scholarly journals Azospirillum zeae sp. nov., a diazotrophic bacterium isolated from rhizosphere soil of Zea mays

2007 ◽  
Vol 57 (12) ◽  
pp. 2805-2809 ◽  
Author(s):  
Samina Mehnaz ◽  
Brian Weselowski ◽  
George Lazarovits
Keyword(s):  
Fatty Acid ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Fatty Acid Analysis ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Gene Sequence Analysis

Two free-living nitrogen-fixing bacterial strains, N6 and N7T, were isolated from corn rhizosphere. A polyphasic taxonomic approach, including morphological characterization, Biolog analysis, DNA–DNA hybridization, and 16S rRNA, cpn60 and nifH gene sequence analysis, was taken to analyse the two strains. 16S rRNA gene sequence analysis indicated that strains N6 and N7T both belonged to the genus Azospirillum and were closely related to Azospirillum oryzae (98.7 and 98.8 % similarity, respectively) and Azospirillum lipoferum (97.5 and 97.6 % similarity, respectively). DNA–DNA hybridization of strains N6 and N7T showed reassociation values of 48 and 37 %, respectively, with A. oryzae and 43 % with A. lipoferum. Sequences of the nifH and cpn60 genes of both strains showed 99 and ~95 % similarity, respectively, with those of A. oryzae. Chemotaxonomic characteristics (Q-10 as quinone system, 18 : 1ω7c as major fatty acid) and G+C content of the DNA (67.6 mol%) were also similar to those of members of the genus Azospirillum. Gene sequences and Biolog and fatty acid analysis showed that strains N6 and N7T differed from the closely related species A. lipoferum and A. oryzae. On the basis of these results, it is proposed that these nitrogen-fixing strains represent a novel species. The name Azospirillum zeae sp. nov. is suggested, with N7T (=NCCB 100147T=LMG 23989T) as the type strain.

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

scholarly journals Lactobacillus similis sp. nov., isolated from fermented cane molasses

2010 ◽  
Vol 60 (1) ◽  
pp. 187-190 ◽  
Author(s):  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cane Molasses ◽  
Gene Sequence Analysis

The taxonomic position of strain JCM 2765T isolated from fermented cane molasses in Thailand was reinvestigated. Strain JCM 2765T was originally identified as representing Lactobacillus buchneri on the basis of biochemical and physiological characteristics. In the present study, 16S rRNA gene sequence analysis of strain JCM 2765T demonstrated a low level of similarity with the type strain of L. buchneri (92.5 %) and high levels with those of Lactobacillus collinoides (97.6 %) and Lactobacillus paracollinoides (98.0 %). Ribotyping was applied to investigate the relationships between strain JCM 2765T, L. collinoides and L. paracollinoides. The dendrogram based on ribotyping patterns showed one cluster for six strains of L. paracollinoides, and that strain JCM 2765T and L. collinoides JCM 1123T were each independent. Based on additional phenotypic findings and DNA–DNA hybridization results, strain JCM 2765T is considered to represent a novel species of the genus Lactobacillus, for which the name Lactobacillus similis sp. nov. is proposed. The type strain is JCM 2765T (=LMG 23904T).

scholarly journals Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque

2005 ◽  
Vol 55 (5) ◽  
pp. 1839-1843 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Makoto Umeda ◽  
Isao Ishikawa ◽  
Yoshimi Benno
Keyword(s):  
Fatty Acid ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Cellular Fatty Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Six bacterial strains isolated from the human oral cavity, PPPA16, PPPA20T, PPPA24, PPPA31, EPPA6 and EPPA7, were characterized by determining phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the isolates represented the same species of the genus Prevotella. The strains were related to Prevotella dentalis with about 89 % similarity. In addition, the isolates were related to Prevotella sp. oral clone IDR-CEC-0032, which is a representative of the numerically dominant cluster VI in carious dentine lesions [Nadkarni et al. (2004). J Clin Microbiol 42, 5238–5244], with about 99 % similarity. The strains were obligately anaerobic, non-pigmenting, non-spore-forming, non-motile, Gram-negative rods. The isolates could be differentiated from other Prevotella species by d-mannitol, d-melezitose, d-sorbitol and d-trehalose fermentation in API 20A tests. The cellular fatty acid composition of strains PPPA16, PPPA20T, PPPA24, PPPA31, EPPA6 and EPPA7 was significantly different from that of other Prevotella species. Compared with other Prevotella species, only these six strains contained dimethyl acetals. The major menaquinones of the clinical isolates were MK-12 and MK-13, whereas the major menaquinones of other Prevotella species were MK-10 and MK-11. On the basis of these data, a novel Prevotella species, Prevotella multisaccharivorax sp. nov., is proposed, with PPPA20T (=JCM 12954T=DSM 17128T) as the type strain.

