A5056130227- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Enzyme Production and Characterization
- Environmental DNA in Biodiversity Studies
- Protist diversity and phylogeny
- Probiotics and Fermented Foods
- Methane Hydrates and Related Phenomena
- Enzyme Catalysis and Immobilization
- Lipid Membrane Structure and Behavior
- Microbial Metabolic Engineering and Bioproduction
- Oral microbiology and periodontitis research
- Aquaculture disease management and microbiota
- Biochemical and Molecular Research
- Photosynthetic Processes and Mechanisms
- Toxin Mechanisms and Immunotoxins
- Microbial Metabolites in Food Biotechnology
- Polyamine Metabolism and Applications
- Biofuel production and bioconversion
- Identification and Quantification in Food
- RNA and protein synthesis mechanisms
- Nanopore and Nanochannel Transport Studies
- Amino Acid Enzymes and Metabolism
- Glycosylation and Glycoproteins Research
- Infections and bacterial resistance
Japan Agency for Marine-Earth Science and Technology
2016-2025
Toyo University
2007-2022
The haloarchaeal genera Natrinema and Haloterrigena were described almost simultaneously by two different research groups some strains studied separately as species of these genera. Furthermore, the description additional assigned to either or Haloterrigena, mainly on basis phylogenetic comparative analysis single genes (16S rRNA gene more recently rpoB' gene), but not adequately separated corresponding genus. Some studies suggested that should be unified into a genus, while other indicated...
Abstract Construction of living artificial cells from genes and molecules can expand our understanding life system establish a new aspect bioengineering. However, growth division cell membrane that are basis proliferation still difficult to reconstruct because high-yielding phospholipid synthesis has not been established. Here, we developed cell-free combines fatty acid gene expression synthesizing acyltransferases. The synthesized acids were sequentially converted into phosphatidic by the...
A strategy based on Poisson statistics enables a rapid and efficient acquisition of enzyme mutants from just few clones.
A novel Gram-stain-negative, aerobic, heterotrophic, stalked and capsulated bacterium with potential denitrification ability, designated strain TAR-002(T), was isolated from deep seafloor sediment in Japan. Colonies lacked lustre, were viscous translucent white. The ranges of temperature, pH salt concentration for growth 8-30 °C, 6.0-10.0 1-3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that TAR-002(T) belongs to the genus Brevundimonas class...
Strain YSM-123 T was isolated from commercial salt made Japanese seawater in Niigata prefecture. Optimal NaCl and Mg 2+ concentrations for growth were 4.0–4.5 M 5 mM, respectively. The isolate a mesophilic slightly alkaliphilic haloarchaeon, whose optimal temperature pH 37 °C 8.0–9.0. Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain is member of the phylogenetic group defined by family Halobacteriaceae , but there low similarities to type strains other genera this...
In many prokaryotic species, 16S rRNA genes are present in multiple copies, and their sequences general do not differ significantly owing to concerted evolution. At the time of writing, genus Haloarcula family Halobacteriaceae comprises nine species with validly published names, all which possess two four highly heterogeneous genes. Existence makes it difficult reconstruct a biological phylogenetic tree using sequence data. If orthologous gene is able be discriminated from paralogous genes,...
A novel halophilic strain, BNERC31(T), was isolated from solar salt, 'Sel marin de Guérande', imported France. Colonies on agar medium containing soluble starch, sodium citrate, glutamate and inorganic salts were non-pigmented transparent, while cells obtained by centrifuging liquid cultures red-pigmented. Cells of strain BNERC31(T) non-motile, pleomorphic, stained Gram-negative lysed in distilled water. Growth occurred with 20-30 % (w/v) NaCl (optimum, 25 %, w/v), 0-500 mM MgCl2 10 mM), at...
Giant vesicles have been widely used for the bottom-up construction of artificial (or synthetic) cells and physicochemical analysis lipid membranes. Although methods formation giant encapsulation molecules within them established, a standardized protocol has not shared among researchers including non-experts. Here we proposed rapid facile that allows 30 min. The quality encapsulating cell-free protein expression system was comparable to ones formed using conventional method, in terms...
