scholarly journals Kocuria salsicia sp. nov., isolated from salt-fermented seafood

2011 ◽  
Vol 61 (2) ◽  
pp. 286-289 ◽  
Author(s):  
Ji-Hyun Yun ◽  
Seong Woon Roh ◽  
Mi-Ja Jung ◽  
Min-Soo Kim ◽  
Eun-Jin Park ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Lemon Yellow ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
16S Rrna Gene Sequences ◽  
Taxonomic Analysis

Strain 104T was isolated from a traditional salt-fermented seafood in Korea. It was a Gram-positive, non-motile, coccus-shaped bacterium. It formed lemon–yellow, opaque colonies that were circular with entire margins. Optimal growth occurred at 30–37 °C, pH 7–8 and in the presence of 0–2 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences from strain 104T and reference species of the genus Kocuria indicated that strain 104T formed an independent line. The G+C content of the chromosomal DNA was 60.6 mol%. MK-7 was the major menaquinone and the predominant fatty acids were anteiso-C15 : 0 (76.7 %), anteiso-C17 : 0 (10.9 %) and iso-C16 : 0 (4.5 %). Strain 104T was most closely related to Kocuria rhizophila TA68T (98.9 % 16S rRNA gene sequence similarity). The DNA–DNA hybridization value between strain 104T and K. rhizophila TA68T was 14.1±3.4 %. On the basis of this polyphasic taxonomic analysis, strain 104T appears to represent a novel species in the genus Kocuria. The name Kocuria salsicia sp. nov. is proposed. The type strain is 104T (=KACC 21128T=JCM 16361T).

scholarly journals Microbacterium enclense sp. nov., isolated from sediment sample

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2064-2070 ◽  
Author(s):  
Rahul R. Mawlankar ◽  
Poonam Mual ◽  
Vidya V. Sonalkar ◽  
Meghana N. Thorat ◽  
Ashish Verma ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sediment Sample ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Phenotypic Analysis ◽  
Novel Bacterium ◽  
Marine Sediment Sample

A novel bacterium (strain NIO-1002T) belonging to the genus Microbacterium was isolated from a marine sediment sample in Chorao Island, Goa Province, India. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Cells of this strain were Gram-stain-positive, non-motile, non-spore-forming rods that formed yellow-pigmented colonies. It grew in 0–12 % (w/v) NaCl and at 25–37 °C, with optimal growth at 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1002T is associated with members of the genus Microbacterium, with highest sequence similarity with Microbacterium hominis CIP 105731T (98.1 %) and Microbacterium testaceum KCTC 9103T (98.0 %). Within the phylogenetic tree, this novel strain shared a branching point with M. hominis CIP 105731T. The DNA G+C content was 66.5 mol% and DNA–DNA hybridization relatedness between NIO-1002T, M. hominis CIP 105731T and M. testaceum KCTC 9103T was 39.0 ± 2.0 % and 41.0 ± 2.0 %, respectively. The major fatty acids were ai-C15 : 0, i-C16 : 0 and ai-C17 : 0 and the diamino acid in the cell-wall peptidoglycan of NIO-1002T was lysine. Data obtained from DNA–DNA hybridization and chemotaxonomic phenotypic analysis support the conclusion that strain NIO-1002T represents a novel species within the genus Microbacterium. The name Microbacterium enclense sp. nov. is proposed, with NIO-1002T ( = NCIM 5454T = DSM 25125T = CCTCC AB 2011120T) as the type strain.

scholarly journals Plantactinospora sonchi sp. nov., an actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.)

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4895-4901 ◽  
Author(s):  
Zhaoxu Ma ◽  
Chongxi Liu ◽  
Jianlong Fan ◽  
Hairong He ◽  
Chuang Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Sonchus Oleraceus

A novel actinobacterium, designated strain NEAU-QY2T, was isolated from the leaves of Sonchus oleraceus L. specimen, collected from Wuchang, Heilongjiang Province, China. A polyphasic study was carried out to establish the taxonomic position of this strain. The organism formed single spores with rough surfaces on substrate mycelia. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-QY2T belonged to the genus Plantactinospora and formed a monophyletic clade with its closest related strains Plantactinospora endophytica YIM 68255T (99.2 % 16S rRNA gene sequence similarity), Plantactinospora veratri NEAU-FHS4T (98.8 %) and Plantactinospora mayteni YIM 61359T (98.7 %), an association that was supported by a bootstrap value of 90 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. However, DNA–DNA hybridization values between strain NEAU-QY2T and the three closely related strains were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA–DNA hybridization results, strain NEAU-QY2T was distinguished from closely related strains and is classified as representing a novel species of the genus Plantactinospora, for which the name Plantactinospora sonchi sp. nov. is proposed. The type strain is NEAU-QY2T ( = CGMCC 4.7216T = JCM 30345T).

