scholarly journals Gordonia humi sp. nov., isolated from soil

2011 ◽  
Vol 61 (1) ◽  
pp. 65-70 ◽  
Author(s):  
P. Kämpfer ◽  
Chiu-Chung Young ◽  
Jiunn-Nan Chu ◽  
A. Frischmann ◽  
H.-J. Busse ◽  
...  
Keyword(s):  
Edible Mushroom ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Phenotypic Differentiation ◽  
Mycolic Acids ◽  
Gordonia Amarae ◽  
Phosphatidylinositol Mannosides ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-positive, non-endospore-forming actinobacterium (CC-12301T) was isolated from soil attached to a spawn used in the laboratory to grow the edible mushroom Agaricus brasiliensis. Based on 16S rRNA gene sequence similarities, strain CC-12301T was shown to belong to the genus Gordonia and was most closely related to the type strains of Gordonia hydrophobica (97.6 % similarity), Gordonia terrae (97.5 %), Gordonia amarae (97.5 %) and Gordonia malaquae (97.4 %). The quinone system was determined to consist predominantly of menaquinone MK-9(H2), minor amounts of MK-8(H2) and MK-7(H2). The polar lipid profile consisted of the major compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of two phosphatidylinositol mannosides and phosphatidylinositol and minor amounts of phosphatidylglycerol, three unidentified glycolipids, two phosphoglycolipids and a phospholipid. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C16 : 1 cis9, C16 : 0, C18 : 1 and tuberculostearic acid (10-methyl C18 : 0), supported the affiliation of strain CC-12301T to the genus Gordonia. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain CC-12301T from the most closely related Gordonia species. Strain CC-12301T therefore represents a novel species, for which the name Gordonia humi sp. nov. is proposed, with the type strain CC-12301T (=DSM 45298T =CCM 7727T).

scholarly journals Citricoccus parietis sp. nov., isolated from a mould-colonized wall and emended description of Citricoccus alkalitolerans Li et al. 2005

2010 ◽  
Vol 60 (2) ◽  
pp. 271-274 ◽  
Author(s):  
Jenny Schäfer ◽  
Karin Martin ◽  
Peter Kämpfer
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Phenotypic Differentiation ◽  
Emended Description ◽  
Diamino Acid ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A Gram-positive, coccoid-shaped organism (strain 02-Je-010T), forming yellow-pigmented colonies was isolated from the wall of an indoor environment. On the basis of 16S rRNA gene sequence similarity studies, it was shown that strain 02-Je-010T belongs to the genus Citricoccus with sequence similarities of 98.9 % to Citricoccus alkalitolerans DSM 15665T and 98.6 % to Citricoccus muralis DSM 14442T. Cell-wall sugars were mannose and glucose. The diagnostic diamino acid of the peptidoglycan was lysine. The major menaquinones detected were MK-9(H2) and MK-8(H2). The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol and moderate amounts of two unknown phospholipids and two unknown glycolipids. The fatty acid profile comprised major amounts of anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. All these data supported the affiliation of strain 02-Je-010T to the genus Citricoccus. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 02-Je-010T from the two recognized Citricoccus species. For these reasons, strain 02-Je-010T represents a novel species, for which the name Citricoccus parietis sp. nov. is proposed, with the type strain 02-Je-010T (=CCUG 57388T=CCM 7609T).

scholarly journals Plantactinospora veratri sp. nov., an actinomycete isolated from black false hellebore root (Veratrum nigrum L.)

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1799-1804 ◽  
Author(s):  
He Xing ◽  
Chongxi Liu ◽  
Yuejing Zhang ◽  
Junwei Zhao ◽  
Chuang Li ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

A novel actinomycete, designated strain NEAU-FHS4T, was isolated from the root of black false hellebore (Veratrum nigrum L.). Strain NEAU-FHS4T formed single spores with smooth surfaces on substrate mycelium. The novel strain contained meso-diaminopimelic as amino acid of the peptidoglycan and xylose and glucose as whole-cell sugars. The predominant menaquinones were MK-10(H6) and MK-10(H8). Mycolic acids were not detected. The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol. The predominant cellular fatty acids were iso-C16 : 0, C16 : 0, C18 : 0 and anteiso-C17 : 0. Phenotypic and chemotaxonomic analysis showed that the novel isolate had characteristics typical of members of the genus Plantactinospora . 16S rRNA gene sequence analysis also indicated that strain NEAU-FHS4T belonged to the genus Plantactinospora , with highest sequence similarities to Plantactinospora mayteni YIM 61359T (98.88 %) and Plantactinospora endophytica YIM 68255T (98.85 %). The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the novel strain from the most closely related strains. Based on morphological, chemotaxonomic and phylogenetic data, strain NEAU-FHS4T is considered to represent a novel species of the genus Plantactinospora , for which the name Plantactinospora veratri sp. nov. is proposed. The type strain is NEAU-FHS4T ( = CGMCC 4.7143T = DSM 46718T).