scholarly journals Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan

2007 ◽  
Vol 57 (6) ◽  
pp. 1351-1354 ◽  
Author(s):  
Fwu-Ling Lee ◽  
Hsiao-Ping Kuo ◽  
Chun-Ju Tai ◽  
Akira Yokota ◽  
Chi-Chu Lo
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile and endospore-forming bacterial strain, designated G-soil-2-3T, was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequence analysis, DNA–DNA hybridization experiments, fatty acid analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belongs within the genus Paenibacillus. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C15 : 0 (40.5 %), iso-C15 : 0 (13.1 %), iso-C16 : 0 (10.8 %) and anteiso-C17 : 0 (7.3 %) as the major fatty acids. Phylogenetically, the closest relatives of strain G-soil-2-3T were the type strains of Paenibacillus assamensis, Paenibacillus alvei and Paenibacillus apiarius, with 16S rRNA gene sequence similarity of 95.7, 95 and 95.2 %, respectively. DNA–DNA hybridization experiments showed levels of relatedness of 2.8–9.0 % of strain G-soil-2-3T with these strains. The G+C content of the DNA was 44.6 mol%. Strain G-soil-2-3T was clearly distinguishable from P. assamensis, P. alvei and P. apiarius and thus represents a novel species of the genus Paenibacillus, for which the name Paenibacillus taiwanensis sp. nov. is proposed. The type strain is G-soil-2-3T (=BCRC 17411T=IAM 15414T=LMG 23799T=DSM 18679T).

scholarly journals Recurrent Bacteremia Caused by a “Flexispira”-Like Organism in a Patient with X-Linked (Bruton’s) Agammaglobulinemia

1999 ◽  
Vol 37 (8) ◽  
pp. 2439-2445 ◽  
Author(s):  
Susan Weir ◽  
Brenda Cuccherini ◽  
Anne M. Whitney ◽  
Marsha L. Ray ◽  
John P. MacGregor ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Gene Sequence ◽  
Optimal Growth ◽  
Rrna Gene ◽  
New Taxon ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Helicobacter spp., except for Helicobacter cinaedi, have only rarely been reported in cases of septicemia. A patient with X-linked (Bruton’s) agammaglobulinemia was found to have persistent sepsis with a Helicobacter-like organism despite multiple courses of antibiotics. His periods of sepsis were associated with leg swelling thought to be consistent with cellulitis. The organism was fastidious and required a microaerophilic environment containing H2 for growth. Optimal growth was observed at 35 to 37°C on sheep blood, CDC anaerobe, and Bordet-Gengou agars. Serial subcultures every 4 to 5 days were required to maintain viability. The organism was strongly urease positive and showed highest relatedness toHelicobacter-like organisms with the vernacular name “Flexispira rappini” by 16S rRNA gene sequence analysis. Genomic DNA hybridization studies, however, found 24 to 37% relatedness to “F. rappini” and even less to otherHelicobacter spp. Although the organism phenotypically resembles “Flexispira” and Helicobacter, it is thought to represent a new taxon. The patient’s infection was eventually cleared with a prolonged (5-month) course of intravenous imipenem and gentamicin.

scholarly journals Ancylobacter polymorphus sp. nov. and Ancylobacter vacuolatus sp. nov.

2006 ◽  
Vol 56 (6) ◽  
pp. 1185-1188 ◽  
Author(s):  
Yu Hua Xin ◽  
Yu Guang Zhou ◽  
Wen Xin Chen
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis

The taxonomic positions of ‘Renobacter vacuolatum’ DSM 1277 and ‘Ancylobacter polymorphus’ DSM 2457 were investigated in this study. 16S rRNA gene sequence analysis indicated that both strains belonged to the genus Ancylobacter. DNA–DNA hybridization showed that they differed from Ancylobacter aquaticus DSM 101T and Ancylobacter rudongensis AS 1.1761T. According to molecular and phenotypic characteristics, strain DSM 1277T (=AS 1.2807T) is proposed as the type strain of Ancylobacter vacuolatus sp. nov. At the same time, valid publication of the name Ancylobacter polymorphus sp. nov. is proposed, with the type strain DSM 2457T (=AS 1.2800T=NCIMB 10516T).

scholarly journals Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa

2006 ◽  
Vol 56 (4) ◽  
pp. 889-893 ◽  
Author(s):  
Cheng-Hui Xie ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Rrna Gene Sequence ◽  
Bacterial Strains

