scholarly journals Evaluation of recA Sequences for Identification of Mycobacterium Species

2000 ◽  
Vol 38 (8) ◽  
pp. 2846-2852 ◽  
Author(s):  
Kym S. Blackwood ◽  
Cheng He ◽  
James Gunton ◽  
Christine Y. Turenne ◽  
Joyce Wolfe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
Genetic Identification ◽  
Rrna Gene ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Accurate Identification

16S rRNA sequence data have been used to provide a molecular basis for an accurate system for identification of members of the genusMycobacterium. Previous studies have shown thatMycobacterium species demonstrate high levels (>94%) of 16S rRNA sequence similarity and that this method cannot differentiate between all species, i.e., M. gastri and M. kansasii. In the present study, we have used the recAgene as an alternative sequencing target in order to complement 16S rRNA sequence-based genetic identification. The recA genes of 30 Mycobacterium species were amplified by PCR, sequenced, and compared with the published recA sequences of M. tuberculosis, M. smegmatis, and M. leprae available from GenBank. By recA sequencing the species showed a lower degree of interspecies similarity than they did by 16S rRNA gene sequence analysis, ranging from 96.2% betweenM. gastri and M. kansasii to 75.7% betweenM. aurum and M. leprae. Exceptions to this were members of the M. tuberculosis complex, which were identical. Two strains of each of 27 species were tested, and the intraspecies similarity ranged from 98.7 to 100%. In addition, we identified new Mycobacterium species that contain a protein intron in their recA genes, similar to M. tuberculosis and M. leprae. We propose thatrecA gene sequencing offers a complementary method to 16S rRNA gene sequencing for the accurate identification of theMycobacterium species.

scholarly journals Fibrisoma limi gen. nov., sp. nov., a filamentous bacterium isolated from tidal flats

2011 ◽  
Vol 61 (6) ◽  
pp. 1418-1424 ◽  
Author(s):  
Manuela Filippini ◽  
Andres Kaech ◽  
Urs Ziegler ◽  
Homayoun C. Bagheri
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The North ◽  
Gram Staining

An orange-pigmented, Gram-staining-negative, non-motile, filament-forming, rod-shaped bacterium (BUZ 3T) was isolated from a coastal mud sample from the North Sea (Fedderwardersiel, Germany) and characterized taxonomically using a polyphasic approach. According to 16S rRNA gene sequence data, it belonged to the family Cytophagaceae, exhibiting low 16S rRNA gene sequence similarity (<90 %) with members of the genera Spirosoma, Rudanella and Fibrella. The DNA G+C content was 52.0 mol%. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 1ω5c and iso-C17 : 0 3-OH. The major polar lipids consisted of phosphatidylethanolamine and several aminolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is proposed that strain BUZ 3T represents a novel genus and species, for which the name Fibrisoma limi gen. nov., sp. nov. is proposed. The type strain is BUZ 3T ( = DSM 22564T  = CCUG 58137T).

scholarly journals “Candidatus Thiobios zoothamnicoli,” an Ectosymbiotic Bacterium Covering the Giant Marine Ciliate Zoothamnium niveum

2006 ◽  
Vol 72 (3) ◽  
pp. 2014-2021 ◽  
Author(s):  
Christian Rinke ◽  
Stephan Schmitz-Esser ◽  
Kilian Stoecker ◽  
Andrea D. Nussbaumer ◽  
Dávid A. Molnár ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
23S Rrna ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Marine Ciliate ◽  
16S Rrna Sequence ◽  
Intergenic Spacer Region

ABSTRACT Zoothamnium niveum is a giant, colonial marine ciliate from sulfide-rich habitats obligatorily covered with chemoautotrophic, sulfide-oxidizing bacteria which appear as coccoid rods and rods with a series of intermediate shapes. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization showed that the ectosymbiont of Z. niveum belongs to only one pleomorphic phylotype. The Z. niveum ectosymbiont is only moderately related to previously identified groups of thiotrophic symbionts within the Gammaproteobacteria, and shows highest 16S rRNA sequence similarity with the free-living sulfur-oxidizing bacterial strain ODIII6 from shallow-water hydrothermal vents of the Mediterranean Sea (94.5%) and an endosymbiont from a deep-sea hydrothermal vent gastropod of the Indian Ocean Ridge (93.1%). A replacement of this specific ectosymbiont by a variety of other bacteria was observed only for senescent basal parts of the host colonies. The taxonomic status “Candidatus Thiobios zoothamnicoli” is proposed for the ectosymbiont of Z. niveum based on its ultrastructure, its 16S rRNA gene, the intergenic spacer region, and its partial 23S rRNA gene sequence.

