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Ken-ichiro Suzuki - One of the best experts on this subject based on the ideXlab platform.
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Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Koji Mori, Atsushi Yamazoe, Akira Hosoyama, Shoko Ohji, Nobuyuki Fujita, Jun-ichiro Ishibashi, Hiroyuki Kimura, Ken-ichiro SuzukiAbstract:Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06T and AZM44c09T, were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06T were 60 °C, pH 7.4 and 0 % additional NaCl, and those for strain AZM44c09T were 70 °C, pH 7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06T) and 2.01 Mbp (AZM44c09T). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga . The closest relatives of strains AZM34c06T and AZM44c09T were the type strains of Thermotoga lettingae (96.0 % similarity based on the 16S rRNA gene and 84.1 % similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7 % similarity), respectively. Using blast, the average nucleotide identity was 70.4–70.5 % when comparing strain AZM34c06T and T. lettingae TMOT and 76.6 % when comparing strain AZM44c09T and T. hypogea NBRC 106472T. Both values are far below the 95 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06T = NBRC 106115T = DSM 23275T) and Thermotoga caldifontis sp. nov. (type strain AZM44c09T = NBRC 106116T = DSM 23272T).
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Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs.
International journal of systematic and evolutionary microbiology, 2014Co-Authors: Koji Mori, Atsushi Yamazoe, Akira Hosoyama, Shoko Ohji, Nobuyuki Fujita, Jun-ichiro Ishibashi, Hiroyuki Kimura, Ken-ichiro SuzukiAbstract:Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06(T) and AZM44c09(T), were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06(T) were 60 °C, pH 7.4 and 0% additional NaCl, and those for strain AZM44c09(T) were 70 °C, pH 7.4 and 0% additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06(T)) and 2.01 Mbp (AZM44c09(T)). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga. The closest relatives of strains AZM34c06(T) and AZM44c09(T) were the type strains of Thermotoga lettingae (96.0% similarity based on the 16S rRNA gene and 84.1% similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7% similarity), respectively. Using blast, the average nucleotide identity was 70.4-70.5% when comparing strain AZM34c06(T) and T. lettingae TMO(T) and 76.6% when comparing strain AZM44c09(T) and T. hypogea NBRC 106472(T). Both values are far below the 95% threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06(T) = NBRC 106115(T) = DSM 23275(T)) and Thermotoga caldifontis sp. nov. (type strain AZM44c09(T) = NBRC 106116(T) = DSM 23272(T)).
Koji Mori - One of the best experts on this subject based on the ideXlab platform.
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Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Koji Mori, Atsushi Yamazoe, Akira Hosoyama, Shoko Ohji, Nobuyuki Fujita, Jun-ichiro Ishibashi, Hiroyuki Kimura, Ken-ichiro SuzukiAbstract:Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06T and AZM44c09T, were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06T were 60 °C, pH 7.4 and 0 % additional NaCl, and those for strain AZM44c09T were 70 °C, pH 7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06T) and 2.01 Mbp (AZM44c09T). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga . The closest relatives of strains AZM34c06T and AZM44c09T were the type strains of Thermotoga lettingae (96.0 % similarity based on the 16S rRNA gene and 84.1 % similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7 % similarity), respectively. Using blast, the average nucleotide identity was 70.4–70.5 % when comparing strain AZM34c06T and T. lettingae TMOT and 76.6 % when comparing strain AZM44c09T and T. hypogea NBRC 106472T. Both values are far below the 95 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06T = NBRC 106115T = DSM 23275T) and Thermotoga caldifontis sp. nov. (type strain AZM44c09T = NBRC 106116T = DSM 23272T).
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Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs.
International journal of systematic and evolutionary microbiology, 2014Co-Authors: Koji Mori, Atsushi Yamazoe, Akira Hosoyama, Shoko Ohji, Nobuyuki Fujita, Jun-ichiro Ishibashi, Hiroyuki Kimura, Ken-ichiro SuzukiAbstract:Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06(T) and AZM44c09(T), were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06(T) were 60 °C, pH 7.4 and 0% additional NaCl, and those for strain AZM44c09(T) were 70 °C, pH 7.4 and 0% additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06(T)) and 2.01 Mbp (AZM44c09(T)). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga. The closest relatives of strains AZM34c06(T) and AZM44c09(T) were the type strains of Thermotoga lettingae (96.0% similarity based on the 16S rRNA gene and 84.1% similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7% similarity), respectively. Using blast, the average nucleotide identity was 70.4-70.5% when comparing strain AZM34c06(T) and T. lettingae TMO(T) and 76.6% when comparing strain AZM44c09(T) and T. hypogea NBRC 106472(T). Both values are far below the 95% threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06(T) = NBRC 106115(T) = DSM 23275(T)) and Thermotoga caldifontis sp. nov. (type strain AZM44c09(T) = NBRC 106116(T) = DSM 23272(T)).
