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Tanasupawat S.,Chulalongkorn University | Kommanee J.,Chulalongkorn University | Yukphan P.,National Science and Technology Development Agency | Nakagawa Y.,National Institute of Technology and Evaluation | And 3 more authors.
Journal of the Science of Food and Agriculture | Year: 2011

Background: Fermented rice flour (khao-khab, a non-glutinous rice) and related products are Thai traditional products. The types of acetic acid bacteria (AAB) microflora in khao-khab have not been reported. In this study, Acetobacter strains were isolated and identified based on the phenotypic and chemotaxonomic characteristics and molecular aspects. Results: Twenty-five acetic acid bacteria isolated from fermented rice products and a starter for sweetened rice in Thailand by an enrichment culture approach, were assigned to the genus Acetobacter by phenotypic and chemotaxonomic characterisations. On the basis of the 16S rRNA gene sequence and 16S-23S rRNA gene ITS restriction analyses, 25 isolates were divided into six groups and identified at the specific level: (1) Group 1 included five isolates, which were identified as A. indonesiensis; (2) Group 2 included two isolates, which were identified as A. lovaniensis; (3) Group 3 included one isolate, which was identified as A. orientalis; (4) Group 4 included eleven isolates, which were identified as A. pasteurianus; (5) Group 5 included three isolates, which were identified as A. syzygii and (6) Group 6 included three isolates, which were unidentified and considered to constitute a new species. Conclusion: Results revealed that various Acetobacter species were distributed in Thai fermented rice flour and related products. A novel Acetobacter species was isolated from the product. © 2011 Society of Chemical Industry.


PubMed | 1National Institute of Agricultural science, National Institute of Technology and Evaluation, 4National Institute of Agricultural science, 5National Institute of Horticultural & Herbal Science and 4 more.
Type: | Journal: International journal of systematic and evolutionary microbiology | Year: 2016

One bacterial strain, designated 5GHs33-3T, was isolated from greenhouse soil collected from Yongin region, Gyeonggi province, South Korea. It was aerobic, Gram-stain-positive, flagellated, rod-shaped bacterium. The strain grew at the range of 4-37 C (optimally 28-30 C), pH 6.0-10.0 (optimally pH 7.0) and 0-7 % (w/v) NaCl concentrations (optimally, 0 %). The 16S rRNA gene sequence analysis revealed that it had high sequence similarity with Actinotalea suaedae EGI 60002T (98.4 %), Actinotalea ferrariae CF5-4T (96.4 %) and Actinotalea fermentans DSM 3133T (96.2 %), and revealed less than 95.5 % sequence similarity against all the other validly named species. Phylogenetic tree revealed that the strain formed a robust independent monophyletic line with Actinotalea suaedae EGI 60002T. The predominant fatty acids were anteiso-C15:0 and iso-C14:0. The only quionone was MK-8(H4). Major polar lipids were diphosphatidylglycerol, unknown phosphoglycolipid and unknown lipid. The peptidoglycan type was A4, with ornithine as the diagnostic diamino acid and an interpeptide bridge comprising L-Glu. DNA G+C content is 69.0 mol%. Based on phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analysis, strain 5GHs33-3T represents a novel species of a novel genus, for which the name Pseudactinotalea terrae gen. nov., sp. nov. is proposed. The type strain is 5GHs33-3T (= KACC 16542T = NBRC 111006T). We also propose the reclassification of Actinotlea suaedae as Pseudactinotalea suaedae comb. nov.


PubMed | National Institute of Technology and Evaluation NBRC, National Institute of Technology and Evaluation and 1National Institute of Technology and Evaluation NITE
Type: | Journal: International journal of systematic and evolutionary microbiology | Year: 2016

The aim of this study is to reclarify the taxonomic relationship among Streptomyces hygroscopicus subsp. hygroscopicus, Streptomyces endus and Streptomyces sporocinereus. Whole genome shotgun sequencing was performed for the type strains of these three taxa. Average nucleotide identity and digital DNA-DNA hybridization values among the three taxa were greater than the thresholds for bacterial species delineation, indicating that they belong to the same genomospecies. In addition, their phenotypic data previously reported also support the synonymy. Therefore, S. endus and S. sporocinereus should be reclassified as later heterotypic synonyms of S. hygroscopicus subsp. hygroscopicus.


