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Akira Yokota

Publications and source records attributed to Akira Yokota.

At least 19 recordsLinked to original sources
PubMed2007

Tateyamaria omphalii gen. nov., sp. nov., an alpha-Proteobacterium isolated from a top shell Omphalius pfeifferi pfeifferi.

A Gram-negative, strictly aerobic, coccoid to short rod-shaped marine bacterium strain MKT107(T) was isolated from the molluscan top shell Omphalius pfeifferi pfeifferi collected on the coast of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MKT107(T) constitutes a new lineage in alpha-Proteobacteria related to the genera Nereida, Roseobacter, Staleya, Oceanibulbus and Sulfitobacter. Strain MKT107(T) was found to require salt for its growth and to be mesophilic. It contained 18:1omega7c and 16:0 as major cellular fatty acids and 3-OH 10:0 and 3-OH 12:0 as hydroxy fatty acids. The DNA base composition of the isolate was 61.6 mol% G+C. The major quinone was Q-10. Sufficient differences existed to distinguish this strain from currently recognized bacterial genera. Therefore, the isolate is classified as representing a new genus and species, Tateyamaria omphalii gen. nov., sp. nov. (type strain MKT107(T) =IAM 15108(T) =KCTC 12333(T); GenBank accession no. AB193438).

Alphaproteobacteria↗
PubMed2007

Paenibacillus terrigena sp. nov., isolated from soil.

A novel Gram-positive bacterium, strain A35(T), was isolated from coastal soil at Chiba, Japan, and was identified as a member of the genus Paenibacillus on the basis of phenotypic and phylogenetic analyses. The bacterium was found to be a facultatively anaerobic and endospore-forming rod. The predominant menaquinone was MK-7, the major cellular fatty acid was anteiso-C(15 : 0) and the DNA G+C content was 48.1 mol%. The levels of 16S rRNA gene sequence similarity between strain A35(T) and Paenibacillus species with validly published names were less than 94 %. Strain A35(T) was clearly distinguishable from reference species for the genus Paenibacillus. Therefore, on the basis of these data, a novel species of the genus Paenibacillus, Paenibacillus terrigena sp. nov., is proposed. The type strain is A35(T) (=IAM 15291(T)=CCTCC AB206026(T)).

Anaerobiosis↗
PubMed2007

Terribacillus saccharophilus gen. nov., sp. nov. and Terribacillus halophilus sp. nov., spore-forming bacteria isolated from field soil in Japan.

Three strains, 002-048(T), RB589 and 002-051(T), isolated from field soil in Japan, were characterized using a polyphasic approach. The isolates were Gram-positive, strictly aerobic, non-motile rods that formed ellipsoidal, subterminal endospores. The chemotaxonomic characteristics of these isolates included the presence of meso-diaminopimelic acid as the cell-wall peptidoglycan, anteiso-C(15 : 0) and anteiso-C(17 : 0) as the major cellular fatty acids and MK-7 as the predominant menaquinone. The DNA G+C content was 44-46 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the isolates represented an independent lineage that is distinct from related taxa and exhibited less than 94.3 % sequence similarity with respect to those taxa. Moreover, a DNA-DNA hybridization analysis showed that the three isolates represented two species. On the basis of their phenotypic and phylogenetic distinctiveness, the isolates represent two species within a novel genus, for which the names Terribacillus saccharophilus gen. nov., sp. nov. and Terribacillus halophilus sp. nov. are proposed. The type strain of T. saccharophilus is 002-048(T) (=IAM 15309(T)=KCTC 13936(T)) and the type strain of T. halophilus is 002-051(T) (=IAM 15310(T)=KCTC 13937(T)).

Bacterial Typing Techniques↗
PubMed2006

A novel highly boron tolerant bacterium, Bacillus boroniphilus sp. nov., isolated from soil, that requires boron for its growth.

Three strains of gram-positive, motile, rod-shaped and boron (B)-tolerant bacterium were isolated from naturally B containing soil of Hisarcik area in the Kutahya Province, Turkey. The strains, designated as T-14A, T-15Z(T) and T-17s, produced spherical or ellipsoidal endospores in a terminal bulging sporangium. The strains required B for the growth and can tolerate more than 450 mM B. These also tolerated up to 7.0% (w/v) NaCl in the presence of 50 mM B in agar medium but grew optimally without NaCl. The temperature range for growth was 16-37 degrees C (optimal of 30 degrees C), whereas the pH range was 6.5-9.0 (optimal of 7.5-8.5). The DNA G + C content was 41.1-42.2 mol% and the predominant cellular fatty acid was iso-C(15:0). The major respiratory quinone system was detected as MK-7 and the diamino acid of the peptidoglycan was meso-diaminopimelic acid. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis of 16S rRNA gene sequences data and DNA-DNA re-association values, we concluded that the three strains belong to a novel species of the genus Bacillus, the type strain of which is T-15Z(T) and for which we proposed the name, B. boroniphilus sp. nov. (DSM 17376(T) = IAM 15287(T) = ATCC BAA-1204(T)).