scholarly journals Brevibacterium sandarakinum sp. nov., isolated from a wall of an indoor environment

2010 ◽  
Vol 60 (4) ◽  
pp. 909-913 ◽  
Author(s):  
Peter Kämpfer ◽  
Jenny Schäfer ◽  
Nicole Lodders ◽  
Hans-Jürgen Busse
Keyword(s):  
Indoor Environment ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Phenotypic Differentiation ◽  
Diamino Acid ◽  
Type Strains

A Gram-stain-positive, rod-shaped, non-endospore-forming, orange-pigmented (coloured) actinobacterium (01-Je-003T) was isolated from the wall of an indoor environment primarily colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 01-Je-003T was shown to belong to the genus Brevibacterium and was most similar to the type strains of Brevibacterium picturae (98.8 % similarity), Brevibacterium marinum (97.3 %) and Brevibacterium aurantiacum (97.2 %). Chemotaxonomic data [predominant quinone menaquinone MK-8(H2); polar lipid profile consisting of major compounds diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid; characteristic cell-wall diamino acid meso-diaminopimelic acid; polyamine pattern showing major compounds putrescine and cadaverine; major fatty acids anteiso-C15 : 0 and anteiso-C17 : 0] supported the affiliation of strain 01-Je-003T to the genus Brevibacterium. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 01-Je-003T from the two most closely related species, B. picturae and B. marinum. Strain 01-Je-003T therefore represents a novel species, for which the name Brevibacterium sandarakinum sp. nov. is proposed, with the type strain 01-Je-003T (=DSM 22082T =CCM 7649T).

scholarly journals Virgibacillus soli sp. nov., isolated from mountain soil

2011 ◽  
Vol 61 (2) ◽  
pp. 275-280 ◽  
Author(s):  
P. Kämpfer ◽  
A. B. Arun ◽  
H.-J. Busse ◽  
S. Langer ◽  
C.-C. Young ◽  
...  
Keyword(s):  
Rrna Gene ◽  
Positive Bacterium ◽  
Biochemical Tests ◽  
Unidentified Phospholipid ◽  
Polar Lipid Profile ◽  
Phenotypic Differentiation ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Physiological And Biochemical

A Gram-positive bacterium (strain CC-YMP-6T) was isolated from soil samples collected from Yang-Ming Mountain, Taiwan. On the basis of 16S rRNA gene sequence analysis, strain CC-YMP-6T clearly belonged to the genus Virgibacillus and was most closely related to the type strains of Virgibacillus halophilus (96.2 % similarity) and Virgibacillus kekensis (96.3 %). The predominant isoprenoid quinone was menaquinone MK-7 and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid plus moderate amounts of two unidentified aminophospholipids and a phospholipid. The polyamine pattern comprised spermidine as the single major component with spermine and putrescine present in minor amounts. The major fatty acids of strain CC-YMP-6T were iso-C15 : 0 and anteiso-C15 : 0. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of strain CC-YMP-6T from all recognized species of the genus Virgibacillus. Strain CC-YMP-6T is therefore considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus soli sp. nov. is proposed. The type strain is CC-YMP-6T (=DSM 22952T=CCM 7714T).

scholarly journals Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea

2007 ◽  
Vol 57 (7) ◽  
pp. 1396-1401 ◽  
Author(s):  
Hyung-Gwan Lee ◽  
Dong-Shan An ◽  
Wan-Taek Im ◽  
Qing-Mei Liu ◽  
Ju-Ryun Na ◽  
...  
Keyword(s):  
South Korea ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Type Strains ◽  
Sequence Similarities

