scholarly journals Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 129-134 ◽  
Author(s):  
Roshan Kumar ◽  
Vatsala Dwivedi ◽  
Namita Nayyar ◽  
Helianthous Verma ◽  
Amit Kumar Singh ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
16S Rrna Sequence Analysis

Strain RK1T, a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium was isolated from a hexachlorocyclohexane (HCH) dumpsite, Lucknow, India. 16S rRNA gene sequence analysis revealed that strain RK1T belongs to the family Sphingobacteriaceae and showed highest sequence similarity to Parapedobacter koreensis Jip14T (95.63 %). The major cellular fatty acids of strain RK1T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH, summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c), iso-C15 : 0 3-OH and C16 : 0. The major respiratory pigment and polyamine of RK1T were menaquinone (MK-7) and homospermidine, respectively. The main polar lipids were phosphatidylethanolamine and sphingolipid. The G+C content of the DNA was 44.5 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly demonstrated that strain RK1T represents a novel species of the genus Parapedobacter , for which the name Parapedobacter indicus sp. nov. is proposed. The type strain is RK1T ( = DSM 28470T = MCC 2546T).

Stappia taiwanensis sp. nov., isolated from a coastal thermal spring

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1350-1354 ◽  
Author(s):  
P. Kämpfer ◽  
A. B. Arun ◽  
A. Frischmann ◽  
H.-J. Busse ◽  
Chiu-Chung Young ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A beige-coloured, Gram-stain-negative, aerobic, non-motile moderately thermotolerant, rod-shaped organism, strain CC-SPIO-10-1T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on Marine Agar 2216. Based on 16S rRNA gene sequence analysis, this organism was grouped into the genus Stappia , showing 98.3 % sequence similarity to Stappia indica B106T and 98.2 % gene sequence similarity to Stappia stellulata IAM 12621T . Ubiquinone Q-10 was the major respiratory quinone and C18 : 1ω7c and C18 : 1ω7c 11-methyl were detected as the major fatty acids. The hydroxylated fatty acid C18 : 0 3-OH was detected as well. Predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, unidentified aminolipid AL1 and unidentified phospholipid PL1. Minor amounts of several unidentified lipids (PL2 and L1–L7) were present as well. The polyamine pattern contained the major compounds spermidine and spermine. Strain CC-SPIO-10-1T could be differentiated from the type strains of S. stellulata and S. indica by a set of biochemical tests. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain CC-SPIO-10T represents a novel species of the genus Stappia for which the name Stappia taiwanensis sp. nov. is proposed. The type strain is CC-SPIO-10 T ( = CCUG 59208T = LMG 25538 T = CCM 7757T).

Thauera humireducens sp. nov., a humus-reducing bacterium isolated from a microbial fuel cell

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 873-878 ◽  
Author(s):  
Gui-Qin Yang ◽  
Jun Zhang ◽  
Soon-Wo Kwon ◽  
Shun-Gui Zhou ◽  
Lu-Chao Han ◽  
...  
Keyword(s):  
Fuel Cell ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Fuel Cell ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type

A Gram-negative, rod-shaped, non-spore-forming bacterium, designated SgZ-1T, was isolated from the anode biofilm of a microbial fuel cell. The strain had the ability to grow under anaerobic condition via the oxidation of various organic compounds coupled to the reduction of anthraquione-2,6-disulfonate (AQDS) to anthrahydroquinone-2,6-disulfonate (AHQDS). Growth occurred in TSB in the presence of 0–5.5 % (w/v) NaCl (optimum 0–1 %), at 10–45 °C (optimum 25–37 °C) and at pH 6.0–10.0 (optimum 8.0–8.5). Based on 16S rRNA gene sequence similarity, strain SgZ-1T belonged to the genus Thauera . The highest level of 16S rRNA gene sequences similarity (96.7 %) was found to be with Thauera aminoaromatica S2 T and Thauera selenatis AXT, and lower values were obtained when compared with other recognized Thauera species. Chemotaxonomic analysis revealed that strain SgZ-1T contained Q-8 as the predominant quinone, and putrescine and 2-hydroxyputrescine as the major polyamines. The major cellular fatty acids (>5 %) were C16 : 1ω6c and/or C16 : 1ω7c (44.6 %), C16 : 0 (18.8 %), and C18 : 1ω6c and/or C18 : 1ω7c (12.7 %). Based on its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-1T ( = KACC 16524T = CCTCC M 2011497T) was designated the type strain of a novel species of the genus Thauera , for which the name Thauera humireducens sp. nov. was proposed.