Flammeovirga pacifica sp. nov., isolated from deep-sea sediment

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 937-941 ◽  
Author(s):  
Hui Xu ◽  
Yuanyuan Fu ◽  
Ning Yang ◽  
Zhixin Ding ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Strain WPAGA1T was isolated from marine sediment of the west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Flammeovirga . Strain WPAGA1T exhibited highest 16S rRNA gene sequence similarity with Flammeovirga yaeyamensis NBRC 100898T (98.1 %) and lower sequence similarity with Flammeovirga arenaria IFO 15982T (94.6 %) and other members of the genus Flammeovirga (<94.2 %). DNA–DNA relatedness studies showed that strain WPAGA1T was distinct from F. yaeyamensis NBRC 100898T and F. arenaria NBRC 15982T (43±4 % and 32±2 % relatedness values, respectively). Strain WPAGA1T could be distinguished from all known members of the genus Flammeovirga by a number of phenotypic features. However, the dominant fatty acids of strain WPAGA1T (iso-C15 : 0, C16 : 0 and C20 : 4ω6,9,12,15c), the major polyamine (cadaverine) and the G+C content of the chromosomal DNA (32.9 mol%) were consistent with those of members of the genus Flammeovirga . Based on phenotypic and chemotaxonomic features and 16S rRNA gene sequences, strain WPAGA1T can be assigned to the genus Flammeovirga as a representative of a novel species, for which the name Flammeovirga pacifica sp. nov. is proposed; the type strain is WPAGA1T ( = CCTCC AB 2010364T = LMG 26175T = DSM 24597T = MCCC 1A06425T).

scholarly journals Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica

2005 ◽  
Vol 55 (6) ◽  
pp. 2531-2538 ◽  
Author(s):  
Neha Singh ◽  
Melissa M. Kendall ◽  
Yitai Liu ◽  
David R. Boone
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Sampling Site ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Range Analysis ◽  
Isolation And Characterization

Three novel strains of methylotrophic methanogens were isolated from Skan Bay, Alaska, by using anaerobic cultivation techniques. The water was 65 m deep at the sampling site. Strains AK-4 (=OCM 774), AK-5T (=OCM 775T=DSM 17273T) and AK-9 (=OCM 793) were isolated from the sulfate-reducing zone of the sediments. Each of the strains was a non-motile coccus and occurred singly. Cells grew with trimethylamine as a catabolic substrate and strain AK-4 could also catabolize methanol. Yeast extract and trypticase peptones were not required for growth, but their addition to the culture medium slightly stimulated growth. Each of the strains grew at temperatures of 5–28 °C; they were slight halophiles and grew fastest in the neutral pH range. Analysis of the 16S rRNA gene sequences indicated that strain AK-4 was most closely related to Methanosarcina baltica. DNA–DNA hybridization studies showed 88 % relatedness, suggesting that strain AK-4 represents a novel strain within this species. Strains AK-5T and AK-9 had identical 16S rRNA gene sequences that were most closely related to the sequence of Methanococcoides burtonii (99·8 % sequence similarity). DNA–DNA hybridization studies showed that strains AK-5T and AK-9 are members of the same species (88 % relatedness value), but strain AK-5T had a DNA–DNA relatedness value of only 55 % to Methanococcoides burtonii. This indicates that strains AK-5T and AK-9 should be considered as members of a novel species in the genus Methanococcoides. We propose the name Methanococcoides alaskense sp. nov., with strain AK-5T (=OCM 775T=DSM 17273T) as the type strain.

scholarly journals Oceanisphaera sediminis sp. nov., isolated from marine sediment

