scholarly journals Flavobacterium restrictum sp. nov., Flavobacterium rhamnosiphilum sp. nov., and Flavobacterium zepuense sp. nov. isolated from glaciers

2020 ◽  
Vol 70 (8) ◽  
pp. 4583-4590 ◽  
Author(s):  
Guo-Qing Zhang ◽  
Lei-Lei Yang ◽  
Qing Liu ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Content Type ◽  
Pr China ◽  
The 16S Rrna Gene

Three strains, designated as LB1R34T, LB3P52T and ZT4R6T, were isolated from glaciers located on the Tibetan Plateau, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile and yellow. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated that they were related to the members of the genus Flavobacterium . The 16S rRNA gene sequences similarities between the three strains were 92.31–96.93 %. The average nucleotide identity values and digital DNA–DNA hybridization values between these three strains and their closest relatives were 76.80–91.33 % and 21.3–44.2 %, respectively. LB1R34T, LB3P52T and ZT4R6T contained MK-6 as the major menaquinone, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and iso-C15 : 0 as the major fatty acids. Phosphatidylethanolamine was present in their polar lipids profiles. On the basis of the phenotypic characteristics, he results of phylogenetic analysis and genotypic data, three novel species, Flavobacterium restrictum sp. nov. (type strain=LB1 R34T=CGMCC 1.11493T=NBRC 113650T), Flavobacterium rhamnosiphilum sp. nov. (type strain=LB3 P52T=CGMCC 1.11446T=NBRC 113776T) and Flavobacterium zepuense sp. nov. (type strain=ZT4 R6T=CGMCC 1.11919T=NBRC 113653T) are proposed.

scholarly journals Paenibacillus algicola sp. nov., a novel alginate lyase-producing marine bacterium

2020 ◽  
Vol 70 (9) ◽  
pp. 5087-5092 ◽  
Author(s):  
Jun Zhu ◽  
Kunlian Mo ◽  
Zhiguo Zheng ◽  
Zixu Wang ◽  
Yonghua Hu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Alginate Lyase ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Sequence Similarities

A Gram-stain-variable, facultatively anaerobic, endospore-forming, rod-shaped bacterium, designated HB172198T, was isolated from brown alga collected at Qishui Bay, Hainan, PR China. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain HB172198T belonged to the genus Paenibacillus , and the closest phylogenetically related species was Paenibacillus lemnae NBRC 109972T (97.6% similarity). The other 16S rRNA gene sequence similarities were under 97.0%. The whole genome average nucleotide identity value between strain HB172198T and the closest type strain was 75.3% and the in silico DNA–DNA hybridization value was 20.2%. The predominant isoprenoid quinone was menaquinone 7 and the major fatty acids were anteiso-C15:0, C16:0, anteiso-C17:0, iso C16:0 and C16:1 ω11c. The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB172198T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus algicola sp. nov. is proposed. The type strain is HB172198T (=CGMCC 1.13583T=JCM 32683T).

Aliifodinibius roseus gen. nov., sp. nov., and Aliifodinibius sediminis sp. nov., two moderately halophilic bacteria isolated from salt mine samples

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2907-2913 ◽  
Author(s):  
Yong-Xia Wang ◽  
Ji-Hui Liu ◽  
Wei Xiao ◽  
Xiao-Liang Ma ◽  
Yong-Hong Lai ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Western China ◽  
Rrna Gene ◽  
Content Type ◽  
Moderately Halophilic ◽  
Link Type