Three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. The nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifH gene detection. The three strains were found to be very closely related, with 99·9 % 16S rRNA gene sequence similarity and greater than 70 % DNA–DNA hybridization values, suggesting that the three strains represent a single species. 16S rRNA gene sequence analysis indicated that the strains were closely related to Sphingomonas trueperi, with 99·5 % similarity. The chemotaxonomic characteristics (G+C content of the DNA of 68·0 mol%, ubiquinone Q-10 system, 2-OH as the only hydroxy fatty acid and homospermidine as the sole polyamine) were similar to those of members of the genus Sphingomonas. Based on DNA–DNA hybridization values and physiological characteristics, the three novel strains could be differentiated from other recognized species of the genus Sphingomonas. The name Sphingomonas azotifigens sp. nov. is proposed to accommodate these bacterial strains; the type strain is Y39T (=NBRC 15497T=IAM 15283T=CCTCC AB205007T).

scholarly journals Novosphingobium soli sp. nov., isolated from soil

2011 ◽  
Vol 61 (2) ◽  
pp. 259-263 ◽  
Author(s):  
Peter Kämpfer ◽  
Chiu-Chung Young ◽  
Hans-Jürgen Busse ◽  
Shi-Yao Lin ◽  
P. D. Rekha ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium, strain CC-TPE-1T, was isolated from oil-contaminated soil near an oil refinery located in Kaohsiung County, Taiwan. 16S rRNA gene sequence analysis of strain CC-TPE-1T showed highest sequence similarity to Novosphingobium naphthalenivorans TUT562T (98.1 %), N. panipatense SM16T (97.9 %) and N. mathurense SM117T (97.6 %) and lower (<97 %) sequence similarity to all other Novosphingobium species. DNA–DNA hybridizations of strain CC-TPE-1T with N. naphthalenivorans DSM 18518T, N. panipatense SM16T and N. mathurense SM117T showed low relatedness of 30 % (reciprocal 35 %), 29.1 % (reciprocal 30.6 %) and 35 % (reciprocal 23.6 %), respectively. The major respiratory quinone was ubiquinone Q-10, the predominant fatty acid was C18 : 1 ω7c (49.9 %) and three 2-hydroxy fatty acids, C14 : 0 2-OH (8.2 %), C15 : 0 2-OH (2.45 %) and C16 : 0 2-OH (1.05 %), were detected. Polar lipids consisted mainly of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, two sphingoglycolipids, phosphatidylmonomethylethanolamine and several unidentified lipids, and a yellow pigment was also detected. The polyamine pattern contained the single major compound spermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis and polyamine, ubiquinone, polar lipid and fatty acid compositions revealed that strain CC-TPE-1T represents a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium soli sp. nov., with the type strain CC-TPE-1T (=DSM 22821T =CCM 7706T =CCUG 58493T).

scholarly journals Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group

2007 ◽  
Vol 57 (8) ◽  
pp. 1846-1850 ◽  
Author(s):  
Li-Ting Wang ◽  
Fwu-Ling Lee ◽  
Chun-Ju Tai ◽  
Hiroaki Kasai
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA–DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid sequence similarities among the eight type strains were 75.4–95.0 % and 88.5–99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1–99.8 %. Results showed that gyrB gene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved by gyrB sequence analysis was in agreement with results obtained with DNA–DNA hybridization. It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group.

scholarly journals Differentiation of Mycobacterium ulcerans, M. marinum, and M. haemophilum: Mapping of Their Relationships to M. tuberculosis by Fatty Acid Profile Analysis, DNA-DNA Hybridization, and 16S rRNA Gene Sequence Analysis

1998 ◽  
Vol 36 (4) ◽  
pp. 918-925 ◽  
Author(s):  
T. Tønjum ◽  
D. B. Welty ◽  
E. Jantzen ◽  
P. L. Small
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Mycobacterium Ulcerans ◽  
Rrna Gene ◽  
Mycobacterial Species ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Although Mycobacterium ulcerans, M. marinum, and M. haemophilum are closely related, their exact taxonomic placements have not been determined. We performed gas chromatography of fatty acids and alcohols, as well as DNA-DNA hybridization and 16S rRNA gene sequence analysis, to clarify their relationships to each other and to M. tuberculosis. M. ulcerans and M. marinum were most closely related to one another, and each displayed very strong genetic affinities toM. tuberculosis; they are actually the two mycobacterial species outside the M. tuberculosis complex most closely related to M. tuberculosis. M. haemophilum was more distinct from M. ulcerans and M. marinum, and it appeared to be as related to these two species as to M. tuberculosis. These results are important with regard to the development of diagnostic and epidemiological tools such as species-specific DNA probes and PCR assays for M. ulcerans,M. marinum, and M. haemophilum. In addition, the finding that M. ulcerans and M. marinum are more closely related to M. tuberculosis than are other pathogenic mycobacterial species suggests that they may be evaluated as useful models for studying the pathogenesis of M. tuberculosis. M. marinum may be particularly useful in this regard since strains of this species grow much more rapidly than M. tuberculosis and yet can cause systemic disease in immunocompromised hosts.

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