scholarly journals Bacillus hisashii sp. nov., isolated from the caeca of gnotobiotic mice fed with thermophile-fermented compost

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3944-3949 ◽  
Author(s):  
Ayaka Nishida ◽  
Hirokuni Miyamoto ◽  
Sankichi Horiuchi ◽  
Ryo Watanabe ◽  
Hidetoshi Morita ◽  
...  
Keyword(s):  
Tween 80 ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Dna Relatedness ◽  
Diamino Acid ◽  
Gnotobiotic Mice ◽  
The 16S Rrna Gene ◽  
Hydrolysis Activity ◽  
Produce Acid

A taxonomic study was performed on 15 bacterial isolates from the caeca of gnotobiotic mice that had been fed with thermophile-fermented compost. The 15 isolates were thermophilic, Gram-stain-positive, facultatively anaerobic, endospore-forming bacteria, and were most closely related to Bacillus thermoamylovorans CNCM I-1378T. The 16S rRNA gene sequence of strain N-11T, selected as representative of this new group, showed a similarity of 99.4 % with Bacillus thermoamylovorans CNCM I-1378T, 94.7 % with Bacillus thermolactis R-6488T, and 94.4 % with Bacillus kokeshiiformis MO-04T. The isolates were then classified into two distinct groups based on a (GTG)5-fingerprint analysis. Two isolates, N-11T and N-21, were the representatives of these two groups, respectively.` The N-11T and N-21 isolates showed 66–71 % DNA–DNA relatedness with one other, but had less than 37 % DNA–DNA relatedness with B. thermoamylovorans LMG 18084T. The other 13 isolates showed DNA–DNA relatedness values above 74 % with the N-11T isolate. All 15 isolates grew at 25–60 °C (optimum 50 °C), pH 6–8 (optimum pH 7) and were capable of growing on a medium containing 6 % (w/v) NaCl (optimum 0.5 %). The 15 isolates could be distinguished from B. thermoamylovorans LMG 18084T because they showed Tween 80 hydrolysis activity and did not produce acid from melibiose. The major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The menaquinone was MK-7. The DNA G+C content was 37.9 mol%. Based on the phenotypic properties, the 15 strains represent a novel species of the genus Bacillus, for which the name Bacillus hisashii sp. nov. is proposed. The type strain is N-11T ( = NRBC 110226T = LMG 28201T).

scholarly journals Paenibacillus physcomitrellae sp. nov., isolated from the moss Physcomitrella patens

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3400-3406 ◽  
Author(s):  
Xun Zhou ◽  
Guan Nan Guo ◽  
Le Qi Wang ◽  
Su Lan Bai ◽  
Chun Li Li ◽  
...  
Keyword(s):  
Physcomitrella Patens ◽  
Optimal Growth ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Diamino Acid ◽  
Beijing China ◽  
The 16S Rrna Gene

A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain XBT, was isolated from Physcomitrella patens growing in Beijing, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inferences. The novel strain was spore-forming, motile, catalase-negative and weakly oxidase-positive. Optimal growth of strain XBT occurred at 28°C and pH 7.0–7.5. The major polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unidentified components, including one phospholipid, two aminophospholipids, three glycolipids, one aminolipid and one lipid. The predominant isoprenoid quinone was MK-7. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acid components (>5 %) were anteiso-C15 : 0 (51.2 %), anteiso-C17 : 0 (20.6 %), iso-C16 : 0 (8.3 %) and C16 : 0 (6.7 %). The G+C content of the genomic DNA was 53.3 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain XBT fell within the evolutionary distances encompassed by the genus Paenibacillus; its closest phylogenetic neighbour was Paenibacillus yonginensis DCY84T (96.6 %). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain XBT is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus physcomitrellae sp. nov., is proposed. The type strain is XBT ( = CGMCC 1.15044T = DSM 29851T).

