike Wenning ◽  
Verena Schmidt ◽  
Siegfried Scherer
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Acid Type

A novel Gram-staining-positive, rod-shaped, motile, strictly aerobic, endospore-forming bacterium, designated WCC 4585T, was isolated from a pharmaceutical production line. The organism grew optimally at 30 °C, at pH 8 and in the presence of 0.5 % (w/v) NaCl. Oval endospores were formed subterminally and terminally in swollen sporangia. The cell-wall diamino acid was meso-diaminopimelic acid (type A1γ) and the genomic DNA G+C content was 38.7 mol%. The major menaquinone was MK-7. The cellular fatty acid profile contained major amounts of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, and the cellular phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. The isolate was most closely related to Bacillus oceanisediminis H2T, Bacillus infantis SMC 4352-1T, Bacillus firmus NCIMB 9366T, Bacillus circulans ATCC 4513T and Bacillus horneckiae DSM 23495T with which it shared less than 98.0 % 16S rRNA gene sequence similarity. DNA–DNA relatedness values between strain WCC 4585T and five type strains of related species were ≤27 % and sequence similarity values based on groEL sequences were ≤88.7 %. On the basis of the characteristics presented, strain WCC 4585T is proposed to represent a novel species, Bacillus gottheilii sp. nov. The type strain is WCC 4585T( = DSM 23668T = CCUG 59876T = LMG 25856T).

Flavobacterium dankookense sp. nov., isolated from a freshwater reservoir, and emended descriptions of Flavobacterium cheonanense , F. chungnamense , F. koreense and F. aquatile

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2378-2382 ◽  
Author(s):  
Siwon Lee ◽  
Hang-Yeon Weon ◽  
Kyudong Han ◽  
Tae-Young Ahn
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Freshwater Reservoir ◽  
Genotypic Characteristics

A novel yellow-pigmented bacterial strain, designated ARSA-19T, was isolated from a freshwater reservoir in Cheonan, Korea. Cells were Gram-staining-negative, rod-shaped, strictly aerobic and positive for catalase and oxidase. The phylogenetic tree based on 16S rRNA gene sequences showed that strain ARSA-19T belonged to the genus Flavobacterium and was related to Flavobacterium macrobrachii an-8T (96.5 % sequence similarity), F. koreense KACC 14969T (96.2 %), F. chungnamense KACC 14971T (96.1 %), F. cheonanense KACC 14972T (96.4 %) and F. aquatile ATCC 11947T (95.6 %). The isolate contained MK-6 as the predominant menaquinone and iso-C15 : 0 (21.8 %), iso-C16 : 0 3-OH (10.4 %), iso-C15 : 1 G (9.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 8.2 %), iso-C15 : 0 3-OH (7.7 %) and iso-C16 : 0 (7.3 %) as the major fatty acids. The polar lipids of strain ARSA-19T were phosphatidylethanolamine, four unknown aminolipids and two unidentified polar lipids. The DNA G+C content of strain ARSA-19T was 33.3 mol%. Based on its phenotypic and genotypic characteristics and on the phylogenetic evidence presented, strain ARSA-19T is considered to represent a novel species in the genus Flavobacterium , for which the name Flavobacterium dankookense sp. nov. is proposed. The type strain is ARSA-19T ( = KCTC 23179T  = JCM 17065T  = KACC 14968T). Emended descriptions of Flavobacterium cheonanense , Flavobacterium chungnamense , Flavobacterium koreense and Flavobacterium aquatile are also proposed.

scholarly journals Mycobacterium celeriflavum sp. nov., a rapidly growing scotochromogenic bacterium isolated from clinical specimens

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 510-515 ◽  
Author(s):  
Abdolrazagh Hashemi Shahraki ◽  
Cengiz Çavuşoğlu ◽  
Emanuele Borroni ◽  
Parvin Heidarieh ◽  
Orhan Kaya Koksalan ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Mycolic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Polyphasic Characterization

Six strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of Mycobacterium moriokaense showed 99.0 % 16S rRNA gene sequence similarity, and 91.5–96.5 % similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of M. moriokaense presented an average nucleotide identity (ANI) of 82.9 %. Phylogenetic analysis produced poorly robust trees in most genes with the exception of rpoB and sodA where Mycobacterium flavescens and Mycobacterium novocastrense were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name Mycobacterium celeriflavum sp. nov. is proposed. The type strain is AFPC-000207T ( = DSM 46765T = JCM 18439T).

Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1639-1645 ◽  
Author(s):  
Lei Zhang ◽  
Xihui Shen ◽  
Yingbao Liu ◽  
Shiqing Li
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
The Family

A Gram-staining-negative, rod-shaped, gliding and pale-pink-pigmented bacterium, designated strain ZLM-10T, was isolated from a soil sample collected from an arid area in Xinjiang province, China, and characterized in a taxonomic study using a polyphasic approach. The novel strain grew optimally at 30–37 °C and in the presence of 2 % (w/v) sea salts. The only respiratory quinone detected was MK-7 and the major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified aminophospholipids. The DNA G+C content was 45.4 mol%. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZLM-10T was a member of the phylum Bacteroidetes and appeared most closely related to Cesiribacter roseus 311T (90.2 % sequence similarity), Marivirga sericea LMG 13021T (89.2 %), Cesiribacter andamanensis AMV16T (89.1 %) and Marivirga tractuosa DSM 4126T (89.1 %). On the basis of phenotypic and genotypic data and phylogenetic inference, strain ZLM-10T should be classified as a novel species of a new genus in the family Flammeovirgaceae , for which the name Nafulsella turpanensis gen. nov., sp. nov. is proposed. The type strain of the type species is ZLM-10T ( = CCTCC AB 208222T = KCTC 23983T).

scholarly journals Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2060-2065 ◽  
Author(s):  
Wei-Chun Hung ◽  
Hsiao-Jan Chen ◽  
Jui-Chang Tsai ◽  
Sung-Pin Tseng ◽  
Tai-Fen Lee ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379T, and 96.7 to 98.6 % similarity with Gemella sanguinis ATCC 700632T, Gemella morbillorum ATCC 27824T or Gemella cuniculi CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.

scholarly journals Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1123-1126 ◽  
Author(s):  
Yochan Joung ◽  
Beom-Il Lee ◽  
Heeyoung Kang ◽  
Haneul Kim ◽  
Kiseong Joh
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Artificial Lake ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Bacterium Strain

A Gram-staining-negative, rod-shaped bacterium, strain HMD2169T, was isolated from a mesotrophic artificial lake in Korea. Strain HMD2169T grew in the presence of 0–3.0 % (w/v) NaCl, at pH 5–10 and at 20–37 °C. The predominant quinone of strain HMD2169T was ubiquinone (UQ)-8. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 59.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD2169T was a representative of a lineage within the genus Chitinimonas . Strain HMD2169T was closely related to Chitinimonas taiwanensis (95.8 % sequence similarity) and Chitinimonas koreensis (94.6 %). On the basis of the evidence presented in this study, strain HMD2169T is a representative of a novel species of the genus Chitinimonas , for which the name Chitinimonas viridis sp. nov. is proposed with the type strain HMD2169T ( = KCTC 22839T = CECT 7703T).

Sphingobacterium hotanense sp. nov., isolated from soil of a Populus euphratica forest, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 815-820 ◽  
Author(s):  
Ting Xiao ◽  
Xiang He ◽  
Gang Cheng ◽  
Haiju Kuang ◽  
Xiangru Ma ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Populus Euphratica ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A novel Gram-staining-negative bacterial strain, designated XH4T, was isolated from soil of a Populus euphratica forest in the Hotan River valley, Xinjiang Uyghur autonomous region, PR China. The cells were strictly aerobic, non-motile, short rods. The isolate grew optimally at 37 °C and at pH 7.0–8.0. Based on 16S rRNA gene sequence analysis, strain XH4T belonged to the genus Sphingobacterium and was closely related to Sphingobacterium mizutaii ATCC 33299T (96.1 % sequence similarity). The DNA G+C content was 41.2 mol%. The major polar lipid of strain XH4T was phosphatidylethanolamine, and several unidentified polar lipids were also present. Strain XH4T showed the typical chemotaxonomic features of the genus Sphingobacterium , with the presence of ceramide phosphorylethanolamine 2 (CerPE-2) as the major ceramide. The major cellular fatty acids of strain XH4T were iso-C15 : 0 (34.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 20.7 %) and iso-C17 : 0 3-OH (14.7 %). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic data and phylogenetic inference, strain XH4T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium hotanense sp. nov. is proposed. The type strain is XH4T ( = NRRL B-59204T  = CCTCC AB 209007T). Emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense are also given.

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