Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 518-521 ◽  
Author(s):  
Zhiyong Ruan ◽  
Yanwei Wang ◽  
Jinlong Song ◽  
Shenghua Jiang ◽  
Huimin Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Large Scale ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biogas Slurry ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Method Analysis ◽  
The 16S Rrna Gene

A novel facultatively anaerobic bacterium, designated strain LAM0618T, was isolated from biogas slurry samples collected from the large-scale anaerobic digester of Modern Farming Corporation in Hebei Province, China. Cells of strain LAM0618T were Gram-stain-positive, motile, non-spore-forming and short-rod-shaped. The optimal temperature and pH for growth were 30 °C and 7.0, respectively. The strain did not require NaCl for growth but tolerated up to 70 g NaCl l−1. The major fatty acids of strain LAM0618T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0, C16 : 0 and C18 : 0. The predominant menaquinones of strain LAM0618T were menaquinone 7 (MK-7) and menaquinone 6 (MK-6). The main polar lipids of strain LAM0618T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and six unknown glycolipids. The genomic DNA G+C content was 41 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence revealed that strain LAM0618T was a member of the genus Kurthia , and was most closely related to ‘ Kurthia massiliensis’ DSM 24639, Kurthia zopfii DSM 20580T, Kurthia gibsonii DSM 20636T and Kurthia sibirica DSM 4747T, with 96.9, 95.7, 95.6 and 94.9 % sequence similarity, respectively. Based on its phenotypic and genotypic properties, strain LAM0618T is suggested to represent a novel species of the genus Kurthia , for which the name Kurthia huakuii sp. nov. is proposed. The type strain is LAM0618T ( = ACCC 06121T = JCM 19187T).

Flavobacterium lacus sp. nov., isolated from a high-altitude lake, and emended description of Flavobacterium filum

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 933-939 ◽  
Author(s):  
Aihua Li ◽  
Hongcan Liu ◽  
Bingda Sun ◽  
Yuguang Zhou ◽  
Yuhua Xin
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
High Altitude Lake ◽  
Nam Co Lake ◽  
The 16S Rrna Gene

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated NP180T and NR80, were isolated from water of Nam Co Lake, located in Tibet, China. Growth of strains NP180T and NR80 occurred at 4–25 °C and at pH 6.5–10.0 (optima, 15–20 °C and pH 7.5–8.5). The 16S rRNA gene sequence similarity to the phylogenetically closest related strains, Flavobacterium filum EMB 34T, F. ponti GSW-R14T and F. gelidilacus LMG 21477T, was 95.1, 94.8 and 94.6 %, respectively. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The major menaquinone of the two strains was menaquinone 6 (MK-6). Phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid were the major polar lipids in both strains. The G+C contents of the genomic DNA were 34.9 and 35.1 mol%, respectively, for strains NP180T and NR80. DNA–DNA relatedness between strains NP180T and NR80 was 99 %, indicating that they belong to the same species. According to phylogenetic inference and phenotypic characteristics, a novel species, Flavobacterium lacus sp. nov., is proposed. The type strain is NP180T ( = CGMCC 1.12504T = NBRC 109715T). An emended description of Flavobacterium filum is also provided.

scholarly journals Nonomuraea solani sp. nov., an actinomycete isolated from eggplant root (Solanum melongena L.)

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2418-2423 ◽  
Author(s):  
Xiangjing Wang ◽  
Junwei Zhao ◽  
Chongxi Liu ◽  
Jidong Wang ◽  
Yue Shen ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Solanum Melongena ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A novel actinomycete, designated strain NEAU-Z6T, was isolated from eggplant (Solanum melongena L.) root. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NEAU-Z6T belonged to the genus Nonomuraea , with highest sequence similarity to Nonomuraea monospora PT 708T (98.83 %), Nonomuraea rosea GW 12687T (98.55 %) and Nonomuraea rhizophila YIM 67092T (98.02 %). Sequence similarities between strain NEAU-Z6T and other species of the genus Nonomuraea ranged from 97.94 % ( Nonomuraea candida HMC10T) to 96.30 % ( Nonomuraea wenchangensis 210417T). Key morphological, physiological and chemotaxonomic characteristics of strain NEAU-Z6T were congruent with the description of the genus Nonomuraea . The G+C content of the genomic DNA was 64.51 mol%. DNA–DNA relatedness and comparative analysis of physiological, biochemical and chemotaxonomic data allowed genotypic and phenotypic differentiation of strain NEAU-Z6T from closely related species. Thus, strain NEAU-Z6T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea solani sp. nov. is proposed. The type strain is NEAU-Z6T ( = CGMCC 4.7037T = DSM 45729T).

