Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana)

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2951-2956 ◽  
Author(s):  
Sei Joon Oh ◽  
Na-Ri Shin ◽  
Dong-Wook Hyun ◽  
Pil Soo Kim ◽  
Joon Yong Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod- or coccoid-shaped bacterium, designated strain ORY33T, was isolated from the gut of a camel cricket (Diestrammena coreana). The 16S rRNA gene sequence analysis showed that strain ORY33T belonged to the genus Weissella , with highest sequence similarity to Weissella koreensis S-5623T (97.7 %). The strain grew optimally at 30 °C and pH 7 in the presence of 0 % (w/v) NaCl. Catalase and oxidase activities were negative. The genomic DNA G+C content of strain ORY33T was 45.1 mol%. DNA–DNA hybridization values between strain ORY33T and closely related members of the genus Weissella were less than 27 %. The major fatty acids of strain ORY33T were C18 : 1ω9c, C16 : 0 and C14 : 0. Based on these phenotypic, phylogenetic and genotypic analyses, strain ORY33T represents a novel species belonging to the genus Weissella , for which the name Weissella diestrammenae sp. nov. is proposed. The type strain is ORY33T ( = KACC 16890T = JCM 18559T).

scholarly journals Halioglobus maricola sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (3) ◽  
pp. 1868-1875 ◽  
Author(s):  
Shan-Hui Li ◽  
Jaeho Song ◽  
Yeonjung Lim ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6–97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA–DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-β-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus , for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

scholarly journals Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China

2019 ◽  
Vol 69 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xiang-yue Zhou ◽  
Zeng-hong Gao ◽  
Mei-hong Chen ◽  
Mei-qi Jian ◽  
Li-hong Qiu
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Broad Leaved Forest ◽  
Gene Sequence Analysis ◽  
Leaved Forest

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.

scholarly journals Herbidospora mongoliensis sp. nov., isolated from soil, and reclassification of Herbidospora osyris and Streptosporangium claviforme as synonyms of Herbidospora cretacea

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2322-2329 ◽  
Author(s):  
Ismet Ara ◽  
Baljinova Tsetseg ◽  
Damdinsuren Daram ◽  
Manabu Suto ◽  
Katsuhiko Ando
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Analyses ◽  
Content Type ◽  
Link Type ◽  
Phospholipid Profile

A Gram-reaction-positive aerobic actinomycete, designated strain MN08-A0118T, which produced short chains of non-motile spores on the tips of long sporophores and formed yellow–brown colonies with branched substrate mycelium, was studied in detail to determine its taxonomic position. On the basis of 16S rRNA gene sequence analyses, strain MN08-A0118T was grouped into the genus Herbidospora , being most closely related to Streptosporangium claviforme (98.2 %), Herbidospora osyris (98.2 %), Herbidospora daliensis (98.2 %), Herbidospora cretacea (97.9 %) and Herbidospora yilanensis (97.4 %). Chemotaxonomic data supported allocation of the strain to the genus Herbidospora . MK-10(H4) was the predominant menaquinone with minor amounts of MK-10(H6), MK-10(H2) and MK-9(H4); the fatty acid profile contained major amounts of iso-C16 : 0, C17 : 0 10-methyl, iso-C14 : 0 and iso-C16 : 0 2-OH; the phospholipid profile contained phosphatidylethanolamine, phosphatidylmethylethanolamine and glucosamine-containing phospholipids; and the whole-cell sugars included ribose, glucose, galactose, madurose and rhamnose (trace). The phylogenetic data, phenotypic and genotypic properties and DNA–DNA hybridization differentiated this strain from its closely related strains, S. claviforme (35–54 % DNA–DNA relatedness), H. osyris (39–51 %), H. daliensis (3–16 %), H. cretacea (34–39 %) and H. yilanensis (34–42 %). Thus, MN08-A0118T represents a novel species of the genus Herbidospora , for which the name Herbidospora mongoliensis sp. nov. is proposed, with MN08-A0118T ( = NBRC 105882T  = VTCC D9-22T) as the type strain. In addition, DNA–DNA hybridization results showed that S. claviforme and H. osyris are synonyms of H. cretacea .

Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2684-2689 ◽  
Author(s):  
V. Venkata Ramana ◽  
P. Shalem Raj ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two strains (JA643T and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10–15 °C) were isolated from freshwater streams from different geographical regions of India. Both strains contain bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid (PL), unidentified amino lipids (AL1–AL6, AL9) and an unidentified lipid (L1) were the polar lipids present in both strains. The major cellular fatty acid was C18 : 1ω7c (76–79 % of the total). Bacteriohopane derivatives (BHD1,2), unidentified hopanoids (UH1–5), diplopterol (DPL) and diploptene (DPE) were the major hopanoids of both strains. The DNA G+C content was 64.2–64.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that both strains are closely related to the genus Rhodomicrobium and clustered with Rhodomicrobium vannielii DSM 162T (99 % sequence similarity). However, both strains exhibited only 46.1 % DNA–DNA hybridization with R. vannielii DSM 162T. Strains JA643T and JA755 shared >99 % 16S rRNA gene sequence similarity and were >85 % related on the basis of DNA–DNA hybridization; they are therefore considered to represent a novel species in the genus Rhodomicrobium , for which the name Rhodomicrobium udaipurense sp. nov. is proposed. The type strain is JA643T ( = KCTC 15219T = NBRC 109057T).