Two novel strains belonging to the phylum Bacteroidetes [formerly the Cytophaga–Flexibacter–Bacteroides (CFB) group], designated Gsoil 040T and Gsoil 052T, were isolated from the soil of a ginseng field in Pocheon province, South Korea. A polyphasic approach was used to characterize the taxonomic position of the novel strains. Both strains were Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolates belong to the genus Chitinophaga but are clearly separated from the recognized species of this genus; gene sequence similarities between the novel isolates and type strains of recognized species ranged from 91.2 to 96.5 %. One exception was found; strain Gsoil 052T and the type strain of Chitinophaga filiformis had a gene sequence similarity of 99.6 % but had a DNA–DNA relatedness value of 38 %. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C15 : 0 and C16 : 1 ω5c; major hydroxy fatty acid, iso-C17 : 0 3-OH and major polyamine, homospermidine) supported the affiliation of both strains Gsoil 040T and Gsoil 052T to the genus Chitinophaga. The results of physiological and biochemical tests enabled the genotypic and phenotypic differentiation of the novel strains from the other recognized species of the genus Chitinophaga. Therefore, it is suggested that the new isolates represent two novel species, for which the names Chitinophaga ginsengisegetis sp. nov. [type strain Gsoil 040T (=KCTC 12654T=DSM 18108T)] and Chitinophaga ginsengisoli sp. nov. [type strain Gsoil 052T (=KCTC 12592T=DSM 18017T)] are proposed.

scholarly journals Pantoea theicola sp. nov., isolated from black tea

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3313-3319 ◽  
Author(s):  
Yuko Kato Tanaka ◽  
Nobuhiro Horie ◽  
Kaoru Mochida ◽  
Yoshihiro Yoshida ◽  
Eri Okugawa ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Black Tea ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Type Strains ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A Gram-negative, facultatively anaerobic strain was isolated from black tea. On the basis of 16S rRNA gene sequence similarity comparisons, strain QC88-366T was grouped into the genus Pantoea, being related most closely to the type strains of Pantoea gaviniae (98.5 %) and Pantoea calida (98.3 %); sequence similarities were ≤ 97.0 % to the type strains of other species of the genus Pantoea. Multilocus sequence analysis based on partial sequences of the gyrB, rpoB, infB and atpD genes also revealed P. gaviniae and P. calida as the closest phylogenetic relatives. The fatty acid profile showed the major fatty acids of strain QC88-366T were C16 : 0, C16 : 1 and C18 : 1, the same as those of its closest related species. However, the ratio of C16 : 1, C17 : 0 cyclo, C18 : 1 and C18 : 2 differed slightly compared with those of the related neighbours. In addition, the results of physiological and biochemical tests also allowed the phenotypic differentiation of strain QC88-366T from its closest phylogenetic neighbours. The G+C content of the DNA was 57.2 mol%. Strain QC88-366T therefore represents a novel species of the genus Pantoea, for which the name Pantoea theicola sp. nov. is proposed. The type strain is QC88-366T ( = DSM 29212T = NBRC 110557T).

scholarly journals Dietzia aerolata sp. nov., isolated from the air of a duck barn, and emended description of the genus Dietzia Rainey et al. 1995

2010 ◽  
Vol 60 (2) ◽  
pp. 393-396 ◽  
Author(s):  
P. Kämpfer ◽  
S. Langer ◽  
E. Martin ◽  
U. Jäckel ◽  
H.-J. Busse
Keyword(s):  
Polar Lipid ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Phenotypic Differentiation ◽  
Emended Description ◽  
Phosphatidylinositol Mannosides ◽  
Physiological And Biochemical

A Gram-stain-positive, coccoid, non-endospore-forming actinobacterium (Sj14aT) was isolated from the air of a duck barn on tryptone soy agar after filter sampling. On the basis of 16S rRNA gene sequence similarity studies, strain Sj14aT was shown to belong to the genus Dietzia and was most closely related to Dietzia schimae (98.7 %), Dietzia cercidiphylli (98.4 %) and Dietzia maris (98.6 %). The major menaquinone was MK-8 (H2). The polar lipid profile included the major components diphosphatidylglycerol, phosphatidylglycerol, an unknown polar lipid and two unknown glycolipids. Phosphatidylinositol and two phosphatidylinositol mannosides, as well as several other unknown lipids, were also detected. The polyamine pattern contained the major compounds spermine and spermidine. The fatty acid profile, containing C16 : 0, C17 : 0, C18 : 1 ω9c and 10-methyl C18 : 0 as major fatty acids, supported the affiliation of strain Sj14aT to the genus Dietzia. The results of physiological and biochemical tests and DNA–DNA hybridizations allowed a clear phenotypic differentiation of strain Sj14aT from the most closely related species of the genus Dietzia. Strain Sj14aT represents a novel species, for which the name Dietzia aerolata sp. nov. is proposed, with the type strain Sj14aT (=DSM 45334T =CCM 7659T).

scholarly journals Segetibacter koreensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes, isolated from the soil of a ginseng field in South Korea