Two rod-shaped, non-motile bacteria were isolated from two separate salt mines in Yunnan, south-western China. These strains, designated YIM D15T and YIM J21T, were Gram-negative and moderately halophilic. The two strains required 6–10 % NaCl (w/v; optimal) for growth. The DNA G+C contents of strains YIM D15T and YIM J21T were 49.0 mol% and 48.4 mol%, respectively. The predominant isoprenoid quinone was MK-7. The polar lipid profiles of strains YIM D15T and YIM J21T were composed predominantly of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, three unknown polar lipids and one glycolipid. Minor amounts of other lipids were also detectable. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c/10 methyl-C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct clade with the genus Fodinibius (in the phylum Bacteroidetes ) and were related to the species Fodinibius salinus , with sequence similarities of 91.9–92.4 %. Analyses of 16S rRNA gene sequences revealed that strains YIM D15T and YIM J21T were related to each other (97.3 % sequence similarity). The DNA–DNA hybridization relatedness between the two isolates was 34 %. On the basis of the phylogenetic analysis, DNA–DNA hybridization relatedness, phenotypic and chemotaxonomic characteristics, strains YIM D15T and YIM J21T should be classified as members of a novel genus and as two novel species, for which the names Aliifodinibius roseus gen. nov., sp. nov. (type strain YIM D15T = ACCC 10715T = KCTC 23442T) and Aliifodinibius sediminis sp. nov. (type strain YIM J21T = ACCC 10714T = DSM 21194T) are proposed.

Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Hisami Kobayashi ◽  
Yasuhiro Tanizawa ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
Masanori Tohno
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

The taxonomic status of the species Clostridium methoxybenzovorans was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection ( C. methoxybenzovorans ATCC 700855T) is a member of the species Eubacterium callanderi . Hence, C. methoxybenzovorans ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of Lacrimispora indolis (recently reclassified from Clostridium indolis ) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA–DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis .

scholarly journals Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov.

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1296-1303 ◽  
Author(s):  
Haruka Horino ◽  
Takashi Fujita ◽  
Akio Tonouchi
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Rice Field ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type

An obligately anaerobic bacterial strain designated T-1-35T was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35T stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8–1.0×3.5–15.0 µm, and motile by means of two to four polar flagella. Cells of strain T-1-35T exhibited pleomorphism: in aged cultures (over 90 days of incubation), almost all cells were irregularly shaped. Although no spore formation was observed, cells tolerated high temperatures, up to 90 °C for 10 min. The temperature range for growth was 15–40 °C, with an optimum at 35 °C. The pH range for growth was 5.5–9.0, with an optimum at pH 8.0–8.5 (slightly alkaliphilic). Strain T-1-35T fermented some carbohydrates to produce ethanol and lactate as the major products. Major cellular fatty acids were iso-C16 : 0 and iso-C13 : 0 3-OH. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain T-1-35T belonged to Clostridium rRNA cluster III. The closest relative of strain T-1-35T was Bacteroides cellulosolvens WM2T, with 16S rRNA gene sequence similarity of 93.4 %. Phenotypic, physiological and molecular genetic methods demonstrated that strain T-1-35T was distinct from its phylogenetic relatives (members of Clostridium rRNA cluster III) because it predominantly produced ethanol, iso-C13 : 0 3-OH was a major cellular fatty acid and it always exhibited pleomorphism. On the basis of the results of a polyphasic taxonomic study, strain T-1-35T is considered to represent a novel genus and species, Anaerobacterium chartisolvens gen. nov., sp. nov. The type strain of Anaerobacterium chartisolvens is T-1-35T ( = DSM 27016T = NBRC 109520T). In addition, from the results of our phylogenetic analysis and its phenotypic features, the species Bacteroides cellulosolvens Murray et al. 1984 is proposed to be reclassified in the new genus Pseudobacteroides as Pseudobacteroides cellulosolvens gen. nov., comb. nov., with the type strain WM2T ( = ATCC 35603T = DSM 2933T = NRCC 2944T).