Arcanobacterium phocisimile sp. nov., isolated from harbour seals

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2019-2024 ◽  
Author(s):  
Muaz Hijazin ◽  
Osama Sammra ◽  
Hivda Ülbegi-Mohyla ◽  
Samy Nagib ◽  
Jörg Alber ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Harbour Seals

A polyphasic taxonomic study was performed on two previously unidentified Arcanobacterium -like Gram-positive strains isolated from harbour seals. Comparative 16S rRNA gene sequencing showed that both bacteria belonged to the genus Arcanobacterium and were most closely related to Arcanobacterium haemolyticum CIP 103370T (98.4 % 16S rRNA gene sequence similarity), A. canis P6775T (97.4 %), A. phocae DSM 10002T (97.4 %), A. pluranimalium M430/94/2T (95.7 %) and A. hippocoleae CCUG 44697T (95.5 %). The presence of the major menaquinone MK-9(H4) supported the affiliation of the isolates with the genus Arcanobacterium . The polar lipid profile consisted of major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phospholipid and two unidentified glycolipids. The major fatty acids were C16 : 0, C18 : 0, C18 : 1ω9c and summed feature 5 (comprising C18 : 2ω6,9c and/or anteiso-C18 : 0). Physiological and biochemical tests clearly distinguished the isolates from other members of the genus Arcanobacterium . Based on the common origin and various physiological properties comparable to those of A. phocae , it is proposed that the isolates are classified as members of a novel species with the name Arcanobacterium phocisimile sp. nov. The type strain is 2698T ( = LMG 27073T  = CCM 8430T).

scholarly journals Taxonomic revision of the genus Geobacillus : emendation of Geobacillus , G. stearothermophilus , G. jurassicus , G. toebii , G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly ‘thermoglucosidasius’); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov.

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1470-1485 ◽  
Author(s):  
An Coorevits ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Liesbeth Lebbe ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

Sixty-two strains of thermophilic aerobic endospore-forming bacteria were subjected to polyphasic taxonomic study including 16S rRNA gene sequence analysis, polar lipid and fatty acid analysis, phenotypic characterization, and DNA–DNA hybridization experiments. Distinct clusters of the species Geobacillus stearothermophilus , Geobacillus thermodenitrificans , Geobacillus toebii and Geobacillus thermoglucosidasius were formed, allowing their descriptions to be emended, and the distinctiveness of the poorly represented species Geobacillus jurassicus , Geobacillus subterraneus and Geobacillus caldoxylosilyticus was confirmed. It is proposed that the name Geobacillus thermoglucosidasius be corrected to Geobacillus thermoglucosidans nom. corrig. Bacillus thermantarcticus clustered between Geobacillus species on the basis of 16S rRNA gene sequence analysis, and its transfer to the genus Geobacillus as Geobacillus thermantarcticus comb. nov. (type strain LMG 23032T = DSM 9572T = strain M1T = R-35644T) is proposed. The above-mentioned species, together with Geobacillus thermoleovorans and Geobacillus thermocatenulatus , form a monophyletic cluster representing the genus Geobacillus . The distinctiveness of ‘Geobacillus caldoproteolyticus’ was confirmed and it is proposed that it be accommodated, along with Geobacillus tepidamans , in the genus Anoxybacillus as Anoxybacillus caldiproteolyticus sp. nov. (type strain DSM 15730T = ATCC BAA-818T = LMG 26209T = R-35652T) and Anoxybacillus tepidamans comb. nov. (type strain LMG 26208T = ATCC BAA-942T = DSM 16325T = R-35643T), respectively. The type strain of Geobacillus debilis was not closely related to any members of the genera Anoxybacillus and Geobacillus , and it is proposed that this species be placed in the new genus Caldibacillus as Caldibacillus debilis gen. nov. comb. nov. The type strain of the type species, Caldibacillus debilis, is LMG 23386T ( = DSM 16016T = NCIMB 13995T = TfT = R-35653T).

Proposal of Motilibacteraceae fam. nov., with the description of Motilibacter rhizosphaerae sp. nov.

