scholarly journals Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species

2004 ◽  
Vol 54 (4) ◽  
pp. 1165-1172 ◽  
Author(s):  
Jesús Caballero-Mellado ◽  
Lourdes Martínez-Aguilar ◽  
Guadalupe Paredes-Valdez ◽  
Paulina Estrada-de los Santos
Keyword(s):  
16S Rdna ◽  
Restriction Analysis ◽  
Cellular Fatty Acid ◽  
Cell Protein ◽  
Enzyme Electrophoresis ◽  
Protein Patterns ◽  
Ph Values ◽  
16S Rdna Sequence Analysis ◽  
Dna Reassociation ◽  
Dry Climates

It was shown recently that the genus Burkholderia is rich in N2-fixing bacteria that are associated with plants. A group of these diazotrophic isolates with identical or very similar 16S rDNA restriction patterns [designated amplified rDNA restriction analysis (ARDRA) genotypes 13, 14 and 15] was selected and a polyphasic taxonomic study was performed, which included new isolates that were recovered from rhizospheres, rhizoplanes or internal tissues of maize, sugarcane and coffee plants. Morphological, physiological and biochemical features, as well as multi-locus enzyme electrophoresis profiles and whole-cell protein patterns, of 20 strains were analysed. In addition, analysis of cellular fatty acid profiles, 16S rDNA sequence analysis and DNA–DNA reassociation experiments were performed with representative strains. The taxonomic data indicated that the strains analysed belong to a novel diazotrophic Burkholderia species, for which the name Burkholderia unamae sp. nov. is proposed. Strain MTl-641T (=ATCC BAA-744T=CIP 107921T), isolated from the rhizosphere of maize, was designated as the type strain. B. unamae was found as an endophyte of plants grown in regions with climates ranging from semi-hot subhumid to hot humid, but not from plants grown in regions with semi-hot or hot dry climates. Moreover, B. unamae was isolated from rhizospheres and plants growing in soils with pH values in the range 4·5–7·1, but not from soils with pH values higher than 7·5.

scholarly journals Molecular Typing of Borrelia burgdorferiSensu Lato: Taxonomic, Epidemiological, and Clinical Implications

1999 ◽  
Vol 12 (4) ◽  
pp. 633-653 ◽  
Author(s):  
Guiqing Wang ◽  
Alje P. van Dam ◽  
Ira Schwartz ◽  
Jacob Dankert
Keyword(s):  
Restriction Analysis ◽  
Clinical Manifestations ◽  
Taxonomic Status ◽  
Sensu Stricto ◽  
Borrelia Burgdorferi Sensu Lato ◽  
Clinical Implications ◽  
Rrna Gene ◽  
Enzyme Electrophoresis ◽  
Borrelia Lusitaniae ◽  
Dna Reassociation

SUMMARY Borrelia burgdorferi sensu lato, the spirochete that causes human Lyme borreliosis (LB), is a genetically and phenotypically divergent species. In the past several years, various molecular approaches have been developed and used to determine the phenotypic and genetic heterogeneity within the LB-related spirochetes and their potential association with distinct clinical syndromes. These methods include serotyping, multilocus enzyme electrophoresis, DNA-DNA reassociation analysis, rRNA gene restriction analysis (ribotyping), pulsed-field gel electrophoresis, plasmid fingerprinting, randomly amplified polymorphic DNA fingerprinting analysis, species-specific PCR and PCR-based restriction fragment length polymorphism (RFLP) analysis, and sequence analysis of 16S rRNA and other conserved genes. On the basis of DNA-DNA reassociation analysis, 10 different Borrelia species have been described within the B. burgdorferi sensu lato complex: B. burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii, Borrelia japonica, Borrelia andersonii, Borrelia valaisiana, Borrelia lusitaniae, Borrelia tanukii, Borrelia turdi, and Borrelia bissettii sp. nov. To date, only B. burgdorferi sensu stricto, B. garinii, and B. afzelii are well known to be responsible for causing human disease. Different Borrelia species have been associated with distinct clinical manifestations of LB. In addition, Borrelia species are differentially distributed worldwide and may be maintained through different transmission cycles in nature. In this paper, the molecular methods used for typing of B. burgdorferi sensu lato are reviewed. The current taxonomic status of B. burgdorferi sensu lato and its epidemiological and clinical implications, especiallly correlation between the variable clinical presentations and the infecting Borrelia species, are discussed in detail.

scholarly journals Paenibacillus cineris sp. nov. and Paenibacillus cookii sp. nov., from Antarctic volcanic soils and a gelatin-processing plant