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1552-1557 ◽  
Author(s):  
Na-Ri Shin ◽  
Tae Woong Whon ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Young-Ok Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Two strains, designated TW92T and TW93, were isolated from marine sediment collected from the south coast of Korea. Cells of both strains were Gram-staining-negative, coccus-shaped, aerobic, motile and catalase- and oxidase-positive. Strain TW92T grew optimally in the presence of 2 % (w/v) NaCl (range 1–5 %) while strain TW93 grew optimally in the presence of 1 % (w/v) NaCl (range 0–12 %), and both strains had an optimal growth temperature of 30 °C (range 4–37 °C). Strains TW92T and TW93 had the same optimum pH (pH 7), but differed in their ability to grow at pH 10. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strains TW92T and TW93 were most closely related to Oceanisphaera donghaensis BL1T, with 98.8 % and 98.7 % similarity, respectively. Pairwise similarity between the 16S rRNA gene sequences of strains TW92T and TW93 was 99.9 %. The major fatty acids of both strains were summed features 3 (comprising C16 : 1ω7c/iso-C15 2-OH), C16 : 0 and C18 : 1ω7c. Both strains possessed the ubiquinone Q-8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the polar lipids. The genomic DNA G+C contents of strains TW92T and TW93 were 58.5 and 59.6 mol%, respectively. Genomic relatedness values based on DNA–DNA hybridization of strains TW92T and TW93 with related species were below 47 % and 31 %, respectively. DNA–DNA hybridization values between strains TW92T and TW93 were above 85 %. On the basis of a taxonomic study using polyphasic analysis, it is proposed that the two isolates represent a novel species, Oceanisphaera sediminis sp. nov., with strain TW92T ( = KACC 15117T = JCM 17329T) as the type strain and strain TW93 ( = KACC 15118 = JCM 17330) as an additional strain.

scholarly journals Biochemical and genetic evidence for the transfer of Enterococcus solitarius Collins et al. 1989 to the genus Tetragenococcus as Tetragenococcus solitarius comb. nov.

2005 ◽  
Vol 55 (2) ◽  
pp. 589-592 ◽  
Author(s):  
Saïd Ennahar ◽  
Yimin Cai
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Separate Species ◽  
Tetragenococcus Muriaticus ◽  
Produce Acid

Phylogenetic analysis of 16S rRNA gene sequences revealed that Enterococcus solitarius is not a member of the genus Enterococcus, but is related to species of the genus Tetragenococcus. On a phylogenetic tree, E. solitarius clustered with Tetragenococcus halophilus and Tetragenococcus muriaticus, with which it showed the highest 16S rRNA gene sequence similarity level (about 94 %). Phenotypic studies indicated that E. solitarius was also unable to produce acid from lactose, providing further evidence of its affiliation to the genus Tetragenococcus. DNA hybridization studies indicated that E. solitarius was clearly a separate species, different from T. halophilus and T. muriaticus (reassociation levels of about 23 and 54 %, respectively). As suggested in previous studies, E. solitarius is closely related to but clearly distinct from T. halophilus. Based upon properties that taxonomically distinguish it from species of the genus Enterococcus, it is proposed that E. solitarius be transferred to the genus Tetragenococcus and reclassified as Tetragenococcus solitarius comb. nov. (type strain, 885/78T=ATCC 49428T=CCUG 29293T=CIP 103330T=DSM 5634T=JCM 8736T=LMG 12890T=NCTC 12193T).

scholarly journals Roseovarius nanhaiticus sp. nov., a member of the Roseobacter clade isolated from marine sediment

2010 ◽  
Vol 60 (6) ◽  
pp. 1289-1295 ◽  
Author(s):  
Baojiang Wang ◽  
Fengqin Sun ◽  
Qiliang Lai ◽  
Yaping Du ◽  
Xiupian Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Gram Staining

An aerobic, Gram-staining-negative, rod or ovoid-shaped bacterial isolate, strain NH52JT, was isolated from a sandy sediment sample from the South China Sea. Strain NH52JT exhibited tumbling motility, formed beige or faint pink colonies, gave a positive reaction in tests for catalase and oxidase and required NaCl for growth. Optimal growth was observed at pH 7.8–9.3, at 30 °C and in the presence of 2.0–4.0 % (w/v) NaCl. The novel strain did not synthesize bacteriochlorophyll a, and the DNA G+C content was 62 %. The major fatty acids were C18 : 1 ω7c, C16 : 0 and C18 : 1 ω7c 11-methyl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NH52JT was affiliated to the genus Roseovarius of the class Alphaproteobacteria. Roseovarius pacificus and Roseovarius aestuarii were the most closely related recognized species to strain NH52JT with 16S rRNA gene sequence similarity values of 95.0 and 95.7 %, respectively. Sequence similarity values between strain NH52JT and other phylogenetically related species were all below 95.0 %. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain NH52JT is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius nanhaiticus sp. nov. is proposed. The type strain is NH52JT (=LMG 24840T=CCTCC AB 208317T=MCCC 1A03543T).