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3818-3822 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type

A rod-shaped actinobacterium, designated strain RS-16T, was isolated from a rhizosphere soil and its taxonomic position was determined by a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis indicated that strain RS-16T was most closely related to the type strain of Motilibacter peucedani (98.3 % sequence similarity). The cell-wall peptidoglycan contained ll-diaminopimelic acid as the diagnostic diamino acid and N-glycolylated murein. The major whole-cell sugars were glucose, galactose and mannose. The predominant menaquinone was MK-9(H4). The major fatty acids were C18 : 1ω9c and C16 : 0. The DNA G+C content was 73.1 mol%. The phenotypic and DNA–DNA hybridization data showed that strain RS-16T ( = KACC 16209T = DSM 45622T) represents a novel species of the genus Motilibacter , for which Motilibacter rhizosphaerae sp. nov. is proposed. Based on the phylogenetic position determined by 16S rRNA gene analysis and the signature nucleotide set of the 16S rRNA sequence, the genus Motilibacter represents a novel family of the suborder Frankineae , for which the name Motilibacteraceae fam. nov. is proposed.

scholarly journals Microbacterium immunditiarum sp. nov., an actinobacterium isolated from landfill surface soil, and emended description of the genus Microbacterium

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2187-2193 ◽  
Author(s):  
Srinivasan Krishnamurthi ◽  
A. Bhattacharya ◽  
P. Schumann ◽  
Syed G. Dastager ◽  
Shu-Kun Tang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Surface Soil ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A Gram-positive, non-endospore-forming bacterium, designated strain SK 18T, was isolated from surface soil of a landfill site by dilution plating on trypticase soy broth agar. Preliminary characterization of strain SK 18T via biochemical tests, analysis of fatty acid methyl esters and partial 16S rRNA gene sequencing placed it within the genus Microbacterium . Analysis of the cell wall indicated that the peptidoglycan was of cross-linkage type B, containing the amino acids lysine and ornithine and with muramic acid in the N-glycolyl form. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. The major fatty acids of the cell membrane were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. These data further strengthened placement of the strain within the genus Microbacterium . Strain SK 18T shared highest 16S rRNA gene sequence similarity (97.2 %) with Microbacterium ulmi DSM 16931T. Levels of similarity with the type strains of all other recognized Microbacterium species were less than 97.0 %. DNA–DNA hybridization experiments with strain SK 18T and its closest relative, M. ulmi DSM 16931T, revealed a low reassociation value of 39.0 % (σ = 3.8 %). Moreover, strain SK 18T showed a number of differences in phenotypic characteristics (colony colour, catalase activity, hydrolysis of polymers, acid production from sugars and oxidation of various substrates), and its DNA G+C content was also higher than that of M. ulmi DSM 16931T. These data indicated that strain SK 18T represents a novel species of the genus Microbacterium , for which the name Microbacterium immunditiarum sp. nov. is proposed. The type strain is SK 18T ( = MTCC 7185T = JCM 14034T). An emended description of the genus Microbacterium is also provided.

scholarly journals Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates

2019 ◽  
Vol 69 (4) ◽  
pp. 964-969 ◽  
Author(s):  
Masanori Tohno ◽  
Yasuhiro Tanizawa ◽  
Yoichiro Kojima ◽  
Mitsuo Sakamoto ◽  
Yasukazu Nakamura ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, strain YK43T, isolated from spent mushroom substrates stored in Nagano, Japan was performed. Growth was detected at 15–45 °C, pH 5.0–8.5, and 0–10 % (w/v) NaCl. The genomic DNA G+C content of strain YK43T was 43.6 mol%. The predominant fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 8. Based on 16S rRNA gene sequence analysis, the type strains of Lactobacillus acidipiscis (sequence similarity, 97.6 %) and Lactobacillus pobuzihii (97.4 %) were most closely related to YK43T. The average nucleotide identities were 74.1 % between strain YK43T and L. acidipiscis DSM 15836T and 74.0 % between YK43T and L. pobuzihii E100301T. Based on a multilocus sequence analysis, comparative genomic analysis and a range of phenotypic and chemotaxonomic characteristics, strain YK43T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus salitolerans sp. nov. is proposed. The type strain is YK43T (=JCM 31331T = DSM 103433T).

scholarly journals Streptococcus oriloxodontae sp. nov., isolated from the oral cavities of elephants

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3755-3759 ◽  
Author(s):  
Noriko Shinozaki-Kuwahara ◽  
Masanori Saito ◽  
Masatomo Hirasawa ◽  
Kazuko Takada
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Streptococcal Species