2004 ◽  
Vol 54 (4) ◽  
pp. 1071-1076 ◽  
Author(s):  
Niall A. Logan ◽  
Elke De Clerck ◽  
Liesbeth Lebbe ◽  
An Verhelst ◽  
Johan Goris ◽  
...  
Keyword(s):  
16S Rdna ◽  
Restriction Analysis ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rdna Sequence ◽  
Processing Plant ◽  
Sequence Comparisons ◽  
16S Rdna Sequence ◽  
Dna Reassociation ◽  
Sds Page

Seven strains of aerobic, endospore-forming bacteria were found in soil taken from an active fumarole on Lucifer Hill, Candlemas Island, South Sandwich archipelago, Antarctica, and four strains were from soil of an inactive fumarole at the foot of the hill. Amplified rDNA restriction analysis, 16S rDNA sequence comparisons, SDS-PAGE and routine phenotypic tests support the proposal of two novel species of Paenibacillus, Paenibacillus cineris sp. nov. and Paenibacillus cookii sp. nov., the type strains of which are LMG 18439T (=CIP 108109T) and LMG 18419T (=CIP 108110T), respectively. A further strain, isolated from a gelatin-production process, showed more than 99 % 16S rDNA sequence similarity to the proposed P. cookii type strain and, although the gelatin isolate was atypical when compared with the fumarole isolates by repeated element primed-PCR, SDS-PAGE and phenotypic analyses, it was shown by DNA–DNA reassociation studies to belong to the same species. Strains of P. cookii produce spreading growth with motile microcolonies. Both species produce swollen sporangia that are typical for the genus, they both show 97·6 % 16S rDNA sequence similarity to Paenibacillus azoreducens, they have 51·5–51·6 mol% G+C in their DNA and their major fatty acid is anteiso-C15 : 0; however, fatty acids C16 : 0 and anteiso-C17 : 0 represent, respectively, 18 and 10 % of the total in P. cineris, but 11 and 20 % in P. cookii.

Validation of a partialrpoBgene sequence as a tool for phylogenetic identification of aeromonads isolated from environmental sources

2010 ◽  
Vol 56 (3) ◽  
pp. 217-228 ◽  
Author(s):  
Brigitte Lamy ◽  
Fréderic Laurent ◽  
Angeli Kodjo
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Restriction Analysis ◽  
Rpob Gene ◽  
Aeromonas Species ◽  
Species Identity ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis ◽  
Aeromonas Caviae ◽  
Phylogenetic Identification

A collection of 50 aeromonads isolated from environmental sources were studied, together with all known Aeromonas nomenspecies, by phenotypic, amplified 16S rDNA restriction analysis (16S rDNA RFLP) and by partial sequence alignment of both 16S rDNA and rpoB genes. Although most of the type strain showed a unique phenotypic pattern, a database constructed on type strain phenotype allowed the identification of only 24% of the isolates. Analysis of 16S rDNA RFLP and the rpoB sequence were almost concordant in identifying environmental isolates at the species level, except for strains belonging to Aeromonas caviae spp., which were not differentiated from Aeromonas aquariorum , nor Aeromonas hydrophila susbsp. dhakensis by 16S rDNA RFLP. In addition, rpoB gene analysis clustered separately a group of isolates found in snails within the A. hydrophila species. In contrast to 16S rDNA RFLP and rpoB, the partial 16S rDNA sequence analysis was weak in resolving species identity. Part of these results, phenotypic and phylogenetic data, showed that Aeromonas molluscorum and Aeromonas sharmana are distant from all other Aeromonas species and that the type species of A. hydrophila subsp. anaerogenes is similar to A. caviae and should be considered synonymous.

scholarly journals Characterization of Leuconostoc gasicomitatum sp. nov., Associated with Spoiled Raw Tomato-Marinated Broiler Meat Strips Packaged under Modified-Atmosphere Conditions

2000 ◽  
Vol 66 (9) ◽  
pp. 3764-3772 ◽  
Author(s):  
K. Johanna Bj�rkroth ◽  
Rolf Geisen ◽  
Ulrich Schillinger ◽  
Norbert Weiss ◽  
Paul De Vos ◽  
...  
Keyword(s):  
16S Rdna ◽  
Sequence Homology ◽  
Type Strain ◽  
Rdna Sequence ◽  
Cell Protein ◽  
Modified Atmosphere ◽  
Broiler Meat ◽  
16S Rdna Sequence ◽  
Dna Reassociation ◽  
Whole Cell Protein