Piero Cammarano - One of the best experts on this subject based on the ideXlab platform.
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Manipulation of the tuf gene provides clues to the localization of sequence element(s) involved in the thermal stability of Thermotoga maritima elongation factor Tu
Microbiology, 1996Co-Authors: Anna M. Sanangelantoni, Piero Cammarano, Orsola TiboniAbstract:Truncated versions of the tuf gene for elongation factor Tu (EF-Tu; 400 aa) from the hyperthermophilic bacterium Thermotoga maritima have been produced by progressive 3′→5′ trimming. The truncated genes have been expressed in Escherichia coli and the thermal stability of the gene products has been assayed by monitoring their GDP-binding capacity after preheating the cell-free extracts at various temperatures (65-95 0C). One of the truncated proteins, corresponding to the nucleotide-binding domain (G domain aa 1-200) appears to be only slightly less stable than the full-length EF-Tu. Replacement of the first 90 N-terminal residues of both the full-length Thermotoga EF-Tu and the isolated G domain with the corresponding sequence of the mesophilic bacterium E. coli, drastically destabilizes both the complete and the truncated protein, indicating that sequence element(s) that are crucial for the attainment of a thermally stable conformation of the Thermotoga EF-Tu lie well within the initial portion of the G domain between residues 1 and 90. The relevant residues defy identification, however, as no amino acid preferences, or exclusive sequence element(s), appear to distinguish the N-terminal region of the thermophilic proteins from those of mesophilic counterparts. It is suggested that the thermal stability of Thermotoga EF-Tu is critically dependent upon unique tertiary structural interactions involving certain N-terminal residues of the molecule.
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Sensitivity of ribosomes of the hyperthermophilic bacterium Aquifex pyrophilus to aminoglycoside antibiotics.
Journal of bacteriology, 1996Co-Authors: M Bocchetta, R Huber, Piero CammaranoAbstract:A poly(U)-programmed cell-free system from the hyperthermophilic bacterium Aquifex pyrophilus has been developed, and the susceptibility of Aquifex ribosomes to the miscoding-inducing and inhibitory actions of all known classes of aminoglycoside antibiotics has been assayed at temperatures (75 to 80 degrees C) close to the physiological optimum for cell growth. Unlike Thermotoga maritima ribosomes, which are systematically refractory to all known classes of aminoglycoside compounds (P. Londei, S. Altamura, R. Huber, K. O. Stetter, and P. Cammarano, J. offteriol. 170-4353-4360, 1988), Aquifex ribosomes are susceptible to all of the aminoglycosides tested (disubstituted 2-deoxystreptamines, monosubstituted 2-deoxystreptamines, sand streptidine compounds). The significance of this result in light of the Aquifex and Thermotoga placements in phylogenetic trees of molecular sequences is discussed.
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Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: Phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences
Journal of molecular evolution, 1995Co-Authors: M Bocchetta, Orsola Tiboni, Anna M. Sanangelantoni, Elena Ceccarelli, Roberta Creti, Piero CammaranoAbstract:The gene fus (for EF-G) of the hyperthermophilic bacterium Aquifex pyrophilus was cloned and sequenced. Unlike the other bacteria, which display the streptomycin-operon arrangement of EF genes (5′-rps12-rps7 fus-tuf-3′), the Aquifex fus gene (700 codons) is not preceded by the two small ribosomal subunit genes although it is still followed by a tuf gene (for EF-Tu). The opposite strand upstream from the EF-G coding locus revealed an open reading frame (ORF) encoding a polypeptide having 52.5% identity with an E. coli protein (the pdxJ gene product) involved in pyridoxine condensation. The Aquifex EF-G was aligned with available homologs representative of Deinococci, high G + C Gram positives, Proteobacteria, cyanobacteria, and several Archaea. Outgroup-rooted phylogenies were constructed from both the amino acid and the DNA sequences using first and second codon positions in the alignments except sites containing synonymous changes. Both datasets and alternative tree-making methods gave a consistent topology, with Aquifex and Thermotoga maritima (a hyperthermophile) as the first and the second deepest offshoots, respectively. However, the robustness of the inferred phylogenies is not impressive. The branching of Aquifex more deeply than Thennotoga and the branching of Thermotoga more deeply than the other taxa examined are given at bootstrap values between 65 and 70% in the fus-based phylogenies, while the EF-G(2)-based phylogenies do not provide a statistically significant level of support (⩽ 50% bootstrap confirmation) for the emergence of Thermotoga between Aquifex and the successive offshoot (Thermus genus). At present, therefore, the placement of Aquifex at the root of the bacterial tree, albeit reproducible, can be asserted only with reservation, while the emergence of Thermotoga between the Aquificales and the Deinococci remains (statistically) indeterminate.