2007 ◽  
Vol 57 (8) ◽  
pp. 1828-1833 ◽  
Author(s):  
Dong-Shan An ◽  
Hyung-Gwan Lee ◽  
Wan-Taek Im ◽  
Qing-Mei Liu ◽  
Sung-Taik Lee
Keyword(s):  
South Korea ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Novel Genus And Species ◽  
Type Strains ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A novel strain, designated Gsoil 664T, isolated from the soil of a ginseng field in South Korea, was characterized by a polyphasic approach to clarify its taxonomic position. The isolate was Gram-negative, strictly aerobic, heterotrophic, non-motile, non-spore-forming and possessed rod-shaped cells. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate formed a cluster with several uncultured bacterial clones and with the established genera Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes. However, the isolate was clearly separated from these genera: the gene sequence similarities with respect to the type strains of recognized species from closely related genera ranged from 86.7 to 90.7 %. The G+C content of the genomic DNA was 40.4 mol%. The predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 and C16 : 1 ω5c. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 664T from recognized species of related genera. On the basis of the polyphasic evidence, Gsoil 664T represents a novel genus and species, for which the name Segetibacter koreensis gen. nov., sp. nov. is proposed. The type strain of S. koreensis is Gsoil 664T (=KCTC 12655T=DSM 18137T).

scholarly journals Nocardia acidivorans sp. nov., isolated from soil of the island of Stromboli

2007 ◽  
Vol 57 (6) ◽  
pp. 1183-1187 ◽  
Author(s):  
Peter Kämpfer ◽  
Birgit Huber ◽  
Sandra Buczolits ◽  
Kathrin Thummes ◽  
Iris Grün-Wollny ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipid ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Phenotypic Differentiation ◽  
Bacterium Strain ◽  
Phosphatidylinositol Mannosides

A Gram-positive, non-spore-forming bacterium (strain GW4-1778T) was isolated from soil of the Italian island of Stromboli. 16S rRNA gene sequence similarity studies showed that strain GW4-1778T is a member of the genus Nocardia, most closely related to Nocardia pseudobrasiliensis (GenBank accession no. DQ659914; 98.6 %), Nocardia nova (Z36930; 98.6 %), Nocardia niigatensis (AB092563; 98.4 %), Nocardia jiangxiensis (AY639902; 98.0 %), Nocardia uniformis (Z46752; 98.0 %) and Nocardia miyunensis (AY639901; 97.8 %). Strain GW4-1778T could be distinguished from any other established Nocardia species by sequence similarity values of less than 97.5 %. Strain GW4-1778T exhibited a quinone system with the predominant compound MK-8 (H4, ω-cycl) (99.5 %) and traces of MK-8 (H4), characteristic for the genus Nocardia. The polar lipid profile of strain GW4-1778T consisted of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides, a unknown polar lipid and trace amounts of two unknown lipids and the major fatty acids were C15 : 0, C16 : 0, C17 : 1 ω8c and 10-methyl C17 : 0. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW4-1778T from related species with 16S rRNA gene similarities of >97.5 %. Therefore, strain GW4-1778T merits species status, for which the name Nocardia acidivorans sp. nov. is proposed, with the type strain GW4-1778T (=CCUG 53410T=CIP 109315T=DSM 45049T).

scholarly journals Nocardioides panacihumi sp. nov., isolated from soil of a ginseng field

2007 ◽  
Vol 57 (9) ◽  
pp. 2143-2146 ◽  
Author(s):  
Dong-Shan An ◽  
Wan-Taek Im ◽  
Sung-Taik Lee ◽  
Min-Ho Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
The Family ◽  
Established Species ◽  
Type Strains

A novel bacterial strain designated Gsoil 616T was isolated from a soil sample of a ginseng field in Pocheon province (South Korea) and was characterized taxonomically by using a polyphasic approach. The isolate was Gram-positive, strictly aerobic, non-motile, non-spore-forming and rod- or coccoid-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Nocardioides in the family Nocardioidaceae but was clearly separated from established species of this genus. The 16S rRNA gene sequence similarities between strain Gsoil 616T and the type strains of Nocardioides species with validly published names ranged from 91.8 to 96.1 %. The G+C content of the genomic DNA was 73 mol%. Phenotypic and chemotaxonomic data [major menaquinone MK-8(H4) and major fatty acid iso-C16 : 0] supported the affiliation of strain Gsoil 616T to the genus Nocardioides. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate from other Nocardioides species. Therefore, strain Gsoil 616T represented a novel species within the genus Nocardioides, for which the name Nocardioides panacihumi sp. nov. is proposed. The type strain is Gsoil 616T (=KCTC 19187T =DSM 18660T).

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