To mitigate marine pollution from single-use plastics, it is crucial to transition next-generation commodity materials that are derived biomass and recyclable biodegradable even at abyssal depths in case of the accidental release ocean. Here, we develop an optically transparent millimeter-thick paperboard called (tPB) through dissolution coagulation cellulose. The tPB made entirely pristine cellulose compositionally identical paper. A cup-shaped can hold just-boiled water without internal...
Strain YSM-79(T) was isolated from commercial salt made seawater in Yonaguni island, Okinawa, Japan. The strain is an aerobic, Gram-negative, chemo-organotrophic and extremely halophilic archaeon. Cells are short rods that lyse distilled water. Growth occurs at 1.5-5.3 M NaCl (optimum 2.5-3.0 M), pH 5.0-8.8 5.2-6.3) 20-55 °C 40 °C). Mg²⁺ required for growth, with maximum growth 200-300 mM Mg²⁺. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate...
A novel Gram-negative, aerobic, psychrotolerant, alkali-tolerant, heterotrophic and dimorphic prosthecate bacterium, designated strain TAR-001(T), was isolated from deep-sea floor sediment in Japan. Cells of this had a life cycle developed an adhesive stalk at site not coincident with the centre cell pole, other type cell, swarm polar flagellum. Colonies were glossy, viscous yellowish-white colour. The temperature, pH salt concentration range for growth 2-41 °C, 6.5-10.0 1-4% (w/v) NaCl....
A Gram-stain-negative, aerobic, heterotrophic and salt-tolerant bacterium, designated strain LL-001(T), was isolated from a deep subseafloor sediment in Japanese waters. Cells were non-motile rods colonies smooth, convex, circular vermilion. The conditions for growth 15-35 °C, pH 5.5-7.5 1-8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that LL-001(T) belonged to the genus Loktanella within family Rhodobacteraceae of class Alphaproteobacteria. sequence...
A thermophilic bacterium, strain Sueoka T , was isolated from steamed Japanese cedar chips a lumber mill in Gobo, Japan. The able to grow on carboxymethyl cellulose at 60 °C, Gram-stain-negative, and grew between 40.0 67.5 °C (optimum 55 °C) pH 3.5 6.5 4.8). Comparative analysis of 16S rRNA gene sequences revealed 91.9 90.9 90.8 % similarity Alicyclobacillus macrosporangiidus pomorum acidocaldarius respectively. major quinone MK-7 the predominant cellular fatty acids were ω -cyclohexane C 19...
Measles virus (MV) causes an acute and highly devastating contagious disease in humans. Employing the crystal structures of three human receptors, signaling lymphocyte-activation molecule (SLAM), CD46, Nectin-4, complex with measles hemagglutinin (MVH), we elucidated computationally details binding energies between amino acid residues MVH those receptors ab initio fragment molecular orbital (FMO) method. The calculated inter-fragment interaction (IFIEs) revealed a number significantly...
A novel filamentous bacterium, designated strain JIR-001(T), was isolated from hemipelagic sediment in deep seawater. This non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form ivory coloured with wrinkles between the centre edge colony on ISP2 medium. The isolate grew aerobically at 55-73 °C formation aerial mycelia; spores produced singly along mycelium. These morphological features show some similarities to those type strains species belonging...
An agar-degrading archaeon Halococcus sp. 197A was isolated from a solar salt sample. The agarase purified by hydrophobic column chromatography using of TOYOPEARL Phenyl-650 M. molecular mass the enzyme, designated as Aga-HC, ~55 kDa on both SDS-PAGE and gel-filtration chromatography. Aga-HC released degradation products in order neoagarohexose, neoagarotetraose small quantity neoagarobiose, indicating that β-type agarase. showed requirement for stability activity, being active 0.3 M NaCl,...
Two marine bacteria, designated strains MBE#61(T) and MBE#74(T), were isolated from a piece of sunken bamboo in the environment Japan. Both these Gram-stain-negative, but had different cell shapes: was spiral, whereas MBE#74(T) rod-shaped. The temperature, pH salt concentration ranges for growth strain 4-38 °C (optimal at 32 °C), 4.5-11.0 7.0-8.0) 1-11 % 2 %) NaCl, those 4-36 30 4.0-10.5 1-12 4 NaCl. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that both belong to...