scholarly journals Bacillus encimensis sp. nov. isolated from marine sediment

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1421-1425 ◽  
Author(s):  
Syed G. Dastager ◽  
Rahul Mawlankar ◽  
Poonam Mual ◽  
Ashish Verma ◽  
Srinivasan Krishnamurthi ◽  
...  
Keyword(s):  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium designated SGD-V-25T was isolated from Veraval sediment sample, India. Strain SGD-V-25T was capable of growing at 25–50 °C (optimum 37 °C), pH 6–12 (optimum pH 7.0) and with 0–5 % (w/v) NaCl. The taxonomic position of this strain was deduced using a polyphasic approach and the 16S rRNA gene sequence analysis showed that the isolate belongs to the phylum Firmicutes , forming the cluster with Bacillus badius MTCC 1548T, with which it shares highest similarity of 99.1 % with 13 nt differences. Other type strains of the genus Bacillus showed less than 96 % similarity. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The polar lipid profile of strain SGD-V-25T showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phsophoglycolipid and two aminophospholipids. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, C16 : 1ω11c and C16 : 0. The genomic DNA G+C content of strain SGD-V-25T was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization, strain SGD-V-25T could be clearly distinguished from closely related members of the genus Bacillus , and the name Bacillus encimensis sp. nov., is proposed to accommodate this strain. The type strain is SGD-V-25T ( = NCIM 5513T = DSM 28241T).

scholarly journals Alkalibacillus flavidus sp. nov., isolated from a marine solar saltern

2010 ◽  
Vol 60 (2) ◽  
pp. 434-438 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Marine Solar Saltern ◽  
Phenotypic Properties ◽  
Diamino Acid

A Gram-stain-positive, motile, rod-shaped bacterial strain, ISL-17T, was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain ISL-17T grew optimally at pH 8.5–9.0, at 37 °C and in the presence of approximately 10 % (w/v) NaCl. It contained meso-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, MK-7 as the predominant menaquinone and iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids. The DNA G+C content was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-17T fell within the genus Alkalibacillus, clustering with Alkalibacillus salilacus BH163T with a bootstrap resampling value of 100 %. Strain ISL-17T exhibited 98.2 % 16S rRNA gene sequence similarity to A. salilacus BH163T and 95.8–96.5 % similarity to the type strains of the other Alkalibacillus species. The mean DNA–DNA relatedness value between strain ISL-17T and A. salilacus KCTC 3916T was 19 %. The phenotypic properties of strain ISL-17T, together with its phylogenetic and genetic distinctiveness, enable this strain to be differentiated from recognized Alkalibacillus species. On the basis of phenotypic, phylogenetic and genetic data, strain ISL-17T represents a novel species within the genus Alkalibacillus, for which the name Alkalibacillus flavidus sp. nov. is proposed; the type strain is ISL-17T (=KCTC 13258T =CCUG 56753T).

scholarly journals Amphibacillus sediminis sp. nov., an endospore-forming bacterium isolated from lake sediment in Japan

2007 ◽  
Vol 57 (11) ◽  
pp. 2489-2492 ◽  
Author(s):  
Sun-Young An ◽  
Shu Ishikawa ◽  
Hiroaki Kasai ◽  
Keiichi Goto ◽  
Akira Yokota
Keyword(s):  
Lake Sediment ◽  
Type Strain ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Diamino Acid ◽  
Isoprenoid Quinones ◽  
Type Strains

A facultatively anaerobic, moderately alkaliphilic, Gram-positive, spore-forming and rod-shaped bacterial strain, Shu-P-Ggiii25-2T, was isolated from lake sediment in Shizuoka, Japan, and was characterized taxonomically using a polyphasic approach. Analysis of the 16S rRNA gene sequence indicated that the novel isolate clustered with the type strain of Amphibacillus xylanus and it exhibited sequence similarities of 94.9–95.6 % to the type strains of species of the genus Amphibacillus. Isoprenoid quinones and oxidase and catalase activities were not detected for strain Shu-P-Ggiii25-2T. The DNA G+C content was 42.3 mol%, the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid and the major cellular fatty acids were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. On the basis of phylogenetic position and phenotypic properties, strain Shu-P-Ggiii25-2T represents a novel species of the genus Amphibacillus, for which the name Amphibacillus sediminis sp. nov. is proposed. The type strain is Shu-P-Ggiii25-2T (=MBIC08269T=IAM 15428T=KCTC 13120T). An emended description of the genus Amphibacillus is also given.

scholarly journals Lapillicoccus jejuensis gen. nov., sp. nov., a novel actinobacterium of the family Intrasporangiaceae, isolated from stone

2007 ◽  
Vol 57 (12) ◽  
pp. 2794-2798 ◽  
Author(s):  
Soon Dong Lee ◽  
Dong Wan Lee
Keyword(s):  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Straight Chain ◽  
Polar Lipid Profile ◽  
The Family ◽  
Small Stone ◽  
Novel Genus And Species ◽  
Diamino Acid ◽  
The 16S Rrna Gene

