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Environmental Metagenome Research Team

Environmental Metagenome Research Team

2014

[Original paper]
  1. Mikihiko Kawai, Taiki Futagami, Atsushi Toyoda, Yoshihiro Takaki, Shinro Nishi, Sayaka Hori, Wataru Arai, Taishi Tsubouchi, Yuki Morono, Ikuo Uchiyama, Takehiko Itoh, Asao Fujiyama, Fumio Inagaki, and Hideto Takami (2014) High frequency of phylogenetically diverse reductive dehalogenasehomologous genes in deep subseafloor sedimentary metagenomes. Front. Microbiol. doi: 10.3389/fmicb.2014.00080, advanced online

  2. Yohta Fukuda, Hiroyasu Koteishi, Ryohei Yoneda, Taro Tamada, Hideto Takami, Tsuyoshi Inoue, Masaki Nojiri (2014) Structural and functional characterization of the Geobacillus copper nitrite reductase: roles of the unique N-terminal region on the interprotein electron transfer with its redox partner. BBA Bioenerg. 1837, 396-405

  3. Yohta Fukuda, Ka Man Tse, Eiichi Mizohata, Hiroyoshi Matsumura, Hideto Takami, Masaki Nojiri, Tsuyoshi Inoue (2014) Structural insights into the function of a thermostable copper-containing nitrite reductase. J. Biochem. 155, (2) 123-135

[Book chapter]
  1. Hideto Takami (2014) New method for comparative functional genomics and metagenomics using KEGG MODULE. In Encylopedia of Metagenomics (Nelson K. ed.) Springer, Tokyo, Dordrecht, Heidelberg, London, New York, (Peer reviewed) in press

2013

[Original paper]
  1. Guiomar Sánchez-Carrón, María Inmaculada García-García, Rubén Zapata-Pérez, Hideto Takami, Francisco García-Carmona, Álvaro Sánchez Ferrer (2013) Biochemical and mutational analysis of a novel nicotinamidase from Oceanobacillus iheyensis HTE831. PLoS ONE 8 (2), e56727

  2. Sayaka Hori, Masashi Tsuchiya, Shinro Nishi, Wataru Arai, Takao Yoshida, and Hideto Takami (2013) Active bacterial flora surrounding foraminifera (Xenophyophorea) living on the deep-sea floor. Biosci. Biotech. Biochem. 77 (2), 381-384

  3. Guiomar Sánchez-Carrón, Ana Belén Martínez-Moñino, Agustín Sola-Carvajal, Hideto Takami, Francisco García-Carmona, Álvaro Sánchez-Ferrer (2013) New insights into the phylogeny and molecular classification of nicotinamide mononucleotide deamidases. PLoS ONE 8 (12): e82705

  4. Nikolaos Anesiadis, Hideki Kobayashi, William R. Cluett, and Radhakrishnan Mahadevan. (2013) Analysis and design of a genetic circuit for dynamic metabolic engineering. ACS Synthetic Biol. 10.1021/sb300129j

2012

[Original paper]
  1. Hideto Takami, Takeaki Taniguchi, Yuki Moriya, Tomomi Kuwahara, Minoru Kanehisa, and Susumu Goto (2012) Evaluation method for potential functionome harbored in genome and metagenome. BMC Genomics 13, 699

  2. Masaaki Konishi, Shinro Nishi, HidetoTakami, Yasuhiro Shimane, Yuriko Nagano, Kozue Mori, Yukari Ohta, Yuji Hatada (2012) Unique substrate specificity of a thermostableglycosyl hydrolase from uncultured Anaerolinea, derived from bacterial mat on a subsurface geothermal water stream. Biotechnol. Lett. 34, 1887-1893