Two strains were isolated from oral cavity samples of healthy elephants. The isolates were Gram-positive, catalase-negative, coccus-shaped organisms that were tentatively identified as a streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequence analysis suggested classification of these organisms in the genus Streptococcus with Streptococcus criceti ATCC 19642T and Streptococcus orisuis NUM 1001T as their closest phylogenetic neighbours with 98.2 and 96.9 % gene sequence similarity, respectively. When multi-locus sequence analysis using four housekeeping genes, groEL, rpoB, gyrB and sodA, was carried out, similarity of concatenated sequences of the four housekeeping genes from the new isolates and Streptococcus mutans was 89.7 %. DNA–DNA hybridization experiments suggested that the new isolates were distinct from S. criceti and other species of the genus Streptococcus . On the basis of genotypic and phenotypic differences, it is proposed that the novel isolates are classified in the genus Streptococcus as representatives of Streptococcus oriloxodontae sp. nov. The type strain of S. oriloxodontae is NUM 2101T ( = JCM 19285T = DSM 27377T).

Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana

2021 ◽  
Author(s):  
Shan Shan Qi ◽  
Margo Cnockaert ◽  
Aurélien Carlier ◽  
Peter Vandamme
Keyword(s):  
Arabidopsis Thaliana ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Maldi Tof Mass Spectra

Three rod-shaped, non-spore-forming, yellow or pale-yellow pigmented bacteria with distinct MALDI-TOF mass spectra were isolated from the phyllosphere of Arabidopsis thaliana seedlings. Their 16S rRNA gene sequences demonstrated that these isolates belong to the genus Pedobacter . The nearest phylogenetic neighbours of strain LMG 31462T were Pedobacter steynii DSM 19110T (98.3 % 16S rRNA sequence similarity) and Pedobacter caeni LMG 22862T (98.3 %); the nearest phylogenetic neighbours of strain LMG 31463T were Pedobacter panaciterrae Gsoil 042T (98.3 %) and Pedobacter nutrimenti DSM 27372T (98.1 %); and the nearest phylogenetic neighbours of strain LMG 31464T were Pedobacter boryungensis BR-9T (99.0 %) and Pedobacter daejeonensis THG-DN3.18T (98.7 %). Average nucleotide identity analyses between the whole genome sequences of the three strains and of the type strains of their respective nearest-neighbour taxa yielded values well below the species delineation threshold and thus confirmed that the three strains represented a novel Pedobacter species each. An extensive phenotypic comparison and an analysis of whole-cell fatty acid components yielded distinctive phenotypic characteristics for each of these strains. We therefore propose to classify these isolates as three novel species, for which we propose the names Pedobacter gandavensis with LMG 31462T (=R-74704T=CECT 30149T) as the type strain, Pedobacter foliorum with LMG 31463T (=R-74623T=CECT 30150T) as the type strain and Pedobacter planticolens with LMG 31464T (=R-74626T=CECT 30151T) as the type strain.

Parabacteroides faecis sp. nov., isolated from human faeces

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1342-1346 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Yoshiki Tanaka ◽  
Yoshimi Benno ◽  
Moriya Ohkuma
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Human Faeces ◽  
Link Type ◽  
Gene Sequence Analysis

A bacterial strain, designated 157T, isolated from human faeces was characterized by using a polyphasic taxonomic approach, which included analysis of physiological and biochemical features, cellular fatty acid profiles, menaquinone profiles and its phylogenetic position, based on 16S rRNA gene sequence analysis. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. The isolate was able to grown on medium containing 20 % (w/v) bile. 16S rRNA gene sequence analysis showed that the strain was a member of the genus Parabacteroides . Strain 157T was closely related to Parabacteroides gordonii JCM 15724T (96 % sequence similarity). The results of hsp60 gene sequence analysis indicated that strain 157T was different from P. gordonii JCM 15724T, with a hsp60 gene sequence similarity of 96.1 %. The major cellular fatty acids of strain 157T were anteiso-C15 : 0, iso-C17 : 0 3-OH, C18 : 1ω9c and anteiso-C17 : 0 3-OH. The major menaquinone of the isolate was MK-9. The DNA G+C content of strain 157T was 41.8 mol%. On the basis of these data, strain 157T represents a novel species of the genus Parabacteroides , for which the name Parabacteroides faecis sp. nov. is proposed; the type strain is 157T ( = JCM 18682T = CCUG 66681T).

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