A novel, yellow-pigmented actinobacterium was isolated from a small stone collected in Jeju, Republic of Korea. The cells of the organism, designated strain R-Ac013T, were Gram-positive, aerobic, non-motile cocci that occurred singly or in pairs. The strain showed growth at 10–37 °C and pH 4.1–11.1, and tolerated 2 % NaCl. On the basis of the 16S rRNA gene sequence, the organism was phylogenetically related to members of the genera Tetrasphaera (94.6–97.1 % sequence similarity), Terrabacter (96.5 %), Knoellia (96.4 %), Terracoccus (96.4 %), Oryzihumus (96.4 %), Janibacter (96.1–96.4 %) and Intrasporangium (96.2 %). The chemotaxonomic results for the organism were as follows: ll-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, acetyl-type murein, MK-8(H4) as the major menaquinone, a DNA G+C content of 74.1 mol%, and a polar lipid profile that comprised diphosphatidylglycerol and phosphatidylinositol. The fatty acid profile consisted of iso- and anteiso-methyl-branched, straight-chain saturated and monounsaturated types, the major components being iso-C16 : 0, C17 : 1 ω8c and iso-C15 : 0. The combination of the phenotypic and phylogenetic data revealed that this strain represents a novel genus and species of the family Intrasporangiaceae, for which the name Lapillicoccus jejuensis gen. nov., sp. nov. is proposed. The type strain is strain R-Ac013T (=KCTC 19200T=DSM 18607T).

scholarly journals Propioniciclava tarda gen. nov., sp. nov., isolated from a methanogenic reactor treating waste from cattle farms

2011 ◽  
Vol 61 (9) ◽  
pp. 2298-2303 ◽  
Author(s):  
Yoshimichi Sugawara ◽  
Atsuko Ueki ◽  
Kunihiro Abe ◽  
Nobuo Kaku ◽  
Kazuya Watanabe ◽  
...  
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Major Respiratory Quinone ◽  
Diamino Acid ◽  
Cattle Farms

Two facultatively anaerobic bacterial strains, designated WR061T and WR054, were isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms in Japan. The two strains were phylogenetically positioned close to one another and had almost the same phenotypic properties. Cells were Gram-reaction-positive, non-motile, non-spore-forming, irregular rods. Cobalamin (vitamin B12) was required for growth. The strains utilized various carbohydrates, including hexoses and disaccharides, and produced acetate and propionate from these carbohydrates. Pentoses and polysaccharides were not utilized. They grew at 20–37 °C (optimum 35 °C) and pH 5.3–8.0 (optimum pH 6.8–7.5). Catalase and nitrate-reducing activities were detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0 and C15 : 0 DMA, the major respiratory quinone was menaquinone MK-9(H4) and the genomic DNA G+C content was 69.3–69.5 mol%. The diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. Phylogenetic analysis based on 16S rRNA gene sequences placed the strains in the phylum Actinobacteria. Both strains were remotely related to the species in the family Propionibacteriaceae and Propionibacterium propionicum JCM 5830T was the most closely related type strain with a sequence similarity of 91.6 %. Based on phylogenetic, physiological and chemotaxonomic analyses, the two novel strains together represent a novel species of a new genus, for which the name Propioniciclava tarda gen. nov., sp. nov. is proposed. The type strain is WR061T ( = JCM 15804T  = DSM 22130T).

scholarly journals Virgibacillus dokdonensis sp. nov., isolated from a Korean island, Dokdo, located at the edge of the East Sea in Korea

2005 ◽  
Vol 55 (5) ◽  
pp. 1833-1837 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
East Sea ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Dna Relatedness ◽  
Type Strains

A Gram-variable, motile, endospore-forming, slightly halophilic bacterial strain, DSW-10T, was isolated from Dokdo, an island located at the edge of the East Sea, Korea, and was characterized taxonomically by using a polyphasic approach. This isolate grew optimally at 37 °C and in the presence of 4–5 % NaCl. Strain DSW-10T had cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone, and anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The DNA G+C content was 36·7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DSW-10T is phylogenetically affiliated to the genus Virgibacillus, and exhibited sequence similarity of 95·3–98·7 % to the type strains of Virgibacillus species. DNA–DNA relatedness levels between strain DSW-10T and the type strains of some phylogenetically related Virgibacillus species were in the range 8·4–17·5 %. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain DSW-10T (=KCTC 3933T=DSM 16826T) was classified as the type strain of a novel Virgibacillus species, for which the name Virgibacillus dokdonensis sp. nov. is proposed.