Bacillus↗
PubMed2006

Endozoicomonas elysicola gen. nov., sp. nov., a gamma-proteobacterium isolated from the sea slug Elysia ornata.

A Gram-negative, strictly aerobic, rod-formed bacterium, strain MKT110(T), was isolated from a mollusk, the sea slug Elysia ornata collected in seawater off the coast of Izu-Miyake Island, Japan at a depth of 15m. Comparative 16S rRNA gene sequences analysis indicated that the isolate MKT110(T) constituted a novel lineage in gamma-proteobacteria related to the genera Zooshikella, Oceanospirillum, Microbulbifer, Marinobacter, Saccharospirillum and Pseudomonas. The strain MKT110(T) was closely related to the clones from marine sponge Halichondria okadai (AB054136, AB054161) and the coral Pocillopora damicornis (AY700600, AY700601). The phylogenetic tree based on the 16S rRNA gene sequences showed that MKT110(T) and four clones formed a sub-lineage related to the genus Zooshikella, with a bootstrap value of 100%. MKT110(T) required salt for its growth and was mesophilic. The bacterium contained 16:1omega7c, 16:0 and 14:0 as major cellular fatty acids, and 3-OH 14:0, 3-OH 10:0 and 3-OH 12:0 as major hydroxy fatty acids. The DNA base composition of the isolate was 50.4 mol% G+C. The major quinone was Q-9. The bacterium is distinguished from currently recognized bacterial genera based on phylogenetic and phenotypic features and should be classified in a novel genus for which the name Endozoicomonas elysicola gen. nov., sp. nov. is proposed. (type strain MKT110(T)=IAM 15107(T)=KCTC 12372(T); GenBank accession no. AB196667).

Animals↗
PubMed2006

Rotational vertigo caused by cerebral lesions: vertigo and areas 3av, 2v, and 7.

We describe two patients complaining of vertigo associated with a small supra-tentorial convexity meningioma. Symptoms disappeared after tumor removal, providing evidence for an association between the vertigo and the cerebral cortical lesions. Tumors were located in the central and parietal areas, respectively, which are probably analogous to the vestibular cortex in the areas designated 3av, 2v, and 7 in animal studies.

Female↗
PubMed2006

Effects of general anesthesia on high-frequency oscillations in somatosensory evoked potentials.

To determine the characteristics of high-frequency oscillations (HFOs) of cortical somatosensory evoked potentials (SEPs), the effect of general anesthesia on HFOs and low-frequency primary cortical responses was studied. The authors recorded SEPs elicited by median nerve stimulation directly from human brains of seven patients who underwent implantation of subdural electrodes before surgical treatment of intractable epilepsy. Recordings were made before and during general anesthesia. Changes in the number of HFOs and amplitude ratios of HFOs/primary cortical responses were analyzed. Under general anesthesia, the number of HFO peaks and the amplitude ratios were significantly decreased. General anesthesia induced remarkably decreased HFO activities when compared to low-frequency SEPs, suggesting that each of those originated from different generators. Possible relations between gamma-amino-butyric acid (GABA)ergic inhibitory interneurons and HFOs are discussed.

Adult↗
PubMed2006

Reclassification of Arthrobacter duodecadis Lochhead 1958 as Tetrasphaera duodecadis comb. nov. and emended description of the genus Tetrasphaera.

Phylogenetic analysis based on 16S rRNA gene sequences and chemotaxonomic features of Arthrobacter duodecadis Lochhead 1958 indicated that the bacterium belonged within the genus Tetrasphaera. A. duodecadis IAM 14868(T) could be distinguished from other species by the presence of 3-hydroxy meso-diaminopimelic acid in the peptidoglycan and a series of 10-methyl fatty acids. In addition, DNA-DNA relatedness studies indicated that the strain belonged to a genomic species that could be readily distinguished from its nearest neighbours, the type strains of Tetrasphaera elongata, Tetrasphaera japonica and Tetrasphaera australiensis. These features support our proposal to reclassify A. duodecadis in the genus Tetrasphaera, as Tetrasphaera duodecadis comb. nov. The type strain is IAM 14868(T) (=NBRC 12959(T) = ATCC 13347(T) = NCIMB 9222(T)). An emended description of the genus Tetrasphaera is given.

