研究成果

中島 信孝 准教授

【代表論文】

  • [1] Nakamura, Y., Yamamoto, N., Kino, Y., Yamamoto, N., Kamei, S., Mori, H., Kurokawa, K., and Nakashima, N. (2016) Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities. Appl. Microbiol. Biotechnol.100, 7263-7279.
  • [2] Akita, H., Nakashima, N., and Hoshino, T. (2015) Bacterial production of isobutanol without expensive reagents. Appl. Microbiol. Biotechnol.99, 991-999.
  • [3] Nakashima, N., Akita, H., and Hoshino, T. (2014) Establishment of a novel gene expression method, BICES (biomass-inducible chromosome-based expression system), and its application to the production of 2,3-butanediol and acetoin. Metab. Eng. 25, 204–214.
  • [4] Nakashima, N., Ohno, S., Yoshikawa, K., Shimizu, H., and Tamura, T. (2014) A vector library for silencing central carbon-metabolism genes with antisense RNAs in Escherichia coli. Appl. Environ. Microbiol. 80, 564–573.
  • [5] Nakashima, N., and Tamura, T. (2013) Gene silencing in Escherichia coli using antisense RNAs expressed from doxycycline-inducible vectors. Lett. Appl. Microbiol. 56, 436–442.
  • [6] Nakashima, N., and Tamura, T. (2012) A new carbon catabolite repression mutation of Escherichia coli, mlc*, and its use for producing isobutanol. J. Biosci. Bioeng. 114, 38–44.
  • [7] Nakashima, N., Goh, S., Good, L., and Tamura, T. (2012) Multiple-gene silencing using antisense RNAs in Escherichia coli. Meth. Mol. Biol. 815, 307-319.
  • [8] Nakashima, N., Goh, S., and Tamura, T. (2012) Subtracting gene function by gene silencing and disruption in bacteria. Curr. Biotechnol. 9, 166-174.