ABSTRACT Lactic acid bacteria (LAB) associated with gaseous spoilage of modified-atmosphere-packaged, raw, tomato-marinated broiler meat strips were identified on the basis of a restriction fragment length polymorphism (RFLP) (ribotyping) database containing DNAs coding for 16S and 23S rRNAs (rDNAs). A mixed LAB population dominated by aLeuconostoc species resembling Leuconostoc gelidum caused the spoilage of the product. Lactobacillus sakei, Lactobacillus curvatus, and a gram-positive rod phenotypically similar to heterofermentativeLactobacillus species were the other main organisms detected. An increase in pH together with the extreme bulging of packages suggested a rare LAB spoilage type called “protein swell.” This spoilage is characterized by excessive production of gas due to amino acid decarboxylation, and the rise in pH is attributed to the subsequent deamination of amino acids. Protein swell has not previously been associated with any kind of meat product. A polyphasic approach, including classical phenotyping, whole-cell protein electrophoresis, 16 and 23S rDNA RFLP, 16S rDNA sequence analysis, and DNA-DNA reassociation analysis, was used for the identification of the dominantLeuconostoc species. In addition to the RFLP analysis, phenotyping, whole-cell protein analysis, and 16S rDNA sequence homology indicated that L. gelidum was most similar to the spoilage-associated species. The two spoilage strains studied possessed 98.8 and 99.0% 16S rDNA sequence homology with the L. gelidum type strain. DNA-DNA reassociation, however, clearly distinguished the two species. The same strains showed only 22 and 34% hybridization with the L. gelidum type strain. These results warrant a separate species status, and we propose the nameLeuconostoc gasicomitatum sp. nov. for this spoilage-associated Leuconostoc species.

scholarly journals Bacillus odysseyi sp. nov., a round-spore-forming bacillus isolated from the Mars Odyssey spacecraft

2004 ◽  
Vol 54 (1) ◽  
pp. 195-201 ◽  
Author(s):  
Myron T. La Duc ◽  
Masataka Satomi ◽  
Kasthuri Venkateswaran
Keyword(s):  
Gamma Radiation ◽  
16S Rdna ◽  
Novel Species ◽  
Rdna Sequence ◽  
Phenotypic Traits ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis ◽  
Novel Bacterium ◽  
Dna Reassociation ◽  
Mars Odyssey

A round-spore-forming Bacillus species that produces an exosporium was isolated from the surface of the Mars Odyssey spacecraft. This novel species has been characterized on the basis of phenotypic traits, 16S rDNA sequence analysis and DNA–DNA hybridization. According to the results of these analyses, this strain belongs to the genus Bacillus and is a Gram-positive, aerobic, rod-shaped, endospore-forming eubacterium. Ultrathin sections of the spores showed the presence of an exosporium, spore coat, cortex and core. 16S rDNA sequence similarities between this strain, Bacillus fusiformis and Bacillus silvestris were ∼96 % and DNA–DNA reassociation values with these two bacilli were 23 and 17 %, respectively. Spores of the novel species were resistant to desiccation, H2O2 and UV and gamma radiation. Of all strains tested, the spores of this strain were the most consistently resistant and survived all of the challenges posed, i.e. exposure to conditions of desiccation (100 % survival), H2O2 (26 % survival), UV radiation (10 % survival at 660 J m−2) and gamma radiation (0·4 % survival). The name proposed for this novel bacterium is Bacillus odysseyi sp. nov.; the type strain is 34hs-1T (=ATCC PTA-4993T=NRRL B-30641T=NBRC 100172T).

scholarly journals Erratum to: Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis

2014 ◽  
Vol 52 (12) ◽  
pp. 1056-1056
Author(s):  
Ok-Hwa Hwang ◽  
Sebastian Raveendar ◽  
Young-Ju Kim ◽  
Ji-Hun Kim ◽  
Tae-Hun Kim ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Bacterial Diversity ◽  
16S Rdna ◽  
Rdna Sequence ◽  
Pig Slurry ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis

scholarly journals Bakteri Simbion Gastropoda Pleuroploca trapesium Dari Perairan Ternate, Sebagai Alternatif Antibakteri MDR (Bacterial Symbiont Gastropoda Pleuroploca trapezium from Ternate, as Alternative Antibacterial MDR)

2014 ◽  
Vol 19 (1) ◽  
pp. 55
Author(s):  
Delianis Pringgenies ◽  
Person Pesona Renta
Keyword(s):  
16S Rdna ◽  
Pathogenic Bacteria ◽  
Dna Amplification ◽  
Sensitivity Test ◽  
Symbiotic Bacteria ◽  
Drug Resistant ◽  
16S Rdna Sequence Analysis ◽  
Close Relationship ◽  
Antibiotic Compounds ◽  
Bacterial Sensitivity