  3. Hideki Kobayashi, Yuji Hatada, TaishiTsubouchi, Takahiko Nagahama, and HidetoTakami (2012) The hadal amphipod Hirondelleagigas possessing a unique cellulase for digesting wooden debris buried in the deepest seafloor.PLoS ONE 7 (8) e42727.
  4. Ken-ichi Yoshida, Azusa Sanbongi, Ayano Murakami, Hirokazu Suzuki, Shinji Takenaka, and HidetoTakami (2012) Three inositol dehydrogenases involved in utilization and interconversion of inositol stereoisomers in a thermophileGeobacilluskaustophilusHTA426. Microbiology 158, 1942-1952.
  5. Junichi Sugahara, Kosuke Fujishima, Takuro Nunoura, Yoshihiro Takaki, Hideto Takami, Ken Takai, Masaru Tomita, and Akio Kanai (2012) Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PLoS ONE 7 (3): e32504

  6. Hideto Takami, Hideki Noguchi, Yoshihiro Takaki, Ikuo Uchiyama, Atsushi Toyoda, Shinro Nishi, Gab-Joo Chee, Wataru Arai, Takuro Nunoura, Takehiko Itoh, Masahira Hattori and Ken Takai (2012) A deeply branching thermophilic bacterium with an ancestral acetyl-CoA pathway dominates a subsurface ecosystem. PLoS ONE 7 (1): e30559, Recommended at Faculty of 1000 (http://f1000.com/13521960)

2011

[Original paper]
  1. Hidetoshi Morita, Akiyo Nakano, Hidehiro Toh, Kenshiro Oshima, Hideto Takami, Masaru Murakami, Tatsuya Takizawa, Tomomi Kuwahara, Soichi Tanabe and Masahira Hattori (2011) Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces. Int. J. System. Evol. Microbiol. 61, 2610-2615
  2. Sakai S., Takaki Y., Shimamura S., Sekine M., Tajima T., Kosugi H., Ichikawa N., Tasumi E., Hiraki AT., Shimizu A., Kato Y., Nishiko R., Mori K., Fujita N., Imachi H., and Takai K. (2011) Genome Sequence of a Mesophilic Hydrogenotrophic Methanogen Methanocella paludicola, the First Cultivated Representative of the Order Methanocellales. PLoS One 6(7): e22898.

  3. Kuwahara H, Takaki Y, Shimamura S, Yoshida T, Maeda T, Kunieda T, Maruyama T. (2011) Loss of genes for DNA recombination and repair in the reductive genome evolution of thioautotrophic symbionts of Calyptogena clams. BMC Evol Biol. 2011 Oct 3; 11(1): 285.

  4. Yohta Fukuda, Taro Tamada, Hideto Takami, Shinnichiro Suzuki, Tsuyoshi Inoue and Masaki Nojiri. (2011) Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of GK0767, the copper-containing nitrite reductase from Geobacillus kaustophilus. Acta Cryst. F. F67, 692-695
  5. Takuro Nunoura, Yoshihiro Takaki, Jungo Kakuta, Shinro Nishi, Junichi, Sugahara, Hiromi Kazama, Gab-Joo Chee, Masahira Hattori, Akio Kanai, Haruyuki Atomi, Ken Takai, Hideto Takami (2011) Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal division. Nucleic Acids Res. 39, 3204-3223
  6. Gab-Joo Chee and Hideto Takami (2011) Alternative splicing by participation of the group II intron ORF in extremely halotolerant and alkaliphilic Oceanobacillus iheyensis. Microbes Environ 26, 54-60
  7. Ruri Tanaka, Takao Kunisad, Nobuaki Kushida, Keiko Yamada, Motoyoshi Noike, Yuusuke Ono, Nobuya Itoh, Hideto Takami, Haruo Seto and Tohru Dairi (2011) Branched fatty acids inhibit the biosynthesis of menaquinone in Helicobacter pylori. J. Antibiotics 64, 151-153

[Book chapter/Peer reviewed]

  1. Hideto Takami (2010) Genomics and Evolution of alkaliphilic Bacillus-related species. Part 2. Extremophiles: Alkaliphiles, 2.9. Extremophiles Handbook (Horikoshi K., Antranikian, G., Bull, A, Robb, F., Stetter, K. eds) Springer, Tokyo, Dordrecht, Heidelberg, London, New York, pp-183-212