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).

scholarly journals Description of Kribbella italica sp. nov., isolated from a Roman catacomb

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 491-496 ◽  
Author(s):  
Gareth J. Everest ◽  
Sarah M. Curtis ◽  
Filomena De Leo ◽  
Clara Urzì ◽  
Paul R. Meyers
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Type Strains ◽  
The 16S Rrna Gene

A novel actinobacterium, strain BC637T, was isolated from a biodeteriogenic biofilm sample collected in 2009 in the Saint Callixstus Roman catacomb. The strain was found to belong to the genus Kribbella by analysis of the 16S rRNA gene. Phylogenetic analysis using the 16S rRNA gene and the gyrB, rpoB, relA, recA and atpD concatenated gene sequences showed that strain BC637T was most closely related to the type strains of Kribbella lupini and Kribbella endophytica . DNA–DNA hybridization experiments confirmed that strain BC637T is a genomic species that is distinct from its closest phylogenetic relatives, K. endophytica DSM 23718T (63 % DNA relatedness) and K. lupini LU14T (63 % DNA relatedness). Physiological comparisons showed that strain BC637T is phenotypically distinct from the type strains of K. endophytica and K. lupini . Thus, strain BC637T represents the type strain of a novel species, for which the name Kribella italica sp. nov. is proposed ( = DSM 28967T = NRRL B-59155T).

scholarly journals Idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer Pseudidiomarina aestuarii to the genus Idiomarina as Idiomarina aestuarii comb. nov.

2011 ◽  
Vol 61 (4) ◽  
pp. 969-973 ◽  
Author(s):  
Liping Wang ◽  
Qiliang Lai ◽  
Yuanyuan Fu ◽  
Hua Chen ◽  
Wanpeng Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Surface Seawater ◽  
Chromosomal Dna ◽  
16S Rrna Gene Sequences ◽  
Pr China ◽  
The 16S Rrna Gene

A taxonomic study was carried out on strain 10-D-4T, which was isolated from a crude oil-degrading consortium enriched from surface seawater collected around Xiamen Island, PR China. Strain 10-D-4T grew optimally at pH 7.0–8.0 and at 25 °C. The 16S rRNA gene sequence of strain 10-D-4T showed the highest similarity to those of Idiomarina salinarum ISL-52T (94.6 %), Idiomarina tainanensis PIN1T (94.2 %) and Idiomarina seosinensis CL-SP19T (94.1 %), and showed lower similarity (92.3–94.0 %) to other members of the genus Idiomarina. The major isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were iso-C13 : 0 (5.2 %), iso-C15 : 0 (15.3 %), C16 : 0 (14.3 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (6.6 %), iso-C17 : 0 (15.4 %) and C18 : 1ω7c (13.5 %). The G+C content of the chromosomal DNA was 50.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain 10-D-4T represents a novel species of the genus Idiomarina, for which the name Idiomarina xiamenensis sp. nov. is proposed. The type strain is 10-D-4T ( = CCTCC AB 209061T  = LMG 25227T  = MCCC 1A01370T). We also propose the transfer of Pseudidiomarina aestuarii, described recently, to the genus Idiomarina as Idiomarina aestuarii comb. nov. (type strain KYW314T  = KCTC 22740T  = JCM 16344T).

Microbacterium chengjingii sp. nov. and Microbacterium fandaimingii sp. nov., isolated from bat faeces of Hipposideros and Rousettus species

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Juan Zhou ◽  
Yuyuan Huang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Pr China

Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60T, HY54, HY82T and HY89) were isolated from bat faeces of Hipposideros and Rousettus species collected in PR China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four novel strains formed two separate but adjacent subclades close to Microbacterium agarici CGMCC 1.12260T (97.6–97.7 % similarity), Microbacterium humi JCM 18706T (97.3–97.5 %) and Microbacterium lindanitolerans JCM 30493T (97.3–97.4 %). The 16S rRNA gene sequence similarity was 98.3 % between strains HY60T and HY82T, and identical within strain pairs HY60T/HY54 and HY82T/HY89. The DNA G+C contents of strains HY60T and HY82T were 61.9 and 63.3 mol%, respectively. The digital DNA–DNA hybridization and average nucleotide identity values between each novel strain and their closest relatives were all below the 70 % and 95–96 % thresholds for species delimitation, respectively. All four novel strains contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the main fatty acids, MK-11 and MK-12 as the major respiratory quinones, and diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid as the predominant polar lipids. The cell-wall peptidoglycan was of B type and contained alanine, glutamate, glycine and ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose and ribose. Based on the foregoing polyphasic analyses, it was concluded that the four uncharacterized strains represented two novel species of the genus Microbacterium , for which the names Microbacterium chengjingii sp. nov. [type strain HY60T (=CGMCC 1.17468T=GDMCC 1.1951T=KACC 22102T)] and Microbacterium fandaimingii sp. nov. [type strain HY82T (=CGMCC 1.17469T=GDMCC 1.1949T=KACC 22101T)] are proposed, respectively.

‘Candidatus Phytoplasma balanitae’ associated with witches’ broom disease of Balanites triflora

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 636-640 ◽  
Author(s):  
Nang Kyu Kyu Win ◽  
Seung-Yeol Lee ◽  
Assunta Bertaccini ◽  
Shigetou Namba ◽  
Hee-Young Jung
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A phytoplasma was identified in naturally infected wild Balanites triflora plants exhibiting typical witches’ broom symptoms (Balanites witches’ broom: BltWB) in Myanmar. The 16S rRNA gene sequence revealed that BltWB phytoplasma had the highest similarity to that of ‘Candidatus Phytoplasma ziziphi’ and it was also closely related to that of ‘Candidatus Phytoplasma ulmi ’. Phylogenetic analysis of the 16S rRNA gene sequences indicated that the BltWB phytoplasma clustered as a discrete subclade with Elm yellows phytoplasmas. RFLP analysis of the 16S rRNA gene including the 16S–23S spacer region differentiated the BltWB phytoplasma from ‘Ca. P. ziziphi ’, ‘Ca. P. ulmi ’ and ‘Candidatus Phytoplasma trifolii ’. Analysis of additional ribosomal protein (rp) and translocase protein (secY) gene sequences and phylogenetic analysis of BltWB showed that this phytoplasma was clearly distinguished from those of other ‘Candidatus Phytoplasma ’ taxa. Taking into consideration the unique plant host and the restricted geographical occurrence in addition to the 16S rRNA gene sequence similarity, the BltWB phytoplasma is proposed to represent a novel taxon, ‘Candidatus Phytoplasma balanitae’.

scholarly journals Streptosporangium jomthongense sp. nov., an actinomycete isolated from rhizospheric soil and emendation of the genus Streptosporangium

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2400-2406 ◽  
Author(s):  
Bungonsiri Intra ◽  
Atsuko Matsumoto ◽  
Yuki Inahashi ◽  
Satoshi Ōmura ◽  
Watanalai Panbangred ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

A novel actinomycete, strain 30EHST, was isolated from the rhizospheric soil under an elephant ear plant (Caladium bicolor) in Jomthong district, Bangkok, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 30EHST fell within the cluster of the genus Streptosporangium . Chemical composition analysis confirmed that the strain represented a member of the genus Streptosporangium even though this strain produced a tightly packed single spore on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain 30EHST was most closely related to Streptosporangium fragile NBRC 14311T (98.1 %), Streptosporangium carneum NBRC 15562T (97.8 %) and Streptosporangium violaceochromogenes NBRC 15560T (97.4 %). The DNA–DNA hybridization relatedness values between strain 30EHST and the above three strains were below 70 %. Based on combined data for phylogenetic analysis, DNA–DNA hybridization relatedness and physiological characteristics, it was concluded that strain 30EHST should be classified as representing a novel species of the genus Streptosporangium . We propose the name Streptosporangium jomthongense sp. nov., with the type strain 30EHST ( = BCC 53154T = NBRC 110047T). An emended description of the genus Streptosporangium is also proposed.

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