Bernard Ollivier - One of the best experts on this subject based on the ideXlab platform.
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A novel Thermotoga strain TFO isolated from a Californian petroleum reservoir phylogenetically related to Thermotoga petrophila and T. naphthophila, two thermophilic anaerobic isolates from a Japanese reservoir: Taxonomic and genomic considerations
Systematic and Applied Microbiology, 2020Co-Authors: Zara Summers, Bernard Ollivier, Alain Dolla, Hassiba Belahbib, Christian Tamburini, Nathalie Pradel, Manon Bartoli, Pooja Mishra, Fabrice ArmougomAbstract:A novel Thermotoga strain TFO isolated from a Californian petroleum reservoir 1 phylogenetically related to Thermotoga petrophila and T. naphthophila, two 2 thermophilic anaerobic isolates from a Japanese reservoir: taxonomic and genomic 3 considerations 4 5
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Towards a congruent reclassification and nomenclature of the thermophilic species of the genus PseudoThermotoga within the order Thermotogales
Systematic and Applied Microbiology, 2018Co-Authors: Hassiba Belahbib, Bernard Ollivier, Alain Dolla, Marielaure Fardeau, Zarath Summers, Manon Joseph, Christian Tamburini, Fabrice ArmougomAbstract:The phylum Thermotogae gathers thermophilic, hyperthermophic, mesophilic, and thermo-acidophilic anaerobic bacteria that are mostly originated from geothermally heated environments. The metabolic and phenotypic properties harbored by the Thermotogae species questions the evolutionary events driving the emergence of this early branch of the universal tree of life. Recent reshaping of the Thermotogae taxonomy has led to the description of a new genus, PseudoThermotoga, a sister group of the genus Thermotoga within the order Thermotogales. Comparative genomics of both PseudoThermotoga and Ther-motoga spp., including 16S-rRNA-based phylogenetic, pan-genomic analysis as well as signature indel conservation, provided evidence that Thermotoga caldifontis and Thermotoga profunda species should be reclassified within the genus PseudoThermotoga and renamed as PseudoThermotoga caldifontis comb. nov. (type strain = AZM44c09 T) and PseudoThermotoga profunda comb. nov. (type strain = AZM34c06 T), respectively. In addition, based upon whole-genome relatedness indices and DNA-DNA Hybridization results, the reclassification of PseudoThermotoga lettingae and PseudoThermotoga subterranea as latter heterotypic synonyms of PseudoThermotoga elfii is proposed. Finally, potential genetic elements resulting from the distinct evolutionary story of the Thermotoga and PseudoThermotoga clades are discussed.
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Thermotoga hypogea sp nov a xylanolytic thermophilic bacterium from an oil producing well
International Journal of Systematic and Evolutionary Microbiology, 1997Co-Authors: Marielaure Fardeau, Bernard Ollivier, Michel Magot, Bharat K C Patel, Pierre Thomas, A Rimbault, F Rocchiccioli, Jeanlouis GarciaAbstract:A new thermophilic, xylanolytic, strictly anaerobic, rod-shaped bacterium, strain SEBR 7054T, was isolated from an African oil-producing well. Based on the presence of an outer sheath (toga) and 16S rRNA sequence analysis data, this organism was identified as a member of the genus Thermotoga. Strain SEBR 7054T possessed lateral flagella, had a G+C content of 50 mol%, produced traces of ethanol from glucose but no lactate, and grew optimally in the presence of 0 to 0.2% NaCl at 70°C. Its phenotypic and phylogenetic characteristics clearly differed from those reported for the five previously validly described Thermotoga species. Therefore, we propose that strain SEBR 7054T is a member of a new species of the genus Thermotoga, Thermotoga hypogea sp. nov. The type strain of T. hypogea is SEBR 7054 (= DSM 11164).