scholarly journals Alkalimicrobium pacificum gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2453-2458 ◽  
Author(s):  
Gaiyun Zhang ◽  
Yanliu Yang ◽  
Shuang Wang ◽  
Zhilei Sun ◽  
Kailin Jiao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Unidentified Phospholipid ◽  
The Family

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated strain F15T, was isolated from a deep-sea sediment of the western Pacific Ocean. The temperature, pH and NaCl ranges for growth were 4–50 °C, pH 6–11 and 0–10 % (w/v), respectively. Strain F15T showed the highest 16S rRNA gene sequence similarity to Sagittula stellata E-37T (96.4 %), followed by Ponticoccus litoralis CL-GR66T (96.4 %), Antarctobacter heliothermus EL-219T (96.3 %) and Thalassococcus lentus YCS-24T (96.0 %). Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain F15T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria. The polar lipid profile of strain F15T comprised significant amounts of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified phospholipid. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 40.2 %), anteiso-C15 : 0 (30.4 %) and anteiso-C17 : 0 (9.7 %). The genomic DNA G+C content of strain F15T was 60.2 mol% and the major respiratory quinone was Q-10. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain F15T is considered to represent a novel species of a new genus within the family Rhodobacteraceae, for which the name Alkalimicrobium pacificum gen. nov., sp. nov. is proposed. The type strain is F15T ( = LMG 28107T = JCM 19851T = CGMCC 1.12763T = MCCC 1A09948T).

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 Planosporangium mesophilum sp. nov., isolated from rhizosphere soil of Bletilla striata

2011 ◽  
Vol 61 (6) ◽  
pp. 1330-1333 ◽  
Author(s):  
Yan-Ru Cao ◽  
Qian Wang ◽  
Rong-Xian Jin ◽  
Yi Jiang ◽  
Hang-Xian Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bletilla Striata

A Gram-stain-positive, non-motile actinomycete, designated strain YIM 48875T, was isolated from rhizosphere soil of Bletilla striata and its taxonomic position was established by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 48875T belonged to the genus Planosporangium, supported by a bootstrap value of 100 %. Cells of strain YIM 48875T showed two kinds of sporangia, which also supported its classification in the genus Planosporangium. Strain YIM 48875T grew optimally at 28 °C, at pH 6.0–8.0 and in the presence of 2 % (w/v) NaCl. The level of 16S rRNA gene sequence similarity between strain YIM 48875T and Planosporangium flavigriseum YIM 46034T was 98.6 %. Strain YIM 48875T exhibited a quinone system with menaquinones MK-9(H4), MK-9(H6) and MK-9(H8) as the predominant compounds, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol mannoside and the major fatty acids iso-C15 : 0 and iso-C16 : 0; these data were markedly different from those for P. flavigriseum YIM 46034T. The level of DNA–DNA relatedness between strain YIM 48875T and P. flavigriseum YIM 46034T was 45.5 %. It is apparent from the genotypic and phenotypic data that strain YIM 48875T represents a novel species of the genus Planosporangium, for which the name Planosporangium mesophilum sp. nov. is proposed. The type strain is YIM 48875T ( = CCTCC AA 209049T  = KCTC 19779T).

scholarly journals Reclassification of Lactobacillus ferintoshensis as a later heterotypic synonym of Lactobacillus parabuchneri

2005 ◽  
Vol 55 (5) ◽  
pp. 2195-2198 ◽  
Author(s):  
Marc Vancanneyt ◽  
Katrien Engelbeen ◽  
Marjan De Wachter ◽  
Katrien Vandemeulebroecke ◽  
Ilse Cleenwerck ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Lactobacillus Kefiri

Lactobacillus ferintoshensis has recently been described as a novel species, distinct from its close phylogenetic neighbours Lactobacillus buchneri, Lactobacillus kefiri and Lactobacillus hilgardii. Two highly related species with validly published names, Lactobacillus parakefiri and Lactobacillus parabuchneri, were not considered in the study due to the lack of 16S rRNA gene sequence data at that time. Since the publication of the study, the sequences have become available and have revealed that L. ferintoshensis and L. parabuchneri share 99·7 % 16S rRNA gene sequence similarity. Further genomic and phenotypic data, derived from fluorescent amplified fragment length polymorphism, DNA–DNA hybridization and API 50 CHL analyses, have demonstrated that the species are synonymous.

scholarly journals Phaeodactylibacter luteus sp. nov., isolated from the oleaginous microalga Picochlorum sp.