Bakteri yang resisten terhadap beberapa jenis antibakteri ini dikenal dengan bakteri multi drug resistant (MDR).Untuk mengatasi permasalahan tersebut, perlu dilakukan pencarian senyawa antibiotik baru yang lebih efektif dan efisien dalam mengatasi permasalahan bakteri MDR. Penelitian bertujuan untuk mengetahui potensi bakteri yang bersimbiosis dengan gastropoda Pleuroploca trapezium sebagai sumber antibakteri MDR. Sampel Moluska dikoleksi dari perairan Ternate, Maluku. Tahapan penelitian meliputi isolasi bakteri, skrining  bakteri simbion yang potensi sebagai anti bakteri MDR, uji antibakteri, isolasi bakteri patogen klinis MDR; uji sensitivitas anti-bakteri, ekstraksi, amplifikasi dan sekuensing DNA. Hasil 16S urutan r-DNA dianalisis dan diedit menggunakan program Genetix dan diikuti dengan analisis urutan 16S rDNA. Hasil menunjukkan bahwa terdapat 19 isolat bakteri dengan 5 bakteri aktif yang berasosiasi dengan Pleuroploca trapezium. Berdasarkan besarnya zona hambat yang dibentuk dan konsistensi munculnya zona hambatan, isolat terbaik adalah TPT 4.7. Isolat ini memiliki hubungan yang dekat dengan Paracoccus  sp. MBIC4019 dengan homologi sebesar 95% yang menunjukkan kekerabatan ditingkat genus. Hasil penelitian ini memberikan harapan adanya potensi besar sebagai bahan antibakteri baru. Kata kunci: antibakteri, simbion, Pleuroploca trapezium, multi drugs resistantThe bacteria resistant to some antibiotics are known as multi drug resistant (MDR). To overcome the problem, it is needed to search for a new antibiotic compounds more effectively and efficiently. This study aims to identify potential from symbionts of Pleuroploca trapezium as a source of antibacteria MDR and identifying the bacteria that were active against the MDR. Samples were collected from Ternate, Maluku. Isolation of symbiotic bacteria, screening for bacteria which producing secondary metabolites as anti-MDR bacteria, antibacterial test, isolation of clinical pathogenic bacteria of MDR. Conducting anti-bacterial sensitivity test,  sensitivity test for antibacterial,  DNA exctraction, DNA amplification based on PCR method, DNA sequencing.  Result of 16S r-DNA sequence was then analyzed and edited using GENETYX program and followed by 16S rDNA sequence analysis. Screening of bacteria associated with P. trapezium resulted in 19 isolates with 5 active bacteria. Based on the size of the zone forming and the consistency of zone, so the best isolate is TPT 4.7. The identification shows that TPT 4.7 has a close relationship with the Paracoccus sp. MBIC4019 with homologi of 95%, which shows the relationship at the genus level. Its suggest that these results are very promising as a new antibacterial material. Keywords: antibacterial, symbiotic bacteria, Pleuroploca trapezium, multi drugs resistant

scholarly journals Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts

2007 ◽  
Vol 57 (12) ◽  
pp. 2908-2911 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Seon-Young Lee ◽  
Byung-Yong Kim ◽  
Hyung-Jun Noh ◽  
Peter Schumann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Phylogenetic Affiliation ◽  
Dna Reassociation ◽  
Compost Facility

Two Gram-negative, rod-shaped, thermophilic bacterial strains, HC145T and HC148T, were isolated from a compost sample from a compost facility in Ichon, Korea. Sequencing of the 16S rRNA genes of HC145T and HC148T and comparative analyses of the resulting sequences clearly showed that these strains had a phylogenetic affiliation to the genus Ureibacillus. The level of 16S rRNA similarity between the two novel strains was 98.4 % and the levels of sequence similarity between them and existing Ureibacillus species were 97.8–98.1 (HC145T) and 97.4–98.7 % (HC148T). The DNA–DNA reassociation values between the two strains and the type strains of Ureibacillus species ranged from 38 to 51 %. The polar lipid profiles for both isolates consisted of phosphatidylglycerol, diphosphatidylglycerol, phospholipids and glycolipids of unknown composition. The major quinones were MK-8, MK-9 and MK-7, the peptidoglycan type was l-Lys←d-Asp and the main cellular fatty acid was iso-C16 : 0. The DNA G+C contents of strains HC145T and HC148T were 42.4 and 38.5 mol%, respectively. On the basis of the data from this polyphasic study, strains HC145T and HC148T represent members of the genus Ureibacillus, for which the names Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., respectively, are proposed. The type strain of U. composti is HC145T (=KACC 11361T =DSM 17951T) and the type strain of U. thermophilus is HC148T (=KACC 11362T =DSM 17952T).

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