Two extremely halophilic archaea, strains MGY-184(T) and MGY-205, were isolated from sea salt produced in Japan rock imported Bolivia, respectively. Both pleomorphic, non-motile, Gram-negative required more than 5 % (w/v) NaCl for growth, with optimum at 9-12 %, the presence of 2 MgCl2 . 6H2O. In 18 6H2O, however, both showed growth even 1.0 NaCl. possessed two 16S rRNA genes (rrnA rrnB), they revealed closest similarity to Halobaculum gomorrense JCM 9908(T), single species a validly...
A moderately halophilic and alkalitolerant bacterium, designated strain HN30(T), was isolated from garden soil in Japan. Cells of HN30(T) were motile, endospore-forming, aerobic, rod-shaped gram-positive, contained A1γ meso-diaminopimelic acid-type murein. Growth occurred 7-23 % (w/v) NaCl (optimum, 10-15 %, w/v), at pH 6.5-10.0 8.0-8.5) 20-40 °C 30 °C). The isoprenoid quinone menaquinone-7. polar lipids phosphatidylglycerol diphosphatidylglycerol. major cellular fatty acids anteiso-C(15 :...
Lignin is one of the most abundant biomasses in nature.It composed aromatic moieties and has great potential for use production chemical alternatives to petroleum products.Because increasing interest biocatalysis, industrial application microbial metabolism lignin-derived compounds gained considerable recent attention.Functional screenings culturable bacteria isolated from sediments sunken wood collected deep sea revealed existence a number previously unidentified capable metabolizing...
Three halophilic archaeal strains, MH2-243-1(T), MH2-93-1 and MH2-91-1 were isolated from commercial salt samples Japan, Australia, Bolivia. Strain MH2-243-1(T) was able to grow in the presence of 12-30% (w/v) NaCl (optimum, 18% NaCl), at pH 4.5-7.0 6.0) 20-60 °C 40 °C). Strains grew slightly different ranges. The orthologous 16S rRNA gene sequences three strains almost identical (99.8-99.9% similarities), closest relative Salarchaeum japonicum JCM 16327(T) with 94.2-94.3% sequence...
Three halophilic archaeal strains, MH1-34-1(T), MH1-16-1 and MH1-224-5 were isolated from commercial salt samples produced seawater in Indonesia, the Philippines Japan, respectively. Cells of three strains pleomorphic stained Gram-negative. Strain MH1-34-1(T) was orange-red pigmented, while pink-pigmented. able to grow at 12-30 % (w/v) NaCl (with optimum 18 NaCl, w/v) pH 4.5-7.2 (optimum, 5.2-5.5) 15-45 °C 42 °C). Strains grew slightly different ranges. These required least 1 mM Mg(2+) for...
A moderately halophilic, slightly acidophilic, aerobic bacterium, designated strain YTM-1(T), was isolated from the body surface of Malacocottus gibber. Cells were Gram-stain-negative, short rods or cocci, approximately 0.9-1.1 µm long and 1.0-1.8 wide. Strain YTM-1(T) able to grow with 1-30% NaCl (optimum, 7.5-10%, w/v), at 4-30 °C 20-25 °C) pH 3.8-9.5 5.0-5.5). Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that belonged genus Salinisphaera low similarity values...
Two chitin-degrading halophilic archaeal strains, MC-74T and MC-23, were isolated from commercial salt samples. Cells motile, rod-shaped stained Gram-negative. Colonies vermillion-pigmented. Strains MC-23 able to grow with 1.5–5.1 M NaCl (optimum, 2.6–3.1 M) at pH 6.0–10.0 7.0) 20–50 °C 40 °C). The orthologous 16S rRNA gene sequence similarity between the two strains was 99.8 %, closest phylogenetic relative Salinarchaeum laminariae JCM 17267T 99.3–99.5 % similarity. level of DNA–DNA...