Actinomycetales↗
PubMed2006

Zoogloea oryzae sp. nov., a nitrogen-fixing bacterium isolated from rice paddy soil, and reclassification of the strain ATCC 19623 as Crabtreella saccharophila gen. nov., sp. nov.

Two strains of free-living diazotrophs isolated from soil from a rice paddy field were characterized by using a polyphasic approach. The novel strains, A-7T and A-4, were found to be very closely related, with 99.9% 16S rRNA gene sequence similarity and a DNA-DNA hybridization value of 89.5%, suggesting that they represent a single species. 16S rRNA gene sequence analyses indicated that the two strains fell within the Zoogloea lineage, with less than 96.7 % sequence similarity to other Zoogloea species. Chemotaxonomic characteristics of the novel strains, including DNA G + C content (65.1 mol%), the major quinone system (Q-8), predominant fatty acids (16:1omega7c and 16:0) and major hydroxy fatty acids (3-OH 10:0 and 3-OH 12:0), are similar to those of the genus Zoogloea. The novel strains showed positive results for floc formation which is accepted as confirmatory for species of the genus Zoogloea. However, the novel strains can be distinguished from the other species of Zoogloea by physiological characteristics. The name Zoogloea oryzae sp. nov. is therefore proposed for the novel strains with strain A-7T (= IAM 15218T = CCTCC AB 2052005T) as the type strain. Phylogenetic and chemotaxonomic analyses indicate that strain ATCC 19623, designated as a reference strain of Zoogloea ramigera, does not belong to the genus Zoogloea but to a new genus of Alphaproteobacteria. The name Crabtreella saccharophila gen. nov., sp. nov. is proposed for strain ATCC 19623T (= IAM 12669T).

Alphaproteobacteria↗
PubMed2006

Pseudovibrio ascidiaceicola sp. nov., isolated from ascidians (sea squirts).

Two bacterial strains, F423T and F10102, were isolated from two ascidians, Polycitor proliferus and Botryllidae sp., respectively, which were collected from a beach on the Boso peninsula in Japan. Cells of both isolates were motile, rod-shaped and formed star-shaped aggregates in the early stage of exponential growth, but were coccoid in stationary growth phase. The results of 16S rRNA gene sequence analysis, fatty acid analysis, DNA-DNA hybridization experiments and physiological and biochemical tests indicated that the two strains were members of a novel species of the genus Pseudovibrio for which the name Pseudovibrio ascidiaceicola sp. nov. is proposed. The type strain is F423T (=NBRC 100514T=IAM 15084T=DSM 16392T=KCTC 12308T).

Animals↗
PubMed2006

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

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).

Bacterial Proteins↗
PubMed2006

Reclassification of [Flavobacterium] ferrugineum as Terrimonas ferruginea gen. nov., comb. nov., and description of Terrimonas lutea sp. nov., isolated from soil.

Strain DY(T), which was isolated from garden soil in Japan, was subjected to a polyphasic taxonomic study. Sequence analysis of the 16S rRNA gene and the GyrB protein revealed that the closest relative of strain DYT was [Flavobacterium] ferrugineum Sickles and Shaw 1934, with 94.8 and 90.1 % similarity, respectively. The two strains had similar chemotaxonomic characteristics, with menaquinone 7 as the major quinone system, 47.2-48.9 mol% DNA G+C content and 15 : 0 iso, 15 : 1 iso, 17 : 0 iso 3-OH and summed feature 3 as the major fatty acids. Based on genotypic and phenotypic characteristics, [Flavobacterium] ferrugineum IAM 15098T could be clearly differentiated from other members of the genus Flavobacterium. Strain DYT and [Flavobacterium] ferrugineum IAM 15098T could be easily distinguished from neighbouring taxa by morphological features (non-motile, non-gliding and non-filamentous single cells). Therefore, it is proposed that [Flavobacterium] ferrugineum IAM 15098T and strain DYT represent two separate species of a new genus, Terrimonas gen. nov., with the names Terrimonas ferruginea comb. nov. (type species; type strain IAM 15098T=ATCC 13524T) and Terrimonas lutea sp. nov. (type strain DYT=IAM 15284T=CCTCC AB205006T), respectively.

Bacterial Typing Techniques↗
PubMed2006

Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov.