Kommanee J.,Chulalongkorn University | Tanasupawat S.,Chulalongkorn University | Yukphan P.,National Center for Genetic Engineering and Biotechnology | Malimas T.,National Center for Genetic Engineering and Biotechnology | And 5 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2011

Three strains, RBY-1 T, PHD-1 and PHD-2, were isolated from fruits in Thailand. The strains were Gram-negative, aerobic rods with polar flagella, produced acetic acid from ethanol and did not oxidize acetate or lactate. In phylogenetic trees based on 16S rRNA gene sequences and 16S-23S rRNA gene internal transcribed spacer (ITS) sequences, the strains formed a cluster separate from the type strains of recognized species of the genus Gluconobacter. The calculated 16S rRNA gene sequence and 16S-23S rRNA gene ITS sequence similarities were respectively 97.7-99.7% and 77.3-98.1%. DNA G+C contents ranged from 57.2 to 57.6 mol%. The strains showed high DNA-DNA relatedness of 100% to one another, but low DNA-DNA relatedness of 11-34% to the tested type strains of recognized Gluconobacter species. Q-10 was the major quinone. On the basis of the genotypic and phenotypic data obtained, the three strains clearly represent a novel species, for which the name Gluconobacter nephelii sp. nov. is proposed. The type strain is RBY-1 T (=BCC 36733 T=NBRC 106061 T=PCU 318 T), whose DNA G+C content is 57.2 mol%. © 2011 IUMS.


Kamino K.,Marine Biotechnology Institute | Kamino K.,National Institute of Technology and Evaluation | Nakano M.,Marine Biotechnology Institute | Kanai S.,Pharma Design Inc.
FEBS Journal | Year: 2012

Barnacles are a unique sessile crustacean that attach irreversibly and firmly to foreign underwater surfaces. Its biological underwater adhesive is a peculiar extracellular multi-protein complex. Here we characterize one of the two major proteins, a 52 kDa protein found in the barnacle cement complex. Cloning of the cDNA revealed that the protein has no homolog in the nonredundant database. The primary structure consists of four long sequence repeats. The process of dissolving the protein at the adhesive joint of the animal by various treatments was monitored in order to obtain insight into the molecular mechanism involved in curing of the adhesive bulk. Treatments with protein denaturant, reducing agents and/or chemical-specific proteolysis in combination with 2D diagonal PAGE indicated no involvement of the protein in intermolecular cross-linkage/polymerization, including formation of intermolecular disulfide bonds. As solubilization of the proteins required high concentrations of denaturing agents, it appears that both the conformation of the protein as building blocks and non-covalent molecular interactions between the building blocks, possibly hydrophobic interactions and hydrogen bonds, are crucial for curing of the cement. It was also suggested that the protein contributes to surface coupling by an anchoring effect to micro- to nanoscopic roughness of surfaces. Database -Sequence of Megabalanus rosa cp52k mRNA for 52 kDa cement protein has been submitted to the DNA Data Bank of Japan under accession number. Barnacle attaches irreversibly and firmly to foreign underwater surfaces. Characterization of the major bulk protein at the adhesive joint of the animal indicated no involvement of the protein in the intermolecular cross-linkage/polymerization. It appeared that both conformation of the protein and non-covalent molecular interactions, possibly hydrophobic interactions and hydrogen bonds, are crucial for curing of the adhesive. © 2012 The Authors Journal compilation © 2012 FEBS.


Okane I.,National Institute of Technology and Evaluation | Srikitikulchai P.,National Center for Genetic Engineering and Biotechnology | Tabuchi Y.,National Institute of Technology and Evaluation | Sivichai S.,National Center for Genetic Engineering and Biotechnology | Nakagiri A.,National Institute of Technology and Evaluation
Mycoscience | Year: 2012

A total of 202 strains of xylariaceous fungi (183 endophytic strains isolated from 25 plant species of 24 genera in 21 families and 19 saprobic strains), segregated into four clades, were examined by nuclear rDNA internal transcribed spacer (ITS) sequence and beta-tubulin coding region analyses to clarify their taxonomic status and species boundaries. Three of the four species clades were assigned to Xylaria cubensis (100 strains), Xylaria grammica (33 strains), and Nemania diffusa (48 strains). Another fungus was tentatively assigned to Nemania cf. bipapillata (21 strains). Comparison of the host plants revealed that X. cubensis inhabited healthy leaves of at least 24 plant species (23 genera of 21 families) as endophytes; N. diffusa was found on 19 plant species (18 genera of 15 families), Nemania cf. bipapillata on 11 species (10 genera of 9 families), and X. grammica on 8 species (8 genera of 7 families). The present results suggest that the major xylariaceous endophytes in tropical plants are likely to be non-host specific, or have a wide range of host plant preferences. © 2011 The Mycological Society of Japan and Springer.