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Priya Lakra ◽  
Helianthous Verma ◽  
Chandni Talwar ◽  
Durgesh Narain Singh ◽  
Nirjara Singhvi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Species Delineation ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .

scholarly journals Flavisolibacter rigui sp. nov., isolated from freshwater of an artificial reservoir and emended description of the genus Flavisolibacter

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4038-4042 ◽  
Author(s):  
Keun Sik Baik ◽  
Mi Sun Kim ◽  
Ji Hee Lee ◽  
Sang Suk Lee ◽  
Wan-Taek Im ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A non-motile and rod-shaped bacterium, designated strain 02SUJ3T, was isolated from freshwater collected from the Juam Reservoir (Republic of Korea). Cells were Gram-stain-negative, aerobic, oxidase-negative and catalase-positive. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The strain contained MK-7 as the major isoprenoid quinone. The main polar lipid was phosphatidylethanolamine. The DNA G+C content was 46.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain 02SUJ3T forms an independent lineage within the genus Flavisolibacter with low sequence similarity to Flavisolibacter ginsengiterrae Gsoil 492T and Flavisolibacter ginsengisoli Gsoil 643T (95.7 %). Phenotypic characteristics distinguished strain 02SUJ3T from members of the genus Flavisolibacter . On the basis of the evidence presented in this study, strain 02SUJ3T is considered to represent a novel species, for which the name Flavisolibacter rigui sp. nov. is proposed. The type strain is 02SUJ3T ( = JCM 17515T = KCTC 23328T). An emended description of the genus Flavisolibacter is also provided.

scholarly journals Rhizobium rhizoryzae sp. nov., isolated from rice roots

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1373-1377 ◽  
Author(s):  
Xiao-Xia Zhang ◽  
Xue Tang ◽  
Rizwan Ali Sheirdil ◽  
Lei Sun ◽  
Xiao-Tong Ma
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
The 16S Rrna Gene

Two strains (J3-AN59T and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59T and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium , and they were most closely related to Rhizobium tarimense ACCC 06128T (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59T and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59T and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA–DNA relatedness value between J3-AN59T and J3-N84 was 89 %, and strain J3-AN59T showed 9 % DNA–DNA relatedness to R. tarimense ACCC 06128T, the most closely related strain. Based on this evidence, we found that J3-AN59T and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59T ( = ACCC 05916T = KCTC 23652T).

scholarly journals Clostridium huakuii sp. nov., an anaerobic, acetogenic bacterium isolated from methanogenic consortia

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4027-4032 ◽  
Author(s):  
Zhiyong Ruan ◽  
Yanwei Wang ◽  
Chi Zhang ◽  
Jinlong Song ◽  
Yi Zhai ◽  
...  
Keyword(s):  
Type Species ◽  
Large Scale ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Acetogenic Bacterium ◽  
Clostridium Subterminale ◽  
The 16S Rrna Gene

A Gram-staining-positive, spore-forming, obligately anaerobic, acetogenic bacterium, designated LAM1030T, was isolated from methanogenic consortia enriched from biogas slurry collected from the large-scale anaerobic digester of Modern Farming Corporation in Hebei Province, China. Cells of strain LAM1030T were motile, straight or spiral-rod-shaped. Strain LAM1030T could utilize glucose, fructose, maltose, galactose, lactose, sucrose, cellobiose, mannitol, pyruvate, succinic acid and tryptophan as the sole carbon source. Acetic acid, isovaleric acid and butanoic acid were the main products of glucose fermentation. Sodium sulfite was used as an electron acceptor. Growth of strain LAM1030T was completely inhibited by the addition of ampicillin, tetracycline, gentamicin or erythromycin at a concentration of 20 µg ml−1. The main polar lipids of strain LAM1030T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, 11 unknown glycolipids and two unknown phospholipids. No respiratory quinone was detected. The major fatty acids of strain LAM1030T were C16 : 0 (21.1 %), C14 : 0 (10.3 %), summed feature 9 (including C16:0 10-methyl and/or iso-C17:1 ω9c) (11.3% ), summed feature 3 (including C16:1 ω7c and/or C16:1 ω6c) (10.6% ) and iso-C15 : 0 (6.6 %). Analysis of the 16S rRNA gene sequence indicated that strain LAM1030T belonged to the genus Clostridium and was most closely related to Clostridium subterminale DSM 6970T, Clostridium thiosulfatireducens DSM 13105T and Clostridium sulfidigenes DSM 18982T, with 97.0, 96.9 and 96.8 % similarity, respectively. The G+C content of the genomic DNA of strain LAM1030T was 31.2±0.3 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characterization, strain LAM1030T is suggested to represent a novel species of the genus Clostridium , for which the name Clostridium huakuii sp. nov. is proposed. The type strain is LAM1030T ( = ACCC 00698T = JCM 19186T).

scholarly journals Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1241-1244 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Moriya Ohkuma
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Single Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Emended Description

Strains of the recently proposed species Bacteroides chinchillae share more than 99.4 % 16S rRNA gene sequence similarity with the type strain of Bacteroides sartorii although these two species do not appear to be similar from their published descriptions. The aim of this study was to perform phenotypic and genetic analyses of both species to clarify their taxonomic position. B. chinchillae JCM 16497T exhibited high hsp60 gene sequence similarity with B. sartorii JCM 17136T (100 %) as well as B. chinchillae JCM 16498 (100 %). The hsp60 gene sequence analysis and levels of DNA–DNA relatedness observed demonstrated B. sartorii JCM 17136T, B. chinchillae JCM 16497T, and B. chinchillae JCM 16498 are members of a single species. Based on these data, we propose Bacteroides chinchillae as a later heterotypic synonym of Bacteroides sartorii . An emended description of B. sartorii is provided.