Cellulosibacter alkalithermophilus gen. nov., sp. nov., an anaerobic alkalithermophilic, cellulolytic-xylanolytic bacterium isolated from soil of a coconut garden

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2330-2335 ◽  
Author(s):  
Amornrat Watthanalamloet ◽  
Chakrit Tachaapaikoon ◽  
Yun Sik Lee ◽  
Akihiko Kosugi ◽  
Yutaka Mori ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
The Family ◽  
A Cell

An obligately anaerobic, cellulolytic-xylanolytic bacterium, designated strain A6T, was isolated from soil of a coconut garden in the Bangkuntien district of Bangkok, Thailand. The strain was Gram-stain positive, catalase-negative, endospore-forming, motile and rod-shaped with a cell size of 0.2–0.3×2.0–3.0 µm. Optimal growth of strain A6T occurred at pH55 °C 9.5, 55 °C. Strain A6T fermented various carbohydrates, and the end products from the fermentation of cellobiose were acetate, ethanol, propionate and a small amount of butyrate. The major cellular fatty acids were iso-C14 : 0 3-OH, iso-C15 : 0, iso-C16 : 0 and C16 : 0. The cell-wall peptidoglycan contained meso-diaminopimelic acid. No respiratory quinones were detected. The DNA G+C content was 30.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain represented a new phyletic sublineage within the family Clostridiaceae , with <93.0 % 16S rRNA gene sequence similarity to recognized species of this family. On the basis of phenotypic, genotypic and physiological evidence, strain A6T represents a novel species of a new genus, for which the name Cellulosibacter alkalithermophilus gen. nov., sp. nov. is proposed. The type strain of the type species is A6T ( = TISTR 1915T = KCTC 5874T).

scholarly journals Haloterrigena daqingensis sp. nov., an extremely haloalkaliphilic archaeon isolated from a saline–alkaline soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2267-2271 ◽  
Author(s):  
Shuang Wang ◽  
Qian Yang ◽  
Zhi-Hua Liu ◽  
Lei Sun ◽  
Dan Wei ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Type Strains ◽  
Physiological And Biochemical

A haloalkaliphilic archaeon, strain JX313T, was isolated from a saline–alkaline soil from Daqing, Heilongjiang Province, China. Its morphological, physiological and biochemical features and 16S rRNA gene sequence were determined. Colonies of the strain were orange–red and cells were non-motile cocci and Gram-stain-variable. The strain required at least 1.7 M NaCl for growth, with optimal growth occurring in 2.0–2.5 M NaCl. Growth was observed at 20–50 °C and pH 8.0–10.5, with optimal growth at 35 °C and pH 10.0. The G+C content of its genomic DNA was 59.3 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain JX313T is associated with the genera Haloterrigena and Natrinema and is most closely related to Haloterrigena salina XH-65T (96.2 % sequence similarity) and Haloterrigena hispanica FP1T (96.2 %). DNA–DNA hybridization experiments revealed that the relatedness of strain JX313T to type strains of related species of the genus Haloterrigena or Natrinema was less than 50 %. Furthermore, the cellular polar lipids of strain JX313T, identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD), were consistent with the polar lipid characteristics of the genus Haloterrigena. Therefore, phylogenetic analysis, phenotypic assessment and chemotaxonomic data showed that JX313T represents a novel species within the genus Haloterrigena, for which the name Haloterrigena daqingensis sp. nov. is proposed. The type strain is JX313T (=CGMCC 1.8909T =NBRC 105739T).

scholarly journals Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus

2010 ◽  
Vol 60 (5) ◽  
pp. 1187-1190 ◽  
Author(s):  
Seong Woon Roh ◽  
Myung-Lip Lee ◽  
Jin-Woo Bae
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
Emended Description ◽  
Extremely Halophilic Archaeon

A novel, extremely halophilic archaeon, D43T, was isolated from traditional salt-fermented seafood in Korea. The cells were Gram-negative-staining and motile. The strain grew at 15–50 °C, 10–30 % (w/v) NaCl and pH 6.0–8.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D43T is affiliated with the family Halobacteriaceae in the domain Archaea and had 95.5 % 16S rRNA gene sequence similarity with Haladaptatus paucihalophilus DX253T. The sequence from strain D43T formed a clade with those from Hap. paucihalophilus regardless of which tree-generating algorithm was used. DNA–DNA hybridization experiments showed 25.8 % relatedness between the isolate and Hap. paucihalophilus KCTC 4006T. Major lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two unidentified glycolipids. The DNA G+C content of the isolate was 56.5 mol%. On the basis of this polyphasic taxonomic study, strain D43T represents a novel species in the genus Haladaptatus, for which the name Haladaptatus cibarius sp. nov. is proposed. The type strain is D43T (=DSM 19505T =JCM 15962T).

Sign in / Sign up

Export Citation Format

Share Document