山田 拓司 准教授

【代表論文】

  • [1] Matsuki T, Yahagi K, Mori H, Matsumoto H, Hara T, Tajima S, Ogawa E, Kodama H, Yamamoto K, Yamada T, Matsumoto S, Kurokawa K. A key genetic factor for fucosyllactose utilization affects infant gut microbiota development. Nat Commun. 2016 Jun 24;7:11939. doi: 10.1038/ncomms11939.
  • [2] Nishimoto Y, Mizutani S, Nakajima T, Hosoda F, Watanabe H, Saito Y, Shibata T, Yachida S, Yamada T . High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy. Gut 2016 Jun 23.
  • [3] Moriya Y, Yamada T, Okuda S, Nakagawa Z, Kotera M, Tokimatsu T, Kanehisa M, Goto S. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs. J Chem Inf Model. 2016 Mar 28;56(3):510-6.
  • [4] Wang T, Mori H, Zhang C, Kurokawa K, Xing XH, Yamada T. DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. BMC Bioinformatics;16(1):96 (2015)
  • [5] Uchiyama T, Irie M, Mori H, Kurokawa K, Yamada T. FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data. PLoS One. 2015 May 14;10(5):e0126967. doi: 10.1371/journal.pone.0126967. PubMed PMID: 25974630
  • [6] Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol;10:766 (2014)
  • [7] Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen, Guarner F, Pedersen O, Doré J, Ehrlich SD, Pons N, Le Chatelier E, Batto JM, Kennedy S, Haimet F, Winogradski Y, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K,Parkhill J, Antolin M, Casellas F, Borruel N, Varela E, Torrejon A, Denariaz G, Derrien M, van Hylckama Vlieg JE, Viega P, Oozeer R, Knoll J,Rescigno M, Brechot C, M'Rini C, Mérieux A, Yamada T, Tims S, Zoetendal EG, Kleerebezem M, de Vos WM, Cultrone A, Leclerc M, Juste C,Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Blottière H, Maguin E, Renault P,Tap J, Mende, Bork P, Wang J. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–41 (2014)
  • [8] Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol.32(8):822-8 (2014)
  • [9] Waller, AS., Yamada, T., Kristensen, DM., Kultima, JR., Sunagawa, S., Koonin, EV., Bork, P. Classification and quantification of bacteriophage taxa in human gut metagenomes. ISME J. 8(7):1391-402 (2014)
  • [10] Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O, Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Maguin E, Haimet F, Winogradski Y, Cultrone A, Leclerc M, Juste C, Blottière H, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K, Parkhill J, Antolin M, Manichanh C, Casellas F, Boruel N, Varela E, Torrejon A, Guarner F, Denariaz G, Derrien M, van Hylckama Vlieg JE, Veiga P, Oozeer R, Knol J, Rescigno M, Brechot C, M'Rini C, Mérieux A, Yamada T. Richness of human gut microbiome correlates with metabolic markers. Nature. 29;500(7464):541-6 (2014)
  • [11] *Yamada, T., Waller, A., Raes, J., Zeleznik, A., Perchat, N., Perret, A., Salanoubat, M., Patil, K.R., Weissenbach, J. and Bork, P. Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighibors; Molecular Systems Biology, 8:581 (2012)
  • [12] *Yamada, T., Letunic, I., Okuda, S., Kanehisa, M. and Bork, P. iPath2.0: interactive pathway explorer; Nucleic Acids Res, 39 W412-415 (2011)
  • [13] Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Junwang, Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Consortium, M., Weissenbach, J., Ehrlich, S.D. and Bork, P. Enterotypes of the human gut microbiome. Nature. 473 (7346), 174-180 (2011)
  • [14] Raes, J., Letunic, I., Yamada, T., Jensen, L.J. and Bork, P. (2011) Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol, 7, 473 (2011).
  • [15] Colbourne, J.K., Pfrender, M.E., Gilbert, D., Thomas, W.K., Tucker, A., Oakley, T.H., Tokishita, S., Aerts, A., Arnold, G.J., Basu, M.K., Bauer, D.J., Caceres, C.E., Carmel, L., Casola, C., Choi, J.H., Detter, J.C., Dong, Q., Dusheyko, S., Eads, B.D., Frohlich, T., Geiler-Samerotte, K.A., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E.V., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J.R., Muller, J., Pangilinan, J., Patwardhan, R.P., Pitluck, S., Pritham, E.J., Rechtsteiner, A., Rho, M., Rogozin, I.B., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y.I., Yamagata, H., Yamada, T., Ye, Y., Shaw, J.R., Andrews, J., Crease, T.J., Tang, H., Lucas, S.M., Robertson, H.M., Bork, P., Koonin, E.V., Zdobnov, E.M., Grigoriev, I.V., Lynch, M. and Boore, J.L. The ecoresponsive genome of Daphnia pulex. Science, 331 (6017), 555-561 (2011)
  • [16] Qin. J., Li. R., Raes. J., Arumugam. M., Burgdorf. KS., Manichanh. C., Nielsen. T., Pons. N., Levenez. F., Yamada. T., Mende. D., Li. J., Xu. J., Li. S., Li. D., Cao. J., Wang. B., Liang. H., Zheng. H., Xie. Y., Tap. J., Lepage. P., Bertalan. M., Batto. J., Hansen. T., Paslier. DL., Linneberg. A., Nielsen. HB., Pelletier. E., Renault. P., Sicheritz-Ponten. T., Turner. K., Zhu. H., Yu. C., Li. S., Jian. M., Zhou. Y., Li. Y., Zhang. X., Li. S., Yang. H., Wang. J., Brunak. S., Doré. J., Guarner. F., Kristiansen. K., Pedersen. O., Parkhill. J., Weissenbach. J., Consortium. M., Bork. P., Ehrlich. SD. and Wang. J; A human gut microbial gene catalog established by deep metagenomic sequencing. Nature 464 (7285), 59-65 (2010)
  • [17] Yus, E., Maier, T., Michalodimitrakis, K., van Noort, V., Yamada, T., Chen, W.-H., Wodke, J. A. H., Guell, M., Martinez, S., Bourgeois, R., Kuhner, S., Raineri, E., Letunic, I., Kalinina, O. V., Rode, M., Herrmann, R., Gutierrez-Gallego, R., Russell, R. B., Gavin, A.-C., Bork, P., Serrano, L.; Impact of genome reduction on bacterial metabolism and its regulation. Science 326 (5957), 1263-1268 (2009)
  • [18] Kuhner, S., van Noort, V., Betts, M. J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P., Castano-Diez, D., Chen, W.-H., Devos, D., Guell, M., Norambuena, T., Racke, I., Rybin, V., Schmidt, A., Yus, E., Aebersold, R., Herrmann, R., Bottcher, B., Frangakis, A. S., Russell, R. B., Serrano, L., Bork, P., Gavin, A.C.; Proteome organization in a genome-reduced bacterium. Science 326 (5957), 1235-1240 (2009).
  • [19] Guell, M., van Noort, V., Yus, E., Chen, W.-H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kuhner, S., Rode, M., Suyama, M., Schmidt, S., Gavin, A.-C., Bork, P., Serrano, L.; Transcriptome complexity in a genome-reduced bacterium. Science 326 (5957), 1268-1271 (2009).
  • [20] *Yamada T., Bork P.; Evolution of biomolecular networks - lessons from metabolic and protein interactions. Nat. Rev. Mol. Cell Biol. 10 (11):791-803 (2009).
  • [21] Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB; Quantifying environmental adaptation of metabolic pathways in metagenomics. PNAS USA. 2009 Feb 3; 106(5): 1374-1379 (2009)

【主な日本語総説】

  • [1] 腸内細菌群集構造のメタゲノム解析:腸内細菌学雑誌 29 : 19-22,2015

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