2010

[Original paper]
  1. Yuriko Nagano, Takahiko Nagahama, Yuji Hatada, Takuro Nunoura, Hideto Takami, Junichi Miyazaki, Ken Takai and Koki Horikoshi (2010) Fungal diversity in de ep-sea sediments – the presence of novel fungal groups. Fungal Ecol. 3, 316-325
  2. Yoshihiro Takaki, Shigeru Shimamura, Satoshi Nakagawa, Yasuo Fukuhara, Hiroshi Horikawa, Akiho Ankai, Takeshi Harada, Akira Hosoyama, Akio Oguchi, Shigehiro Fukui, Nobuyuki Fujita, Hideto Takami, and Ken Takai (2010) Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1. DNA Res. 17,123-137
[Patent]
  1. U.S. Patent Application.
    Patent No.: 7693664 (April 6, 2010)
    Application No.: 11/062833
    For: Method of predicting thermostable protein from methophilic bacteria based on amino acid composition of thermophilic bacteria and its closely related mesophilic bacteria, predicting program therefore and recoding medium thereof.
    Inventors: Hideto Takami, Koki Horikoshi, Yoshihiro Takaki, Gab-Joo Chee, Shinro Nishi, Shigeru Shimamura, Hiroko Suzuki, Ikuo Uchiyama, and Zhi Jun Li
    Filing or 371(c) date: February 23, 2005

2009

[Original paper]
  1. Hidetoshi Morita, Akiyo Nakano, Mitsuharu Shimazu, Hidehiro Toh, Fumihiko Nakajima, Masahiro Nagayama, Shin Hisamatsu, Yukio Kato, Misako Takagi, Hideto Takami, Hiroaki Akita, Minoru Matsumoto, Toshio Masaoka and Masaru Murakami (2009) Lactobacillus hayakitensis, L. equigenerosi and L. equi, predominant lactobacilli in the intestinal flora of healthy Thoroughbreds. Animal Science J. 80, 339-346
  2. Silvia Montoro-Garcîa, Irene Martínez-Martínez, José Navarro-Fernández, Hideto Takami, Francisco García-Carmona, and Álvaro Sánchez-Ferrer (2009) Characterization of a novel thermostable carxyesterase from Geobacillus kaustophilus HTA426 shows the existence of a new carboxyesterase family. J. Bacteriol. 191, 3076-3085
  3. Maiko Harada, Takao Yoshida, Hirokazu Kuwahara, Shigeru Shimamura, Yoshihiro Takaki, Chiaki Kato, Tetsuya Miwa, Hiroshi Miyake and Tadashi Maruyama (2009) Expression of genes for sulfur oxidation in the intracellular chemoautotrophic symbiont of the deep-sea bivalve Calyptogena okutanii, Extremophiles, 13, 895-903.
[Book chapter]
  1. Satoshi Nakagawa and Yoshihiro Takaki (2009) Nonpathogenic epsilonproteobacteria, Encyclopedia of Life Sciences, DOI: 10.1002/9780470015902.a0021895.