Transfer of Bacillus schlegelii to a novel genus and proposal of Hydrogenibacillus schlegelii gen. nov., comb. nov.

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1723-1727 ◽  
Author(s):  
Peter Kämpfer ◽  
Stefanie P. Glaeser ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Novel Genus ◽  
Content Type ◽  
Link Type ◽  
Bacillus Schlegelii ◽  
The 16S Rrna Gene

Analysis of the 16S rRNA gene sequences of species currently assigned to the genus Bacillus has shown an extensive intrageneric phylogenetic heterogeneity. The 16S rRNA gene sequence of Bacillus schlegelii ATCC 43741T shows only 82.2–85.9 % sequence similarity to type strains of other members of the genus Bacillus and <88.5 % sequence similarity to recognised species of the most closely related genera, Calditerricola (88.4–88.5 %), Planifilum (87.3–87.8 %) and Caldalkalibacillus (87.2−87.9 %). Furthermore, B. schlegelii ATCC 43741T could not be assigned to an existing family by phylogenetic analysis. The predominant menaquinone was MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and two unidentified glycolipids. The major fatty acids were iso-C16 : 0, C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. Both the polar lipid profile and the fatty acid composition clearly distinguished B. schlegelii DSM 2000T from the type species of the genus Bacillus , Bacillus subtilis . Hence, there is no evidence for a clear phenotypic grouping of this organism into the genus Bacillus nor to the genera Calditerricola , Caldalkalibacillus or Planifilum . A proposal is made to transfer Bacillus schlegelii to a novel genus and species, Hydrogenibacillus schlegelii gen. nov., comb. nov., and to emend the species description. The type strain of the type species is DSM 2000T ( = ATCC 43741T = CCUG 26017T = CIP 106933T).

Mucilaginibacter inviolabilis sp. nov., isolated from the phycosphere of Haematococcus lacustris NIES 144 culture

2021 ◽  
Author(s):  
Sang-Ah Lee ◽  
Ve Van Le ◽  
So-Ra Ko ◽  
Nakyeong Lee ◽  
Hee-Mock Oh ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Haematococcus Lacustris ◽  
The 16S Rrna Gene

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated HC2T, was isolated from the phycosphere of Haematococcus lacustris NIES 144 culture. Strain HC2T was able to grow at pH 4.5–8.0, at 4–32 °C and in the presence of 0–2 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain HC2T was affiliated to the genus Mucilaginibacter and shared the highest sequence similarity with Mucilaginibacter lappiensis ANJKI2T (98.20 %) and Mucilaginibacter sabulilitoris SMS-12T (98.06 %). Strain HC2T contained summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 0 as the major fatty acids (>10.0 %). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. The respiratory quinone was menaquinone 7 (MK-7). The genomic DNA G+C content was 42.0 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain HC2T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter inviolabilis sp. nov. is proposed. The type strain is HC2T (=KCTC 82084T=JCM 34116T).

Flavobacterium anatoliense sp. nov., isolated from fresh water, and emended description of Flavobacterium ceti

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2075-2081 ◽  
Author(s):  
Murat Kacagan ◽  
Kadriye Inan ◽  
Ali Osman Belduz ◽  
Sabriye Canakci
Keyword(s):  
Fresh Water ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A Gram-staining-negative, catalase- and oxidase-positive, strictly aerobic, rod-shaped bacterial strain isolated from fresh water in Trabzon, Turkey and designated MK3T was characterized by phenotypic and molecular methods in order to determine its phylogenetic position. On the basis of 16S rRNA gene sequence similarity, strain MK3T was shown to belong to the genus Flavobacterium , being most closely related to Flavobacterium ceti CECT 7184T (93.6 %). Sequence similarity with other species of the genus Flavobacterium with validly published names was less than 91.6 %. Phenotypic and chemotaxonomic data supported the affiliation of strain MK3T to the genus Flavobacterium . The only menaquinone was MK-6; the major fatty acids were iso-C15 : 0 (45.2 %), summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c; 20.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 13.3 %) and the major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified phospholipids. The G+C content of the genomic DNA was 38.6 mol%. The results of physiological and biochemical tests allowed strain MK3T to be distinguished phenotypically from Flavobacterium ceti CECT 7184T. Strain MK3T, therefore, represents a novel species of the genus Flavobacterium , for which the name Flavobacterium anatoliense sp. nov. is proposed. The type strain is MK3T ( = LMG 26441T = NCCB 100384T). An emended description of Flavobacterium ceti is also proposed.

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