scholarly journals Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid

2006 ◽  
Vol 56 (6) ◽  
pp. 1305-1310 ◽  
Author(s):  
Jan Hendrik Wübbeler ◽  
Tina Lütke-Eversloh ◽  
Stefanie Van Trappen ◽  
Peter Vandamme ◽  
Alexander Steinbüchel
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Rrna Gene Sequence ◽  
Nearest Neighbours ◽  
The 16S Rrna Gene

In this study, a novel betaproteobacterium, strain DPN7T, was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3′-dithiodipropionic acid. Analysis of the 16S rRNA gene sequence of strain DPN7T revealed 98.5 % similarity to that of Tetrathiobacter kashmirensis LMG 22695T. Values for sequence similarity to members of the genera Alcaligenes, Castellaniella and Taylorella, the nearest neighbours of the genus Tetrathiobacter, were about 95 % or less. The DNA G+C content of strain DPN7T was 55.1 mol%. The level of DNA–DNA hybridization between strain DPN7T and T. kashmirensis LMG 22695T was 41 %, whereas it was much lower between strain DPN7T and Alcaligenes faecalis LMG 1229T (7 %) or Castellaniella defragrans LMG 18538T (5 %). This genotypic divergence was supported by differences in biochemical and chemotaxonomic characteristics. For this reason, and because of the differences in the protein and fatty acid profiles, strain DPN7T should be classified within a novel species of Tetrathiobacter, for which the name Tetrathiobacter mimigardefordensis sp. nov. is proposed. The type strain is strain DPN7T (=DSM 17166T=LMG 22922T).

scholarly journals Agromyces arachidissp. nov. Isolated from a Peanut (Arachis hypogaea) Crop Field

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Chandandeep Kaur ◽  
Anil Kumar Pinnaka ◽  
Nitin Kumar Singh ◽  
Monu Bala ◽  
Shanmugam Mayilraj
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Crop Field ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A Gram-positive, yellowish bacterium strain AK-1Twas isolated from soil sample collected from peanut (Arachis hypogaea) crop field and studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genusAgromyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AK-1Twas closely related toAgromyces aurantiacus(98.6%) followed byAgromyces soli(98.3%),Agromyces tropicus(97.6%),Agromyces ulmi(97.3%),Agromyces flavus(97.2%), andAgromyces italicus(97.0%), whereas the sequence similarity values with respect to the otherAgromycesspecies with validly published names were between 95.3 and 96.7 %. However, the DNA-DNA hybridization values obtained between strain AK-1Tand other related strains were well below the threshold that is required for the proposal of a novel species. The DNAG+Ccontent of the strain is 71.8 mol%. The above data in combination with the phenotypic distinctiveness of AK-1Tclearly indicate that the strain represents a novel species, for which the nameAgromyces arachidissp. nov. is proposed. The type strain is AK-1T(=MTCC 10524T= JCM 19251T).

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).

Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov.

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 208-211 ◽  
Author(s):  
Lourdes Martínez-Aguilar ◽  
Jesús Caballero-Mellado ◽  
Paulina Estrada-de los Santos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Phylogenetic analysis of the 16S rRNA gene sequences of strains TE26T and K6 belonging to Wautersia numazuensis Kageyama et al. 2005 showed the strains to be deeply intermingled among the species of the genus Cupriavidus . The comparison showed that strain TE26T was closely related to the type strains of Cupriavidus pinatubonensis (99.1 % 16S rRNA gene sequence similarity), C. basilensis (98.7 %), C. necator (98.7 %) and C. gilardii (98.0 %). However, DNA–DNA hybridization experiments (less than 20 % relatedness) demonstrated that strain TE26T is different from these Cupriavidus species. A comparative phenotypic and chemotaxonomic analysis (based on fatty acid profiles) in combination with the 16S rRNA gene sequence phylogenetic analysis and the DNA–DNA hybridization results supported the incorporation of Wautersia numazuensis into the genus Cupriavidus as Cupriavidus numazuensis comb. nov.; the type strain is TE26T ( = LMG 26411T  = DSM 15562T  = CIP 108892T).

Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2457-2462 ◽  
Author(s):  
Om Prakash ◽  
Stefan J. Green ◽  
Puja Jasrotia ◽  
Will A. Overholt ◽  
Andy Canion ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Contaminated Aquifer ◽  
Content Type ◽  
Link Type ◽  
Characteristic Features

Bacterial strains 2APBS1T and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus Rhodanobacter shown to be capable of complete denitrification. Cells of strain 2APBS1T and 116-2 were Gram-negative, non-spore-forming rods, 3–5 µm long and 0.25–0.5 µm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 °C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1T and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus Rhodanobacter . Although strains 2APBS1T and 116-2 shared high 16S rRNA gene sequence similarity with Rhodanobacter thiooxydans LCS2T (>99 %), levels of DNA–DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1T and 116-2 are considered to represent a single novel species of the genus Rhodanobacter , for which the name Rhodanobacter denitrificans sp. nov. is proposed. The type strain is 2APBS1T ( = DSM 23569T = JCM 17641T).

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.

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