2008

[Original paper]
  1. Hidetoshi Morita, Chiharu Shiratori, Masaru Murakami, Hideto Takami, Hidehiro Toh, Yukio Kato, Fumihiko Nakajima, Misako Takagi, Hiroaki Akita, Toshio Masaoka and Masahira Hattori (2008) Sharpea azabuensis gen. nov., sp. nov., a Gram-positive strict anaerobic bacterium isolated from the faeces of Thoroughbred horses. Int. J. System. Evol. Microbiol. 58, 2682-2686
  2. Irene Martínez-Martínez, José Navarro-Fernández, Francisco García-Carmona, Hideto Takami, and Álvaro Sánchez-Ferrer (2008) Characterization and structural modeling of a novel thermostable glycine oxidase from Geobacillus kaustophilus HTA426. Proteins-Structure, Function, and Bioinformatics 70, 1429-1441
  3. José Navarro-Fernández, Irene Martínez-Martínez, Silvia Montoro-García, Francisco García-Carmona, Hideto Takami and Álvaro Sánchez-Ferrer (2008) Characterization of a new Rhamnogalacturonan Acetyl Esterase from Bacillus halodurans C-1.326 with a new putative carbohydrate binding domain. J. Bacteriol. 190, 1375-1382
  4. Hirokazu Kuwahara, Yoshihiro Takaki, Takao Yoshida, Shigeru Shimamura1, Kiyotaka Takishita, James D. Reimer, Chiaki Kato and Tadashi Maruyama (2008) Reductive genome evolution in chemoautotrophic intracellular symbionts of deep-sea Calyptogena clams. Extremophiles 12, 365-74
  5. Toru Kobayashi, Kozue Mori, Shigeru Shimamura, Takae Matsuura, Takeshi Miura, Yoshihiro Takaki, Yuki Morono, Takuro Nunoura, Hiroyuki Imachi, Fumio Inagaki, Ken Takai, Koki Horikoshi (2008) Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. Extremophiles 12, 519-27
[Book chapter]
  1. Hideto Takami (2008) Genomic diversity of Bacillus-related species. NOVA Science Publisher, New York, U.S.A.

2007

[Original paper]
  1. Ken Kurokawa, Takehiko Itoh, Tomomi Kuwahara, Kenshiro Oshima, Hidehiro Toh, Atsushi Toyoda, Hideto Takami, Hidetoshi Morita, Vineet K. Sharma, Tulika P. Srivastava, Todd D. Taylor, Hideki Noguchi, Hiroshi Mori, Yoshitoshi Ogura, Dusko E. Ehrilich, Kikuji Itoh, Toshihisa Takagi, Yoshiyuki Sakaki, Tetsuya Hayashi, Masahira Hattori (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiome. DNA Res 14, 169-181, Recommended at Faculty of 1000 (http://f1000.com/1097479#evaluations)
  2. Hidetoshi Morita, Tomomi Kuwahara, Kenshiro Ohshima, Hiroyuki Sasamoto, Kikuji Itoh, Masahira Hattori, Tetsuya Hayashi, and Hideto Takami (2007) An improved DNA isolation method for metagenomic analysis of the microbial flora of the human intestine. Microbes Environ. 22, 214-222
  3. Irene Martinez-Martinez, Jose Navarro-Fernandez, Francisco Garcia-Carmona, Hideto Takami, and Alvaro Sanchez- Ferrer (2007) Characterization and structural modeling of a novel thermostable glycine oxidase from Geobacillus kaustophilus HTA426. Proteins: Structure, Function, and Bioinformatics 70, 1429-1441
  4. Hidetoshi Morita, Chiharu Shiratori, Masaru Murakami, Hideto Takami, Yukio Kato, Akihiko Endo, Fumiko Nakajima, Hiroaki Akita, Sanae Okada and Toshio Masaoka (2007) Lactobacillus hayakitensis sp. nov., isolated from healthy Thoroughbred intestine. Int. J. System. Evol. Microbiol. Int. J. System. Evol. Microbiol. 57, 2836-2839
  5. Hideki Kobayashi, Yuichi Nogi and Koki Horikoshi (2007) New violet 3, 3’-bipyridyl pigment purified from deep-sea microorganism Shewanella violacea DSS12. Extremophiles 11, 245-250
  6. Satoshi Nakagawa, Yoshihiro Takaki, Shigeru Shimamura, et al. (2007) Deep-sea vent epsilon- proteobacterial genomes provide insights into emergence of pathogens. Proc Natl Acad Sci USA 104, 12146-12150

2006

[Book chapter]
  1. Hideto Takami (2006) Genomic diversity of extremophilic Gram-positive endospore-forming Bacillus-related species. In: Trends in Genome Research (C. R. Williams ed.), NOVA Publisher, New York, U.S.A. pp. 25-85