Kamino K.,National Institute of Technology and Evaluation
Journal of Adhesion | Year: 2010

Various organisms are known to attach themselves to a wide range of foreign materials in water as one of their essential physiological functions. To accomplish this, these organisms have acquired their specialized molecular systems in the process of their evolution. The molecular systems of sessile organisms are excellently designed for the purpose of underwater adhesion from the macroscopic scale to the molecular level. This review focuses on the unique sessile crustacean, the barnacle, in which a molecular system called cement was found for the underwater adhesion, which is completely different from the molecular system found in the mussel and tubeworm. The components, properties, and unique functions of the cement proteins from barnacles in comparison with those of the mussel and tubeworm are discussed.


Kamino K.,National Institute of Technology and Evaluation
Biofouling | Year: 2013

Barnacles are intriguing, not only with respect to their importance as fouling organisms, but also in terms of the mechanism of underwater adhesion, which provides a platform for biomimetic and bioinspired research. These aspects have prompted questions regarding how adult barnacles attach to surfaces under water. The multidisciplinary and interdisciplinary nature of the studies makes an overview covering all aspects challenging. This mini-review, therefore, attempts to bring together aspects of the adhesion of adult barnacles by looking at the achievements of research focused on both fouling and adhesion. Biological and biochemical studies, which have been motivated mainly by understanding the nature of the adhesion, indicate that the molecular characteristics of barnacle adhesive are unique. However, it is apparent from recent advances in molecular techniques that much remains undiscovered regarding the complex event of underwater attachment. Barnacles attached to silicone-based elastomeric coatings have been studied widely, particularly with respect to fouling-release technology. The fact that barnacles fail to attach tenaciously to silicone coatings, combined with the fact that the mode of attachment to these substrata is different to that for most other materials, indicates that knowledge about the natural mechanism of barnacle attachment is still incomplete. Further research on barnacles will enable a more comprehensive understanding of both the process of attachment and the adhesives used. Results from such studies will have a strong impact on technology aimed at fouling prevention as well as adhesion science and engineering. © 2013 Copyright Taylor and Francis Group, LLC.


Yamazaki A.,National Institute of Technology and Evaluation | Toyama K.,National Institute of Technology and Evaluation | Nakagiri A.,National Institute of Technology and Evaluation
Mycoscience | Year: 2010

A novel acidophilic fungus was isolated by an acidic enrichment culture of microbial mats and biofilms collected at an extremely acidic and high temperature hot spring. In culture studies, this fungus was revealed to produce ascomycetous teleomorph structures. Molecular phylogenetic study and morphological observation showed this fungus is a new species of the genus Teratosphaeria (Capnodiales, Dothideomycetes) and is phylogenetically close to Acidomyces acidophilus and Bispora sp., which were previously reported as acidophilic anamorphic fungi. This new fungus is described here as a new species of Teratosphaeria, and its physiological properties adapting to its habitat are demonstrated. This is the first report of a teleomorphic fungus having highly acidophilic and thermophilic properties. © 2010 The Mycological Society of Japan and Springer.


PubMed | National Institute of Technology and Evaluation
Type: Journal Article | Journal: Microbes and environments | Year: 2015

Dehalococcoides spp. are currently the only organisms known to completely reduce cis-1,2-dichloroethene (cis-DCE) and vinyl chloride (VC) to non-toxic ethene. However, the activation of fermenting bacteria that generate acetate, hydrogen, and CO2 is considered necessary to enhance the dechlorination activity of Dehalococcoides and enable the complete dechlorination of chloroethenes. In the present study, we stimulated chloroethene-contaminated groundwater by injecting different nutrients prepared from yeast extract or polylactate ester using a semicontinuous culture system. We then evaluated changes in the bacterial community structure and their relationship with dechlorination activity during the biostimulation. The populations of Dehalococcoides and the phyla Bacteroidetes, Firmicutes, and Spirochaetes increased in the yeast extract-amended cultures and chloroethenes were completely dechlorinated. However, the phylum Proteobacteria was dominant in polylactate ester-amended cultures, in which almost no cis-DCE and VC were dechlorinated. These results provide fundamental information regarding possible interactions among bacterial community members involved in the dechlorination process and support the design of successful biostimulation strategies.

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