A study was carried out to clarify the taxonomy of four Gram-positive, heterotrophic mesophiles isolated from marine lakes in the Republic of Palau. The strains, designated YM3-251(T), YM3-653, YM3-671 and YM11-542(T), formed aerial and substrate mycelia. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. The G+C content of their genomic DNA was approximately 45 mol%. The major fatty acid was iso-C(15 : 0) and the major isoprenoid quinone was MK-9. The strains formed a distinct group in the 16S rRNA gene tree and shared a range of phenotypic properties that distinguished them from members of related genera in Thermoactinomycetaceae fam. nov. The name proposed to accommodate the new isolates is Mechercharimyces gen. nov., comprising two species based on genotypic and phenotypic criteria, including comparative gyrB and DNA-DNA relatedness data. The names proposed for these taxa are Mechercharimyces mesophilus sp. nov., the type species, and Mechercharimyces asporophorigenens sp. nov., with the type strains YM3-251(T) (=MBIC06230(T)=DSM 44894(T)) and YM11-542(T) (=MBIC06487(T)=DSM 44955(T)), respectively.

Antineoplastic Agents↗
PubMed2006

Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan.

Among a large collection of Taiwanese soil isolates, a novel Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterial strain, Soil-3-27(T), was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, fatty acid analysis and comparative phenotypic characterization. The 16S rRNA gene sequence analysis indicated that the organism belongs to the genus Chryseobacterium. The organism contains menaquinone MK-6 as the predominant isoprenoid quinone and 15 : 0 iso (43 %), 17 : 1 isoomega9c (17.5 %) and 17 : 0 iso 3-OH (16.6 %) as the major fatty acids. Phylogenetically, the closest relatives of strain Soil-3-27(T) are Chryseobacterium daecheongense, Chryseobacterium defluvii and Chryseobacterium taichungense with 96.7-97.2 % sequence similarity. DNA-DNA hybridization showed relatedness values of 8.5-24.2 % with these species. The DNA G+C content is 36.8 mol%. Strain Soil-3-27(T) is clearly distinguishable from other Chryseobacterium species and represents a novel species, for which the name Chryseobacterium taiwanense sp. nov. is proposed. The type strain is strain Soil-3-27(T) (=BCRC 17412(T)=IAM 15317(T)=LMG 23355(T)).

Base Composition↗
PubMed2006

Myroides pelagicus sp. nov., isolated from seawater in Thailand.

An aerobic, Gram-negative, non-motile, yellow-to-orange pigmented and rod-shaped bacterium, designated strain SM1(T), was isolated from seawater in Thailand and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolate shared 93-95 % sequence similarity with species of the genus Myroides. The DNA-DNA relatedness values of strain SM1(T) with Myroides odoratimimus JCM 7460(T) and Myroides odoratus JCM 7458(T) were below 70 %. The DNA G+C content of strain SM1(T) was 33.6 mol%, the major menaquinone was MK-6 and the major fatty acids were C(15 : 0) iso, C(17 : 1)omega9c iso and C(17 : 0) iso 3-OH. Based on its phenotypic and chemotaxonomic characteristics, strain SM1(T) was classified as representing a novel species of the genus Myroides, for which the name Myroides pelagicus sp. nov. is proposed. The type strain is SM1(T) (=IAM 15337(T)=KCTC 12661(T)).

Bacteroidetes↗
PubMed2006

Plantibacter auratus sp. nov., in the family Microbacteriaceae.

Strain NCIMB 9991(T) is a Gram-positive, short rod-shaped, yellow-pigmented bacterium, with a high DNA G+C content, and was originally deposited in 1967 as Arthrobacter sp. The bacterium is aerobic, non-motile, catalase-positive and oxidase-negative. Comparative 16S rRNA gene sequencing studies demonstrated that this strain was highly related genealogically to Plantibacter flavus DSM 14012(T). Strain IAM 14817(T) (=NCIMB 9991(T)) has the following characteristics: the predominant menaquinones are MK-9 and MK-10, the DNA G+C content is 68 mol%, the diamino acid in the cell wall is 2,4-l-diaminobutyric acid and the muramic acid in the peptidoglycan is of an acetyl type. The major fatty acid is 12-methyl tetradecanoic acid (anteiso-C(15 : 0)), followed by 14-methyl hexadecanoic acid (anteiso-C(17 : 0)), 14-methyl pentadecanoic acid (iso-C(16 : 0)) and hexadecanoic acid (C(16 : 0)). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA-DNA hybridization and 16S rRNA gene sequence comparison, strain IAM 14817(T) represents a novel species within the genus Plantibacter, for which the name Plantibacter auratus sp. nov. is proposed, with the type strain IAM 14817(T) (=NCIMB 9991(T)=NBRC 15702(T)).

Actinomycetales↗