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2666-2670 ◽  
Author(s):  
Xueqian Lei ◽  
Yi Li ◽  
Guanghua Wang ◽  
Yao Chen ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Biodiesel Production ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Respiratory Quinone ◽  
Gram Staining ◽  
Rrna Gene Sequencing

A Gram-staining-negative, orange-pigmented, non-motile, aerobic bacterial strain, designated GYP20T, was isolated from a culture of the alga Picochlorum sp., a promising feedstock for biodiesel production, which was isolated from the India Ocean. Growth was observed at temperatures from 20 to 37 °C, salinities from 0 to 3  % and pH from 5 to 9.Mg 2+ and Ca2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain was a member of the genus Phaeodactylibacter, which belongs to the family Saprospiraceae. Strain GYP20T was most closely related to Phaeodactylibacter xiamenensis KD52T (95.5  % sequence similarity). The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3. The predominant respiratory quinone was menaquinone-7 (MK-7). The polar lipids of strain GYP20T were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified glycolipids, two unidentified phospholipids and three unidentified aminolipids. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence data, the novel strain most appropriately belongs to the genus Phaeodactylibacter, but can readily be distinguished from Phaeodactylibacter xiamenensis GYP20T. The name Phaeodactylibacter luteus sp. nov. is proposed with the type strain GYP20T ( = MCCC 1F01222T = KCTC 42180T).

scholarly journals Morphological and Phylogenetic Characterizations of Freshwater Thioploca Species from Lake Biwa, Japan, and Lake Constance, Germany

2003 ◽  
Vol 69 (1) ◽  
pp. 390-398 ◽  
Author(s):  
Hisaya Kojima ◽  
Andreas Teske ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Lake Biwa ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Uranyl Acetate ◽  
Lake Constance ◽  
Rrna Gene ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Gradient Gel Electrophoresis

ABSTRACT Filamentous, gliding, sulfide-oxidizing bacteria of the genus Thioploca were found on sediments in profundal areas of Lake Biwa, a Japanese freshwater mesotrophic lake, and were characterized morphologically and phylogenetically. The Lake Biwa Thioploca resembled morphologically Thioploca ingrica, a brackish water species from a Danish fjord. The diameters of individual trichomes were 3 to 5.6 μm; the diameters of complete Thioploca filaments ranged from 18 to 75 μm. The cell lengths ranged from 1.2 to 3.8 μm. In transmission electron microscope specimens stained with uranyl acetate, dense intracellular particles were found, which did not show any positive signals for phosphorus and sulfur in an X-ray analysis. The 16S rRNA gene of the Thioploca from Lake Biwa was amplified by using newly designed Thioploca-specific primers (706-Thioploca, Biwa160F, and Biwa829R) in combination with general bacterial primers in order to avoid nonspecific amplification of contaminating bacterial DNA. Denaturing gradient gel electrophoresis (DGGE) analysis of the three overlapping PCR products resulted in single DGGE bands, indicating that a single 16S rRNA gene had been amplified. With the same method, the Thioploca from Lake Constance was examined. The 16S rRNA sequence was verified by performing fluorescence in situ hybridization targeted at specific motifs of the Lake Biwa Thioploca. Positive signals were obtained with the bacterial probe EUB-338, the γ-proteobacterial probe GAM42a, and probe Biwa829 targeting the Lake Biwa Thioploca. Based on the nearly complete 16S rRNA sequence and on morphological similarities, the Thioploca from Lake Biwa and the Thioploca from Lake Constance are closely related to T. ingrica and to each other.

scholarly journals Roseomonas aquatica sp. nov., isolated from drinking water

2006 ◽  
Vol 56 (10) ◽  
pp. 2291-2295 ◽  
Author(s):  
Virginia Gallego ◽  
Cristina Sánchez-Porro ◽  
Maria Teresa García ◽  
Antonio Ventosa
Keyword(s):  
Drinking Water ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Distribution System ◽  
Water Distribution ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Drinking Water Distribution

Strain TR53T, a Gram-negative, non-motile, non-spore-forming and strictly aerobic coccobacillus, isolated from the drinking water distribution system of Seville, Spain, was subjected to polyphasic taxonomic analysis using a combination of phenotypic, genotypic and phylogenetic features. Phylogenetic analysis of 16S rRNA gene sequences showed that strain TR53T had highest similarity to members of the genus Roseomonas, with sequence similarity values between 95.7 % (to Roseomonas genomospecies 5 strain ATCC 49960) and 94.0 % (to Roseomonas gilardii subsp. rosea ATCC 49956T). On the basis of its phenotypic characteristics, 16S rRNA gene sequence data and DNA G+C content (68.6 mol%), strain TR53T represents a novel species of the genus Roseomonas, for which the name Roseomonas aquatica sp. nov. is proposed. The type strain of Roseomonas aquatica is TR53T (=CECT 7131T=JCM 13556T).

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