scholarly journals Rhodococcus antrifimi sp. nov., isolated from dried bat dung of a cave

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4043-4048 ◽  
Author(s):  
Kwan Su Ko ◽  
Youngju Kim ◽  
Chi Nam Seong ◽  
Soon Dong Lee
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Taxonomic Status ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Mycolic Acids ◽  
Diamino Acid ◽  
Gene Similarity ◽  
Sequence Study ◽  
The 16S Rrna Gene

A Gram-reaction-positive, high DNA G+C content, non-motile actinobacterium, strain D7-21T, was isolated from dried bat dung inside a natural cave and its taxonomic status was examined by using a polyphasic approach. The 16S rRNA gene sequence study showed that the isolate belonged to the genus Rhodococcus and formed a cluster with Rhodococcus defluvii (98.98 % gene similarity), Rhodococcus equi (98.62 %) and Rhodococcus kunmingensis (97.66 %). Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H2) was the predominant menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unknown phosphoglycolipid and an unknown glycolipid. Mycolic acids were present. The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0. The DNA G+C content was 70.1 mol%. A battery of phenotypic features and DNA–DNA relatedness data support that strain D7-21T ( = KCTC 29469T = DSM 46727T) represents a novel species of the genus Rhodococcus, for which Rhodococcus antrifimi sp. nov. is proposed.

Reclassification of Marinococcus albus Hao et al. 1985 as Salimicrobium album gen. nov., comb. nov. and Bacillus halophilus Ventosa et al. 1990 as Salimicrobium halophilum comb. nov., and description of Salimicrobium luteum sp. nov.

2007 ◽  
Vol 57 (10) ◽  
pp. 2406-2411 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New Genus ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Separate Species ◽  
Diamino Acid

A Gram-positive, non-motile, coccoid-shaped, non-spore-forming halophilic bacterial strain, BY-5T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated by using a polyphasic approach. The novel strain grew optimally at 37 °C and in the presence of 10 % (w/v) NaCl. Strain BY-5T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C content was 47.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BY-5T formed a coherent cluster with Bacillus halophilus and Marinococcus albus. Strain BY-5T exhibited 16S rRNA gene sequence similarity values of 98.7 and 97.4 % to the type strains of B. halophilus and M. albus, respectively. Strain BY-5T was distinguished from B. halophilus and M. albus by several phenotypic properties and DNA–DNA relatedness data. On the basis of the combined chemotaxonomic and phylogenetic data, it is proposed that M. albus, B. halophilus and strain BY-5T should be placed in a new genus as three separate species. Marinococcus albus and Bacillus halophilus are reclassified in a new genus, Salimicrobium gen. nov., as Salimicrobium album comb. nov. and Salimicrobium halophilum comb. nov., respectively. The type species of the new genus is Salimicrobium album. Strain BY-5T (=KCTC 3989T=CIP 108918T) is placed in the genus Salimicrobium as a novel species Salimicrobium luteum sp. nov.

Amphibacillus marinus sp. nov., a member of the genus Amphibacillus isolated from marine mud

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1485-1491 ◽  
Author(s):  
Biao Ren ◽  
Na Yang ◽  
Jian Wang ◽  
Xiao-Long Ma ◽  
Qian Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Sea Mud ◽  
Diamino Acid ◽  
Marine Mud

A Gram-positive, spore-forming, rod-shaped bacterium, designated J1T was isolated from deep-sea mud collected from the South China Sea and subjected to polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences revealed that J1T clustered with the type strains of Amphibacillus cookii , Amphibacillus sediminis and Amphibacillus jilinensis and exhibited a range of similarity of 93.9–97.0 % to members of the genus Amphibacillus . The DNA G+C content was 36.7 mol%. Chemotaxonomic analysis showed no quinones, and the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid for strain J1T. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Strain J1T was positive for catalase activity and negative for oxidase activity. On the basis of phylogenetic position and phenotypic properties, strain J1T represents a novel species of the genus Amphibacillus and the name Amphibacillus marinus sp. nov. is proposed. The type strain is J1T ( = CGMCC 1.10434T = JCM 17099T).

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