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thiosulfate reduction an important physiological feature shared by members of the order Thermotogales
Applied and Environmental Microbiology, 1995Co-Authors: Gilles Ravot, Bernard Ollivier, Michel Magot, Bharat K C Patel, J L Crolet, Marielaure Fardeau, Jeanlouis GarciaAbstract:Several members of the order Thermotogales in the domain Bacteria, viz., Thermotoga neapolitana, Thermotoga maritima, Thermosipho africanus, Fervidobacterium islandicum, and Thermotoga strain SEBR 2665, an isolate from an oil well, reduced thiosulfate to sulfide. This reductive process enhanced cellular yields and growth rates of all the members but was more significant with the two hyperthermophiles T. neapolitana and T. maritima. This is the first report of such an occurrence in this group of thermophilic and hyperthermophilic anaerobic bacteria. The results suggest that thiosulfate reduction is important in the geochemical cycling of sulfur in anaerobic thermal environments such as the slightly acidic and neutral-pH volcanic hot springs and oil reservoirs.
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Thermotoga elfii sp. nov., a Novel Thermophilic Bacterium from an African Oil-producing Well
International journal of systematic bacteriology, 1995Co-Authors: Gilles Ravot, Michel Magot, Bharat K C Patel, Marielaure Fardeau, Jeanlouis Garcia, Gérard Prensier, A. Egan, Bernard OllivierAbstract:A thermophilic, glucose-fermenting, strictly anaerobic, rod-shaped bacterium, strain SEBR 6459T (T = type strain), was isolated from an African oil-producing well. This organism was identified as a member of the genus Thermotoga on the basis of the presence of the typical outer sheath-like structure (toga) and 16S rRNA signature sequences and its ability to grow on carbohydrates (glucose, arabinose, fructose, lactose, maltose, and xylose). Major differences in its 16S rRNA gene sequence, its lower optimum temperature for growth (66 degrees C), its sodium chloride range for growth (0 to 2.8%), its lack of lactate as an end product from glucose fermentation, and its peritrichous flagella indicate that strain SEBR 6459T is not similar to the three previously described Thermotoga species. Furthermore, this organism does not belong to any of the other genera related to the order Thermotogales that have been described. On the basis of these findings, we propose that this strain should be described as a new species, Thermotoga elfii. The type strain of T. elfii is SEBR 6459 (= DSM 9442).
Atsushi Yamazoe - One of the best experts on this subject based on the ideXlab platform.
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Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Koji Mori, Atsushi Yamazoe, Akira Hosoyama, Shoko Ohji, Nobuyuki Fujita, Jun-ichiro Ishibashi, Hiroyuki Kimura, Ken-ichiro SuzukiAbstract:Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06T and AZM44c09T, were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06T were 60 °C, pH 7.4 and 0 % additional NaCl, and those for strain AZM44c09T were 70 °C, pH 7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06T) and 2.01 Mbp (AZM44c09T). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga . The closest relatives of strains AZM34c06T and AZM44c09T were the type strains of Thermotoga lettingae (96.0 % similarity based on the 16S rRNA gene and 84.1 % similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7 % similarity), respectively. Using blast, the average nucleotide identity was 70.4–70.5 % when comparing strain AZM34c06T and T. lettingae TMOT and 76.6 % when comparing strain AZM44c09T and T. hypogea NBRC 106472T. Both values are far below the 95 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06T = NBRC 106115T = DSM 23275T) and Thermotoga caldifontis sp. nov. (type strain AZM44c09T = NBRC 106116T = DSM 23272T).
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Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs.
International journal of systematic and evolutionary microbiology, 2014Co-Authors: Koji Mori, Atsushi Yamazoe, Akira Hosoyama, Shoko Ohji, Nobuyuki Fujita, Jun-ichiro Ishibashi, Hiroyuki Kimura, Ken-ichiro SuzukiAbstract:Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06(T) and AZM44c09(T), were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06(T) were 60 °C, pH 7.4 and 0% additional NaCl, and those for strain AZM44c09(T) were 70 °C, pH 7.4 and 0% additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06(T)) and 2.01 Mbp (AZM44c09(T)). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga. The closest relatives of strains AZM34c06(T) and AZM44c09(T) were the type strains of Thermotoga lettingae (96.0% similarity based on the 16S rRNA gene and 84.1% similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7% similarity), respectively. Using blast, the average nucleotide identity was 70.4-70.5% when comparing strain AZM34c06(T) and T. lettingae TMO(T) and 76.6% when comparing strain AZM44c09(T) and T. hypogea NBRC 106472(T). Both values are far below the 95% threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06(T) = NBRC 106115(T) = DSM 23275(T)) and Thermotoga caldifontis sp. nov. (type strain AZM44c09(T) = NBRC 106116(T) = DSM 23272(T)).
